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2008 ANNUAL REPORTARC CentRe of exCellenCe in BioinfoRmAtiCs

ARC Centre of Excellence in Bioinformatics Institute for Molecular Bioscience The University of Queensland Brisbane Qld 4072

Telephone: (07) 3346 2617

Facsimile: (07) 3346 2101

Email: [email protected]

Website: http://bioinformatics.org.au

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Contents

ChaIR’S FOREwORd 2

dIRECtOR’S REvIEw and hIghlIghtS 3

ORganISatIOn and gOvERnanCE 4Organisational chart 4advisory Board 5Research Committee 8director 8Chief Investigators 8Partner Investigators 13Special advisor 14Information infrastructure 14Centre Manager 14Postdoctoral Fellows / Research Officers 15Research assistants 15Masters/Phd students 15honours students 16International & national interns 16Undergraduate research trainees and volunteers 17visiting scholars, associates 17

StRatEgIC dIRECtIOn (2008-2010) 18vision 18Mission 18aims 18Objectives 18Capabilities — core technologies and infrastructure 18

RESEaRCh PROgRaMS 19Program 1 –the visible Cell®: linking genome and phenome 201.1 generation of subcellular localisation data in

mammalian cells 201.2 Project and data management for visible Cell® 221.3 data analysis and knowledge discovery in very large

biological network databases 24

Program 2 – Phenotype-informed discovery of networks and systems 262.1 Computational discovery and modelling of

gene-regulatory networks 262.2 differential expression of genes towards

pathway discovery 272.3 discovery and modelling of Rna-based regulatory

networks 28

Program 3 – Modelling dynamic cellular processes 303.1 Mathematical modelling of genetic regulatory

networks and biochemical pathways 303.2 Modelling and visualising biological processes in

complex spatial environments 32

Program 4 – algorithms for graphs and networks 344.1 discrete optimisation and graph clustering 344.2 Optimisation-based approaches to large systems 354.3 External-memory algorithms for analysis of

massive graphs 37

KEy PERFORManCE IndICatORS 391. Research findings and competitiveness 40Publications 40

Quality of publications 40number of publications 40

Patents and trademarks 40Invitations to address and participate in conferences 41

International conferences 41national conferences 44

Invitations to visit leading international laboratories, major research groups and centres 44Commentaries about the Centre’s achievements 46Evidence of interdisciplinary linkages within the Centre 46

2. Research training and professional education 47Recruitment 47Professional/technical training and advanced career development 47 Seminar/Symposium hosted and/or sponsored by aCB 47 Other research and training and professional education 49 Postgraduate and undergraduate courses in the

Centre’s area 49 Scientists in Schools Partnership 49

3. International, national and regional links and networks 50visitors 50

International visitors 50national visitors to one or more aCB nodes 50

Collaborative national and international workshops and exchanges 50Other research linkages 51Membership on national and international professional committees 53Research projects with international partners 54

4. End-user links 55Commercialisation activities 55government, industry and business briefings 55trained/ing in technology transfer and commercialisation 55Public awareness programs 55

5. Organisational support 56new organisations recruited to or involved in the Centre 56Infrastructure 56annual cash contributions from other organisations 2008–2010 57annual in-kind contributions: collaborating organisations 2008–2010 57

6. national benefit 58Measures of expansion of australia’s capability in the priority area(s) 58

aPPEndIX 1: PUBlICatIOnS 60aPPEndIX 2: FInanCIal StatEMEnt 73

Cont

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2 2008 ANNUAL REPORTARC CentRe of exCellenCe in BioinfoRmAtiCs


Chair’s Foreword

I am pleased to be able to introduce you to the 2008 annual Report of the aRC Centre for Bioinformatics (“aCB”).

2008 was a year of transition for aCB. In 2007, aCB was awarded a three-year extension by aRC, and was upgraded by aRC to an aRC Centre of Excellence. therefore, this 2008 annual Report provides an overview of the Centre’s first year of operation as the “aRC Centre of Excellence in Bioinformatics”.

this second round of Federal government support now permits aCB to build on its existing research portfolio and to reinforce its capabilities and the interests of its Investigators and their research teams across both existing and new interdisciplinary research programs and between geographical nodes. new Investigators have joined the Centre from three institutions new to the aCB: Macquarie University, the University of auckland, and the University of tennessee. Collaborations have also continued to grow outside the Centre, as the co-authorship of grants and research publications, listed later in this report, amply demonstrates.

aCB was the local host of the 19th International Conference on genome Informatics (gIw-2008). the conference attracted 220 registrants, almost 50% of whom were international. Roundtable forums at the conference focused on innovation and commercialisation in genome-scale bioinformatics, and the development of genome-scale bioinformatics in China and India.

the Centre’s annual winter School in Mathematical and Computational Biology, held in 2008 at aCB’s University of newcastle node, attracted 82 participants from 25 institutions and 6 countries.

aCB continued to grow its highly regarded research publication record, and continued to play an active role in the evolution of the Queensland Facility for advanced Bioinformatics.

aCB became a key node in the EU’s Sixth Framework Information Society technology project “Quasi-opportunistic supercomputing for complex systems in grid environments” (QosCosgRId). the technical manager, Chris Kurowski, worked out of aCB during 2008 to manage the project from australia.

aCB director Mark Ragan represented the University of Queensland on the working group of EMBl australia, the body that manages australia’s associate membership in the European Molecular Biology laboratory (EMBl).

Most importantly, aCB’s research excellence continued to be recognised internationally in 2008. Professor Michael Fellows and dr Frances Rosamond worked in Jena, germany for much of 2008 in support of Michael’s von humboldt research award. Professor John Mattick was elected a Fellow of the australian academy of Science, and became the inaugural gutenberg Chair at the Université louis Pasteur in Strasbourg. Professor geoff Mclachlan became president-elect of the International Federation of Classification Societies. Professor Kevin Burrage continued his joint appointment at Oxford University as Professor of Computational Systems Biology. Professor Mark Ragan facilitated the national technology Roadmap for Bioinformatics with the Ministry of Science technology and Innovation in Malaysia.

I anticipate that 2009 will be another year of considerable achievement for the Centre as it continues to develop its activities under the second term of its support from aRC.

dr gregory R. Smith Chair, advisory Board March 2009

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most part these are not universities, but established companies, medical research institutions, primary industries bodies, biotech start-ups, consultancies and others. the national health and Medical Research Council, the national Breast Cancer Foundation, and several state governments have funded programs or centres in bioinformatics. Bioinformatics australia, our national society organised within ausBiotech, is now an affiliate of the International Society for Computational Biology, and – fresh from hosting the 19th International Conference on genome Informatics (gIw-2008) in december 2008, is busily planning its fourth annual conference (to be held in Melbourne). and on the research front, next-generation dna sequencing is onshore in a big way – we are all very soon to see how robust and scalable our bioinformatics really is.

On behalf of my colleagues in the aRC Centre of Excellence in Bioinformatics, I encourage you to peruse this report of our 2008 activities, and invite your comments.

Professor Mark Ragan director aRC Centre of Excellence in Bioinformatics March 2009

director’s Review and highlights

2008 was a year of transition for our Centre. In its first phase (2003-2007), the aRC Centre in Bioinformatics brought together researchers from diverse disciplines, institutions and regions to build new research programs in bioinformatics, linking the mammalian genome with its expression in the cellular phenome. we learned to see problems from each others’ perspectives, work in new scientific languages, and apply unfamiliar tools. we engaged researchers outside our Centre and institutions, contributed to new partnerships and the development of national research infrastructure, and initiated our successful winter School in Mathematical and Computational Biology. In mid-2006 we applied for a more-ambitious three-year extension of our Centre, and on 16 March 2007 we learned that aRC would fund our proposed extension – and upgrade our status to that of an aRC Centre of Excellence. these pages report on our first year as the aRC Centre of Excellence in Bioinformatics.

this second phase of our Centre differs in several respects from the first:

Firstly, we are joined by Investigators at three institutions new to our Centre: Professor Shoba Ranganathan (Macquarie University), Professor allen Rodrigo (the University of auckland), and Professor Michael langston (the University of tennessee). associate Professor Pablo Moscato, a longstanding collaborator, has formally joined us via our founding partner, the University of newcastle; and at the University of Queensland we welcome new Investigators dr Brad Marsh and Professor John Mattick, while dr Sean grimmond, dr Ralf Muhlberger and Professor Bernard Pailthorpe did not continue with us into Phase II. Collaborations continue (and indeed are growing) with Sean and Bernard, and I’m confident that upcoming annual Reports will continue to show their names as co-authors on grants and research publications, and as collaborators in infrastructure initiatives.

two new members, whom I had the privilege of introducing in last year’s annual Report, augmented our distinguished advisory Board in 2008: Professor Peter donnelly FRS, director of the wellcome trust Centre for human genetics, and Professor of Statistical Science at Oxford University, and Professor Barney glover, deputy vice-Chancellor of the University of newcastle.

Phase II of our Centre will see a progressive shift in emphasis from method and tool development, to application; from integrating large datasets, to their common use by multiple Investigators in our Centre; from building data infrastructure, to using it to address complex problems. In Phase I our external alliances emphasized technology; while valuing their continuance, we now add new alliances in data-generation, experimental validation and (perhaps) large-scale service provision.

Establishing – and during 2008, expanding – a Centre necessarily involves legal formalities, and I’m pleased to report that the funding contract and inter-institutional agreement formally extending our Centre as the aRC Centre of Excellence in Bioinformatics were signed by all parties in late december 2008. with these in place, we can now flow research funds to our new programs and projects. In 2008 we wrapped-up projects from Phase I, and began to put our plans for Phase II into action; 2009 will be a year of consolidation and scaling-up. Early outcomes will appear from some of our new projects.

Change continues to accelerate in our external environment: 2009 is radically different from mid-2006, when we wrote the application for extension to Phase II. the national Collaborative Research Infrastructure Strategy has engaged bioinformatics not only through Bioplatforms australia, but also through the australian national data Service and national Computational Infrastructure. EMBl australia is operational, and an initiative is underway to establish a major data services mirror in australia. the victorian life Science Computing Initiative has been announced, and bioinformatics is firmly on the radar in Innovation departments within several state governments. at any given point in time, several institutions in australia are recruiting bioinformaticians – and for the

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Organisation and governance

Organisational Chart

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Information Infrastructure

Centre Manager

director (RC Chair + COO)

Research Committee (RC)

UQ – dvC (R) advisory Board

PROgRaM 2 Phenotype-

informed discovery of networks and

systems

Coordinator Regulatory networks

Research groups

PROgRaM 1 the visible Cell®:

linking genome and phenome

Coordinator data Integration

visible Cell® Project Manager

Research team Research groups

Coordinator Cell Function

Research groups

PROgRaM 3 Modelling dynamic cellular processes

Coordinator Modelling

Research groups

PROgRaM 4 algorithms for

graphs and networks

Coordinator networks

Research groups





advisory Boardthe 8th advisory Board meeting was held on thursday 28 august 2008. the members of the advisory Board are:

1 Dr Gregory R. Smith (Chair)

directorSciventures Investments Pty ltdMelbourne vIC, australia

dr greg Smith is a cofounder and director of Sciventures Investments Pty ltd, the manager of the Sciventures Pre-Seed Fund. he also is a director or chair of four start-up companies into which Sciventures has invested. greg has been a member of the Commonwealth government’s Industrial Research & development Board and of its advisory Council for Intellectual Property. he is the Board Chair for the australian Microscopy and Microanalysis Research Facility. greg was awarded the Maurice holland award of Industrial Research Institute (washington dC, USa) in 2000 for his “front-end innovation” at alliedSignal (now honeywell) and at alcoa.

2 Prof. Ross Coppel

director, victorian Bioinformatics Consortium

department of MicrobiologyMonash UniversityMelbourne vIC, australia

Prof. Ross Coppel is a recipient of the glaxo award for advanced Research in Infectious diseases and of an International Investigator award from the howard hughes Medical Institute. he is a named inventor on nine patents for inventions in malaria, primary biliary cirrhosis and novel antibiotics, and is internationally recognised for his work in these fields and in malaria genomics. Ross is Professor of Microbiology at Monash University, director of the victorian Bioinformatics Consortium, and co-founder of the biotechnology company glykoz.

3 Prof. Peter Donnelly FRS

director, wellcome trust Centre for human genetics

Professor of Statistical ScienceUniversity of Oxford, UK

Professor donnelly is director of the wellcome trust Centre for human genetics and Professor of Statistical Science at the University of Oxford. Peter is a Fellow of both the Royal Society and academy of Medical Sciences. he has been awarded the Mitchell Prize of the aSa and International Society for Bayesian analysis and the guy Medal in Silver of the Royal Statistical Society. his early work was in applied probability, particularly stochastic models in genetics, but, for some years, his research has focused on genetics. he played a major role in the hapMap project, an international collaboration that followed the human genome Project in studying genetic diversity in worldwide populations. he currently chairs the wellcome trust Case Control Consortium, a collaboration of over 200 UK scientists studying the genetics of 12 common human diseases. Other research interests include human population structure and histories, bacterial variation, human recombination, and the development of statistical methodology for modern genetics.

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4 Prof. Simon Easteal

John Curtin School of Medical Research

the australian national UniversityCanberra aCt, australia

Prof. Simon Easteal is deputy director of the John Curtin School of Medical Research at the australian national University. his research is focused on how the evolutionary dynamic between humans and their environments has shaped the complexity of human biology, given rise to human diversity and left a lasting impact on human health. Simon was founding co-director of anU’s Centre for Bioinformation Science, director of the genetic Epidemiology Unit at the Menzies Centre for Population health Research in hobart, and Editor-in-Chief of Molecular Biology and Evolution. his work as a trusted Intermediary in the australian Industry group’s InnovationXchange network involved business intermediation, innovation management and advising on R&d commercialisation. he has served on numerous committees and boards in both private and public sectors.

5 Prof. Barney Glover

deputy vice-Chancellor (Research) the University of newcastlenewcastle, nSw, australia

Prof glover holds a Bachelor of Science (honours), a diploma of Education, a Master of Science and a doctor of Philosophy from the University of Melbourne, and was a Professorial Fellow with the western australian Centre of Excellence in Industrial Optimization. Professor glover also has extensive industry networks and has held a number of corporate appointments including board membership of the australian Biosecurity Cooperative Research Centre, the John Curtin Institute for Public Policy, and the Cooperative Research Centre for Coal in Sustainable development.

6 Prof. Mark Ragan FLS

director, aRC Centre in Bioinformatics (ex officio)

Institute for Molecular Biosciencethe University of QueenslandBrisbane Qld, australia

Prof. Mark Ragan joined IMB in 2000 after 28 years with national Research Council Canada, where he co-founded and developed programs in bioactive compounds, molecular biology, genomics and bioinformatics, including Canadian Bioinformatics Resource. with Prof. w. Ford doolittle and dr Robert Charlebois he received the largest single grant under the first Canadian genome program (Cgat) and sequenced Sulfolobus solfataricus. Mark has been President of two international scientific societies, and a Fellow of the Canadian Institute for advanced Research. Mark is vice-president of Bioinformatics australia, and in 2008 was Chair of the Executive group of the association of asian Societies of Bioinformatics. Under the overall theme of comparative and computational genomics, research in his group includes projects on whole-genome duplication, genetic recombination, the cellular localisation of molecular-interaction networks, and applications of semantic web technologies to large-scale biomolecular, chemical and structural data.

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7 Prof. David Siddle FASSA

deputy vice-Chancellor (Research)the University of Queensland Brisbane Qld, australia

Prof. david Siddle was appointed deputy vice-Chancellor (Research) in 2002. he is responsible for enhancement of the University’s research and research training profile, and development of research collaborations. Previously david was University of Queensland Pro-vice-Chancellor (Research) 2001; University of Sydney Pro-vice-Chancellor (Research) 1997-2001; and University of Queensland dean, Postgraduate Studies 1993-1997. he was chair of the aRC Social Sciences and humanities Panel 1993-94, and deputy chair of the aRC Research grants Committee 1994. he chaired the national Committee of dvCs/PvCs (Research) in 2001 and was convenor of the go8 dvCs(R) until december 2007. Currently, david is a director of the australian Synchrotron Company and australian Synchrotron holding Company; ahURI Queensland Research Centre ltd; CRCMining; and australian genome Research Facility ltd.

8 Prof. Brandon Wainwright

directorInstitute for Molecular Biosciencethe University of QueenslandBrisbane Qld, australia

In 2006 Professor wainwright was appointed director of the Institute for Molecular Bioscience (IMB) at the University of Queensland, and before that was IMB’s deputy director (Research). IMB, recognised nationally and internationally as one of australia’s leading centres for molecular bioscience research, has around 500 research staff and research students with an annual budget in the order of $40M. Professor wainwright currently serves on a number of boards including those of the australian genome Research Facility, the australian Phenomics Facility, and the health and Medical Research Council of Queensland. In 2007 he was Chair of the dESt Research Quality Framework Panel 6.

Professor wainwright’s major research focus is the use of genomic approaches to dissect the basis of common genetic disease, in particular cystic fibrosis and basal-cell carcinoma of the skin. through the mapping and isolation of the genes which are responsible for these diseases, he has continued to follow-through on each to understand how the genetic defects lead to the disease. the aim of his work is to discover the genes which when altered cause the tumour cell to grow in an uncontrolled fashion. Ultimately this will provide validated targets against which potential therapeutics can be developed.

9 Prof. Marc Wilkins

department of Biotechnology and Biomolecular Sciences

University of new South walesSydney nSw, australia

Prof. Marc wilkins developed the concept of the proteome and coined the term. he is author of more than 90 publications, and co-editor of two books. he is the director of the nSw Systems Biology Initiative, a member of the advisory Board of the australian Proteomics Computational Facility (aPCF) and the Management Committee of the Ramaciotti Centre for gene Function analysis. Marc is a Senior Editor of the journal Proteomics, and serves on the Editorial Boards of Practical Proteomics and Bioinformatics and Biology Insights. he has six years experience in industry, and has co-founded two biotechnology companies, one of which, Proteome Systems, employs ~30 staff and is listed on the australian Securities Exchange. his current research interests are in the dynamics of the interactome and the role that protein post-translational modifications play in the control of protein-protein interactions. O

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Research Committeethe Research Committee met 12 times during 2008. Members of the aRC Centre of Excellence in Bioinformatics Research Committee for 2008 were:

Chair Prof. Mark RaganProgram 1 dr Rohan teasdaleProgram 1 Prof. Shoba RanganathanProgram 2 dr timothy Bailey (from September 2008)Program 2 a/Prof. Phoebe Chen (to September 2008)Program 2 Prof. geoff MclachlanProgram 2 Prof. John MattickProgram 3 Prof. Kevin BurrageProgram 4 a/Prof. Pablo MoscatoSecretary Ms lanna wong

director

1 Prof. Mark Ragan FLS

Institute for Molecular Biosciencethe University of Queensland

Please refer to page 6 for profile.

Chief Investigators

2 Dr Timothy L. Bailey

Institute for Molecular Bioscience the University of Queensland

dr timothy Bailey has been active in bioinformatics and computational biology since the early 1990s, and since 2004 he has been a senior research fellow at the Institute for Molecular Bioscience. he is well-known as an expert in pattern recognition in biological sequences, and as the author of several important bioinformatics software programs, most notably MEME, one of the most heavily used tools in sequence analysis. tim’s major areas of expertise are machine learning, statistical pattern recognition (discovery), and the statistics of sequence alignment scores. he is experienced in developing parallel algorithms for massively parallel computer architectures, and in development and support of web-based algorithms for bioinformatics. during the past year, dr Bailey’s group, in collaboration with the noble group at the University of washington, introduced a new website featuring a suite of sequence analysis tools. this “MEME suite of motif-bases sequence analysis tools” includes motif discovery algorithms (MEME and glaM2), motif-based sequence search tools (MaSt, FIMO and glaM2SCan) and tools for analysing the functions of dna sequence motifs in regulatory networks (tOMtOM and gOMO). the new MEME suite website is currently used by about 1,000 biologists per month.

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3 Prof. Kevin Burrage

Institute for Molecular Biosciencethe University of Queensland; andProfessor of Computational Systems

BiologyCOMlaB, Oxford University, UK

Prof. Kevin Burrage was founding CEO of the Queensland Parallel Supercomputer Foundation (now Queensland Cyber Infrastructure Foundation), director of the advanced Computational Modelling Centre (aCMC) at UQ, and director of the viSaC visualisation laboratory. In 2003 he was awarded a prestigious Federation Fellowship by the australian Research Council. Kevin has co-authored more than 180 papers in the fields of computational science, computational biology, mathematical modelling and complex systems. this oeuvre consists of fundamental work on the numerical solution of both ordinary differential equations and stochastic differential equations, and algorithms for linear systems. he is author of a monograph on parallel and sequential methods for ordinary differential equations. In a computational biological context he is interested in the modelling and simulation of complex cellular processes, and the role of noise in molecular systems. In 2007 Kevin accepted a joint appointment as Professor of Computational Systems Biology at Oxford University.

4 A/Prof. Yi-Ping Phoebe Chen

School of Engineering and Information technology

deakin University

associate Professor (Reader) yi-Ping Phoebe Chen is Bioinformatics group leader, and head of Multimedia information retrieval at deakin University in Melbourne. She was director of Research (acting associate head of Research) in deakin’s School of Information technology. a/Prof. Chen has been working in bioinformatics since 1997. Prior to that, she conducted significant research in knowledge discovery, information retrieval, database query languages, data visualisation, and data integration systems. She has written about 120 refereed journal articles and international conference papers including papers in Nucleic Acids Research and BMC Bioinformatics, and serves on the editorial boards of IEEE Transactions on Multimedia, Current Bioinformatics, Journal of Research and Practice in Information Technology, International Journal of Intelligent Computing in Medical Sciences, and Image Processing. a/Prof. Chen founded asia-Pacific Bioinformatics Conference and continues to chair its Steering Committee. She also serves on the national steering committee of Bioinformatics australia.

5 Prof. Michael R. Fellows

Parameterised Complexity Research Unit

Office of the deputy vice-Chancellor (Research)

the University of newcastle

Prof. Mike Fellows is internationally recognised for his foundational work on parameterised complexity, for which he and collaborator Prof. Rod downey (victoria University, new Zealand) were nominated for the gödel Prize in 2005. they co-authored the foundational papers and the first comprehensive monograph for the field, now considered one of the main branches of theoretical computer science concerned with algorithms and complexity. For more than a decade, this area has had strong applications in bioinformatics and computational biology, both in the design of effective algorithms for large datasets, and in the formation and evaluation of theory for natural computing systems. Mike is also recognised for major contributions to cryptography, algebraic graph theory, and the popularisation of mathematical sciences. a recipient in 2006 of an alexander von humboldt Research award, and in 2007 of an Inaugural Fellowship to the durham University Institute of advanced Studies, Prof. Fellows spent much of 2007 and 2008 with research groups in Europe as an invited distinguished visiting researcher. he is an associate Editor for the Journal of Computer and Systems Sciences, and (since 2008) for the A.C.M. Transactions on Algorithms.

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8 Dr Brad Marsh

Senior Research Fellow and group leader

Institute for Molecular Bioscience the University of Queensland

dr Brad Marsh heads the Beta Cell Structural Biology/Cellular tomography group at the Institute for Molecular Bioscience at UQ. Brad is recognised internationally in the beta cell biology, membrane traffic and microscopy communities for his role in the groundbreaking development/application of large-area EM tomography for the detailed study of the 3d organization of the insulin-secreting pancreatic beta cell at high resolution. his research remains focused on understanding structure-function relationships related to insulin biosynthesis, processing and trafficking in situ in the beta cells of the endocrine pancreas. his work has been featured on the covers of Proceedings of the National Academy of Sciences USA (2001), Proceedings of Microscopy & Microanalysis (2001), Materials Today (2002), Traffic (2004, 2008), BBA Molecular Cell Research (2005) and Nucleic Acids Research (2006), and has been highlighted in high-impact publications including La Recherche (2001), Nature Reviews Molecular Cell Biology (2001, 2006), Journal of Cell Biology (2001), Current Opinion in Structural Biology (2002), Current Opinion in Cell Biology (2003), Molecular Cell Biology 5th Edition (2003), Essential Cell Biology 2nd Edition (2004), Genome Biology (2005), Australian Life Scientist (2006), Nature Chemical Biology (2007) and the 150th anniversary edition of Gray’s Anatomy (2008). his inaugural PNAS article (2001) has been lauded as a landmark (150 citations) by seminal leaders across a range of disciplines including structural biology, cell biology, diabetes research, and computational biology.

6 Dr Markus Hegland

Centre for Mathematics and its applications

Mathematical Sciences Institutethe australian national University

dr Markus hegland is a member of the Computational Mathematics Program at the anU’s Centre for Mathematics and Its applications. he is known internationally for his work on ill-posed problems, parallel solution of linear systems of equations and fast Fourier transforms, and, most recently in high-dimensional approximation. he has pioneered the application of numerical techniques, in particular sparse grids, in data mining applications. Finally he has developed chemical master equation solvers which were shown to work for up to 100 different chemical species. he was co-initiator of the australasian data Mining Conference (ausdM) and of the high-dimensional approximation workshop (hda), which annually attracts some of the most prominent researchers of the field world-wide to australia.

7 Prof. Geoffrey J. McLachlan

australian Professorial FellowProfessor and head, Mathematicsthe University of Queensland

Prof. geoff Mclachlan is internationally known for his research in statistics applied in the fields of classification, cluster and discriminant analysis, image analysis, intelligent systems, machine learning, neural networks, pattern recognition, and statistical inference. the focus in the latter has been on the theory and applications of finite mixture models, and on estimation via the EM (expectation-maximisation) algorithm. a common theme has been statistical computation, with particular attention to computational aspects of statistical methodology. this computational theme extends to the field of data mining. More recently, geoff has been actively involved in bioinformatics, focusing on the statistical analysis of microarray gene expression data. a joint wiley monograph on the analysis of microarray data was published in 2004. In 2006 he was awarded a Professorial Research Fellowship for the period 2007-2011 by the australian Research Council, and in 2007 was appointed to the aRC College of Experts. he is also Fellow of american Statistical association, australian Mathematical Society, Royal Statistical Society, and President-elect of the International Federation of Classification Societies.




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9 Prof. John Mattick FAA AO

Professor of Molecular Biology and aRC Federation Fellow


Prof. John Mattick stepped down as director of the Institute for Molecular Bioscience at the end of 2005 to take up an aRC Federation Fellowship, after serving as Foundation Co-director (together with Prof. Peter andrews) from 2000-2002, and as director from 2003-2005. he was Foundation director of the Centre for Molecular and Cellular Biology (previously the Centre for Molecular Biology and Biotechnology) from 1988-1999, Foundation director of the australian genome Research Facility from 1996-2002, and Foundation director of the aRC Special Research Centre for Functional and applied genomics from 2000-2002. his main research interest is the role of non-protein-coding Rna in the evolution and development of humans and other complex organisms. he was awarded the 1989 Pharmacia-lKB Biotechnology Medal from the australian Biochemical Society, an honorary Fellowship of the Royal College of Pathologists of australasia (2002), the Centenary Medal by the australian government (2003), the CSIRO Eureka Prize for leadership in Science (2006) and the Julian wells Medal of the lorne genome Society (2009). he was appointed an Officer in the Order of australia (aO) in 2001 for service to molecular biology and biotechnology, and elected as an associate Member of the European Molecular Biology Organisation in 2007 and a Fellow of the australian academy of Science in 2008. Prof. Mattick serves on the advisory boards of several institutes in australia and abroad. Professor Mattick receives no direct funding from the Centre.

10 A/Prof. Pablo Moscato

Priority Research Centre for Bioinformatics,

Biomarker discovery and Information-Based Medicine

the University of newcastle andInformation-based Medicine Programhunter Medical Research Institute

a/Prof. Pablo Moscato was founding director of the newcastle Bioinformatics Initiative (2002) and, in 2006, become the Co-director and Founder of the Priority Research Centre for Bioinformatics, Biomarker discovery and Information-Based Medicine of the University of newcastle, australia. he is also one of the four members of the Strategic Research advisory Panel of the hunter Medical Research Institute. he is a member of the editorial boards of Journal of Mathematical Modelling and Algorithms, Journal of Heuristics, and in 2008 Memetic Computing. Pablo introduced memetic algorithms in 1989 when he was a member of the Caltech Concurrent Computation Program, and has championed this field for two decades. he has shown how successful the application of these hybrid computing methodologies to large-scale problems in combinatorial optimisation and bioinformatics can be. Pablo has served on program committees of numerous international conferences in bioinformatics, heuristics and optimisation and is currently leading research programs in data analysis from high-throughput technologies as applied to the study of samples from alzheimer disease, multiple sclerosis, melanoma, and breast and prostate cancer.



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13 Prof. Xiaofang Zhou

School of Information technology & Electrical Engineering

the University of Queensland

Prof. Xiaofang Zhou is Professor of Computer Science at UQ, and head of the data and Knowledge Engineering program in the School of ItEE. he is also Convenor of the aRC Research network in Enterprise Information Infrastructure (EII), and Chair of the Steering Committee of the asia-Pacific web Conferences. Until 1999, Xiaofang was Principal Researcher and head of Spatial Information Systems within the Commonwealth Scientific and Industrial Research Organisation (CSIRO). Xiaofang is author of over 100 publications in spatial databases and information systems, grid computing, and bioinformatics.

11 Prof. Shoba Ranganathan

department of Chemistry and Biomolecular Sciences & Biotechnology Research Institute

Macquarie University

Prof. Shoba Ranganathan holds the first Chair in Bioinformatics in australia, at Macquarie University. She holds an adjunct Professor position at the national University of Singapore (since 2004). her research interests include genome annotation, transcriptome analysis, structural bioinformatics, immunoinformatics and genome-phenome analysis. Shoba’s achievements include the development of graph-theoretical methods for alternative splicing analysis, a rapid and accurate docking protocol for vaccine design, software tools for the analysis of protein sequence and for modelling protein structure, and the development of boutique databases. She pursues collaborations with research groups at the national University of Singapore and the Institute for Infocomm Research, Singapore. Shoba serves on the editorial boards of several bioinformatics journals including Briefings in Bioinformatics and BMC Bioinformatics, and contributes to the organisation and scientific program of several international bioinformatics conferences. She was re-elected as President of the asia-Pacific Bioinformatics network (2008-2011).

12 Dr Rohan D. Teasdale


dr Rohan teasdale holds a Senior Research Fellowship a from the national health & Medical Research Council. he leads a multidisciplinary research group at IMB that applies both cellular and computational techniques to investigate how subcellular compartments are generated and how proteins are trafficked within the mammalian cell. Rohan played a key role in the formation of Bioinformatics australia and is a member of its steering committee. Rohan has 65 research publications, with many papers in high-profile and leading bioinformatics and cell biology journals. these publications have focused on how individual proteins are compartmentalised within the cell and defining the protein trafficking machinery responsible for this process. In addition he has numerous publications outlining novel bioinformatics methodologies, database resources and collaborative projects.




15 Prof. Michael Langston

department of Computer ScienceUniversity of tennessee, USa

Professor Mike langston’s research interests include computational biology, graph theory, discrete optimization and high-performance computation. he is currently Professor of Electrical Engineering and Computer Science at the University of tennessee, and Collaborating Scientist in the Biosciences division at Oak Ridge national laboratory. Mike is lead investigator on a variety of research projects focused on the design and synthesis of combinatorial algorithms used to process high-throughput biological data. his collaborations extend across the US and to research groups in australia, Canada, Europe and the Middle East. he has worked closely for over twenty years with Professor Mike Fellows, and has authored over 200 refereed journal articles, conference papers, book chapters and other reports. Beginning in 2007, Mike led the development of the Bertinoro Systems Biology series of workshops. his work has been funded in the US by the national Science Foundation, the national Institutes of health, the department of defence and the department of Energy, and internationally by the australian Research Council and the European Commission.

Partner Investigators

14 Dr Isidore Rigoutsos

IBM thomas J. watson Research Center

yorktown heights, new york USa

dr Isidore Rigoutsos manages the Bioinformatics and Pattern discovery group at IBM’s thomas J. watson Research Center, and has been a visiting lecturer at MIt since 2000, where he teaches a Spring semester course and a Summer professional class in bioinformatics. Isidore is a Fulbright Scholar, and in 2003 was elected a Fellow of the american Institute for Medical and Biological Engineering. he serves on editorial boards of several journals in bioinformatics, and is a member of the advisory Board for the Master’s program in bioinformatics of Oxford University. he recently edited a two-volume book on Systems Biology (Oxford University Press, September 2006). his research activities currently focus on the computational study of Rna interference (Rnai) and its application to regenerative medicine and therapy, the study of cancer as a disruption of normal regulatory processes, the analysis of “junk” dna in animal and plant genomes, and meta-phylogenomics.

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16 Prof. Allen Rodrigo

director, Bioinformatics Institutethe University of auckland,

new Zealand

allen Rodrigo is Professor of Computational Biology and Bioinformatics, and associate dean of It at the Faculty of Science at the University of auckland. he has over 80 international publications on bioinformatics and computational biology, phylogenetics and evolutionary genetics, and the molecular evolution of viruses. allen is an associate Editor of Evolutionary Bioinformatics and on the Editorial Board of Mathematical Biosciences. he also sits on the Scientific advisory Board of two bioinformatics companies, is a Principal Investigator of the allan wilson Centre for Molecular Ecology and Evolution, and is involved in national and international collaborative projects on genomics and bioinformatics. his major research contributions are in the area of virus evolutionary genetics, where he has spearheaded the development of new methods to analyse time-series genetic data from viral populations.

Special advisor

17 Prof. Gene Myers

Janelia Farms Research Campushoward hughes Medical Institutesasburn, virginia USa

Prof. gene Myers was a foundation group leader at Janelia Farms Research Campus of the howard hughes Medical Institutes, near washington dC. gene has made fundamental contributions to computational molecular biology and bioinformatics, notably the BlaSt algorithm (1990) and whole-genome assembly (1999). he designed and led computer-based assembly of large genome sequences including those of fruit fly (2000), human (2001) and mosquito (2002). his research is now focusing on algorithms for fast image searching and comparison. gene’s numerous awards include the aCM Kannellakis theory and Practice award (2002), membership in the US national academy of Engineering (2003), the Max Planck Research Prize for International Cooperation (2004), induction into leopoldina, the german national academy (2006), and most recently an honorary doctorate from Eth Zürich. gene has been an honorary Professor in the Institute for Molecular Bioscience at UQ since 2003.

Information infrastructure

Mr Matthew Bryant System administrator, high-performance computing

Mr Oliver Cairncross Project Manager, visible Cell®

Ms Mhairi Marshall grid & database developer

Mr tim McComb (to October 2008) application developer

dr andrew newman (from december 2008) application developer

Mr timothy Sullivan (to October 2008) application developer

Mr david wood database administrator/developer

Centre Manager

Ms lanna wong, MBa

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Postdoctoral Fellows / Research Officers

dr Marjan asakarian-amiri

dr John Belward (part-time)

dr Mikael Bodén

dr Pamela Burrage

dr Qingfeng Chen

dr adrian Cootes

dr larry Croft

dr aaron darling

dr Melissa davis

dr Marcel dinger

dr gabriel Fung

dr Martin gómez-Ravetti

dr nicholas hamilton

dr Martin hansen

dr John hawkins

dr Karin Kassahn

dr Krzysztof Kurowski (to november 2008)

dr Kim-anh lê Cao (from november 2008)

dr Fawang liu (part-time)

dr Shev Macnamara

dr Igor Makunin

dr lorenzo Malquori

dr harald Oey

dr neelima Pottekkat Sidharthan

dr Fran Rosamond

dr Osvaldo anibal Rosso (to august 2008)

dr Muhammad Shoaib Sehgal

dr Zheng yuan

Research assistants

dr Cheong Xin Chan (to april 2008)

Ms Seetha Karunarathne

Mr lloyd Flack

Mr daniel Johnstone (from november 2008)

Ms Ranjeeta Menon

Ms Chikako Ragan

Masters/Phd students

Supervision/Associate supervision (principal advisor in ACB):

Farah abdullah (Phd awarded, 2008) advisor: Prof. Kevin Burrage

Paulo amaral (due to complete in 2010) advisor: Prof. John Mattick

Isye arieshanti (MPhil) (due to complete in 2009) advisor: dr Mikael Bodén associate advisors: dr timothy Bailey & dr Stefan Maetschke

Rajith aturaliya (Phd awarded, 2008) advisor: dr Rohan teasdale

denis Bauer (due to complete in 2009) advisor: dr timothy Bailey

durgaprasad Bollina (Phd awarded, 2008) advisor: Prof. Shoba Ranganathan

Fabian Buske (due to complete in 2012) advisor: Prof. John Mattick associate advisor: dr timothy Bailey

alhadi Bustamam (due to complete in 2009) advisor: Prof. Kevin Burrage associate advisors: dr nicholas hamilton & dr Shoaib Sehgal

Pierre Cattenoz (due to complete in 2011) (Co-tutelle with the University of Strasbourg) advisors: Prof. John Mattick, Prof. Eric westhof (University of Strasbourg)

Elsa Chacko (due to complete in 2011) advisor: Prof. Shoba Ranganathan

Cheong Xin Chan (Phd awarded, 2008) advisor: Prof. Mark Ragan associate advisor: dr Robert Beiko

Feng Chen (due to complete in 2010) advisor: a/Prof. Phoebe Chen

yan Chen (due to complete in 2009) advisor: a/Prof. Phoebe Chen

Joo-young Choi (due to complete in 2009) advisor: Prof. Mark Ragan associate advisor: dr Melissa davis

Khar heng Choo (due to complete in 2009) advisor: Prof. Shoba Ranganathan associate advisor: a/Prof. tan tin wee

Michael Clark (due to complete in 2010) advisor: Prof. John Mattick associate advisor: dr Rohan teasdale

adam Costin (due to complete in 2010) advisor: dr Brad Marsh

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alex Foo (due to complete in 2010) advisor: dr Brad Marsh

Jitendra gaikwad (due to complete in 2010) advisor: Prof. Shoba Ranganathan

Mohammad Islam (due to complete in 2010) advisor: Prof. Shoba Ranganathan associate advisor: dr abhaya nayak

Chol hee Jung (due to complete in 2009) advisor: Prof. John Mattick

John hawkins (Phd awarded, 2008) advisor: dr Mikael Bodén associate advisors: dr Rohan teasdale & Prof. Janet wiles

Mario Inostroza-Ponta (Phd thesis submitted, 2008) advisor: a/Prof. Pablo Moscato associate advisor: dr Regina Berretta

Javed M. Khan (due to complete in 2011) advisor: Prof. Shoba Ranganathan

varun Khanna (due to complete in 2011) advisor: Prof. Shoba Ranganathan

Keith Knapp (Phd to be awarded in april 2009) advisor: a/Prof. Phoebe Chen

Chin Foon Khoo (due to complete in 2009) advisor: dr Markus hegland

gaurav Kumar (due to complete in 2012) advisor: Prof. Shoba Ranganathan

Shev Macnamara (Phd awarded, 2008) advisor: Prof. Kevin Burrage

Robert Mcleay (due to complete in 2011) advisor: dr timothy Bailey

Scott Mann (due to complete in 2009) advisor: a/Prof. Phoebe Chen

Ranjeeta Menon (due to complete in 2011) advisor: Prof. Shoba Ranganathan

tim Mercer (due to complete in 2009) advisor: Prof. John Mattick

nurul Mohamad (MPhil) (due to complete in 2009) advisor: dr Mikael Bodén associate advisor: dr Rohan teasdale

Katrina Monico (due to complete in 2009) advisor: Prof. geoff Mclachlan

Shivashankar h. nagaraj (Phd awarded 2008) advisor: Prof. Shoba Ranganathan associate advisor: Prof. Robin gasser

Satu nahkuri (due to complete in 2009) advisor: Prof. John Mattick



Co-supervision (principal advisor not an ACB investigator)

agnes Boskovitz (Phd awarded, 2008) associate advisor: dr Markus hegland advisor: dr Rajeev goré

Michael Bode (Phd awarded, 2008) associate advisor: Prof Kevin Burrage advisor: Prof hugh Possingham

luke hammond (due to complete in 2009) associate advisor: dr nicholas hamilton advisor: Prof Jenny Stow

duncan Mortimer (Phd thesis submitted, 2008) associate advisor: Prof Kevin Burrage advisor: dr geoffrey goodhill

Radosav Pantelic (Phd awarded, 2008) associate advisor: dr nicholas hamilton advisor: dr Ben hankamer

Mitchell Stanton-Cook (due to complete in 2009) associate advisor: dr nicholas hamilton advisor: dr thomas huber

daniel Johnstone (due to complete in 2009) associate advisors: a/Prof. Pablo Moscato & Prof. Rodney Scott advisor: dr Elizabeth adrienne Milward

honours students

Rees Butterworth Geometric hashing for the discovery of protein binding surfaces advisor: dr Mikael Bodén

vinh dang Divergence in expression patterns and functions of duplicated genes in zebrafish (Danio rerio) advisors: Prof. Mark Ragan & dr Karin Kassahn

James Johnson Volunteer computing for statistical phylogenetics advisors: Prof. Mark Ragan & dr aaron darling

Pratishtha vedalankar The distribution of phosphoinositide binding proteins in the mammalian endosomes advisor: dr Rohan teasdale

International & national interns

International

Pricilia Boerleinder hogeschool Rotterdam, University of Rotterdam (the netherlands) advisor: dr Rohan teasdale

Khar heng Choo national University of Singapore (Singapore) advisor: Prof. Shoba Ranganathan associate advisor: a/Prof. tan tin wee

nikhil lilaria Indian Institute of technology, Bombay (India) advisor: Prof. Mark Ragan

Camille Maumet Institut national des Sciences appliqueés (France) advisor: Prof. geoff Mclachlan

National

nicole Maggacis the University of Queensland advisor: dr Rohan teasdale

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andrew noske (due to complete in 2009) advisor: dr Brad Marsh associate advisors: Prof. Mark Ragan & Prof. Kevin Burrage

timothy Pan (due to complete in 2011) advisor: dr Brad Marsh

Chang Jin Shin (due to complete in 2009) advisor: Prof. Mark Ragan associate advisors: dr Simon wong (to 2007) & dr Melissa davis

Elizabeth Skippington (due to complete in 2011) advisor: Prof. Mark Ragan associate advisor: dr thomas huber

Cas Simons (Phd awarded, 2008) advisor: Prof. John Mattick

Martin Smith (due to complete in 2011) advisor: Prof. John Mattick

Josefine Sprenger (due to complete in 2009) advisor: dr Rohan teasdale associate advisor: dr nicholas hamilton

Stuart Stephen (Phd awarded, 2008) advisor: Prof. John Mattick associate advisor: Prof. Mark Ragan

Chinnu Subramaniam (due to complete in 2012) advisor: a/Prof. Phoebe Chen

Sharnsheer Syed (part-time due to complete in 2012) advisor: Prof. Xiaofang Zhou

Ryan taft (due to complete in 2009) advisor: Prof. John Mattick

Selene Fernandez valverde (due to complete in 2011) advisor: Prof. John Mattick

Peter van der heide (due to complete in 2009) advisor: dr Brad Marsh

lawrence wee (Phd thesis submitted, 2009) advisor: Prof. Shoba Ranganathan associate advisor: a/Prof. tan tin wee

tom whitington (due to complete in 2011) advisor: dr timothy Bailey

Emily Zhou (Phd awarded, 2008) advisor: Prof. Xiaofang Zhou associate advisor: dr heng tao Shen

Jia Zhu (part-time, due to complete in 2011) advisor: Prof. Xiaofang Zhou

Justin Xi Zhu (due to complete in 2009) advisor: Prof. geoff Mclachlan associate advisor: dr angus ng





Undergraduate research trainees and volunteers

Zoran Boskovic Research trainee A software suite to integrate various regulatory network inference models advisor: dr Mohammad Shoaib Sehgal

andres Esteban Marcos Research trainee SeEvolution, 3D visualization of genomic evolution advisor: dr aaron darling

Michal lorenc Research trainee A plasma membrane visualisation advisor: dr Pamela Burrage

Cindy yan Undergraduate trainee/volunteer Conserved non-coding elements associated with duplicated zebrafish genes advisor: dr Karin Kassahn

visiting scholars, associates

Visiting sabbatical scholars

Prof. Michael Zuker, Professor of Mathematical Sciences, Rensselaer Polytechnic Institute (USa)

Associates

dr Jonathan arthur, Sesqui lecturer in Bioinformatics, University of Sydney

a/Prof. Ian atkinson, Information technology, James Cook University

Prof. Kaye Basford, head, School of land & Food Sciences, the University of Queensland

dr Robert Beiko, Faculty of Computer Science, dalhousie University (Canada)

Prof. lindsay Botten, director, national Computational Infrastructure, australian national University

dr Christopher Bouton, head, Integrative data Mining, Pfizer Research technology Center (USa)

Prof. vladimir Brusic, director of Bioinformatics, dana Farber Cancer Institute, Boston (USa)

Mr geoff Bulow, Queensland department of Primary Industries and Fisheries

Prof. gillian Bushell, dean (Research), Science, Environment, Engineering and technology, griffith University

dr Robert Charlebois, Sanofi Pasteur (Canada)

dr Brian dalrymple, CSIRO livestock Industries

Prof. Bernie degnan, School of Integrative Biology, the University of Queensland

Prof. werner dubitzky, head, Bioinformatics and Systems Biology, University of Ulster (northern Ireland)

dr dave Edwards, australian Centre for Plant Functional genomics

Prof. Charles Elkan, department of Computer Science and Engineering, University of California, San diego (USa)

dr Martin Frith, Computational Biology Research Center, national Institute of advanced Industrial Science and technology (Japan)

dr david green, high Performance Computing group, Information technology Services, the University of Queensland

Prof. Michael gribskov, Purdue University (USa)

dr Ben hankamer, Institute for Molecular Bioscience, the University of Queensland

dr david hansen, e-health Research Centre, CSIRO

dr James hogan, School of Software Engineering & data Communications, Queensland University of technology

dr lindsay hood, Cray Inc., Canberra

dr thomas huber, School of Molecular & Microbial Sciences, the University of Queensland

dr Philip hugenholtz, head, Microbial Ecology Program, US dOE Joint genome Institute (USa)

Prof. Jane hunter, School of Information technology & Electrical Engineering, the University of Queensland

dr lars Jermiin, School of Biological Sciences, the University of Sydney

Prof. Simon Kaplan, Executive dean, Faculty of Information technology, Queensland University of technology.

dr Jonathan Keith, Faculty of Science, Queensland University of technology

Prof. do han Kim, department of life Science, Seoul national University (Korea)

Prof. Sang yup lee, director, Bioinformatics Research Center, KaISt (Korea)

Prof. Peter lindsay, School of Information technology & Electrical Engineering, the University of Queensland; and director, aRC Centre for Complex Systems

dr alex loukas, Queensland Institute of Medical Research

Prof. Satoru Miyano, Institute of Medical Science, University of tokyo (Japan)

dr gary Morgan, director, australian e-health Research Centre, CSIRO

Prof. Mark Morrison, Science leader Metagenomics, CSIRO livestock Industries

a/Prof. william noble, department of genome Sciences, School of Medicine, University of washington, USa

Prof. Bernard Pailthorpe, CEO, Queensland Cyber Infrastructure Foundation

Prof. Jenny Stow, Institute for Molecular Bioscience, the University of Queensland

dr anne trefethen, Executive director, Oxford e-Research Centre (UK)

Prof. ah Chung tsoi, vice-President, Research & Institutional advancement, hong Kong Baptist University (hong Kong)

dr Mark wilkinson, department of Medical genetics, University of British Columbia and St Paul’s hospital vancouver (Canada)

Prof. Janet wiles, School of Information technology & Electrical Engineering, the University of Queensland

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visionthe aRC Centre of Excellence in Bioinformatics is a multi-nodal interdisciplinary Centre that applies genome-scale bioinformatics, computational science and advanced data technologies to empirical data on cellular structure and function, yielding a deep understanding of the mammalian cell as an information system.

Missionthe aRC Centre of Excellence in Bioinformatics is committed to research excellence, advanced education and training, interdisciplinarity, improved access to skills, tools and facilities, and building critical mass and national focus for cellular and ‘omic’ bioinformatics in australia.

aimswithin this mission, we aim to:

• Buildapowerfulnewbioinformaticsthat integrates insights and key developments in mathematics, statistics, computing science, information technology, genomics and molecular cell biology.

• Mutuallyenrichbiomolecularresearch,mathematics, computer science and It.

• Applythisnewbioinformaticstomake innovative use of advanced biomolecular technologies, with the result of illuminating the development and differentiation of the mammalian cell.

• Playaleadingroleinthenationalandinternational bioinformatics agenda and in the generation of human capital, enhancing critical mass and national focus in bioinformatics.

ObjectivesMore specifically, our objectives for the extension period will be to:

• Buildonthecapabilitiesandinterdisciplinary perspectives we have developed in the first phase of the Centre (2003-2007).

• Useempiricaldatafromadvancedmicroarray and tomographic technologies to construct quantitative dynamic models of selected cellular regulatory networks and subcellular systems.

• Developadvancedalgorithmic,statistical and computational methods and knowledge engineering systems, and apply them to extend, refine and inter-relate these models.

• Deliveradvancedprototypesofourintegrated data and visual framework for hypothesis-testing, validation and discovery, the visible Cell®, and use them to understand more fundamentally the mammalian cell as an information system.

Capabilities — core technologies and infrastructurethe integrated research programs of the aRC Centre of Excellence in Bioinformatics are underpinned by established strengths in mathematics, computing science, information technologies, cell and structural biology, and molecular and genomic biosciences.

Key capabilities include:

• Algorithmicsandcomputationalcomplexity

• Statistics,includingexpressionmicroarray statistics

• Patterndiscovery,machinelearningand adaptive optimisation

• Advanceddatabasearchitectures,including distributed and visual databases

• Specialisedmark-uplanguages,ontologies and semantic web technologies

• Computationalmodelling,includingstochastic, deterministic, and agent-based approaches

• Computationalsimulationusinghigh-performance parallel and distributed architectures

• Automateddiscoverypipelinesandworkflows in bioinformatics

• Advancedscientificvisualisation• Advancedmicroscopic,tomographic

and imaging technologies in cell biology• High-throughputmicroarray-based

genomic technologies• Multipleinterfacestoempirical

“wet” biology

Strategic direction 2008–2010

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Research Programs

Research programs highlightsthe Centre’s research in 2008 was delivered through four programs, each of which was further organized as two or three projects. the following pages describe the aims of each of these projects, the Centre and other personnel involved, and the main achievements during 2008.

as described elsewhere in this Report, 2008 was a year of transition from the initial phase of our Centre to our new Centre of Excellence. we welcomed four new Chief Investigators and their research groups, while three of our former Chief Investigators did not continue with us. this renewal is strongly reflected in our realigned Research Programs and Projects. In place of three Programs we now have four, and in place of 13 Projects we now have 11.

no simple mapping exists between our former Projects and those in our new Centre of Excellence. two have been brought forward largely intact, and three were discontinued. the other eight, however, have been re-mixed with the goal of better exploiting synergies, whether arising from our previous work or from our new Investigators and directions. we sharpen our research focus on cellular networks, separating discovery and inference (our new Program 2) from mathematical modelling (our new Program 3), with the latter incorporating modelling activity formerly managed as part of our visible Cell® project. two Projects in our Centre of Excellence are entirely new.

Chief Investigators in our new Programs 2 and 4 met in newcastle on 22 august 2008 to refine program goals, agree on datasets, and develop timelines. Personnel in Programs 1 and 3 similarly met in Brisbane on 10 October 2008. Our detailed activity plans for 2009 are set out in a separate, closed document that will be submitted to aRC concurrently with this annual Report.

In Program 1, we develop an integrative data and visualisation framework, the visible Cell®, that allows biologists and modellers to interact with mammalian cells reconstructed from 3d electron tomographic or fluorescence confocal images, annotate cell structures using federated data (sequences, structures, pathways, networks, literature), and conduct quantitative analyses. we also develop tools and an interface to manage the analysis and integration of very large biomolecular data.

Information flows from genome to phenome through complex molecular networks and systems, and in Program 2 we examine the signals, pathways and regulatory mechanisms by which these networks operate and interconnect. algorithmic and statistical approaches are being focused on understanding which pathways and networks are up- or down-regulated in complex disease including cancer, and on the discovery of new pathways and sub-networks. this Program includes innovative approaches to the discovery and modelling of Rna-based regulatory networks in mammalian cells.

Computational modelling and simulation allow us to describe the operation of these networks in dynamic, quantitative terms. Key biomolecules often occur transiently, in extremely small numbers and/or in highly restricted locations. Cellular structures move too, driven by mechanical or thermodynamic forces that are highly susceptible to mathematical modelling. In Program 3 we construct computational models of molecular networks and of the subcellular structures through which they transduce information to the cellular phenome. One of the main goals of our extended Centre will be to embed these models in the visible Cell®, making it a dynamic environment for hypothesis-generation and -testing.

Representing molecular networks and systems mathematically requires us to work with large numbers of graphs, and Program 4 develops powerful algorithmic and combinatorial approaches that will make our models computationally tractable. these include data-reduction strategies, implementation of scalable algorithms for problems on very large graphs, and novel computational techniques to make very large problems computable on actual hardware.

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Research programs 2008-2010

Program 1 The Visible Cell®: linking genome and phenome

1.1 generation of subcellular localisation data in mammalian cells

1.2 Project and data management for visible Cell®

1.3 data analysis and knowledge discovery in very large biological network databases

Program 2 Phenotype-informed discovery of networks and systems

2.1 Computational discovery and modelling of gene-regulatory networks

2.2 differential expression of genes towards pathway discovery

2.3 discovery and modelling of Rna-based regulatory networks

Program 3 Modelling dynamic cellular processes

3.1 Mathematical modelling of genetic regulatory networks and biochemical pathways

3.2 Modelling and visualising biological processes in complex spatial environments

Program 4 Algorithms for graphs and networks

4.1 discrete optimisation and graph clustering

4.2 Optimisation-based approaches to large systems

4.3 External-memory algorithms for analysis of massive graphs





Program 1 –the visible Cell®: linking genome and phenome

1.1 generation of subcellular localisation data in mammalian cells

Investigators:

dr Rohan teasdale (the University of Queensland)

Prof. Mark Ragan (the University of Queensland)

In collaboration with:dr Christopher Bouton (Pfizer RtC, Cambridge, Ma USa)

Prof. Kevin Burrage (the University of Queensland)

Prof. Jane hunter (the University of Queensland)

Prof. John Mattick (the University of Queensland)

Prof. Shoba Ranganathan (Macquarie University)

Prof. Mark Smythe (the University of Queensland)

Prof. Xiaofang Zhou (the University of Queensland)

Researchers:

Research Associates:dr Melissa davis (the University of Queensland)

dr nicholas hamilton (the University of Queensland)

Ms Seetha Karunaratne (the University of Queensland)

dr Karin Kassahn (the University of Queensland)

dr Zheng yuan (the University of Queensland)

PhD students:Ms Joo-young Choi (the University of Queensland)

Mr Chang Jin Shin (the University of Queensland)

Ms Josefine Sprenger (the University of Queensland)

Aims:

Because eukaryotic cells are highly compartmentalised, a protein’s function is tightly enmeshed with its location (more precisely, the distribution of its location). Knowing the latter can greatly improve prediction of its function, while conversely, a comprehensive protein inventory is critical to understanding the function of cellular compartments. this project aims to generate unique primary data on subcellular localisation of proteins in mammalian cells, and make these data available via value-added data resources for further integration, analysis, computational modelling, simulation and visualisation.

Achievements (2008):

(a) we developed novel statistical tests for distinguishing subcellular imaging, and used them in the automatic discovery of proteins whose localisation has changed under e.g. drug treatment. we showed these tests to be more sensitive than any other available, and to be able to detect subtle changes such as endosomal redistribution. a paper describing the methods is currently under review for BMC Bioinformatics, and software supporting the methodology is being made available under open source license (hamilton, teasdale).

(b) a paper describing the iCluster high throughput image visualisation tool appeared in BMC Bioinformatics and was rated highly accessed. iCluster enables large image sets (~1500 images) to be viewed and interacted with in 3d. a presentation on iCluster at the inaugural hunter Imaging workshop (March 2008) led to an invited review by hamilton on quantification of subcellular imaging for the journal Traffic; the manuscript is under review (hamilton, teasdale).

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(c) we developed high-throughput microarray-based screening of ~12,000 ncRnas and ~30,000 mRnas to determine their nuclear or cytoplasmic location, and are initiating medium-throughput semi-automated in situ hybridisation approaches, combined with computational algorithms developed by nick hamilton, to identify ncRnas associated with known and novel cellular compartments. In association with dr Bodo lange (Max Planck Institute for Molecular genetics, Berlin) we identified three ncRnas associated with centrosomes, and in association with dr david Spector (Cold Spring harbor laboratories) showed that a ncRna induced upon muscle differentiation is an essential structural component of a sub-nuclear domain called paraspecles (Genome Research 2009) (Mattick, teasdale).

(d) we applied the ElPP pipeline, generating subcellular localisation data for an additional 50 proteins within the mouse proteome. within 2008 we redirected this project to a focused set of proteins predicted to encode phosphoinositide-binding domains (teasdale, Karunaratne).

(e) we defined the nuclear proteome by integrating data from the lOCatE database with data generated from the ElPP and literature-mining (teasdale, Karunaratne). this major body of work was published in the high-impact journal Genome Biology.

(f) we maintained the lOCatE Subcellular localisation database, and added predictive subcellular localisation data based on the most-accurate prediction algorithms (teasdale, Sprenger).

(g) we predicted features of proteins relevant to their subcellular localisation, e.g. transmembrane domains (tMds) and localisation signals (teasdale, yuan).

(h) we are developing resources to enable a systems biology approach targeted at the mammalian endosome. By combining protein-protein and gene expression networks we are developing target sets of interest for shRna knockdown phenotype assays (teasdale, Sprenger).





(i) we are currently developing experimental methodologies to determine the subcellular distribution of ncRna with the cell (Mattick, teasdale).

(j) By computational analysis of five fish genomes, postdoctoral researcher dr Karin Kassahn identified mechanisms by which genes that have arisen by whole-genome duplication have partitioned existing function or taken on new function. novel regulatory control was identified by new patterns of temporal and/or spatial expression during embryogenesis. a comprehensive manuscript was submitted in december 2008 (Ragan).

(k) Phd student Chang Jin Shin completed the mapping of orthologs from proteomes of model organisms where subcellular localisation is well-known, to the human proteome, and identified six parameters (three biological, three annotation-related) that strongly influence the quality of the mapping. the lOCatE database, developed within aCB by CI Rohan teasdale and colleagues, provided data for validation. a manuscript was accepted at BMC Systems Biology for publication in 2009. analysis of interologs was largely completed during 2008, and a manuscript has been invited for a special issue of Proteomics (Ragan).

(l) Because determining ortholog sets is computationally expensive, we collaborated with CI Mike Fellows to explore FPt versions of VeRtex CoVeR algorithms (Project 4.1). a joint manuscript was submitted for publication in a tier a mathematics journal (Fellows, Ragan).

(m) Because interacting proteins must at least transiently or conditionally be physically co-located, subcellular localisation constrains inference of protein-protein interaction (PPI). Postdoctoral researcher Muhammad Shoaib Sehgal implemented subcellular localisation information within a multi-stage Bayesian classifier for inference of network function; MatlaB code was developed and made available to collaborators, and a manuscript was initiated (Burrage, Ragan).

(n) data resources including for protein-protein interactions and pathways were migrated to Resource description Framework (RdF). with Professor Jane hunter and dr Christopher Bouton we demonstrated the use of Semantic web technologies SPaRQl and SwRl to query and reason-over subsets of these data. although the BioManta collaboration with Pfizer was concluded, these technologies were transferred to the core visible Cell® environment (Project 1.2) leading to an applications note in Bioinformatics (2009) focused on semantic capabilities of the visible Cell® visualisation environment Illoura™ (Cairncross, Marsh, Ragan).

(o) Separately from the BioManta collaboration, MSc student Joo-young Choi and postdoctoral researcher Melissa davis identified data sources and standards for description of small molecules (e.g. drugs and drug-like compounds), converted them to RdF, and demonstrated the use of SPaRQl and SwRl to query jointly over small-molecule and biomolecular data. Ms Choi demonstrated that complex rule sets, e.g. lipinski’s Rule of Five, can be represented as SwRl rules and used within a reasoning framework. Posters were presented at two international conferences. we continue to work with IMBcom to protect intellectual property in this project (Ragan).

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1.2 Project and data management for visible Cell®

Investigators:

dr Brad Marsh (the University of Queensland)


Project Manager:

Mr Oliver Cairncross (aRC Centre of Excellence in Bioinformatics)

In collaboration with:dr Melissa davis (the University of Queensland)



Researchers:

Research Associate:dr neelima Sidharthan (the University of Queensland)

Research staff:dr tim McComb (aRC Centre of Excellence in Bioinformatics)

Mr david wood (Queensland Facility for advanced Bioinformatics)

PhD students:Mr andrew noske (the University of Queensland)

Mr timothy Pan (the University of Queensland)

Mr Peter van der heide (the University of Queensland)

Aims:

a defining characteristic of our visible Cell® is its spatial matrix: an actual mammalian cell, imaged at high resolution using the advanced cryo-electron microscopy facilities at UQ. For each cell this matrix can be up to 10 tB in size, depending on how we compress certain data. In the first phase of our Centre, we designed, constructed and implemented a computational and data infrastructure that can handle tB image files and links to scaleable data grid environments.

this Project aims to integrate cellular reconstruction and bioinformatic data by incorporating a specific ontology and novel methods of processing semantic data, yielding a world-first visible Cell® prototype environment. this environment will streamline querying, analysis and visualisation of cellular reconstructions enriched with external sequence, structure, pathway, network and functional data. It will provide data and parameters to drive simulations based on the enriched data, support semantic querying and other application in systems biology (Project 1.1), and utilise national e-research and other infrastructure initiatives.


(a) neelima Sidharthan, timothy Pan and Brad Marsh established an in-house program for identifying factors that regulate/modulate key functions of the mammalian pancreatic beta cell, using a natural product discovery/multi-modal screening approach.

(b) andrew noske, Peter van der heide and Brad Marsh developed methods and generated primary data that provide proof-of-concept for a 3d visible Cell® atlas. this will involve technology development and proof-of-concept for high-resolution (<5 nm) and intermediate resolution (10-20 nm) whole-cell electron microscope tomography.

(c) the same group developed mathematical methods for pre- and post-processing cellular electron tomography data that expedite segmentation, quantitative analysis and computational simulation.

(d) to provide high-speed access to arbitrary subsets of large topographic data, in 2008 the visible Cell® development team led by Oliver Cairncross coded and implemented an export utility from Oracle into IMOd format. we can now build a tomogram file (or a subsection of one) much more quickly than can be done using the command-line utilities in IMOd.

(e) In 2008 we completed the implementation of the Illoura™ data structure in RdF. Oliver Cairncross and tim McComb developed and implemented a reasoner in lISP and SPaRQl that makes spatial data that do not natively have semantic value available, in semantic format, on-demand to inference engines. this solution appears to be general for spatially resolved data, not only in bioscience. we demonstrated semantic querying jointly over spatial (cell tomographic) and biomolecular pathway data. an applications note was submitted to Bioinformatics and will appear in early 2009.

(f) we explored out-of-memory execution of queries over tomographic data using new Semantic web functionality in Oracle 11g, but have postponed decision on whether to integrate it into Illoura™.

(g) david wood, Oliver Cairncross and tim McComb implemented a bridge between the Illoura™ visualiser and SRS, allowing SPaRQl queries to seamlessly incorporate information found in federated data sources. this bridge is described in some detail in the Illoura™ web pages.

(h) we continue work to extend the query engine so queries can be distributed across multiple machines and query handlers; this will add scalability to the query engine and will allow e.g. the offloading of a computationally complex routine to a purpose-built query handler. In 2008 we re-implemented some computationally intensive aspects of key queries in C++.

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(i) we shifted functionality in the vtK visualisation library from Illoura™ to external J3d code. In view of other priorities, we chose not to undertake major modification of the user interface during 2008.

(j) with the wrap-up of BioManta, we did not further augment the visible Cell® ontology to support queries of protein accessibility for intercellular components, or refine protein-protein interaction maps. we continue to develop the core architecture to enable better interaction with external data stores, modelling environments and software.

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1.3 Data analysis and knowledge discovery in very large biological network databases

Investigators:


Prof. Xiaofang Zhou (The University of Queensland)

In collaboration with:Prof. Alon Halevy (University of Washington)

Dr Brad Marsh (The University of Queensland)

Prof. Mark Ragan (The University of Queensland)

Dr Rohan Teasdale (The University of Queensland)

A/Prof. Wei Wang (University of North Carolina)

Researchers:

Research Associates:Dr Adrian Cootes (Macquarie University)

Dr Gabriel Fung (The University of Queensland)

PhD student:Mr Gaurav Kumar (Macquarie University)

Aims:

The Visible Cell® project typifies the data-analysis and knowledge-discovery challenges of omic bioinformatics, including demands for efficiency with very large data, complex data types and relationships, and multiplicity of sources and formats – problems exacerbated by the explorative nature of data analysis in biology. This project addresses these issues by (1) development of a portal that will investigate a new “pay-as-you-go” approach to data integration, allowing biologists to specify just-enough data mappings for a task. It thereby offers low upfront overhead and the ability to evolve with changes in data sources. The key to this incremental, collaborative approach will be a tool that supports online community annotation, automatic consistency enforcement for data mappings, dataset and resource discovery, dynamic dataset membership, data uncertainty and lineage analysis; and (2) data mining that models data and metadata as graphs, and automates the detection of frequent sub-graphs. Initial application will be to RDF diagrams, to sub-structures of protein surfaces indexed by frequency of geometric graphs, and to semi-automatic data linking (where topological structure similarity among annotations labelled differently due to semantic heterogeneity can be automatically detected and reported for the human user to verify). These tools will allow users of our Visible Cell® to specify only the biological data needed to address each question, without our having to incur the upfront cost of fully inter-relating all data across the hundreds of data sources we are mirroring.


(a) Dr Gabriel Fung was co-located with Visible Cell® core development team (Project 1.2) for around 3 months in early 2008 to establish common objectives and mutual understanding of problems and technologies. We identified some major datasets (bio-literature, protein data) and scenarios (literature mining, name entity resolution, data integration) for problem formulation, characterisation, prototyping and testing. We identified potential users, and surveyed basic user requirements for usability and scalability. Several papers and posters appeared in 2008, and a manuscript dealing with entity resolution was prepared (Fung, Zhou).

(b) We constructed an integrated database linking SCL data from the LOCATE database (developed within the project) with protein interaction and metabolic reaction network data for human and mouse, and conducted preliminary analyses examining the utility of applying protein interaction and metabolic networks to the problem of SCL prediction. Details of the integrated database and some of the preliminary analysis were presented as a poster at GIW-2008. We are currently using this work as the basis for a network-based SCL prediction scheme, and are using InParanoid ortholog-prediction algorithm to extend both experimental and literature-based SCL data for human and mouse in the LOCATE database to a number of other species (Ranganathan).

(c) We identified conserved functional modules in human, fly and yeast protein interaction networks using the PHUNKEE network-comparison algorithm, developed previously by members of the project. We analysed SCL of the conserved functional modules using data from the LOCATE database, and demonstrated that the modules from these species mostly represented processes taking place in the cell nucleus, e.g. DNA repair. This work was presented as a poster at ECCB-2008 in Italy (Ranganathan).

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(d) we constructed another integrated database designed specifically for network-based protein function prediction across multiple species. the database integrates protein interaction, sequence similarity relationships, function and SCl data from a variety of sources. we conducted a detailed preliminary analysis of this data for the purpose of evaluating various techniques for function prediction. we developed a sophisticated network-based function prediction methodology based on this initial work; the function-prediction analysis is ongoing. this work will eventually be integrated with the SCl work mentioned in (b) above (Ranganathan).

(e) we reviewed the literature on protein function and disease in relation to biological networks, and initiated writing a manuscript “Protein networks, function and disease” (Cootes, Ranganathan).

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Transcriptionfactor

Count matrix

DNA

A 2 1 20 10 5 5 30

C 30 2 10 10 5 10 5

G 5 30 5 10 20 15 4

T 3 7 5 10 10 10 1

Regulatoryregion

Quantitative TF concentrations

Predicted quantitativegene output

Model

TF1 TF2 TF3

Concentration

Output

Concentration



Program 2 – Phenotype-informed discovery of networks and systems

2.1 Computational discovery and modelling of gene-regulatory networks

Investigator:

dr timothy Bailey (the University of Queensland)

In collaboration with:a/Prof. Phoebe Chen (deakin University)

Prof. geoff Mclachlan (the University of Queensland)


a/Prof. Osamu Maruyamu (University of Kyushu)

a/Prof. Pablo Moscato (the University of newcastle)

a/Prof. andrew Perkins (the University of Queensland)

Researchers:

Research Associates:dr Mikael Bodén (the University of Queensland)

dr John hawkins (the University of Queensland)

Research staff:Mr david wood (Queensland Facility for advanced Bioinformatics)

PhD students:Ms denis Bauer (the University of Queensland)

Mr Robert Mcleay (the University of Queensland)

Mr thomas whitington (the University of Queensland)

Aims:

this project aims to:

(a) Construct gene-regulatory sub-networks incorporating regulation by transcription factors (tFs) and non-coding Rnas (ncRnas).

(b) Build static computational models of the transcriptional output of a gene under the control of tFs and ncRnas.

(c) develop useful software tools implementing the above prediction and modelling tasks, and make them available to the international research community


(a) thomas whitington developed and published in Nucleic Acids Research an approach for making tissue-specific predictions of functional transcription factor binding sites. his method combines tissue-specific chromatin modification data (histone methylation) with standard in silico binding site prediction.

(b) dr John hawkins developed and published theoretical analyses of the power of comparative genomics-based transcription factor binding site prediction methods. this work confirmed the high degree to which functional binding sites are not fixed in the genome, but “drift” or are lost during evolution. dr hawkins implemented a new sequence search algorithm that takes these facts into account in order to improve in silico prediction accuracy. the first part of this work was published in RECOMB, and the second part has been submitted to ISMB, the premier conference in bioinformatics.

(c) dr Mikael Bodén developed an algorithm for predicting the association of gene Ontology terms with transcription factors. this aids in the discovery and characterisation of transcription factor motifs, which are vital components in building gene-regulatory models. this work was published in Nucleic Acids Research. Fabian Buske integrated this algorithm into the MEME suite of motif-based sequence analysis tools, making its functionality available via the web to biologists worldwide. Fabian also extended the method to utilize conservation information, and a manuscript is in preparation.

(d) Robert Mcleay studied improved ways to discover transcription factor binding motifs in chromatin immunoprecipitation data. this work revealed that the sensitive statistical methods for scoring motifs suggested by other researchers do not work as reported. a simpler scoring method developed by our colleague dr Martin Frith is superior. Robert is preparing a manuscript describing these results.

(e) denis Bauer continued the development and testing of a model of transcriptional output of the Drosophila EvE gene. She demonstrated that the model can predict regulatory modules in other species, and explored numerous model optimisation strategies. denis also created, published and made freely available STREAM, the first workbench for constructing static regulatory models. this work resulted in articles in Bioinformatics and BMC Bioinformatics, and a third manuscript has been submitted for review.

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2.2 differential expression of genes towards pathway discovery

Investigator:


In collaboration with: dr Regina Berretta (the University of newcastle)

a/Prof. Phoebe Chen (deakin University)


dr Muhammad Shoaib Sehgal (the University of Queensland)

Researchers:

Research Associate:dr Kim-anh lê Cao (the University of Queensland)

Research Assistant:Mr lloyd Flack (the University of Queensland)

Aims:

this project aims to:

(a) Extend statistical methods based on estimates of the empirical null appropriate for non-independent samples, and develop guidelines for their use.

(b) develop pathway-aware modifications to the minimum class entropy approach to univariate quantisation developed jointly by Chen and Moscato, and to the combinatorial approach pioneered by Moscato.

(c) thereupon undertake a unique cross-comparison of these three approaches based on public-domain microarray datasets, comparing results against annotated pathways to find the conditions under which each approach best recovers known genetic regulatory pathways or modules.

(d) More generally, investigate the benefits of pathway-centric methodologies for improving classification in data from microarray expression studies.


(a) we developed and applied new statistical methods to analyse biological data produced by CIs in the Centre, in particular by the Mattick laboratory (Mclachlan).

(b) during 2008, Moscato and Berretta collaborated on a study using a prostate cancer gene expression data (true et al., PNAS 2006). the overarching aim was to investigate the link between the tP53 network, its robustness, and its putative role to stratify the samples into groups. analysis of the tP53 network of Kuhn et al. (first proposed in 1999) led to a new “pathway-aware” method to uncover the consequences of altered signalling events. a manuscript will be submitted in 2009 (Moscato).

(c) the newcastle group analysed four genome-wide microarray datasets in prostate cancer; they will be integrated with other datasets available centrally in aCB, with the goals of helping new members of our groups to understand the available information, and facilitating collaborative analysis using both statistical and combinatorial optimisation approaches (Mclachlan, Moscato).

(d) we considered the formal development of statistical methods for inferring networks, including measures of uncertainty about each link in the inferred network. these methods will be applied to inferring gene networks and miRna networks using corresponding expression data (Mclachlan).

(e) we continued with the development of user-friendly software implementing EMMIX-FdR, EMMIX-gEnE and EMMIX-wIRE for use in the statistical analysis of gene-expression and other high-throughput data (Mclachlan).

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2.3 discovery and modelling of Rna-based regulatory networks

Investigators:




In collaboration with:dr tim Bailey (the University of Queensland)

dr Regina Berretta (the University of newcastle)


dr Colleen nelson (translational Research Institute, Princess alexandra hospital)

dr Carlos Riveros (the University of newcastle)

Researchers:

Research Associates:dr Qingfeng Chen (deakin University)

dr Marcel dinger (the University of Queensland)

Research Assistant:Mr david wood (Queensland Facility for advanced Bioinformatics)

PhD student:Mr Feng Chen (deakin University)

Aims:

(a) apply microarray technologies to discover novel non-protein-coding Rnas (ncRnas) involved in the control of in mammalian systems under selected conditions of development, health and disease.

(b) Infer and characterise Rna-based regulatory networks involved in these systems, and identify the molecular interactions by which this control is transduced.

(c) Characterise candidate ncRnas transcripts in human, and identify their homologs in other mammalian and vertebrate genomes and transcriptomes.

(d) Identify evolutionarily conserved secondary structures in ncRnas and construct hypotheses concerning their function.


(a) Using the v1 and v2 microarray chips, we generated novel expression signatures encompassing both protein-coding and non-protein-coding transcripts in tissue samples from breast cancer (Mattick), as well as a variety of differentiating cell systems including embryonal stem cells, neural stem cells, t-lymphocytes, muscle cells, epithelial cells, and the developing gonadal ridge. we are developing our collaboration with dr Colleen nelson (QUt) to extend these studies to prostate cancer, as well as with dr Charles Perou (University of north Carolina) and dr Jeff Rosen (Baylor College of Medicine) to further the analysis of ncRna expression and function in breast development and breast cancer.

(b) we developed a database of ncRna expression (dinger et al., Nucleic Acids Research, 2009) and recruited a dedicated postdoctoral scientist (due to start in april 2009) to integrate and deposit data from all available sources (including in-house experiments) into a central data store, annotate them, via linkage to genomic coordinates, with predicted binding sites for transcription factors, miRnas, ncRnas and other novel regulators, and make them available for analysis using a range of approaches available within the Centre (Bailey, Chen, Mclachlan, Moscato), and with advanced network inference and visualisation tools provided by the Queensland Facility for advanced Bioinformatics.

(c) Using data sources including Rnadb (Mattick) and nOnCOdE (liu et al.), we formalised and standardised the description of ncRna secondary-structure features including bulges, stems and loops. we applied data-mining technologies to extract these features, and related them to annotated function. we developed filters specific to organisms, developmental states and diseases, and used these reduced data for further data-mining. From this we developed a causality matrix that relates a putative ncRna to an identified ncRna class or group. a manuscript was accepted for publication in IEEE Transactions on Knowledge and Data Engineering (Chen).

(d) we developed methods to predict the function of ncRnas by similarity of expression pattern with ncRnas of known function, characterised these ncRnas based on the annotation of their transcripts, and cluster them into groups. a manuscript was submitted (Chen).

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(f) during 2008 we explored external funding possibilities for a project that would use v1 and v2 chips to generate novel expression signatures encompassing both protein-coding and non-protein-coding genomic regions in tissue samples from prostate cancer, melanoma and breast cancer (Mattick, Moscato). an agreement now exists to put this forward for 2010, while we try to collect more evidence and pilot data on the role of non-coding Rna in the diseases currently studied by Moscato at the newcastle node of aCB. at present, thanks to a collaboration also involving dr Marcel dinger (UQ) and dr Carlos Riveros (CIBM-newcastle), we are trying to establish a pilot study from existing Illumina datasets on the role of non-protein-coding genomic regions as markers of disease subtypes in prostate cancer, melanoma and breast cancer (Mattick, Moscato). the datasets have been obtained thanks to an existing collaboration with Prof. Peter hersey (CIBM-newcastle) or are in the public domain. we expect the analysis to be first priority by mid-2009, when the newcastle node concludes a set of three manuscripts, currently in preparation, on protein-coding regions and their differential expression in melanoma metastasis.

(g) In a separate project, Moscato and his group are developing a method to find a minimum set of putative transcription factors that can be linked to a set of differentially expressed genes, i.e. to identify putative subsets of gene-expression regulators, of minimal cardinality, that “explain” a major transcriptional change between groups of samples. the method is general and can be applied to regulation by miRnas. the Bailey group will provide lists of predicted target genes for selected human transcription factors with known binding motifs; target predictions will use the comparative genomics-based methodology developed by Centre postdoctoral researcher John hawkins (Project 2.1).

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Program 3 – Modelling dynamic cellular processes

3.1 Mathematical modelling of genetic regulatory networks and biochemical pathways

Investigators:


dr Markus hegland (australian national University)

In collaboration with:Prof. Manuel Barrio (vallodolid University, Spain)

Prof. Simon davis (Oxford University, UK)

Prof. James dehnam (the University of newcastle)

dr nicholas hamilton (the University of Queensland)

Prof. John hancock (University of texas, houston)

Prof. des higham (University of Strathclyde, UK)

dr tatiana Marquez lago (Eth, Switzerland)

dr andré leier (Eth, Switzerland)

dr grant lythe (University of leeds, UK)


dr Carmen Molina-Paris (University of leeds, UK)


dr tianhai tian (Monash University)

Prof. Jordi villa (University of Barcelona, Spain)

Researchers:

Research Associates:dr John Belward (the University of Queensland)

dr Pamela Burrage (the University of Queensland)

dr Fawang liu (the University of Queensland)

dr Shev Macnamara (the University of Queensland)

dr Muhammad Shoaib Seghal (aRC Centre of Excellence in Bioinformatics)

Research staff:Mr tim Sullivan (aRC Centre of Excellence in Bioinformatics)

PhD students:Mr alhadi Bustamam (the University of Queensland)

Ms Chin Foon Khoo (australian national University)

Aims:

(a) we will explore quantitative mathematical models of genetic regulatory networks and kinase signalling pathways using stochastic differential equations and other mathematical formalisms, and simulate these models in computer code, in some cases marked-up in MathMl so that they can be imported, via SMBl, into the visible Cell® environment (Program 1).

(b) we will develop new stochastic models for understanding the behaviour of molecular clocks in mouse, and somite formation in zebrafish, that incorporate delayed effects that arise from delays in transcription and translation.

(c) we will develop collaborations with immunologists in the UK with the aim of studying the immune system via modelling of the interrelationships among t cells, d cells and B cells.

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(a) we developed new stochastic simulation techniques for solving a wide class of important stochastic differential equation problems (Burrage, lythe), and applied some of these simulation techniques to examine how the effects of intrinsic and extrinsic noise can accelerate and stabilise juxtracrine pattern formation (Burrage, Rudge).

(b) we developed multiscale methods for biochemical kinetics based on tau leaping and other approaches, with the aim of improving performance so that larger biochemical problems can be solved over longer time periods (Burrage, villa).

(c) we developed delayed stochastic models for molecular clocks in mouse (hes1 gene) and somite formation in zebrafish (Burrage, leier, Marquez lago). these techniques are of a multi-scale nature, so we can simulate much larger problems than was previously the case.

(d) we developed efficient and effective Krylov and steady-state techniques for solving the Chemical Master Equation for the mitogen-activated protein kinase cascade (Burrage, hegland, Macnamara, Sidje). this is the first time that such large chemical-kinetic problems have become solvable by these techniques.

(e) we developed spatial and temporal models for investigating the human immune system, and the interrelationships among t cells, d cells and B cells (Burrage, Macnamara, davis, lythe, Molina-Paris).

(f) we developed new, computationally efficient techniques for studying the properties of large molecular-interaction networks (Seghal, Burrage, Bustamam).

(g) during 2008, Moscato and Phd student Mario Inostroza-Ponta developed a parallel, scalable algorithm for non-hierarchical clustering. gene-expression datasets with relatively good annotation (e.g. yeast) were studied for validation of the technique in a real scenario with very good success. later the method was used in cancer datasets to find deregulated sets of genes and their associated putative common regulators (transcription factors and miRnas). the methods were discussed in Mario’s Phd thesis, which was examined and approved in late 2008. Several publications are likely to arise from these results.

(h) In a collaboration involving Prof. James denham (newcastle), Moscato and Phd student Mario Inostroza-Ponta analysed data from a prostate cancer trial. the purpose was to categorize longitudinal radiation-induced rectal toxicity data obtained from men participating in tROg 96.01, a randomised controlled trial for locally advanced prostate cancer. Our algorithm showed seven well-defined clusters of rectal symptoms, with 25 seen immediately following radiation and 7 at years 1, 2 and 3 following radiation. the conclusion is then that the widely used CtC grading does not accord with the degree of rectal “distress” and “problems’” at all time points, and reveals serious shortcomings for clinical use. On the positive side, our results open opportunities for us to develop genomic profiling and detailed patho-physiological studies in prostate cancer management. a paper in Radiotherapy & Oncology was published electronically (24 October 2008) ahead of print publication in 2009 (Capp, Inostroza-Ponta et al.).

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3.2 Modelling and visualising biological processes in complex spatial environments

Investigators:


dr Markus hegland (australian national University)

In collaboration with:dr nicholas hamilton (the University of Queensland)

Prof. John hancock (University of texas, houston)

dr tatiana Marquez lago (Eth, Switzerland)

dr andré leier (Eth, Switzerland)


Mr dan nicolau Jr (Oxford University)

dr Rohan teasdale (the University of Queensland)

a/Prof. Peter thorn (the University of Queensland)

Researchers:

Research Associates:dr John Belward (the University of Queensland)

dr Pamela Burrage (the University of Queensland)

dr Fawang liu (the University of Queensland)

dr Shev Macnamara (the University of Queensland)

dr Muhammad Shoaib Seghal (aRC Centre of Excellence in Bioinformatics)

Research staff:Mr tim Sullivan (aRC Centre of Excellence in Bioinformatics)

PhD students:Mr alhadi Bustamam (the University of Queensland)

Ms Chin Foon Koo (australian national University)

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Aims:

the core goal of this theme is to develop novel methodologies for geometric, stochastic and statistical modelling of cellular processes based, where possible, on live cell imaging data in order to deepen our understanding of the processes being observed, and extend the range of inference that can be made from such data.

Some biological processes map readily to familiar mathematical formalisms (e.g. genetic regulatory networks as graphs). It is often less obvious how to model dynamic processes that involve complex cellular structures and spatial relationships. within the aRC Centre of Excellence in Bioinformatics we have established genuine collaborations of experimentalists and mathematicians that have yielded new modelling techniques, new mathematics for generating experimentally verifiable hypotheses, and (collaboratively with IMB’s virtual Membrane strategic program) models for the kinetics of lipid raft mobility, tubular-vesicle formation from endosomes, macropinosome biogenesis and vesicle recycling. these models are parameterised using live cell imaging, high-resolution confocal and EM data.

(a) we will analyse the large numbers of 3d movies of processes such as macropinocytosis and golgi events that are currently being captured in the laboratory of dr Rohan teasdale, with the aim of getting deeper insights into the nature of the complex spatial and temporal dynamics of these cellular processes.

(b) we will extend this work to whole beta-cell tomograms at 5-nm resolution (Program 1) and to 4d live images, producing and applying novel protocols, automated image-analysis and visualisation tools, and voxel-based stochastic simulators. In this way, the ultrastructural matrix of our visible Cell® will by 2010 become model-driven.

(c) we will extend our virtual membrane models so that simulations can be run on larger problems and over more-appropriate longer time scales.





(a) In collaboration with group Stow (IMB), a paper describing OBCOl, a system for segmenting and quantifying multi-fluorophore 3d and 4d cell imaging, was submitted to Cytometry A. OBCOl is unique in that it is the first system that can quantify whole-cell images to give detailed co-localisation information at the organelle level. In future work, the OBCOl quantification methods will form the basis for data generation for mathematical modelling. Supporting software is being released under an open source license (hamilton).

(b) we developed methods that automatically quantify the recruitment and expulsion in live cells of phosphoinositides from endosomes, an important subcellular organelle implicated in a number of major diseases, and submitted a manuscript (Kerr et al.). these methods enable the first detailed view of the rates of recruitment and transformations of the phosphoinositides, as well as their relationships and timings. Currently these data are being used as a basis for mathematical modelling of the phosphoinositide transformations (Fawang liu, John Belward). the systems have not previously been modelled, and preliminary differential equation models created show much promise in replicating the behaviours and timings found in the experimental data (hamilton, teasdale, Burrage).

(c) we developed new computational methods for modelling the transport and kinetics of processes in crowded spatial environments, particularly the plasma membrane. these new methods are based around the concept of fractional differential equations (liu, Burrage), and attempt to capture complicated spatial effects by a deterministic fractional partial differential equation framework. this is a very general approach that could be important wherever there is molecular crowding. this general description of non-classical diffusion more easily interprets experimental diffusion studies than do existing approaches.

(d) we developed new parallel simulation techniques that allow us to perform very complex simulations of processes on the plasma membrane by decomposing the problem into a number of sub-problems that communicate asynchronously. this allows us to tackle much larger simulation problems than via a purely sequential simulation (P. Burrage)

(e) we developed new stochastic simulation techniques for chemical reactions in spatially complex media such as the plasma membrane. we extended the Stochastic Simulation algorithm so it can be applied in a spatially constrained environment (nicolau, Burrage). this approach will allow us to evaluate the potential of various interactions (notably barriers, lipid rafts, and molecular crowding) to explain experimental observations of protein confinement and anomalous diffusion on the membrane.

(f) we developed a novel optimisation algorithm called extremotaxis that was inspired by how some bacteria move, and applied it to several very difficult optimisation problems with impressive results (nicolau, Maini, Burrage).

(g) we carried out computational simulations within the visible Cell® (Burrage, hegland, Macnamara, Sullivan, Sehgal) focusing on simulations of granular transport and insulin release at the plasma membrane, and development of temporal stochastic and deterministic models that explore the dynamics between glucose uptake and insulin release.

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Program 4 – algorithms for graphs and networks

4.1 discrete optimisation and graph clustering

Investigator:

Prof. Michael Fellows (the University of newcastle)

In collaboration with:Prof. Mike langston (University of tennessee and ORnl)

Researcher:

Research Associate:dr Frances Rosamond (the University of newcastle)

Aims:

(a) develop and implement algorithms for discrete clustering problems related to the VeRtex CoVeR problem, especially FPt algorithms that can be applied to very large datasets due to effective data-reduction subroutines.

(b) Integrate discrete clustering models with problems concerning motif identification for sequence-based datasets.

(c) develop general algorithmic approaches to classes of discrete clustering problems, such as minimum edge deletion editing to a graph of maximum degree d (the VeRtex CoVeR problem is the special case d = 0).

(d) develop algorithms for problems on coloured graphs, such as the graph-based Biochemical Motif Identification problem (a relaxed form of coloured subgraph isomorphism), and problems on convex recolouring of trees applicable in phylogenetic modelling and analysis.

(e) Integrate novel algorithmic strategies for identifying key nodes in networks, with broader strategies for experimentally verifying interpretations of the data suggested by the algorithmic outputs.

(f) develop algorithms for multiple-interval graph-based analysis of sequence data.

(g) develop new algorithms for realistic discrete graph-based modelling of haplotype data in the presence of errors.


(a) we made some first applications of FPt algorithmics to sequence consensus problems; these have applications in voting systems, and internet search engines as well as in the study of gene sequences. Results were published at prominent conferences.

(b) we found linear kernelisation algorithms for several strong generalisations of the VeRtex CoVeR problem, including the problem of deleting k vertices so that the resulting graph has maximum degree at most d (VeRtex CoVeR is the case of d = 0). Using the systematic technology of crown reduction (developed in recent years in Centre programs) we were able to achieve linear vertex kernels for every fixed d in quadratic time. these results were accepted at StaCS 2009.

(c) we continued to investigate graph motif problems (modelled by coloured graphs) with several bioinformatics applications. Our results were published at CPM 2008, and a full version prepared and submitted to Algorithmica.

(d) Our 2007 results on multiple interval graph problems relevant to sequence analysis were prepared for, submitted and accepted to Theoretical Computer Science (published January 2009).

(e) a paper on FPt algorithms for analysing haplotype data in a realistic model where plausible haplotypes are constrained, was prepared and submitted to CPM 2009.

(f) new applications (to new datasets) of our discrete clustering algorithms were obtained by the implementations of our algorithms by PI Mike langston.

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From left: Professor helmut Schwarz, President of the alexander von humboldt Foundation, Prof. Michael Fellows, dr Frances Rosamond, and Professor dr Rolf niedermeier, Friedrich-Schiller-Universität Jena, Institut für Informatik.




4.2 Optimisation-based approaches to large systems

Investigators:


In collaboration with:dr timothy Bailey (the University of Queensland)

dr Regina Berretta (the University of newcastle)


Prof. hugh Craig (the University of newcastle)

Prof. Mike langston (University of tennessee and ORnl)



Researcher:

Research Associate:dr Osvaldo Rosso (the University of newcastle)

Research Assistants:Mr daniel Johnstone (the University of newcastle)

dr Martin gómez-Ravetti (the University of newcastle)

Aims:

(a) develop a comprehensive methodology based on combinatorial optimization approaches for the identification of “oncosystems”, networks of highly correlated gene expression patterns in cancer samples as measured from microarray and miRna datasets.

(b) address the open problems including the development of powerful semi-supervised methods that identify subgroups representing potentially under-sampled phenotypes.

(c) develop more-robust pattern recognition methods that allow platform-independent recognition of molecular profiles characterising phenome subtypes, and will combine unsupervised and semi-supervised approaches to identify pathways that are differentially expressed according to disease state.


(a) we developed a metaheuristics-based method for identification of large molecular signatures in microarray datasets. the method will be tested with real datasets for which an assumed solution is known (e.g. the nCI-60 panel), with simulated data, and with real datasets to which a supervised method has been already applied (e.g. the 2006 dataset on prostate cancer by hood et al.). we will attempt to identify further datasets suitable for analyses to validate the method (Moscato, Berretta).

(b) we developed a novel methodology for identifying, from gene-expression data, biomarkers that correlate with disease progression. this method uses of information-theory-based quantifiers, Shannon entropies, and generalised statistical complexity quantifiers based on Jensen-Shannon divergence (Berretta, Rosso and Moscato). a large manuscript covering methodology, implementation and results for both prostate cancer and melanoma is in preparation. the method will greatly enrich the capabilities of this group in support of Projects 2.2 and 2.3.

(c) we verified our hypothesis that there exist large molecular correlates to sudden transitions in Shannon entropy and statistical complexity, and have been able to understand dysregulated biological processes, using Pathway

Studio. we also investigated the relevance of the (a,b)-k-FeAtuRe set as a model to identify genes for which expression behaviour changes in these transitions (Moscato, Rosso, gómez-Ravetti, Berretta). analysing two different datasets, we uncovered small, yet very predictive, molecular signatures, and from the union of the two signatures we identified an overrepresentation of binding motifs for v-MaF. the increasing down-regulation of MaF in primary tumors becomes even more pronounced in lymph-node metastatic prostate cancer, and was verified on a third dataset contributed by lapointe and colleagues.

(d) as part of the Phd thesis of Mario Inostroza-Ponta, we investigated the connection of these large molecular signatures with putative miRnas that target those genes. Our aim was to bridge the identification of these systems with putative regulators of these genes, and to enrich the biological hypotheses to be tested in Projects 2.2 and 2.3 (Moscato). we will attempt to validate these results on different datasets before submitting a manuscript for publication.

(e) we explored the combined use of approaches based on cliques and biclique identification to obtain better molecular correlates of bad prognosis from vijver’s breast cancer dataset (langston, Moscato). to that end, we developed a program to find best practice in combining literature information within the framework of the (a,b)-k-FeAtuRe set approach for biomarker selection. Using a dataset on protein abundance in blood, we showed that we have established the existence of a five-protein molecular signature that can predict the onset of clinical alzheimer’s disease two to five years before it is declared; our results were published in PLoS ONE (gómez-Ravetti, Moscato).

(f) we tested new algorithmic ideas based on the Jensen-Shannon divergence and Shannon entropy to study gene-expression data. as a case study, we carried out a computational linguistic study involving a large corpus of English Renaissance literature: the 185 texts (136 plays and 49 poems between 1580-1640) include 30 texts unquestionably written by Shakespeare.

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we also included a lover’s Complaint, a poem which generally appears in Shakespeare collections but whose authorship is in dispute. Our statistical complexity quantifiers combine the power of Jensen-Shannon’s divergence with the entropy variations as computed from a probability distribution function of observed word-use frequencies. we found that for a given entropy, poems display higher complexity than plays, that Shakespeare’s work falls into two distinct entropy clusters, and that his work is remarkable for its homogeneity and for its closeness to overall means. a manuscript (Rosso, Craig, Moscato) will appear in Physica A (2009).

(g) we analysed background electroencephalography (EEg), recorded with scalp electrodes, in children with childhood absence epilepsy (CaE) and in control individuals. Functional activity between electrodes was evaluated using wavelet decomposition in conjunction with the wootters distance, then pairs of electrodes with differentiated behaviour between CaE and controls were identified using a test statistic-based feature selection technique. this approach identified clear differences between CaE and healthy control background EEg in the frontocentral electrodes, as measured by Principal Component analysis. the findings of this pilot study have strong implications for clinical practice. a paper (Rosso et al.) will appear in Journal Neuroscience Methods (2009), and a follow-up study has been initiated to explore the use of (a,b)-k-FeAtuRe set to identify a smaller, yet more predictive, set of electrode pairs to discriminate cases from controls.

(h) we dealt with randomness-quantifiers and concentrate on their ability to discern chaos in time-series used in connection with pseudorandom number generators (PRng). workers in the field are motivated to use chaotic maps for generating PRngs because they are simple to implement. Our analysis shed light on the importance of the two main statistical characteristics of a chaotic map, namely its invariant measure and the mixing constant. this helps to answer two questions that arise

in applications: which is the best PRng among those available, and if a given PRng turns out not to be good enough and a randomisation procedure must still be applied to it, which is randomisation procedure is best? a paper (de Micco et al.) will appear in Philosophical Transactions of The Royal Society A (2009).

(i) we evaluated multifractality degree (Md) in a collection of developed and emerging stock market indices. Empirical results suggest that Md can serve as a quantifier to characterise the stage of market development. we develop a model to test the relationship between stage of market development and Md, and found robust evidence that the relationship is negative, i.e. Md is associated with a less-developed market. thus, an inefficiency ranking can be derived from multifractal analysis. we also established a link with previous volatility time series. a paper (Zunino et al.) appeared in Physica A.

(j) two important stochastic processes, the fractional Brownian motion and fractional gaussian noise, were analysed within the framework of the tsallis permutation entropy. this entropic measure, evaluated after using the Bandt & Pompe method to extract the associated probability distribution, was shown to be a powerful tool to characterise fractal stochastic processes. It allows for a better discrimination of the processes than the Shannon counterpart for appropriate ranges of values of the entropic index. Moreover, we find the optimum value of this entropic index for the stochastic processes under study. a paper (Zunino et al.) appeared in Physica A (2008).

(k) we worked out theoretical curves for the permutation entropy of the fractional Brownian motion and fractional gaussian noise by using the Bandt & Shiha theoretical predictions for their corresponding relative frequencies. Comparisons with numerical simulations show excellent agreement. we could also theoretically validate the entropy gap in the transition between these processes, observed previously via numerical results. we analysed behaviour of the

permutation entropy of the fractional gaussian noise for different time delays. a paper (Zunino et al.) appeared in Physics Letter A (2008).

(l) Even in healthy individuals, erythrocytes in capillaries continually change their shape in a synchronised erratic fashion. we studied this cell behaviour from the perspective of a bounded correlated random walk, assuming that diffractometric data involve both deterministic and stochastic components. we obtained photometric data ektacytometry over several million shear-elongated cells, using a home-made device called an erythrodeformeter. as we have only a scalar signal and no governing equations, we reconstructed behaviour in an artificial phase space. the results suggest that on a random-walk approach, samples from healthy controls exhibit significant differences from those from diabetic patients; thus we can claim to have linked nonlinear mathematical tools with clinically relevant rheological properties of erythrocytes from diabetics. a paper (Korol et al.) appeared in The Open Medical Informatics Journal (2008).

(m) Moscato and gómez-Ravetti began developing a new method to identify biomarkers for the progression of diseases, this time using microarray datasets of brain-tissue samples from patients who had died with alzheimer’s disease. we initiated a manuscript on the newly found genes and their relationship to the disease and its progression.

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a/Prof. Pablo Moscato at 2008 winter School in Mathematical and Computational Biology, newcastle.




4.3 External-memory algorithms for analysis of massive graphs

Investigator:


In collaboration with:dr tim Bailey (the University of Queensland)



Prof. Mike langston (University of tennessee and ORnl)


dr Isidore Rigoutsos (IBM tJ watson Research Center)


dr luciana Buriol (University. Fed. de Rio grande, Brazil)

dr Matt Ritt (Univ. Fed. de Rio grande do Sul, Brazil)

Researchers:

PhD student:Mr Mario Inostroza-Ponta (the University of newcastle)

MSc student:Mr leomar Costa (Univ. Fed. de Rio grande do Sul, Brazil)

Aims:

Since 2003, the meaning of large graph has changed by at least an order of magnitude. the gene co-expression graphs analysed by Mike langston and Pablo Moscato typically have 25K-200K nodes and ~1M edges, while problems in protein-protein interaction graphs and MaChOS (wong & Ragan) can be 1-2 orders of magnitude larger yet.

at least initially, this project will constitute a watching brief on technologies potentially useful for the analysis of graphs of this order. we will study the feasibility of translating to bioinformatics new algorithmic advances in advanced telecommunications, including external memory algorithms and novel data structures now being implemented by at&t for clique and quasi-clique computations in multi-digraphs of ~200M edges, and biclique partitioning in massive weighted bipartite graphs as potentially applied to multiple microarray datasets.


although this project constitutes as a watching brief and no specific funds have been associated, it has already produced some interesting results thanks to a collaboration between Moscato and other members of the newcastle aCB node, with drs luciana Buriol and Matt Ritt at Universidade Federal de Rio grande do Sul, Brazil, where MSc student leomar Costa has implemented an external memory algorithm version of the clustering method developed by Moscato and Inostroza-Ponta (2005-2008). this algorithm uses StXXl (Standard template library for Extra large data Sets), a free, open-source program available under the Boost Software license 1.0. we are now evaluating the feasibility of using this algorithm for problems involving genome-wide association studies and microarray data analysis. the newcastle node is likely to host some of our Brazilian collaborators in 2009, to explore the use of the algorithm in some datasets in melanoma and multiple sclerosis.

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gold Coast (1–3 december 2008)aCB was local host and a sponsor of the 19th International Conference on genome Informatics (gIw-2008), held on gold Coast from 1–3 december 2008. gIw, held annually under the auspices of the asian association of Societies of Bioinformatics (aaSBi), is the world’s oldest continuing conference series in bioinformatics. Until gIw-2006, annual gIw conferences were held in tokyo, then later yokohama. at that point aaSBi decided that gIw should circulate through the aaSBi countries. gIw-2007 was held at the Biopolis in Singapore, and gIw-2008 was hosted in australia under sponsorship of Bioinformatics australia, our national bioinformatics society organised within ausBiotech.

Mark Ragan served as conference Chair, while aCB Chief Investigators timothy Bailey, Kevin Burrage, Phoebe Chen, geoff Mclachlan, John Mattick, Pablo Moscato, Shoba Ranganathan, Rohan teasdale and Xiaofang Zhou were members of the national Organisation Committee. the conference was opened by Professor Peter andrews aO, Queensland Chief Scientist.

the australian bioinformatics community, companies and institutions provided brilliant support for gIw-2008. Financial sponsorship and support was secured from the department of Innovation, Industry, Science and Research (dIISR), Queensland government, the University of Queensland, CSIRO, alexander technology, SgI, the Computational Biology Research Center of the national Institute of advanced Industrial Science and technology (Japan), aRC Research network in Enterprise Information Infrastructure, australian Centre for Plant Functional genomics, australian genome Research Facility ltd, national ICt australia, Queensland Facility for advanced Bioinformatics, the Queensland Cyber Infrastructure Foundation (QCIF), Queensland University of technology, Sydney Bioinformatics, aaRnet, and Cisco Systems. the institutional and commercial displays added a further dimension that vitalised the conference and added great value for all participants. a portable tiled-wall OptIPortal operated by aaRnet and QCIF was particularly popular.

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19th International Conference on genome Informatics (gIw-2008)

gIw-2008 featured six leading keynote speakers. International keynote speakers were Julio Collado-vides (UnaM Universidad nacional autonóma de México), Ming li (Canada Research Chair in Bioinformatics, University of waterloo), yi-xue li (director, Shanghai Center for Bioinformation technology, Shanghai Institutes for Biological Sciences, Chinese academy of Sciences; and Shanghai Jiaotong University) and Cliona Molony (Rosetta Inpharmatics/Merck Research labs, Seattle, USa). Rounding out the roster of distinguished keynote speakers were Sean grimmond (Institute for Molecular Bioscience, the University of Queensland – a CI in the first phase of aCB) and CI John Mattick.

Open round-table discussion forums were held on the topics Innovation and commercialisation in genome-scale informatics and Development of genome-scale bioinformatics in China and India. Please see pages 70 to 72 for summaries of these sessions.

gIw-2008 attracted 220 registrants, almost half from overseas (Canada, China, France, India, Japan, Korea, Mexico, Malaysia, new Zealand, Russia, Singapore, taiwan, USa). within australia, all mainland states (plus aCt), almost all major bioinformatics groups, and many genomics and other “omics” groups were represented.

Prof. allen Rodrigo, University of auckland, chairing a session at gIw-2008.




19th International Conference on genome Informatics (gIw-2008)

aCB’s Key Performance Indicators (KPIs) encompass the following areas:

1. Research findings and competitiveness2. Research training and professional

education3. International, national and regional

links and networks4. End-user links5. Organisational support6. national benefit

highlights for 2008: the aRC Centre of Excellence in Bioinformatics again organised and sponsored our annual national winter School in Mathematical and Computational Biology. the 2008 winter School was hosted by our node at the University of newcastle, the first time winter School has been held elsewhere than at the University of Queensland. winter School is designed to introduce topics in mathematical and computational biology to postgraduate and advanced undergraduate students, postdoctoral researchers, and others working in mathematics, statistics, computer science, information technology, and biological, chemical or medical sciences and engineering. Our fifth winter School attracted 82 participants from 35 institutions in six countries, including PI Michael langston.

2008 was a good year for publications from the Centre, with 102 C1 journal articles (59 of which were co-authored with overseas collaborators) and 37 E1 conference papers.

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Prof. Michael Fellows continued his longstanding activity in science communication and popularisation. his books Computer Science Unplugged! (written with Prof. tim Bell, University of Canterbury and Prof. Ian witten, University of waikato) and This is MEGA-Mathematics! (with nancy Casey) convey sophisticated concepts such as intractability, sorting networks, and cryptography. they have won several international awards for science popularisation, and have been translated into Chinese, French, Japanese, Korean, norwegian, Polish, Russian, Spanish, Swedish and Urdu, with more translations underway. Professor Christopher M. Bishop (UK Microsoft Research) used material from Computer Science Unplugged! in his 2008 Faraday Christmas lectures; this lecture series, a tradition in london since 1825, is sponsored by the Royal Institution of great Britain and the leverhulme trust.

during 2007-2008 Prof. Fellows and dr Frances Rosamond were based largely in Jena (germany) with support from his von humboldt Research award awarded in 2007. Mike and Fran and visited a number of research centres across Europe during 2008, taking time out from research collaboration to lead a number of workshops for schoolchildren or teachers.

Prof. John Mattick was elected a Fellow of the australian academy of Science. John was appointed as inaugural gutenberg Chair at the Université louis Pasteur de Strasbourg, and was based in Strasbourg for a number of weeks.

Prof. geoff Mclachlan was elected President-Elect of the International Federation of Classification Societies.

Prof. Kevin Burrage took up a joint appointment at Oxford University as Professor of Computational Systems Biology, and was based at Oxford for several months during 2008. Kevin took the lead in developing plans for student exchange between the Institute for Molecular Bioscience and the systems biology program at Oxford. the first student exchanges could take place during 2009.

In recognition of the excellence of his research carried out within aCB, dr nick hamilton was appointed a group leader at the Institute for Molecular Bioscience.

In august 2008 Prof. Mark Ragan facilitated the national technology Roadmap for Bioinformatics process hosted by the Ministry of Science technology & Innovation Malaysia. leaders of most bioinformatics research groups came together in Shah alam, near Kuala lumpur, to develop a detailed “roadmap” for bioinformatics in Malaysia (http://www.mosti.gov.my/mosti/images/ICt_roadmap/Bioinformatics.pdf).

dr Melissa davis received a dean’s award for Excellence for her Phd thesis Defining the membrane organisation of eukaryotic proteins. her thesis research was advised by dr Rohan teasdale.

dr Stefan Maetschke received a dean’s award for Excellence for his Phd thesis (submitted in late 2007) Topological models of transmembrane proteins for subcellular localization prediction. Prof. geoff Mclachlan and dr Mikael Bodén were his associate advisors.

dr timothy Bailey’s students denis Bauer and Fabian Buske won the best student paper award for their paper “Predicting SUMOylation Sites” at the third International association for Pattern Recognition (IaPR) Conference on Pattern Recognition in Bioinformatics (PRIB 2008) held in Melbourne.

Key Performance Indicators



1. Research findings and competitiveness

Publications

Quality of publications

aCB researchers continue to perform well in peer-reviewed publication. Our Investigators and their research groups were authors of 102 Category C1 journal articles in 2008, of which 54 (53%) appeared in journals with 2007 impact factor ≥3.0, 30 (29%) with IF ≥5.0, and 8 (8%) with IF ≥10.0. In all, 59 (58%) of our C1 journal articles were co-authored with overseas collaborators.

Our Investigators demonstrated strong research performance in bioinformatics by publications in Bioinformatics (2), BMC Bioinformatics (8), Briefings in Bioinformatics, Journal of Computational Biology (2) and PLoS Computational Biology (3). Our impact beyond bioinformatics per se is reflected by publications in prestigious journals including Genome Biology, Genome Research (2), Nature, Nature Biotechnology (2), Nature Protocols, Philosophical Transactions of the Royal Society of London, Proceedings of the National Academy of Sciences USA, PLoS Genetics, Systematic Biology (2), and Science.

Number of publications

the table on this page summarises the published output by our investigators and research groups that appeared with a 2008 publication date. we do not count papers that at the end of december 2008 were available only electronically in advance of print publication, or were in press, under review, submitted or in preparation. For details, please refer to appendix 1: Publications and Papers.

Patents and trademarksno patents were awarded to our investigators during 2008.

Centre students Joo-young Choi and Elizabeth Skippington attended the BioBusiness day Out held by IMBcom Pty ltd on 13 november 2008. the introductory workshop introductory workshop provides first-year Phd students with an overview of the concepts of bio-business.

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Category Quantity

a1 Book – authored research 1

a3 Book – edited 2

B Book chapter 14

C1 Journal articles – articles in scholarly refereed journal 102

C2 Journal article – other contribution to refereed journal 2

C3 Journal article – non-refereed article 1

C5 Unpublished reports (including commercial consultancies) 3

E1 Conference – full written paper – refereed proceedings 37

E2 Conference – full written paper – non-refereed proceedings 2

E4i Conference – edited volume of conference proceedings 2

E4 Conference – unpublished presentations 8

g Computer software 3

Other academic outputs

– demos 1

– newsletter 1

– Posters 29

– Postgraduate theses 9

tOtal 217




Invitations to address and participate in conferences

International conferences

Chief and Partner Investigatorsdr timothy Bailey• ProgramCommittee,3rdInternational

association for Pattern Recognition (IaPR) Conference sponsored conference on Pattern Recognition in Bioinformatics (PRIB 2008), Melbourne (October)

• OrganisingCommittee,19thInternational Conference on genome Informatics (gIw-2008), gold Coast (december)

Prof. Kevin Burrage• InternationalConferenceon

Computational Cell Biology, hinxton, UK (March)

• SecondBertinoroSystemsBiologyworkshop (BSB 2008), Bertinoro, Italy (april)

• LymphocyteKineticsinHealthanddisease, london, UK (May)

• eResearchAustralasia2008,Melbourne (September)

• ProgramCommittee,SixthConferenceon Computational Methods in Systems Biology, Rostock, germany (October)

a/Prof. Phoebe Chen• Chair,SteeringCommittee,SixthAsia-

Pacific Bioinformatics Conference (aPBC2008), Kyoto (January)

• Chair,SteeringCommittee,14thInternational Conference on Multimedia Modelling (MMM2008), Kyoto (January)

• ProgramCommittee,24thInternationalConference on data Engineering (ICdE2008), Cancun, México (april)

• ProgramCommittee,12thPacific-AsiaConference on Knowledge discovery and data Mining (PaKdd2008), Osaka (May)

• ProgramCommittee,SecondInternational Conference on Bioinformatics Research and development (BIRd 2008), vienna (July)

• IASTEDInternationalConferenceonInternet and Multimedia Systems and applications (IMSa 2008), Kailua-Kona, hawaii, USa (august)

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• Keynote,21stRepublicofChinaImageProcessing and Pattern Recognition Society Conference on Computer vision, graphics and Image Processing, taiwan (august)

• PublicityCo-Chair,3rdInternationalassociation for Pattern Recognition (IaPR) Conference on Pattern Recognition in Bioinformatics (PRIB 2008), Melbourne (October)


• ProgramCommittee,19thInternationalConference on Pattern Recognition (ICPR 2008), tampa, Florida (december)

• ProgramCommittee,10thPacificRim International Conference on artificial Intelligence (PRICaI2008), hanoi (december)

Prof. Michael Fellows• TechnicalSymposiumonComputer

Science Education (SIgCSE 2008), Portland, Oregon, USa (March)

• FourthInternationalConferenceonalgorithmic aspects in Information and Management (aaIM 2008), Shanghai (June)

• InternationalConferenceonDiscreteMathematics (ICdM 2008), Mysore, India (July)

• ProgramCommittee,2ndAnnualInternational Conference on Combinatorial Optimization and applications (COCOa’08), newfoundland, Canada (august)

• ProgramCommittee,9thInternationalConference for young Computer Scientists (ICyCS 2008), hunan, China (november)

dr Markus hegland• Keynote,ChemnitzSymposium

on Inverse Problems, Chemnitz, germany (September)

• SessionOrganiser,7thAustralia-NewZealand Mathematics Convention, Christchurch, new Zealand (december)

Prof. geoff Mclachlan• 18thInternationalConferenceon

Computational Statistics (Compstat 2008), Porto, Portugal (august)

• GermanClassificationSociety32ndannual Conference (gfKl-2008), hamburg (July)

• XXIVInternationalBiometricConference, dublin, Ireland (July)

• ProgramCommittee,3rdInternationalassociation for Pattern Recognition (IaPR) Conference, Melbourne (October)


dr Brad Marsh• Keynote,NinthInternational

Symposium on Parallel architectures, algorithms, and networks (ISPan’08), Sydney (May)

• AmericanDiabetesAssociationAnnualMeeting 2008, San Francisco (June)

• InternationalCongressofhistochemistry & Cytochemisry (IChC 2008), gdansk, Poland (august)

• The2008GolgiMeeting:Membranetrafficking in global Cellular Responses, Pavia, Italy (September)

• SessionChair,9thAsia-PacificMicroscopy Conference (aPMC9), Jeju Island, Korea (november)

• Plenary,DutchSocietyforMicroscopyannual Meeting, lunteren, the netherlands (november)

Prof. John Mattick• Plenary,FoundationdesTreilles

Meeting “new catalytic and regulatory functions of Rna in eukaryotes”, nice, France (March)

• Plenary,GenomestoSystemsConference, Manchester, UK (March)

• OpeningPlenary,CellCultureEngineering XI, Coolum (april)

• Invitedspeaker,2008ASBMB(american Society for Biochemistry and Molecular Biology) annual Meeting, San diego, USa (april)

• Invitedspeaker,QueenstownEpigenetics Meeting, Queenstown, new Zealand (June)



• Invitedspeaker,EMBONewMembersMeeting, tampere, Finland (September)

• Plenary,EuropeanBioPerspectives,hannover (October)

• Keynote,TheRiGHTSymposium:Rna Interference technology as human therapeutic tool, Brussels, Belgium (november)

• OpeningKeynote,8thAnnualaustralasian Microarray and associated technologies (aMata) Conference, dunedin, new Zealand (november)

• PlenaryandNationalOrganisingCommittee, 19th International Conference on genome Informatics (gIw-2008), gold Coast (december)

a/Prof. Pablo Moscato• ProgramCommittee,SixthEuropean

Conference on Evolutionary Computation, Machine learning and data Mining in Bioinformatics (EvOBIO 2008), napoli, Italy (March)

• ProgramCommittee,EighthEuropeanConference on Evolutionary Computation in Combinational Optimisation (EvoCOP 2008), napoli, Italy (March)

• ScientificProgramCommittee,SpecialSession on Memetic algorithms, 2008 IEEE world Congress on Computational Intelligence, hong Kong (June)

• ProgramCommittee,CongressonEvolutionary Computation, IEEE world Congress on Computational Intelligence, hong Kong (June)

• ProgramCommittee,BrazilianSymposium on Bioinformatics (BSB 2008), Santo andré, Brazil (august)

Prof. Mark Ragan• ProgramCommittee,SixthAsia-Pacific

Bioinformatics Conference (aPBC2008), Kyoto (January)

• SecondBertinoroSystemsBiologyworkshop (BSB 2008), Bertinoro, Italy (april)

• Australia-BrazilWorkshoponBiotechnology Innovation for agriculture, Brasília (May)

• 16thInternationalConferenceonIntelligent Systems for Molecular Biology (ISMB2008), toronto (July)

• ProgramCommittee,eResearch australasia 2008, Melbourne (September)

• Chair,OrganisingCommittee,19th International Conference on genome Informatics (gIw-2008), gold Coast (december)

Prof. Shoba Ranganathan• ProgramCommittee,6thAsia-Pacific

Bioinformatics Conference (aPBC) 2008, Kyoto, Japan (January)

• ProgramCommittee,2ndInternationalConference on Bioinformatics Research and development (BIRd) 2008, vienna, austria (July)

• Chair,ProgramCommittee,7thInternational Conference on Bioinformatics (InCoB 2008), taipei, taiwan (October)

• ProgramCommittee,IEEEInternationalConference on Bioinformatics and Biomedicine (BIBM) 2008, Philadelphia, USa (november)

• ProgramCommitteeandWorkshopChair, 19th International Conference on. genome Informatics (gIw-2008), gold Coast, australia (december)

dr Rohan teasdale• CellularMicrobiology

– EMBO Meeting, villars-sur-Ollon, Switzerland (September)

• 6thInternationalDrugDiscoveryScience and technology (IddSt) 2008, Beijing (October)

Prof. Xiaofang Zhou• ProgramCommittee,17thInternational

world wide web Conference (www2008), Beijing (april)

• ProgramCommittee,28thACMSIgMOd International Conference on Management of data (SIgMOd 2008), vancouver (June)

• GeneralCo-Chair,FourthInternationalConference on advanced data Mining and applications (adMa 2008), Chengdu, China (July)

• ProgramCommitteeandTutorialChair,34th International Conference on very large databases (vldB 2008), auckland (august)

• Keynote,9thInternationalConference on web Information Systems Engineering (wISE 2008), auckland (September)

• TutorialChair,6thInternationalConference on Service Oriented Computing (ISOC 2008), Sydney (december)

Postdoctoral fellows, Research Officers and studentsMr Paulo amaral• 29thLorneGenomeConference,Lorne,

australia (July)• XXInternationalCongressofGenetics,

Berlin, germany (July)

dr Mikael Bodén• Asia-PacificBioinformaticsConference

(aPBC 2008), Kyoto (January)• ProgramCommittee,3rdInternational

association for Pattern Recognition (IaPR) Conference on Pattern Recognition in Bioinformatics (PRIB 2008), Melbourne (October)

• Programcommittee,9thInternationalConference on Intelligent data Engineering and automated learning (IdEal 2008), daejeon, Korea (november)

dr Pamela Burrage• SecondBertinoroSystemsBiology

workshop (BSB 2008), Bertinoro, Italy (april)

• eResearchAustralasia2008,Melbourne (September)

Ms Elsa Chacko • 16thAnnualInternationalConference

on Intelligent Systems for Molecular Biology (ISMB) 2008, toronto, Canada (July)

Mr. Khar heng Choo• ProgramCommittee,7thInternational

Conference on Bioinformatics, taipei, taiwan (October)

dr adrian Cootes• 7thEuropeanConferenceon

Computational Biology (ECCB) 2008, Cagliari, Italy (September)

• ProgramCommittee,7thInternationalConference on Bioinformatics, taipei, taiwan (October)

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dr aaron darling• StatisticalGeneticsforMetagenomics

workshop, Berlin (July)• InternationalCongressofGenetics,

Berlin (July)• 16thArrowheadMeetingonMicrobial

genomics, lake arrowhead, California (September)

• 6thRECOMBComparativeGenomicsSatellite Meeting, Paris (October)

• ProgramCommittee,19thInternationalConference on genome Informatics (gIw-2008), gold Coast (december)

dr Melissa davis• Asia-PacificBioinformaticsConference

(aPBC 2008), Kyoto (January)

dr Mercer dinger• KeystoneSymposium:RNAi,MicroRNA,

and non-Coding Rna, whistler, Canada (March)

Mr. Jitendra gaikwad• ProgramCommittee,7thInternational


dr Karin Kassahn• SocietyforMolecularBiologyand

Evolution 2008, Barcelona (June)

Mr. Javed Khan• 12thAnnualInternationalResearch

in Computational Molecular Biology (RECOMB) Conference 2008, Singapore (March/april)

• ProgramCommittee,7thInternationalConference on Bioinformatics, taipei, taiwan (October)

Mr. varun Khanna• StrasbourgSummerSchoolon

Chemoinformatics 2008, Obernai, France (June)

• ProgramCommitteeMember,7th International Conference on Bioinformatics, taipei, taiwan (October)

• InternationalConferenceonNewdevelopments in drug discovery from natural Products and traditional Medicines 2008, Mohali, India (november)

Mr. gaurav Kumar• ProgramCommittee,7thInternational


dr Krzysztof Kurowski• eResearchAustralasia2008

Conference, Melbourne (September)

dr Shev Macnamara • SocietyforMathematicalBiology

Conference , toronto, Canada (august)• SIAMConferenceontheLifeSciences,

Montreal, Canada (august)

Ms Ranjeeta Menon• ProgramCommittee,7thInternational


dr timothy Mercer• QueenstownEpigeneticsMeeting,

Queenstown, new Zealand (June)• QueenstownMolecular

Biology Meeting, Queenstown, new Zealand (September)

Mr. Shivashankar nagaraj• ProgramCommittee,7thInternational


Mr Satu nahkuri• FirstInternationalEURASNET

Conference on alternative Splicing, Krakow, Poland (May)

Mr andrew noske• SystemsBiologySymposium,

Queenstown, new Zealand (September)

dr Osvaldo Rosso• IIInternationalConferenceNet-Works

2008, Pamplona, Spain (June) • OrganisingCommittee,XVIConference

on nonequilibrium Statistical Mechanics and nonlinear Physics (MEdyFInOl’08), Punta del Este, Uruguay (december)

Mr. lawrence wee• ProgramCommittee,7thInternational


dr Simon wong• 16thInternationalConferenceon

Intelligent Systems for Molecular Biology (ISMB2008), toronto (July)

Centre staff (Mr Oliver Cairncross, Mr david wood), postdoctoral fellows (dr Melissa davis, dr nicholas hamilton, dr Karin Kassahn, dr Shev Macnamara, dr Muhammad Shoaib Sehgal) and students (gaurav Kumar, Elizabeth Skippington, Joo-young Choi, Isye arieshanti, alhadi Bustamam) participated in the 19th International Conference on genome Informatics (gIw-2008), gold Coast (december).

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National conferences

Chief InvestigatorsProf. Kevin Burrage• 2008WinterSchoolinMathematical

and Computational Biology, newcastle (July)

a/Prof. Phoebe Chen• FirstAustraliaVideoConference

(ausvideo), Brisbane (October 2008)

dr Markus hegland• Organiseroflocaltwo-daymeeting

as part of the “gene golub around the world day”, Canberra (February)

• Treasurer,ComputationalTechniquesand applications Conference (CtaC 2008), Canberra (July)

Prof. geoff Mclachlan• JointorganiserofProgramon

Bioinformatics and Statistical genetics, australian Statistical Conference, Melbourne (July)

• SymposiumCelebratingProf.Suewilson’s 34 years, Canberra (december)

dr Brad Marsh• SessionChair,AustralianConference

on Microscopy & Microanalysis, Perth (February)

Prof. John Mattick• Plenary,AustralianGenomeResearch

Facility tenth anniversary genomics Symposium, Melbourne (april)

• OpeningPlenary,The18thStVincent’s& Mater health Research Symposium, Sydney (September)

a/Prof. Pablo Moscato• 2008WinterSchoolinMathematical


Prof. Mark Ragan• 2008WinterSchoolinMathematical


Prof. Shoba Ranganathan• 2008WinterSchoolinMathematical


Prof. Xiaofang Zhou• 2008EIIWinterSchoolinDataQuality

and Management, Kioloa, nSw (august)

• 200EIIEarlyCareerDevelopmentworkshop, Kioloa, nSw (august)

Postdoctoral fellows, Research Officers and studentsMr. Jitendra gaikwad• BiodiversityInformationStandards

(tdwg) annual Conference 2008, Perth (October)

dr nick hamilton• The8thHunterMeeting,HunterValley,

nSw (april)

Mr andrew noske• SessionChair,MitochondrialImaging

and dynamics, ‘aussieMit’ workshop, Melbourne (november)

dr Cheong Xin Chan and dr aaron darling attended adelaide Conference on Mathematical Evolutionary Biology 2008, adelaide (March)

Centre postdoctoral fellows dr Osvaldo Rosso and dr Martin gómez-Ravetti, and students vinh dang, nikhil lilaria and Elizabeth Skippington attended the 2008 winter School in Mathematical and Computational Biology, newcastle (July)

Invitations to visit leading international laboratories, major research groups and centres

Chief Investigatorsdr timothy Bailey• NobleLaboratory,Universityof

washington, USa (november)

Prof. Kevin Burrage• ComputerScienceDepartment,

University of Rostock, germany (november)

• MathematicsDepartment,Universityofnottingham, UK (november)

• MathematicsDepartment,Universityofleeds, UK (november)

• SystemsBiologyCentre,UniversityofEdinburgh, UK (december)

• BiomedicalSciencePark,Barcelona,Spain (december)

a/Prof. Phoebe Chen• DepartmentofComputerScience,

Fudan University, China (March)• NationalTsingHuaUniversity,

taiwan (november)• AcademiaSinicaTaiwan(November)• NationalChiaoTungUniversity,

taiwan (november)• NationalTaiwanOceanUniversity,

taiwan (november)• NationalChungHsingUniversity,

taiwan (november)

Prof. Michael Fellows• AsHumboldtResearchAwardinvited

guest lecturer: Universität Berlin, Universität dusseldorf, Universität Jena, Universität Karlsruhe, Universität Kiel, Universität lubeck, Universität Rostock, Universität Saarbrücken, and Max-Planck Institut für Informatik (Saarbrücken), germany

• Prof.HenningFernau,UniversitätTrier,germany (March)

• CentreInternationaldeRencontresMathématiques, Marseille (april)

• Humboldt-UniversitätzuBerlin,germany (april)

• Prof.MichaelLangston,Universityoftennessee (december)

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dr Markus hegland• InstituteforNumericalSimulation,

University of Bonn, germany (august, September)

• DepartmentofInformationtechnology, University of Uppsala, Sweden (September)

Prof. geoff Mclachlan• Invitedfellowintheprogramme

Statistical theory and Methods for Complex, high-dimensional data held at the Isaac newton Institute for Mathematical Sciences, Cambridge University (March-June)

• UniversityofWarwick,UK(May)• UniversityofReading,UK(June)

dr Brad Marsh• Walter&ElizaHallInstituteofMedical

Research, Melbourne (June)• SystemsBiologyLaboratory,Hagedorn

Research Institute, novo nordisk, denmark (September)

Prof. John Mattick• AsLeonardoLecturer,Istituto

Scientifico San Raffaele and Universitá vita-Salute San Raffaele, Milan, Italy (March)

• CambridgeBiologicalSociety,Cambridge UK (March)

• AsGutenbergProfessor,UniversityofStrasbourg, France (June)

• FriedrichMiescherInstitute(FMI),Basel Switzerland (June)

• InstitutdeGénétiqueetdeBiologieMoléculaire et Cellulaire (IgBMC), Strasbourg, France (June)

• InstitutdeBiologieMoléculaireetCellulaire (IBMC), Centre national de la Recherche Scientifique, Strasbourg France (June)

• UniversitéPierreetMarieCurie,Paris,France (June)

• MaxPlanckInstituteforMoleculargenetics, Berlin, germany (June)

• DepartmentofBiology,UniversityofCopenhagen, denmark (September)

• MaxPlanckInstituteofMolecularCell Biology and genetics, dresden, germany (October)

• InstitutdeGénétiqueetdeBiologieMoléculaire et Cellulaire (IgBMC), Strasbourg, France (October)

a/Prof. Pablo Moscato• InstitutodeCienciasMatematicas

e de Computacao, Universidade de Sao Paulo, Sao Carlos, Sao Paulo, Brazil (September)

• DepartamentodeBioquimica,Universidad nacional de Quilmes, Buenos aires, argentina (September)

• DepartamentodeComputacion,Universidad de Buenos aires, Buenos aires, argentina (September)

Prof. Mark Ragan• Murzingroup(StructuralClassification

of Proteins database), MRC laboratory of Molecular Biology and Cambridge Centre for Protein Engineering, Cambridge UK (January)

• EuropeanBioinformaticsInstitute,hinxton, UK (January)

• EMBRAPA(BrazilianAgriculturalResearch Corporation) headquarters, laboratories and field station, Brasilia, Brazil (May)

• MinistryofScience,Technologyand Innovation, Shah alam, Malaysia (august)

Prof. Shoba Ranganathan• BioinformaticsInstitute,

Singapore (September)• UniversitiTeknologiMalaysia

(September)• SangerCentre,Hinxton,UK(September)• EuropeanBioinformaticsInstitute,

hinxton, UK (September)• AcademiaSinica,Taiwan(October)

Prof. Xiaofang Zhou• NagoyaUniversity,Japan(November

2008–January 2009)• InstituteofSoftware,ChineseAcademy

of Sciences, Beijing, China (January)• AalborgUniversity,Denmark(March)• ChineseAcademyofScienceInstitute

of Software, Beijing, China (april)• PekingUniversity,Beijing,China(April)• RenminUniversity,Beijing,China(April• IBMResearch,Beijing,China(April)• GISCompany,Wuhan,China(April)• WuhanUniversity,Wuhan,China(April)• HuazhongUniversityofScienceand

technology, wuhan, China (april)

Postdoctoral fellows, Research Officers and studentsMr Javed Khan• InstituteforInfocommResearch,

Singapore (april)

dr Osvaldo a Rosso• DepartamentdeFisicaiEnginyeria

nuclear, Universitat Politècnica de Catalunya,terrassa, Barcelona, Spain (June)

• DepartamentodeFísicayMatemáticaaplicada, Universidad de navarra, Spain (June)

• DepartamentodeInformáticaeIngeniería de Sistemas, Universidad de Zaragoza, Zaragoza, Spain (June)

• InstitutodelDesarrolloHumano,Universidad nacional de general Sarmiento, Buenos aires, argentina (december)

• EscueladeCienciayTecnología,Universidad nacional de San Martín, Buenos aires, argentina (december)

• LaboratoriodeSistemasComplejos,Facultad de Ingeniería, Universidad de Buenos aires, Buenos aires, argentina (december)

• ServiciodeNeurologíaPediátrica,hospital Italiano, Buenos aires, argentina (december)

• InstitutodeCálculo,UniversidaddeBuenos aires, argentina (december)

• CentroInvestigacionesÓpticas,Universidad nacional de la Plata, la Plata, argentina (december)

• InstitutodeFísica,Universidadnacional de la Plata, la Plata, argentina (december)

dr Martin gómez-Ravetti• HongKongUniversityofScienceand

technology, hong Kong (april)• FederalUniversityofMinasGerais,

Brazil (May)Ke

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dr Christophe lefèvre, Prof. Mark Ragan and a/Prof. Phoebe Chen (front row from left) with deakin Bioinformatics group members.



Commentaries about the Centre’s achievements Professor John Mattick was one of seventeen of australia’s leading scientists honoured on 19 March by election to the australian academy of Science. John’s nomination cites his work on the structure of genetic systems in higher organisms. Election to the academy recognises a career that has significantly advanced, and continues to advance, the world’s scientific knowledge.

John was also quoted in two articles in the new york times, “the promise and power of Rna” and “now: the rest of the genome” (11 november 2008). the same issue depicted John in a cartoon accompanied by the quotation “this [the many new roles found for Rna] is potentially the biggest change in our understanding of biology since the discovery of the double helix”.

dr aaron darling appeared on the Channel 7 news program “Catalyst” regarding the genetic basis of antibiotic resistance in bacteria (wednesday, 13 February 2008).

dr Brad Marsh’s work on high-resolution cell tomography of mammalian cells was featured in the leading textbook Physical Biology of the Cell (Phillips, Kondev & theriot, Eds) and in the 150th anniversary edition of Gray’s Anatomy. his work was also featured in a Queensland weekender feature article on diabetes management and research (30 October 2008).

a paper by noske, Costin, Morgan & Marsh (Expedited approaches to whole cell electron tomography and organelle mark-up in situ in high-pressure frozen pancreatic islets. Journal of Structural Biology 161:298-313, 2008) was highlighted in Faculty of 1000 Biology (http://www.f1000 biology.com/article/id/1100294).

a letter from Professor Mark Ragan in response to “gM concerns continue to crop up” (allen greer, The Australian Higher Education Supplement, 13 February 2008) was published in HES on 20 February 2008.

Mark was also briefly quoted in The Australian Financial Review (13 October 2008) as part of coverage of the visit of Professor larry Smarr (director, California Institute for telecommunications and Information technology) to australia. Professor Smarr, the australian american leadership dialogue 2008 Scholar, toured australia to make the case for national investment in grid fabric, specifically ultra-fast broadband networks linking major research infrastructure and high-performance computers, with visualisation based on tiled-wall lCd displays such as the OptIPortal.

Professor Michael langston was featured in the Spring 2008 issue of the University of tennessee’s faculty newsletter, available online at http://www.cs.utk.edu/~langston/faculty-focus.pdf

dr nick hamilton coordinated aCB presentations for the OptiPortal visualisation cluster at the gIw-2008 conference in december 2008.

Evidence of interdisciplinary linkages within the CentreMuch of aCB’s research is conducted by interdisciplinary teams within which many of our postgraduate and postdoctoral researchers are co-supervised or mentored by researchers from different fields, e.g. bioscience and mathematics, or bioscience and ICt. In this way we prepare the next generation of researchers to recognise and appreciate problems in systems biology, to think laterally into other fields and leverage insights and methods from multiple disciplines, and to work in and lead multi-disciplinary teams.

Of our 11 projects and sub-projects active during 2008, 8 (73%) included personnel with advanced degrees in different disciplines; 20 of our 28 PdFs (71%), 13 of our 55 postgraduate students (24%), and 4 international interns worked in these 11 projects. Of our 57 papers and posters during 2008 with at least two Centre investigators or students as co-authors, 38 (67%) of those co-authors hold advanced degrees in different disciplines. two-thirds (20 of 30) of our co-authored C1 journal publications were interdisciplinary in this sense. Our winter School is intentionally interdisciplinary, and all aCB students and postdoctoral researchers are strongly encouraged to attend.

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2. Research training and professional education

RecruitmentIn 2008, aCB recruited:

• DrAdrianCootes,ResearchOfficerinto Project 1.3 (data analysis and knowledge discovery in very large biological datasets) with Prof. Shoba Ranganathan.

• DrGabrielFung,ResearchOfficerinto Project 1.3 (data analysis and knowledge discovery in very large biological datasets) with Prof. Xiaofang Zhou.

• DrJohnHawkins,ResearchOfficerintoProject 2.1 (Computational discovery of gene-regulatory motifs and motif clusters) with dr timothy Bailey.

• MrAndrewNewman,Researchassistant into Project 1.2 (data and process management for the visible Cell®) with Prof. Mark Ragan.

• DrKim-AnhLêCao,ResearchOfficerinto Project 2.2 (differential expression of genes towards pathway discovery) with Prof. geoff Mclachlan.

• DrShevMacNamara,ResearchOfficer into Project 3.1 (Mathematical modelling of genetic regulatory networks) with Prof. Kevin Burrage.

• DrJohnBelwardandDrFawangLiu,Research Officers into Program 3 (Modelling dynamic cellular processes) with Prof. Kevin Burrage.

• MrDanielJohnstoneandDrMartingómez-Ravetti, Research assistants into Project 4.2 (Optimisation-based approaches to large systems) with a/Prof. Pablo Moscato.

Each of the five days focused on a different theme:

day 1: Entropy and statistical complexityday 2: data mining, machine learning and

new technologiesday 3: Combinatorial optimisation and

applicationsday 4: network pathway analysis in

bioinformaticsday 5: advances in proteomics and

genomics

Our distinguished invited speakers were:

• Prof.VladimirBrusic harvard University, USa

• A/Prof.CarlosCotta University of Malaga, Spain

• Prof.CharlesCantor Chief Scientific Officer, Sequenom, USa

• DrMartinGómez-Ravetti aCB and the University of newcastle, australia

• Prof.MichaelLangston aCB and the University of tennessee, USa

• A/Prof.JoergMattes the University of newcastle, australia

• A/Prof.PabloMoscato aCB and the University of newcastle, australia

• DrFerranteNeri University of Jyväskylä, Finland

• DrMichaelNorman CEO, Scapa technologies, UK

• Prof.ShobaRanganathan aCB and Macquarie University, australia

• DrCarlosRiveros the University of newcastle, australia

• DrOsvaldoRosso University of Buenos aires, argentina

• Prof.RodneyScott the University of newcastle, australia

• DrMuhammadShoiabSehgal aCB and the University of Queensland, australia

• Prof.ConstantinoTsallis,BrazilianCenter for Physics Research Brazil

• Prof.MichaelZuker Rensselaer Polytechnic Institute, USa

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Professional/technical training and advanced career development

Seminar/Symposium hosted and/or sponsored by ACB

9th International Symposium on Parallel Architectures, Algorithms and NetworksIn 2008 aCB sponsored the travel of CI dr Brad Marsh, a keynote speaker at the 9th International Symposium on Parallel architectures, algorithms and networks, Sydney (7–9 May 2008).

3rd IAPR Conference on Pattern Recognition in BioinformaticsaCB financially supported student participation in the 3rd International association for Pattern Recognition (IaPR) Conference on Pattern Recognition in Bioinformatics (PRIB 2008), Melbourne (15–17 October 2008).

19th International Conference on Genome InformaticsPlease see page 38.

2008 Winter School in Mathematical and Computational Biology (7–11 July 2008)Our 2008 winter School in Mathematical and Computational Biology was held first time in newcastle, hosted by CI a/Prof. Pablo Moscato with the local support of colleagues from aCB, the University of newcastle’s School of Electrical Engineering and Computer Science, and the newcastle Priority Research Centre for Bioinformatics, Biomarker discovery and Information-Based Medicine.

winter School 2008 featured 14 speakers (9 international, 5 national), and attracted 81 participants from 35 institutions across australia and from Finland, India, Spain, UK and USa. Of these 78% were researchers or postgraduate students, and 22% advanced undergraduates. One-third identified a biological background, with most others from mathematics, statistics, computer science or It. about 41% represented australian universities. again, we received highly positive written feedback from the participants about the topics and quality of presentations.



a public lecture was held on day 4 featuring Professor John Forbes, director of Research for the australian new Zealand Breast Cancer trials group (anZ BCtg), Professor of Surgical Oncology at the University of newcastle, and director, department of Surgical Oncology at the Calvary Mater hospital.

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2008 winter School in Mathematical and Computational Biology, newcastle. From left: vinh dang, nikhil lilaria, dr Muhammad Shoaib Sehgal, Prof. Shoba Ranganathan, Prof. Michael Zuker (Rensselaer Polytechnic Institute, USa), Prof. Michael langston (University of tennessee) and Prof. Mark Ragan.

2008 winter School in Mathematical and Computational Biology, newcastle. From left: dr Ferrante neri (University of Jyväskylä, Finland), Prof. Constantino tsallis (Santa Fe Institute, USa and Brasilian Center for Physics Research, Rio de Janeiro, Brazil), Ms armita Zarnegar (Phd student, University of Ballarat), dr Osvaldo Rosso (Universidad nacional de Buenos aires, argentina and Centre for Bioinformatics, Biomarker discovery and Information-based Medicine, the University of newcastle (CIBM)), dr Carlos Riveros (CIBM), a/Prof. Pablo Moscato, dr Michael norman (Chief Executive Officer, Scapa technologies, Scotland); and a/Prof. Carlos Cotta (University of Malaga, Spain).




Other research and training and professional education

apart from our winter School, our CIs and researchers participated in:

Prof. Kevin Burrage• Doctoraltrainingprograms,University

of Oxford (March)

Prof. Michael Fellows• InternationalSummerSchoolon

Fixed Parameter tractable algorithms (FPt2008), Shanghai (June)

dr nick hamilton• FutureResearchLeadersProgram,

University of Queensland (november)

dr Markus hegland• CourseonApproximationTheoryat

the aMSI Summer School, Monash University (January)

Prof. geoff Mclachlan• ProgrammeonStatisticalTheory

and Methods for Complex, high-dimensional data, Isaac newton Institute for Mathematical Sciences, Cambridge (January-June)

Prof. John Mattick• CentreforMilitary&VeteransHealth

think tank, Canberra (May)• QueenslandInstitutesofHealth

Symposium, Coolum (august)• NewSouthWalesSupremeCourt

annual Conference, Shoal Bay (august)

Postgraduate and undergraduate courses in the Centre’s area

Our investigators and researchers participated in the following for-credit courses and programs in 2008:

dr timothy Bailey and dr Mikael Bodén re-designed and taught the University of Queensland undergraduate course “advanced Bioinformatics”.

dr timothy Bailey• BIOL3014AdvancedBioinformatics

(lecturer/coordinator)

dr Mikael Bodén• BScBioinformaticsdualmajor

(convener)• BInfTechBioinformaticsdualmajor

(convenor)• BIOL3014AdvancedBioinformatics

(lecturer/coordinator)

a/Prof. Phoebe Chen• SIT781IntroductiontoBioinformatics

(unit chair and lecturer)• SIT772DatabaseandInformation

Retrieval (unit chair and lecturer)• SIT362AdvancesinInteractiveMedia

(unit chair and lecturer)

dr gabriel Fung• INFS4203/7203DataMining

dr Markus hegland• 3359TopicsinComputational

Mathematics

dr Karin Kassahn• BIOL3010EcologicalandEvolutionary

genetics (two guest lectures)

dr Brad Marsh• BIOL3006MolecularCellBiology

(lecturer)• BIOC3004StructuralBiology:

Macromolecular Structure (lecturer)• UndergraduateResearchOpportunities

Program (UROP) scholarship student projects

a/Prof. Pablo Moscato• COMP4120KnowledgeDiscoveryand

data Mining (lecturer/coordinator)• COMP2270,COMP6270Formal

languages and automata (lecturer/coordinator)

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Prof. Mark Ragan• BIOL3004GenomicsandBioinformatics

(introductory lecture)

Prof. Shoba Ranganathan• CBMS223BiochemistryandMolecular

Biology I (Unit coordinator and lecturer)• CBMS301TechnologyMiniproject(Unit

coordinator)• CBMS880SelectedTopicsin

Biotechnology (lecturer)

dr Mohammad Shoaib Sehgal• COMP3702ArtificialIntelligence

(lecturer)

Prof. Xiaofang Zhou• INFS4203/7203DataMining

Scientists in Schools Partnership

dr Brad Marsh is the Centre’s point of contact for the CSIRO Scientists in Schools Partnership program. he gave two presentations explaining basic cell biology and how we image insulin-secreting cells in 3d to the combined 6/7 advanced learning class at graceville State School, graceville, Brisbane (april 2008). Brad and science teacher Ms Sandra davey assisted the class in extracting dna from strawberries, and loaned them some laboratory equipment and glassware for the experiments (august 2008). Brad also organised an on-site visit and tour of the IMB and electron microscopy facilities for the class (30 students, teacher, and accompanying parents) in august 2008.

dr Melissa davis was also involved with the CSIRO Scientists in Schools Partnership. working with Ms andrea O’Brien, faculty organiser of the Ironside Science Club (Ironside State School, Brisbane), Melissa made several presentations through the year on molecular biology and genetics, and gave three presentations at their 2008 Science day.



3. International, national and regional links and networks

visitors

International visitors

• WagnerAioffi,UniversidadeFederaldeMinas gerais (UFMg), Brazil

• Prof.VladimirBrusic,HarvardUniversity, USa

• DrJulioCollado-Vides,UNAMUniversidad nacional autonóma de México, Mexico

• MrGrahamCameron,Associatedirector, EMBl-EBI, UK

• Prof.CharlesCantor,ChiefScientificOfficer, Sequenom, USa

• DrCheongXinChan,UniversityofIowa,USa

• Prof.VickiChandler,Universityofarizona, USa

• A/Prof.CarlosCotta,UniversityofMalaga, Spain

• DrPaulHorton,ComputationalBiologyResearch Center, aISt, Japan

• Prof.DavidKeyes,ColumbiaUniversity,new york

• Prof.MingLi,CanadaResearchChairinBioinformatics, University of waterloo, Canada

• DrYi-xueLi,ShanghaiCenterforBioinformation technology, Shanghai Institutes for Biological Sciences, Chinese academy of Sciences, Shanghai Jiaotong University, China

• DrClionaMolony,HeadofStatisticalgenetics, Rosetta Inpharmatics/Merck Research labs, USa

• Prof.NancyMoran,Universityofarizona, USa

• DrFerranteNeri,UniversityofJyväskylä, Finland

• DrMichaelNorman,CEO,Scapatechnologies, UK

• Prof.HowardOchman,Universityofarizona, USa

• Prof.LindaPetzold,UniversityofCalifornia Santa Barbara

• DrJuergenPlitzko,MaxPlanckInstituteof Biochemistry, Martinsried, germany

• Prof.MikePowell,UniversityofCambridge

• DrXiangtongQi-HongKongUniversityof Science and technology (USt), hong Kong.

• Prof.UlrichRüde,UniversitätErlangen-nürnberg

• Prof.AllenRodrigo,BioinformaticsInstitute, new Zealand

• DrJoãoSarubbi-CEFET/MG,Brazil• Prof.ErnstStephan,LeibnizUniversity,

hannover• DrMartinSwain,SchoolofBiomedical

Sciences, University of Ulster, UK• GeorgeTeodoro,UniversidadeFederal

de Minas gerais (UFMg), Brazil• Prof.ConstantinoTsallis,Brazilian

Center for Physics Research, Brazil• Prof.AlexisVandenbon,Universityof

tokyo, Japan• Prof.MichaelZuker,Rensselaer

Polytechnic Institute, USa

National visitors to one or more ACB nodes

• DrIanAtkinson,JamesCookUniversity• DrEricChu,MonashUniversity• A/Prof.ChristineClarke,Westmead

Institute for Cancer Research, Sydney• Prof.LarryForbes,Universityof

tasmania• DrMarcusHeisler,EMBLAustralia• DrElizabethMurchison,Australian

national University• DrKenPang,LudwigInstitute,

Melbourne• ProfessorDavidRavine,Universityof

western australia• DrWilliamRitchie,CentenaryInstitute,

Sydney• Prof.IanSloan,UniversityofNewSouth

wales• DrRohanWilliams,TheJohnCurtin

School of Medical Research, australian national University

• Prof.RobWomersley,UniversityofNewSouth wales

Collaborative national and international workshops and exchangesIn addition to the 2008 winter School and Student Symposium, our CIs, PdFs, Phds presented at or participated in workshops as follows:

Chief Investigators

Prof. Kevin Burrage• NumericalModellingofComplex

dynamical Systems, leiden, netherlands (May)

a/Prof. Phoebe Chen• EigthInternationalWorkshoponData

Mining in Bioinformatics (BIOKdd 2008), las vegas, USa (august)

• Co-Chair,SecondInternationalworkshop on Conceptual Modelling for life Sciences applications (CMlSa2008), Barcelona, Spain (October)

• 2008InternationalComputerSymposium(ICS’08), workshop on Medical and Bio-Informatics, taipei, taiwan (november)

Prof. Michael Fellows• 34thInternationalWorkshopon

graph-theoretic Concepts in Computer Science (wg2008), durham, UK (July)

• SecondInternationalFrontiersofalgorithmics workshop (Faw 2008), Changsha, China (June)

dr Markus hegland• “DayshonouringthelivesofGene

golub and Ron Mitchell”, Canberra (February)

• Sessionsoninformationbasedcomplexity and on linear algebra and inverse problems at FOCM 09, hong Kong, City University (March)

• ComputationalTechniquesandapplications Conference (CtaC 2009) conference, Canberra, (July)

• ConferenceonModeling,Simulationand Optimization of Complex Processes (MOSOCOP 08), University of heidelberg, germany (July)

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Prof. geoff Mclachlan• HighDimensionalStatisticsinBiology

workshop, Cambridge (March-april)• QuantitativeBiologyandApplied

Statistics Seminar, the University of Reading, UK (May)

• CRiSM(CentreforResearchinStatistical Methodology) Seminar, the University of warwick, UK (May)

• SecondAnnualWorkshoponStatisticalMethods for genetic analysis, QUt (november)

dr Brad Marsh• SessionChair,MitochondrialImaging

and dynamics, ‘aussieMit’ workshop, Melbourne (november)

a/Prof. Pablo Moscato• 2008NSWSydneyBioinformatics

Research Symposium, Sydney (november)

Prof. John Mattick• FoundationdesTreillesMeeting

on “new catalytic and regulatory functions of Rna in eukaryotes,” nice, France (March)

Prof. Shoba Ranganathan• WorkshoponEducationin

Bioinformatics and Computational Biology (wEBCB) 2008, taipei, taiwan (October)

Prof. Xiaofang Zhou• 1stInternationalWorkshopon

Information-explosion and next generation Search (IngS), Shenyang, China (april)

Postdoctoral fellows, Research Officers and studentsMr. Khar heng Choo• WorkshoponEducationin

Bioinformatics and Computational Biology (wEBCB) 2008, taipei, taiwan (October)

Other research linkagesOur investigators and senior members of their research groups maintain active research linkages in australia with essentially every research-active university, many other research institutions, several divisions within CSIRO, and with companies. In addition we have active research linkages with numerous institutions as follows. Please see also to page 44, Invitations to visit leading international laboratories.

National collaborating institutions:

agilent technologiesaRC Centre for Complex Systems aRC Research network in Enterprise

Information Infrastructure aRC Special Research Centre for Functional

and applied genomicsaustralian Centre for Plant Functional

genomicsaustralian e-health Research Centre,

CSIROaustralian Microscopy & Microanalysis

Research Facilityaustralian Regenerative Medicine Institute,

Monash Universityaustralian Stem Cell CentreBio21 Molecular Science and

Biotechnology InstituteCSIRO Mathematical and Information

SciencesElizabeth Macarthur agricultural Institute,

nSw department of Primary IndustriesEnergy Edge Pty ltdFlinders University of South australiagriffith UniversityIBM australiaInvitrogen life technologiesJames Cook Universityludwig Institute for Cancer ResearchMicrosoft australiaMonash UniversityMurdoch Childrens Research InstituteMuseum victorianational ICt australianielson MediaQueensland Brain InstituteQueensland Cyber Infrastructure

Foundation Queensland Institute of Medical Research Queensland University of technology Rulequest Research Pty ltdSwinburne University of technologytasmania ICt Centre, CSIROthe Bionic Ear Institutethe University of Melbournethe University of Sydneythe University of western australiathe walter and Eliza hall Institute of

Medical ResearchUniversity of technology Sydneywestmead hospital, Sydney

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International collaborating institutions:

aalborg University, denmarkacademia Sinica, Institute of Information

Science, taiwanacademia Sinica, Institute of Software,

Chinaaghia Sophia Children’s hospital, greeceaItIa International Informatics Inc.,

hungaryalbert Einstein College of Medicine, USaalbert ludwigs Universität Freiburg,

germanyalfréd Rényi Institute of Mathematics,

hungarian academy of Sciences, hungary

allen Institute for Brain Science, Seattle, USa

arkansas State University, USaat&t laboratories, USaBanco Central do Brazil, BrazilBaylor College of Medicine, USaBioinformatics Institute of Singapore,

SingaporeBroad Institute of MIt and harvard, USaBuenos aires Scientific Research

Commission, argentinaBurnham Institute for Medical Research,

USaCalifornia Institute of technology, USaCentro de Regulación genómica, SpainChao Family Comprehensive Cancer Center,

USaChinese University of hong Kong, ChinaChonnam national University, KoreaClausthal University of technology,

germanyCnR-Fondazione scuola di S. giorgio,

venezia, ItalyCold Spring harbor laboratory, USaCollegium Budapest, hungaryCombiMatrix Corporation, USaComputational Sciences Center of

Emphasis, Pfizer, USaCranfield School of Management, UKdalhousie University, Canadadana Farber Cancer Institute, USa dokuz Eylul University, Izmir, turkeydublin Institute of technology, Irelanddurham University, UKEidgenössische technische hochschule

Zürich, SwitzerlandEötvös loránd University, hungaryFlorida State University, USaFreie Universität Berlin, germanyFriedrich-Schiller-Universität Jena,

germany

genome Institute of Singapore, Singaporehacettepe Üniversitesi, turkeyharbin Institute of technology, Chinaharvard University, USaháskóli Íslands, Icelandhohai University, Chinahong Kong University of Science and

technology, Chinahospital Italiano, Buenos aires, argentinahospital Ramos Mejía, Buenos aires,

argentinahoward University, USaImperial College london, UKInstitut national de Recherche en

Informatique et en automatique, FranceInstituto Balseiro, Centro atómico

Bariloche, argentinaInstitute of neurobiology, Bulgarian

academy of Sciences, BulgariaInstitute for Infocomm Research, SingaporeIsaac newton Institute for Mathematical

Sciences, UKISIS Pharmaceuticals, USaIstituto Italiano di tecnologia, genoa, ItalyJoint genome Institute, US department of

Energy, USaJohn Radcliffe hospital, Oxford, UKJohns hopkins University, USaKarolinska Institutet, SwedenKültür University, turkeyKwangju Institute of Science and

technology, KoreaKyoto University, Japanlawrence Berkeley national laboratory,

USalerner Research Institute, USaMax-Planck-Institut für Informatik, germanyMax-Planck-Institut für Molekulare genetik,

germanyMax-Planck-Institut für Molekulare

Zellbiologie und genetik, germanyMcgill University, CanadaMoredun Research Institute, UKnanjing University, Chinananyang technological University,

Singaporenational Institute of advanced Industrial

Science and technology, Japan national Institutes of health, USanational University of Singapore, Singaporenational yang-Ming University, taiwanOak Ridge national laboratory, USaOsaka University, JapanOtto-von-guericke Universität Magdeburg,

germanyParahyangan Catholic University, IndonesiaPeking University, ChinaPlatform Computing SaRl, France/germany

Pontificia Universidad Católica de Chile, Chile

Pontificia Universidad Católica de valparaíso, Chile

Poznan Supercomputing and networking Center, Poland

Purdue University, USaQueen Silvia Children’s hospital, göteborg,

SwedenRaytheon Inc., USaRIKEn genomic Sciences Center, JapanRIKEn wako Institute, JapanSalford Systems, USaSandia national laboratory, USaScripps Institution of Oceanography, USaSichuan University, ChinaSingapore Management University,

SingaporeSRa International Inc., USatechnion – Israel Institute of technology,

Israeltechnischen Universität Berlin, germanytemasek life Sciences laboratory,

Singaporetsinghua University, Chinathe Open University, UKUniversidad autónoma de Madrid, SpainUniversidad de Buenos aires, argentinaUniversidad de la Republica, UruguayUniversidad de los andes, ChileUniversidad de navarra, SpainUniversidad de valladolid, SpainUniversidad de valparaíso, ChileUniversidad de Zaragoza, SpainUniversidad Favaloro, argentinaUniversidad nacional de Córdoba,

argentinaUniversidad nacional de general

Sarmiento, argentinaUniversidad nacional de la Plata, argentinaUniversidad nacional de Mar del Plata,

argentinaUniversidad nacional de Quilmes, argentinaUniversidad nacional de Rosario, argentinaUniversidad nacional de San Martín,

argentinaUniversidad nacional de tucumán,

argentinaUniversidade Catolica de Brasilia, BrazilUniversidade Federal de Rio grande do Sul,

BrazilUniversidade Federal de Minas gerais,

BrazilUniversità di Perugia, ItalyUniversità di Roma “la Sapienza”, ItalyUniversitat de les Illes Balears, SpainUniversitat Politècnica de Catalunya, SpainUniversitat Pompeu Fabra, SpainUniversität Bonn, germany

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Universität lübeck, germanyUniversität trier, germanyUniversité des Sciences of d’Orsay, FranceUniversité Pierre et Marie Curie, FranceUniversité de Rennes, FranceUniversité de Strasbourg, FranceUniversiteit van amsterdam, the

netherlandsUniversiteit Utrecht, the netherlandsUniversitetet Bergen, norwayUniversity of alabama at Birmingham, USaUniversity of auckland, new ZealandUniversity of British Columbia, CanadaUniversity of California at Berkeley, USaUniversity of California at Irvine, USaUniversity of California at San diego, USaUniversity of California at Santa Barbara,

USaUniversity of Cambridge, UKUniversity of Canterbury, new ZealandUniversity of Chicago, USaUniversity of Colorado, USaUniversity of dar es Salaam, tanzaniaUniversity of dayton, USaUniversity of dublin, IrelandUniversity of Florida, USaUniversity of georgia, USaUniversity of haifa, IsraelUniversity of Illinois at Chicago, USaUniversity of Iowa, USaUniversity of Kentucky, USaUniversity of leeds, UKUniversity of liverpool, UKUniversity of Maryland at Eastern Shore,

USaUniversity of Minnesota, USaUniversity of Montana, USaUniversity of north Carolina, USaUniversity of Oxford, UKUniversity of Reading, UKUniversity of Southampton, UKUniversity of texas at austin, USaUniversity of Ulster, UKUniversity of vermont, USaUniversity of victoria, CanadaUniversity of waikato, nZUniversity of warwick, UKUniversity of washington, USaUniversity of waterloo, CanadaUniversity of western Ontario, CanadaUniversity of wisconsin, USaUppsala Universitet, Swedenvictoria University of wellington, new

Zealandwake Forest University, USaXiamen University, Chinayale University, USa

Membership on national and international professional committeesIn addition to participation on organising or program committees for specific conferences or workshops, aCB Chief Investigators were actively engaged in 2008 with executive, management and professional committees, advisory and review committees, and similar continuing bodies (excludes fellowships, journal editorial boards and learned societies):

Prof. Kevin Burrage• ResearchCommittee,OxfordCentrefor

Integrative Systems Biology

a/Prof. Phoebe Chen• Chair,SteeringCommittee,Asia-Pacific

Bioinformatics Conference• Chair,SteeringCommittee,International

Conference of Multimedia Modelling• SteeringCommittee,

Bioinformatics australia

Prof. Michael Fellows• SteeringCommittee,International

workshop on Parameterized and Exact Computation

dr Markus hegland• Internationalpanelofassessors,

deutsche Forschungsgemeinschaft SPP 1243

• SteeringCommittee,ComputationalMathematics group

Prof. geoff Mclachlan• President-Elect,International

Federation of Classification Societies• CollegeofExperts,Australian

Research Council

dr Brad Marsh• Chair,Communications&Program

awareness Sub-committee, network for Pancreatic Organ donors with diabetes (Juvenile diabetes Research Foundation, USa)

Prof. John Mattick• CouncilofScientists,HumanFrontier

Science Program

a/Prof. Pablo Moscato• StrategicAdvisoryCommittee,Hunter

Medical Research Institute. • DeputyLeader,Information-based

Medicine Program, hunter Medical Research Institute.

Prof. Mark Ragan• Vice-president,BioinformaticsAustralia

(ausBiotech)• Chair,ExecutiveGroup,Associationof

asian Societies of Bioinformatics • CommitteeonGlobalCollaborations,

European life Sciences Infrastructure for Biological Information (ElIXIR)

• SteeringCommittee,AustralianNationaldata Service

• BoardofManagement,AustralianResearch Enabling Environment (aRChER)

• NationalWorkingGroupandQueensland Coordinator, EMBl australia

• Chair,ManagementCommittee,and Member, Industrial Research advisory Panel, Queensland Facility for advanced Bioinformatics

• AdvisoryBoard,QosCosGRID(Quasi-Opportunistic Supercomputing for Complex Systems in grid Environments) project, European Sixth Framework

• ExternalExaminer,MastersofBiotechnology Programme, Universiti Malaya (2005-2010)

Prof. Shoba Ranganathan• President,Asia-Pacific

Bioinformatics network• Chair,InternationalConferencein

Bioinformatics Executive Committee• Chair,S*LifeScience

Informatics alliance• SteeringCommittee,

Bioinformatics australia

dr Rohan teasdale• SteeringCommittee,International

Conference on Bioinformatics• SteeringCommittee,

Bioinformatics australia• NationalAssociationofResearch

Fellows of nhMRC

Prof. Xiaofang Zhou• ExecutiveCommittee,WebInformation

Systems Engineering Society (wISE Society)

• ExpertConsultant,MidandLongTermStrategic Planning for Science and technology development, Ministry of Science and technology of the People’s Republic of China

• AdvisoryCommittee,AdaptiveServiceagreement and Process Management in Services grids Project, an EU-dESt project hosted by Swinburne University

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Research projects with international partnerslisted below are research projects with international partners that are underway in 2008:

dr timothy Bailey• A/Prof.WilliamNoble,Department

of genome Sciences, University of washington (USa) MEME suite of motif-based sequence analysis tools

Prof. Kevin Burrage• DrChristopherBouton&DrVictor

Farutin, Pfizer Research technology Center (USa) BioMANTA: modelling and analysis of biological network activity

• ProfessorSimonDavis,JohnRadcliffehospital, Oxford (UK) Computational Immunology

• Prof.JohnHancock(UniversityofTexashealth Sciences Center, houston) & dr dan nicolau Jr, University of California at Berkeley, USa) Stochastic simulations for modelling anomalous diffusion and exploring the role of lipid rafts in the plasma membrane

• DrAndréLeier&DrTatianaMarquezlago, Eth Zürich (Switzerland) Dynamics of the Her1 and Her7 complex in somite formation in zebrafish

• DrGrantLythe,UniversityofLeeds(UK) New numerical methods for second-order stochastic equations

• DrTatianaMarquezLago,ETHZürich(Switzerland) Multiscale algorithms for the spatial modelling of discrete chemical kinetics in a cell

• ManuelBarrioSolórzano,Universidadde valladolid (Spain) Dynamics of the Hes1 molecular clock in mouse

• ProfessorJordiVilla,UniversitatPompeu Fabra (Spain) Multiscale simulation of cellular processes

a/Prof. Phoebe Chen• Prof.LimsoonWong,National

University of Singapore & dr J. li, nanyang technological University (Singapore) Development of knowledge discovery for high-dimensional biomedical data

Prof. Michael Fellows• Prof.JanArneTelle&Prof.Pinar

heggernes, University of Bergen (norway) PARALGO: Parameterized Algorithms and FPT Kernelization

• Prof.RolfNiedermeier,Friedrich-Schiller-Universität Jena (germany) Parameterized graph clustering algorithms for bioinformatics applications

dr Markus hegland• Prof.MichaelGriebel,Universityof

Bonn (germany) MAP density estimation with Gaussian Process Priors

• Prof.PerLotstedt,UniversityofUppsala(Sweden) Numerical CME solvers

• Prof.MartinGutknecht,ETHZürich(Switzerland) Efficient Algorithms for Large Linear Additive Models

• DrJochenGarcke,TechnischeUniversität Berlin (germany) Sparse grid combination technique

dr Karin Kassahn• DrStéphaneGuindon,Universityof

auckland (new Zealand) Estimating selection in vertebrate protein families

Prof. geoff Mclachlan• DrJillMesirov,BroadInstituteofMIT

and harvard (USa) Automated high-dimensional flow cytometric data analysis

Prof. Brad Marsh• Prof.MichaelHaydenandA/Prof.Bruce

verchere, University of British Columbia (Canada) Structure-function studies of intracellular cholesterol accumulation in ACBA1 KO mice

• A/Prof.MaryannMartone,NationalCenter for Microscopy and Imaging Research, University of California at San diego (USa) Cell Centered DataBase (http://ccdb.ucsd.edu/CCDBWebSite/index.html)

• Prof.DavidMastronarde,Boulderlaboratory for 3d Electron Microscopy of Cells, University of Colorado (USa) Supermontaging: reconstructing large cellular volumes by lateral stitching of adjacent tomograms

• Prof.ChristopherRhodes,UniversityofChicago (USa) Elucidating regulated autophagy in pancreatic islet beta cells from mice and humans

• A/Prof.NielsVolkmann,BurnhamInstitute for Medical Research (USa) Semi-automated pre- and post-processing approaches to segmentation of cellular tomographic data

Prof. John Mattick• ProfessorMarkMehler,Institute

for Brain disorders and neural Regeneration, albert Einstein College of Medicine of yeshiva University (USa) Noncoding RNA expression, function and editing in brain development and cognition

• DrBodoLange,Max-PlanckInstituteforMolecular genetics (germany) Noncoding RNAs in centrosomes

• DrCharlesPerou,UniversityofNorthCarolina (USa) Noncoding RNA expression and function in breast cancer

• DrJeffRosen,BaylorCollegeofMedicine, houston (USa) Noncoding RNA expression and function in breast development

• DrDavidSpector,ColdSpringHarborlaboratories (USa) Noncoding RNAs in muscle development and paraspeckle function

• Prof.EricWesthof,UniversityofStrasbourg (France) Structure-based genome alignments and estimation of conservation, deep sequencing and analysis of brain small RNAs

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Prof. Mark Ragan• AITIAInternationalInformaticsInc.

(hungary), Collegium Budapest (hungary), Cranfield School of Management (UK), Eötvös loránd University (hungary), Institut national de Recherche en Informatique et en automatique (InRIa) (France), Platform Computing SaRl (France/germany), Poznan Supercomputing and networking Center (Poland), technion – Israel Institute of technology (Israel), Universitat Pompeu Fabra (Spain), Universiteit van amsterdam (netherlands) & University of Ulster (UK) EU-FP6 project Quasi-Opportunistic Supercomputing for Complex Systems in Grid Environments (QosCosGRID)

• DrChristopherBouton,PfizerResearchtechnology Center (USa) BioMANTA: modelling and analysis of biological network activity

Prof. Shoba Ranganathan• USNationalInstitutesofHealth(USA)

Large-scale antibody and T-cell epitope discovery program

dr Rohan teasdale• DrHarukazuSuzuki&Prof.Yoshihide

hayashizaki, RIKEn genomic Sciences Center (Japan) Systematic determination of the subcellular localisation of transcriptional regulators

4. End-user links

Commercialisation activitiesaCB was directly involved with a number of commercial partners in 2008:

• Prof.KevinBurrageandProf.MarkRagan collaborated with Pfizer Research technology Center (USa) in the BioManta project (see our 2007 annual Report, page 41).

• DrNickHamiltonmetwithDrStephanKuppig (Carl Zeiss ag, germany) to discuss commercialisation potential of his iCluster and OBCOl software (September 2008).

• Prof.JohnMattickworkedwithInvitrogen life technologies (USa) in the development and commercialisation of mouse and human noncoding Rna arrays (“nCode”).

• Prof.MarkRaganandcolleaguescollaborated with commercial partners in the QosCosgRId project funded by the EU Sixth Framework Programme.

government, industry and business briefingsthe events below are in addition to the numerous meetings, teleconferences and interactions with colleagues in government, industry and business implicit in the above collaborations and links.

Prof. Mark Ragan• Australiandelegationorganisedby

the australian academy of Science on behalf of the department of Innovation, Industry, Science and Research (dIISR) – australia-Brazil workshop on Biotechnology Innovations for agriculture, Brasília (May)

• ExecutivebriefingandpresentationPfizer, Brisbane (May)

• Facilitator,NationalTechnologyRoadmap for Bioinformatics, Ministry of Science technology & Innovation Malaysia, Kuala lumpur (august)

• Forumoninnovationandcommercialisation in genome-scale bioinformatics, 19th International Conference on genome Informatics (gIw-2008), gold Coast (december)

Prof. Shoba Ranganathan• Forumonthedevelopmentofgenome-

scale bioinformatics in China and India, 19th International Conference on genome Informatics (gIw-2008), gold Coast (december)

trained/ing in technology transfer and commercialisationdr Melissa davis attended the “Engineering your IP” hosted by IP australia and Institute of Engineers australia in June 2008.

Public awareness programsdr Melissa davis and dr Karin Kassahn participated in the “talking Scientists” public outreach programme sponsored by Queensland government (September 2008), as well as preparatory workshops.

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5. Organisational support

new organisations recruited to or involved in the Centrethree new organisations began formal involvement with the aRC Centre of Excellence in Bioinformatics in 2008: Macquarie University, the University of auckland, and the University of tennessee.

Infrastructure

World-class expertise

Bioinformatics is a key research technology, particularly in enabling advances in life sciences and biotechnology. aCB researchers, students and collaborators have access to top australian experts in many areas of bioinformatics, statistics, high-performance computing, and data integration. this expertise is being aggregated further through the aRC Research network in Enterprise Information Infrastructure, QFaB and other initiatives.

Computing

the aRC Centre of Excellence in Bioinformatics is headquartered on level 6-west of the Queensland Bioscience Precinct (QBP) on the St lucia campus of the University of Queensland. QBP-6w has been purpose-built for bioinformatics, with space for more than 75 researchers and students. all aCB researchers access some of the best computing facilities in australia, including more than 600 research-dedicated compute cores and nearly 100 tB research-dedicated storage at IMB, newly upgraded SgI altix systems at UQ/QCIF, a new cluster at newcastle Bioinformatics Initiative, and (via merit allocation) the 2200-processor national computing facility (nCI/nCRIS). we are a partner in the European Union Sixth Framework project Quasi-Opportunistic Supercomputing for Complex Systems in gRId Environments (www.qoscosgrid.eu) and in early 2008, the UQ node of aCB was physically connected to the European testbed.

Data infrastructure

aCB has built significant data environments, database mirrors and specialised software, some of which are exposed on our research website. Many of these have been partnered-into QFaB, which is further developing this infrastructure with commercial bioinformatics software (e.g. SRS) and data sources. QFaB has also adopted some of the aRChER e-research tools (www.archer.edu.au) including Plone. we have access to storage at anU and UQ currently at 100s-tB scale, and being developed toward PB scale.

Microscopy

the $1.4M aCRF/IMB dynamic Imaging Facility and the high-content Screening facility were established with active involvement of CI Rohan teasdale. the former includes two state-of-the-art Zeiss Meta 510 confocal microscope systems with two-photon and motorised stage capabilities. this live-cell imaging facility complements the advanced Cryo-Electron Microscopy laboratory at IMB, a peak node of the nCRIS-funded australian Microscopy & Microanalysis Research Facility (aMMRF) that provides instruments and expertise for high-resolution 3d reconstruction and analysis of molecules, cells and tissues. Equipment includes tecnai 300 kev and 120 kev scopes, 4K×4K gatan CCd and Baltec high-pressure freezing. dr Brad Marsh has a key role in providing strategic advice on facility management and personnel, new/major instrument acquisition and future R&d directions - including collaborations with industry – to ensure these facilities remain internationally competitive at the highest levels.

Microarrays and other wet-lab technologies

Queensland Bioscience Precinct has state-of-the-art facilities and infrastructure to undertake a wide range of experimental phenomic research, including the affymetrix, agilent, Illumina and spotted-array platforms, protein expression and crystallisation, Rigaku FR-E and hU-2R x-ray sources, eight advanced mass spectrometry platforms with capillary separation front-ends and robotics, single-particle analysis, robotic high-content chemical screening, transgenic animals, and the zebrafish model system. IMB is one of three international reference sites for next-generation high-throughput dna sequencing using the applied Biosystems SOlid platform, with two SOlid systems in place during 2008.

Network analysis for systems biology

the University of newcastle node has purchased two individual licences of Pathway Studio for three years, to help develop the program on pathway-aware investigation of differential patterns of gene expression in microarray data. QFaB has signed an agreement to become the australasian reference site and distributor for genego, and will host a local mirror.

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annual cash contributions from other organisations 2008–2010 2008 2009 2010ARC* 1,144,719 1,167,613 1,190,966TheUniversityofQueensland** 525,000 525,000 525,000australian national University 10,000 10,000 10,000deakin University 30,000 30,000 30,000Macquarie University 70,000 70,000 70,000University of newcastle 80,000 80,000 80,000TOTAL 1,859,719 1,882,613 1,905,966

annual in-kind contributions: collaborating organisations 2008–2010 2008 2009* 2010*the University of Queensland Personnel 551,499 579,074 608,027 Equipment 20,000 20,000 20,000 Other 212,105 73,000 73,000 Total 783,604 672,074 701,027australian national University Personnel 22,988 24,138 25,345 Equipment 0 0 0 Other 8,800 0 0 Total 31,788 24,138 25,345deakin University Personnel 22,052 23,155 24,312 Equipment 0 0 0 Other 12,750 0 0 Total 34,802 23,155 24,312Macquarie University Personnel 34,420 36,141 37,948 Equipment 0 0 0 Other 48,618 10,000 10,000 Total 83,038 46,141 47,948University of newcastle Personnel 74,796 78,536 82,463 Equipment 0 0 0 Other 21,738 0 0 Total 96,534 78,536 82,463University of auckland Personnel 6,985 7,334 7,700 Equipment 0 0 0 Other 0 0 0 Total 6,985 7,334 7,700University of tennessee Personnel 32,416 33,389 34,391 Equipment 0 0 0 Other 0 0 0 Total 32,416 33,389 34,391IBM Personnel 20,000 20,000 20,000 Equipment 0 0 0 Other 133,353 133,353 133,353 Other – tivoli application 30,000 0 0 Total 183,353 153,353 153,353TOTAL 1,252,521 1,038,119 1,076,539

*Thenumbersshownassumeindexingat5%peryearforthepersonnelcomponentonly,inadditiontoprobablesalaryincrementswhereknown.

TOTAL (annual cash + annual in-kind contributions) 3,112,240 2,920,732 2,982,505

* Thenumbersshownassumeindexingat2%per year.

**Inadditiontothecashsupportidentifiedhere,theCentrewillbenefitfromIGSgenerated by the core aRC grant funds at UQ distributed via IMB.



6. national benefit

Measures of expansion of australia’s capability in the priority area(s)

Review paper

at the request of PLoS Computational Biology Editor-in-Chief Prof. Phil Bourne, aCB director Mark Ragan and two colleagues based in industry, dr tim littlejohn (IBM australia) and dr Bruce Ross (Microsoft australia), prepared a review of genome-scale computational biology and bioinformatics in australia. the review summarises major characteristics and features of these fields in australia, and calls attention to the significant expansion in capability since the previous review (littlejohn tg, Bioinformatics in australia. Bioinformatics 16:849-850, 2000). the review appeared in PLoS Computational Biology on 29 august 2008.

National Collaborative Research Infrastructure Scheme (NCRIS)

the strategic role of bioinformatics in the development of “omic” biology was explicitly recognised in the scoping of nCRIS capability area 5.1 (Emerging Biomolecular Platforms and Informatics) and is implicit in several activities within capability area 5.16 (Platforms for Collaboration). the former will be managed by the new australian Bioinformatics Facility, which is headquartered at Murdoch University in Perth, under contract to BioPlatforms australia, the entity that arose from nCRIS 5.1. In mid-2008 national Computational Infrastructure (nCI), successor under nCRIS to australian Partnership in advanced Computing (aPaC), called for expressions of interest in developing and hosting Specialised Facilities; it is a measure of the expansion of australia’s capability that at least two expressions of interest were submitted for an nCI SF in bioinformatics.

EMBL Australia

In conjunction with the nCRIS process, australia became an associate Member of the European Molecular Biology laboratory (EMBl) on 1 March 2008. Monash University has been lead institution in this process pending formalisation of a new body, EMBl australia. the founding members of EMBl australia are CSIRO, Monash University, the University of Queensland, the University of Sydney and the University of western australia, as well as dIISR. the national health and Medical Research Council (nhMRC) and the australian Research Council (aRC) have committed support for an initiative under australia’s associate membership. the profile of bioinformatics within EMBl australia has been high, led by an initiative to mirror substantial components of the European Bioinformatics Institute (EBI) data facility in australia. during 2008 Mark Ragan represented UQ on the EMBl australia working group. dr graham Cameron, deputy director of EBI, visited australia (including aCB) in September-October 2008 and was a keynote speaker at the e-Research australasia conference in Melbourne. dr Ewan Birney, a senior scientist at EBI and key driver of major bioinformatics environments including Ensembl, will spend almost one month in australia in early 2009 under the sponsorship of EMBl australia; his visit will raise of the profile of bioinformatics as an area of potentially enhanced research collaboration between australia and Europe.

Australian Bioinformatics Network and Bioinformatics Australia

Following a recommendation in the national Bioinformatics Strategy (2005), in mid-2006 dESt contracted Bioinformatics australia to manage an australian Bioinformatics network “that would, in consultation with government agencies, researchers, and industry implement elements of [the national Bioinformatics] Strategy; coordinate bioinformatics activities; facilitate collaboration with and between key national and international organisations and networks; and improve awareness of bioinformatics”. as part of this contract, aBn/Ba held a series of consultative workshops in Melbourne, Canberra, Brisbane, Sydney and Perth, and a roundtable discussion at the 2007 Bioinformatics australia annual conference. a summary of the community response was reported to dIISR in early 2008, and follow-up actions form part of the proposal for extension of aBn funding to be submitted to dIISR. aCB supports Bioinformatics australia in multiple ways, particularly in its coordination role within the national bioinformatics community and outreach to government, research and industrial sectors, as these are strongly synergistic with our own mission and aims. aCB CIs Phoebe Chen, Shoba Ranganathan and Rohan teasdale are members of the Ba Committee, while Mark Ragan was elected vice-President (tim littlejohn is President). Bioinformatics australia hosted the 2008 International Conference on genome Informatics (gIw-2008), with the 2008 annual Ba conference combined into gIw-2008.

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Queensland Facility for Advanced Bioinformatics

as described in our 2006 annual Report, QFaB has been established to provide advanced infrastructure and service to partners and clients. aCB has supported this start-up by seconding certain infrastructure staff on a term basis; in return QFaB is managing the corresponding components of our infrastructure requirements, originally focusing on the visible Cell® project but during 2008 transitioning to support of aCB’s Research Program 2 (Phenotype-informed discovery of networks and systems). QFaB’s institutional partners have instituted an Industry Research advisory Panel, which met for the first time in late 2007; members are dr Rhys Francis, Executive director, australian eResearch Infrastructure Council, chair; dr greg harper, Meat & livestock australia; dr tim littlejohn, IBM australia; dr warren Parker, CEO, landcare new Zealand; Prof. Mark Ragan, UQ; and Prof. nadia Rosenthal, director, australian Regenerative Medicine Institute, Monash University. QFaB is using Plone, a highly capable portal developed in the aRChER e-research project, to provide data to partners in adelaide, Brisbane, Melbourne, Perth and Sydney as part of a large project on nuclear receptor signalling funded by the national Breast Cancer Foundation. the latter program is likewise highly synergistic with our Research Program 2, and with parallel work in research groups at the University of newcastle and the University of Queensland.

QosCosGRID

during 2008 aCB became a key node in the EU Sixth Framework Information Society technology project “Quasi-opportunistic supercomputing for complex systems in grid environments”. QosCosgRId technical Manager dr Krzysztof (Chris) Kurowski was based within the UQ node of aCB during 2008 and managed the project from australia. an early outcome is that a small cluster in IMB is now part of the QosCosgRId computing network, and research within aCB’s Program 3 (spatial models of diffusion in lipid membranes) was demonstrated at the 2008 EU review in Brussels. Chris built on earlier links with Prof. david abramson (Monash University), and joint proposals have been submitted within national research and infrastructure funding contexts. new links among the aaF, aaRnet, aPaC/nCI, nCRIS Platforms for Collaboration, and national e-research capability represent an expansion of australia’s capacity in bioinformatics.

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names of aCB investigators, postdoctoral researchers and students are shown in boldface. we do not list papers that at the end of december 2008 were available only electronically in advance of print publication, or were in press, under review, submitted or in preparation.

a. BOOKS

a1. BOOK – aUthOREd RESEaRChMcLachlan, G.J. & Krishnan, t. (2008) The EM Algorithm and Extensions. Second Edition. new york: wiley. ISBn 978-0-471-20170-0.

a3. BOOK – EdItEddowney, R.g., Fellows, M.R. & Langston, M.A., Eds (2008) The Computer Journal Special Issues on Parameterized Complexity: The Computer Journal, 51(1) and 51(3). British Computer Society. Online ISSn 1460-2067 Print ISSn 0010-4620.

Schönbach, C., Ranganathan, S. & Brusic, v., Eds (2008) Immunoinformatics (Immunomics Reviews) volume 1. Springer. ISBn 978-0-387-72967-1.

B. BOOK ChaPtERSBailey, T.L. (2008) discovering sequence motifs. In: Bioinformatics: data, Sequence analysis and Evolution (J.M. Keith, Ed.), humana Press. Methods in Molecular Biology Series 452, Chapter 12, pp. 231-251. ISBn 978-1-58829-707-5.

Berretta, R., Costa w. & Moscato, P. (2008) Combinatorial optimization models for finding genetic signatures from gene expression datasets. In: Bioinformatics: Structure, Function and applications (J.M. Keith, Ed.), humana Press. Methods in Molecular Biology Series 453, Chapter 19, pp. 363-377. ISBn 978-1-60327-428-9.

Beiko, R.G. & Ragan, M.A. (2008) detecting lateral genetic transfer: a phylogenetic approach. In: Methods in Bioinformatics (J.M. Keith, Ed.), humana Press. Methods in Molecular Biology Series 453, Chapter 21, pp. 457-469. ISBn 978-1-60327-428-9.

Flack, L.K. & McLachlan, G.J. (2008) Clustering methods for gene-expression data. In: handbook of Research on Systems Biology applications in Medicine (a. daskalaki, Ed.), hershey, Pennsylvania: Idea group Publishing, Chapter XI, pp. 209-220. ISBn 978-1-60566-076-9.

Hamilton, N. & huber, t. (2008) an introduction to protein contact prediction. In: Bioinformatics: Structure, Function and applications (J.M. Keith, Ed.), humana Press. Methods in Molecular Biology Series 453, Chapter 3, pp. 87-104. ISBn 978-1-60327-428-9.

Hamilton, N., Kerr, M.C., Burrage, K. & Teasdale, R.D. (2008) analysing real-time video microscopy: the dynamics and geometry of vesicles and tubules in endocytosis. In: Current Protocols in Cell Biology Series (K. Morgan, Ed.), wiley Interscience, Unit 4.16. ISSn: 1934-2500. Online ISSn: 1934-2616.

hourani, M., Berretta, R., Mendes, a. & Moscato, P. (2008) genetic signatures for a rodent model of Parkinson’s disease using combinatorial optimization methods. In: Bioinformatics: Structure, Function and applications (J.M. Keith, Ed.), humana Press. Methods in Molecular Biology Series 453, Chapter 20, pp. 379-392. ISBn 978-1-60327-428-9.

McLachlan, G.J., Bean, R. & ng, S.K. (2008) Clustering of microarray data via mixture models. In: Statistical advances in Biomedical Sciences: Clinical trials, Epidemiology, Survival analysis, and Bioinformatics (a. Biswas, S. datta, J.P. Fine & M.R. Segal, Eds), hoboken, new Jersey: wiley, Chapter 21, pp. 365-383. ISBn 9780471947530.

McLachlan, G.J., Bean, R. & ng, S.K. (2008) Clustering. In: Bioinformatics: Structure, Function and applications, (J.M. Keith, Ed.), humana Press. Methods in Molecular Biology Series 453, Chapter 22, pp. 423-439. ISBn 978-1-60327-428-9.

McLachlan, G.J., Chevelu, J. & Zhu, J. (2008) Correcting for selection bias via cross-validation in the classification of microarray data. In: Beyond Parametrics in Interdisciplinary Research: Festschrift in honour of Professor Pranab K. Sen (n. Balakrishnan, E. Pena & M.J. Silvapulle, Eds), hayward Ca: IMS Collections 1:383-395. ISBn 978-0-940600-73-7.

Mendes, a., Scott, R.J. & Moscato, P. (2008) Microarrays–identifying molecular portraits for prostate tumors with different gleason patterns. In: Clinical Bioinformatics (R.J.a. trent, Ed.), humana Press. Methods in Molecular Medicine Series 141, Chapter 8, pp. 131-151. ISBn 978-1-58829-791-4.

ng, S.K. & McLachlan, G.J. (2008) Expert networks with mixed continuous and categorical feature variables: a location modeling approach. In: Machine learning Research Progress (h. Peters and M. vogel, Eds), nova, pp. 1-14. ISBn 978-1-60456-646-8.

Ranganathan, S., tong, J.C. & tan, t.w. (2008) Structural Immunoinformatics. In: Immunoinformatics (Immunomics Reviews) volume 1 (C. Schönbach, S. Ranganathan & v. Brusic, Eds), Springer, new york, Chapter 3, pp. 51-61. ISBn 978-0-387-72967-1.

Rosamond, F. (2008) Max leaf Spanning tree. In: Encyclopedia of algorithms (Ming-yang Kao, Ed.), Springer, Part 12, pp. 297-305. ISBn 978-0-387-30770-1.

C. JOURnal aRtIClES

C1. Journal articles in scholarly refereed publicationsAmaral, P.P. & Mattick, J.S. (2008) noncoding Rna in development. Mammalian Genome 19:454-492.

Amaral, P.P., Dinger, M.E., Mercer, T.R. & Mattick, J.S. (2008) the eukaryotic genome as an Rna machine. Science 319:1787-1789.

An, J. & Chen, Y.-P.P. (2008) Finding edging genes from microarray data. Journal of Biotechnology 135:233-240.

Barrenäs, F., andersson, B., Cardell, l.O., Langston, M., Mobini, R., Perkins, a., Soini, J., Ståhl, a. & Benson, M. (2008) gender differences in inflammatory proteins and pathways in seasonal allergic rhinitis. Cytokine 42:325-329.

Bauer, D. & Bailey, T.L. (2008) StREaM: static thermodynamic regulatory model of transcription. Bioinformatics 24:2544-2545.

Bauer, D.C. & Bailey, T.L. (2008) Studying the functional conservation of cis-regulatory modules and their transcriptional output. BMC Bioinformatics 9:220.

appendix 1: Publications

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Bode, M., Burrage, K. & Possingham, h.P. (2008) Using complex network metrics to predict the persistence of metapopulations with asymmetric connectivity patterns. Ecological Modelling 214:201-209.

Bodén, M. & Bailey, T.L. (2008) associating transcription factor binding site motifs with target gO terms and target genes. Nucleic Acids Research 36:4108-4117.

Bodén, M., Teasdale, R.D. (2008) determining nucleolar association from sequence by leveraging protein-protein interactions. Journal of Computational Biology 15:291-304.

Bordewich, M., Rodrigo, A.G. & Semple, C. (2008) Selecting taxa to save or sequence: desirable criteria and a greedy solution. Systematic Biology 57:825-834.

Brusic, v. & Ranganathan, S. (2008) Critical technologies for bioinformatics. Briefings in Bioinformatics 9:261-262.

Cai, l., huang, X., liu, C., Rosamond, F. & Song, y. (2008) Parameterized complexity and biopolymer sequence comparison. The Computer Journal 51:3:270-291.

Campbell, B.E., Nagaraj, S.H., hu, M., Zhong, w., Sternberg, P.w., Ong, B, loukas, a., Ranganathan, S., Beveridge, I. & gasser, R.B. (2008) gender-enriched transcripts in adult Haemonchus contortus – predicted functions and genetic interactions based on comparative analyses with Caenorhabditis elegans. International Journal for Parasitology 38:65-83.

Caprania, C.C., O’Brien, E. & McLachlan, G.J. (2008) Characteristic traffic load effects from a mixture of loading events on short to medium span bridges. Structural Safety 30:394-404.

Chen, C.-M., liu, F. & Burrage, K. (2008) Finite difference method and a new Fourier analysis for the Fractional Reaction-diffusion Equation. Applied Mathematics and Computation 198:754-769.

Chen, Q., Zhang, S. & Chen, Y.-P.P. (2008) Rule-based dependency models for security protocol analysis. Integrated Computer-Aided Engineering 15:369-380.

Chen, Y.-P.P. & Chen, F. (2008) Identifying targets for drug discovery using bioinformatics. Expert Opinion on Therapeutic Targets 12:383-389.

Chen, Y.-P.P. & Chen, F. (2008) Using bioinformatics techniques for gene identification in drug discovery and development. Current Drug Metabolism 9:567-573.

Chin, F.K. & Hegland, M. (2008) the total quasi-steady state assumption: its justification by singular perturbation theory and its application to the chemical master equation. ANZIAM Journal 50:C429-C443.

Choo, K.H. & Ranganathan, S. (2008) Flanking signal and mature peptide residues influence signal peptide cleavage. BMC Bioinformatics 9:S15.

Choo, K.H., tong, J.C. & Ranganathan, S. (2008) Modeling Escherichia coli signal peptidase complex with bound substrate: determinants in the mature peptide influencing signal peptide cleavage. BMC Bioinformatics 9:S15.

Dang, V.T., Kassahn, K.S., Esteban Marcos, A. & Ragan, M.A. (2008) Identification of human haploinsufficient genes and their genomic proximity to segmental duplications. European Journal of Human Genetics 16:1350-1357.

Darling, A.E., Miklós, I. & Ragan, M.A. (2008) dynamics of genome arrangement in bacterial populations. PLoS Genetics 4:e1000128. doi:10.1371/journal.pgen.1000128.

datu, B.J.d., gasser, R.B., Nagaraj, S.H., Ong, E., O’donoghue, P., McInness, R., Ranganathan, S. & loukas, a. (2008) transcriptional changes in the hookworm, ancylostoma caninum, during the transition from a free-living to a parasitic larva. PLoS Neglected Tropical Diseases 2:e130.

de Micco, l., gonzález, C. M., larrondo, h. a., Martín, M. t., Plastino, a. & Rosso, O.A. (2008) Randomizing nonlinear maps via symbolic dynamics. Physica A 387:3373-3383

deng, K., Zhou, X., Xhen, h.t., liu, Q., Xu, K. & lin, X. (2008) a multi-resolution surface distribution model for k-nn query processing. The VLDB Journal 17:1101-1119.

Dinger, M.E., Amaral, P.P., Mercer, T.R., Pang, K.C., Bruce, S.J., gardiner, B.B., askarian-amiri, M.E., Ru, K., Soldà, g., Simons, C., Sunkin, S.M., Crowe, M.l., grimmond, S.M., Perkins, a.C. & Mattick, J.S. (2008) long noncoding Rnas in mouse embryonic stem cell pluripotency and differentiation. Genome Research 18:1433–1445.

Dinger, M.E., Mercer, T.R. & Mattick, J.S. (2008) Rnas as extracellular signaling molecules. Journal of Molecular Endocrinology 40:151-159.

Dinger, M.E., Pang, K.C., Mercer, T.R. & Mattick, J.S. (2008) differentiating protein-coding and noncoding Rna: challenges and ambiguities. PLoS Computational Biology 4:e1000176.

downey, R.g., Fellows, M.R., McCartin, C. & Rosamond, F. (2008) Parameterized approximation of dominating set problems. Information Processing Letters 109:68-70.

dujmovic, v., Fellows, M.R., Kitching, M., liotta, g., McCartin, C., nishimura, n., Ragde, P., Rosamond, F., whitesides, S. & wood, d.R. (2008) On the parameterized complexity of layered graph drawing. Algorithmica 52:267-292.

Fellows, M.R., hermelin, d., Rosamond, F. & vialette, S. (2008) On the parameterized complexity of multiple-interval graph problems. Theoretical Computer Science 410:53-61.

Fellows, M.R., Knauer, C., nishimura, n., Ragde, P., Rosamond, F., Stege, U., thilikos, d. & whitesides, S. (2008) Faster fixed-parameter tractable algorithms for matching and packing problems. Algorithmica 52:167-176.

Fink, J.L., Karunaratne, S., Mittal, a., gardiner, d., Hamilton, N., Mahony, d., Kai, C., Suzuki, h., hayashizaki, y. & Teasdale, R.D. (2008) towards defining the nuclear proteome. Genome Biology 9:R15.

Frith, M.C., Saunders, n.F.w., Kobe, B. & Bailey, T.L. (2008) discovering sequence motifs with arbitrary insertions and deletions. PLoS Computational Biology 4:e1000071.

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Gaikwad, J., Khanna, V., vemulpad, S., Jamie, J., Kohen, J. & Ranganathan, S. (2008) CMKb: a web-based prototype for integrating australian aboriginal customary medicinal plant knowledge. BMC Bioinformatics 9:S25.

glasner, J.d., Plunkett III, g., anderson, B.d., Baumler, d.J., Biehl, B.S., Burland, v., Cabot, E.l., Darling, A.E., Mau, B., neeno-Eckwall, E.C., Pot, d., Qui, y., Rissman, a.I., worzella, S., Zaremba, S., Fedorko, J., hampton, t., liss, P., Rusch, M., Shaker, M., Shaull, l., Shetty, P. thotakura, S., whitmore, J., Blattner, F.R., greene, J.M. & Perna, n.t. (2007) Enteropathogen Resource Integration Center (ERIC): bioinformatics support for research on biodefence-relevant enterobacteria. Nucleic Acids Research 36:d519-523.

Gómez-Ravetti, M. & Moscato, P. (2008) Identification of a 5-protein biomarker molecular signature for predicting alzheimer’s disease. PLoS ONE 3:e3111.

guipponi, M., toh, M.y., tan, J., Park, d., Hanson, K., Ballana, E., Kwong, d., Cannon, P.Z., wu, Q., gout, a., delorenzi, M., Speed, t.P., Smith, R.J., dahl, h.h., Petersen, M., Teasdale, R.D., Estivill, X., Park, w.J., Scott, h.S. (2008) an integrated genetic and functional analysis of the role of type II transmembrane serine proteases (tMPRSSs) in hearing loss. Human Mutation 29:130-41.

Hamilton, N. & Teasdale, R.D. (2008) visualising and clustering high throughput sub-cellular localization imaging. BMC Bioinformatics 9:81.

hayward, J.J. & Rodrigo, A.G. (2008) Recombination in feline immunodeficiency virus from feral and companion domestic cats. Virology Journal 5:76.

Hegland, M. (2008) approximating the solution of the chemical master equation by aggregation. ANZIAM Journal 50:C371-C384.

Hegland, M., hellander, a. & lötstedt (2008) Sparse grids and hybrid methods for the chemical master equation. BIT Numerical Mathematics 48:265-283.

holland, l.Z., albalat, R. … [35 authors]… Rigoutsos, I., et al. [26 more authors] (2008) the amphioxus genome illuminates vertebrate origins and cephalochordate biology. Genome Research 18:1100-1111 (Erratum p. 1380).

huang, Z., Shen, h.t. & Zhou, X. (2008) localized co-occurrence model for fast approximate search in structure databases. IEEE Transactions on Knowledge and Data Engineering 20:519-431.

Jorgensen, M. & McLachlan, G.J. (2008) wallace’s approach to unsupervised learning: the Snob program. Computer Journal 51:571-578.

Jueng, h., yiu, M.l., Zhou, X., Jensen, C.S. & Shen, h.t. (2008) discovery of convoys in trajectory databases. The VLDB Journal 1:1068-1080.

Kalyuzhnaya, M.g., lapidus, a., Ivanova, n., Copeland, a.C., Mchardy, a.C., Szeto, E., Salamov, a., grigoriev, I.v., Suciu, d., levine, S.R., Markowitz, v.M., Rigoutsos, I., tringe, S.g., Bruce, d.C., Richardson, P.M., lidstrom, M.E., Chistoserdova, l. (2008) high-resolution metagenomics targets specific functional types in complex microbial communities. Nature Biotechnology 26:1029-1034.

Kassahn, K.S. (2008) Microarrays for comparative and ecological genomics: beyond single-species applications of array technologies. Journal of Fish Biology 72:2407-2434.

Keith, J.M., adams, P., Stephen, S. & Mattick, J.S. (2008) delineating slowly and rapidly evolving fractions of the Drosophila genome. Journal of Computational Biology 15:407-430.

Knapp, K., Chonka, a. & Chen, Y.-P.P. (2008) POEM, a 3-dimensional exon taxonomy and patterns in untranslated exons. BMC Genomics 9:428.

Kong, l. & Ranganathan, S. (2008) tandem duplication, circular permutation, molecular adaptation: how Solanaceae resist pests via inhibitors. BMC Bioinformatics 9:S22.

Korbie, d.J. & Mattick, J.S. (2008) touchdown PCR for increased specificity and sensitivity in PCR amplification. Nature Protocols 3:1452-1456.

Korol, a. M., Foresto, P., darrigo, M. & Rosso, O.A. (2008) diabetic erythrocytes test by correlation coefficient. The Open Medical Informatics Journal 2:105-111

Langston, M.A., Perkins, a.d., Saxton, a.M., Scharff, J.a. & voy, B.h. (2008) Innovative computational methods for transcriptomic data analysis: a case study in the use of FPt for practical algorithm design and implementation. Computer Journal 51:26-38.

leier, a., Marquez-lago, t.t. & Burrage, K. (2008) generalized binomial tau-leap method for biochemical kinetics incorporating both delay and intrinsic noise. Journal of Chemical Physics 128:205107.

leier, a., Marquez-lago, t.t., Burrage, K. & Burrage, P. (2008) Modeling intrinsic noise and delays in chemical kinetics of coupled autoregulated oscillating cells. International Journal for Multiscale Computational Engineering 6: 77-86.

lesmono, d., tonkes, E. & Burrage, K. (2008) Opportunistic timing and manipulation in australian federal elections. European Journal of Operational Research 192:677-691.

lim, J.P., wang, J.t., Kerr, M.C., Teasdale, R.D., gleeson, P.a. (2008) a role for SnX5 in the regulation of macropinocytosis. BMC Cell Biology 9:58.

MacNamara, S., Bersani, a.M., Burrage, K. & Sidje, R.B. (2008) Stochastic chemical kinetics and the total quasi-steady-state assumption: application to the stochastic simulation algorithm and chemical master equation. Journal of Chemical Physics 129:095105.

MacNamara, S., Burrage, K. & Sidje, R.B. (2008) application of Strang splitting to the chemical master equation for simulating biochemical kinetics. International Journal of Computational Science 2:402-421.

MacNamara, S., Burrage, K. & Sidje, R.B. (2008) Multiscale modeling of chemical kinetics via the master equation. SIAM Journal Multiscale Modelling and Simulation Multiscale Modeling & Simulation 6:1146-1168.

Mattick, J.S. & Mehler, M.F. (2008) Rna editing, dna recoding and the evolution of human cognition. Trends in Neuroscience 31:227-233.

Mattick, J.S. & Mehler, M.F. (2008) Rna editing, dna recoding and the evolution of human cognition. Trends in Neuroscience 31:227-233.

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Mattick, J.S., Amaral, P.P., Dinger, M.E., Mercer, T.R. & Mehler, M.F. (2008) Rna control of epigenetic processes. Australian Biochemist 39:4-8.

Mclaren, C.E., gordeuk, v.R., Chen, w.-P., Barton, J.C., acton, R.t., Speechley, M., Castro, O., adams, P.C., Snively, B.M., harris, E.M., Reboussin, d.M., McLachlan, G.J. & Bean, R. (2008) Bivariate mixture modeling of transferrin saturation and serum ferritin concentration in asians, african-americans, hispanics, and whites in the hemochromatosis and Iron Overload Screening (hEIRS) Study. Translational Research 151:97-109.

Mercer, T.R., Dinger, M.E., Mariani, J., Kosik, K.S., Mehler, M.F. & Mattick, J.S. (2008) non-coding Rnas in long-term memory formation. The Neuroscientist 14:434-445.

Mercer, T.R., Dinger, M.E., Sunkin, S.M., Mehler, M.F. & Mattick, J.S. (2008) Specific expression of non-coding Rnas in mouse brain. Proceedings of the National Academy of Sciences USA 105:716-721.

Nagaraj, S., gasser, R.B., nisbet, a.J. & Ranganathan, S. (2008) In silico analysis of expressed sequence tags from Trichostrongylus vitrinus (nematoda): comparison of the automated EStExplorer workflow platform with conventional database searches. BMC Bioinformatics 9:S10.

Nagaraj, S.H., gasser, R.B. & Ranganathan, S. (2008) needles in the ESt haystack: large-scale identification and analysis of excretory-secretory (ES) proteins in parasitic nematodes using expressed sequence tags (ESts). PLoS Neglected Tropical Diseases 2:e301.

nahkuri, S., taft, R.J., Korbie, d.J. & Mattick, J.S. (2008) Molecular evolution of the hBII-52 snoRna cluster. Journal of Molecular Biology 381:810-815.

Nicolau, D.V., Jr & Burrage, K. (2008) Stochastic simulation of chemical reactions in spatially complex media. Computers and Mathematics with Applications 55:1007-1018.

Nicolau, D.V., Jr, Burrage, K., nicolau, d.v. & Maini, P.K (2008) ‘Extremotaxis’: computing with a bacterial-inspired algorithm. BioSystems 94:47-54.

Noske, A.B., Costin, a.J., Morgan, g.P. & Marsh, B.J. (2008) Expedited approaches to whole cell electron tomography and organelle mark-up in situ in high- pressure frozen pancreatic islets. Journal of Structural Biology 161:298–313

Ormsby, R.J., Ranganathan, S., tong, J.C., griggs, K.M., dimasi, d.P., hewitt, a.w., Burdon, K.P., Craig, J.E., hoh, J. & gordon, d.l. (2008) Functional and structural implications of the complement factor h y402h polymorphism associated with age-related macular degeneration. Investigative Ophthalmology & Visual Science 49:1763-70. (joint first authors)

Poss, M., Ross, h., Rodrigo, A.G., terwee, J.a. & vandewoude, S. (2008) the molecular biology and evolution of feline immunodeficiency viruses of cougars. Veterinary Immunology and Immunopathology 123:154-158.

Ragan, M.A., littlejohn, t. & Ross, B. (2008) genome-scale computational biology and bioinformatics in australia. PLoS Computational Biology 4:e1000068. doi:10.1371/journal.pcbi.1000068

Ranganathan, S., gribskov, M. & tan, t.w. (2008) Bioinformatics research in the asia Pacific – an update. BMC Bioinformatics 9:S1.

Richter, t., Floetenmeyer, M., Fergusion, C., galea, J., goh, J., lindsay, M.R., Morgan, g.P., Marsh, B.J. & Parton, R.g. (2008) high-resolution 3d quantitative analysis of caveolar ultrastructure and caveola-cytoskeleton interactions. Traffic 6:893-909.

Rodrigo, A., Bertels, F., heled, J., noder, R., Shearman, h. & tsai, P. (2008) the perils of plenty: what are we going to do with all these genes? Philosophical Transactions of the Royal Society of London Series B: Biological Sciences 363:3893-3902.

Rosso, O.A., vicente, R. & Mirasso, C. (2008) Encryption test of pseudo-aleatory messages embedded on chaotic laser signals: an information theory approach. Physics Letter A 372:1018-1023.

Rudge, t. & Burrage, K. (2008) Effects of intrinsic and extrinsic noise can accelerate juxtacrine pattern formation. Bulletin of Mathematical Biology 70:971-991.

Shen, h.t., Jiang, S., tan, K.-l., huang, Z. & Zhou, X. (2008) Speed up interactive image retrieval. The VLDB Journal 18:329-343.

Sidje, R.B., williams, a.B. & Burrage, K. (2008) Fast generalized cross validation using Krylov subspace methods. Numerical Algorithms 47:109-131.

Sprenger, J., Fink, J.L., Karunaratne, S., Hanson, K., Hamilton, N.A., Teasdale, R.D. (2008) lOCatE: a mammalian protein subcellular localization database. Nucleic Acids Research 36(database issue):d230-d233.

Steel, M. & Rodrigo, A., (2008) Maximum likelihood supertrees. Systematic Biology 57:243-250.

Stephen, S., Pheasant, M., Makunin, I.v. & Mattick, J.S. (2008) large-scale appearance of ultraconserved elements in tetrapod genomes and slowdown of the molecular clock. Molecular Biology and Evolution 25:402-408.

Styczynski, M.P., Jensen, K.l., Rigoutsos, I. & Stephanopoulos, g. (2008) BlOSUM62 miscalculations improve search performance. Nature Biotechnology 26:274-275.

tay, y., Zhang, J., thomson, a.M., lim, B. & Rigoutsos, I. (2008) MicroRnas to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation. Nature 455:1124-1128.

tay, y.M-S., tam, w.-l., ang, y.-S., gaughwin, P.M., yang, h., weijia, w., Rubing, l., george, J., ng, h.-h., Perera, R.J., lufkin, t., Rigoutsos, I., thomson, a.M. & lim, B. (2008) MicroRna-134 modulates the differentiation of mouse embryonic stem cells where it causes post-transcriptional attenuation of nanog and lRh1. Stem Cells 26:17-29.

tian, t. & Burrage, K. (2008) an effective stepsize selection procedure for discrete simulation of biochemical reaction. ANZIAM J. 48:1022-1040.

tsirigos, a. & Rigoutsos, I. (2008) human and mouse introns are linked to the same processes and functions through each genomes most frequent non-conserved motifs. Nucleic Acids Research 36:3848-3493.

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wang, w.X., Rajeev, B.w., Stromberg, a.J., Ren, n., tang, g., huang, Q., Rigoutsos, I. & nelson, P.t. (2008) the expression of microRna miR-107 decreases early in alzheimer’s disease and may accelerate disease progression through regulation of beta-site amyloid precursor protein-cleaving enzyme 1. Journal of Neuroscience 30:1213-1223.

Whitington, T., Perkins, a.C. & Bailey, T.L. (2008) high-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites. Nucleic Acids Research 37:14-25.

Wong, S. & Ragan, M.A. (2008) MaChOS: Markov clusters of homologous subsequences. Bioinformatics 24:i77-85.

wu, X., Kumar, v., Quinlan, J.R., ghosh, J., yang, Q., Motoda, h., McLachlan, G.J., ng, S.K., liu, B., yu, P.S., Zhou, Z.-h., Steinbach, M., hand, d.J. & Steinberg, d. (2008) top 10 algorithms in data mining. Knowledge and Information Systems 14:1-37.

Yuan, Z. & wang, Z.-X. (2008) Quantifying the relationship of protein burying depth and sequence. Proteins – Structure Function and Bioinformatics 70:509-516.

Zhao, J. huang, Z., Shen, h.t., Zhou, X., li, y. & lim, E.-P. (2008) Batch nearest neighbor search for video retrieval. IEEE Transactions on Multimedia 10:409-420.

Zhu, J.X., McLachlan, G.J., Ben-Tovim, L. & wood, I. (2008) On selection biases with prediction rules formed from gene expression data. Journal of Statistical Planning and Inference 3:374-386.

Zunino, l., B. M. tabak, B.M., Figliola, a., Pérez, d.g., garavaglia, M. & Rosso, O.A. (2008) a multifractal approach for the stock market inefficiency. Physica A 387:6558-6566

Zunino, l., Pérez, d. g., Kowalski, a., Martín, M. t., garavaglia, M., Plastino, a. & Rosso, O.A. (2008) Fractional Brownian motion, fractional gaussian noise, and tsallis permutation entropy. Physica A 387:6057-6068.

Zunino,l., Pérez, d. g., Martín, M. t., garavaglia, M., Plastino, a. & Rosso, O.A. (2008) Permutation entropy of fractional Brownian motion and fractional gaussian noise. Physics Letters A 372:4768-4774

C2. Journal article – other contribution to refereed journaldowney, R.g., Fellows, M.R. & Langston, M.A. (2008) the Computer Journal Special Issues on Parameterized Complexity: Foreword by the guest Editors. The Computer Journal 51:1-6.

McLachlan, G.J., wang, K. & ng, S.K. (2008) Contribution to the discussion of the paper by F. Chiaromonte & S. tyekucheva. Comments on: augmenting the bootstrap to analyse high dimensional genomic data. TEST 17:1:43-46.

C3. Journal article – non-refereed articleFellows, M.R., Fomin, F.v., lokshtanov, d., losievskaja, E., Rosamond, F. & Saurabh, S. (2008) Parameterized low-distortion Embeddings - graph metrics into lines and trees. In: the Computing Research Repository (CoRR) abs/0804.3028.

C5. Unpublished reports (including commercial consultancies)Baek, J. & McLachlan, G.J. (2008) Mixtures of factor analyzers with common factor loadings for the clustering and visualisation of high-dimensional data. Technical Report NI08018-SCH, Preprint Series of the Isaac newton Institute for Mathematical Sciences, Cambridge.

Bodlaender, h. l., demaine, E., Fellows, M., guo, J., hermelin, d., lokshtanov, d., Müller, M., Raman, v., van Rooij, J. & Rosamond, F. (2008) Open problems in parameterized and exact computation from IwPEC 2008. Technical Reports: H.L. Bodlaender. Faculty of Science: Information and Computing Sciences, University Utrecht, the netherlands.

Fellows, M., Rosamond, F. & Slinko, a. (2008) Sensing god’s will is fixed parameter tractable. Report series – Information Processing Letters. department of Mathematics, University of auckland.

E. COnFEREnCE PROCEEdIngS

E1. Conference – full written paper – refereed proceedings Bauer, D.C., Buske, F.A. & Bodén, M. (2008) Predicting SUMOylation sites. In: Proceedings of third International association for Pattern Recognition (IaPR) Conference International Conference on Pattern Recognition in Bioinformatics (PRIB 2008), Melbourne, australia, 15-17 October 2008. Lecture Notes in Bioinformatics, 5265:28-40 (M. Chetty, a. ngom & S. ahmad, Eds). Springer. ISBn 978-3-540-88434-7.

Betzler, n., Fellows, M.R., guo, J., niedermeier, R. & Rosamond, F.A. (2008) Computing Kemeny rankings, parameterized by the average K-t distance. In: Proceedings of 2nd International workshop on Computational Social Choice, liverpool, UK 3-5 September 2008 (U. Endriss & P.w. goldberg, Eds), pp. 85-96. University of liverpool.

Betzler, n., Fellows, M.R., guo, J., niedermeier, R. & Rosamond, F.A. (2008) Fixed-parameter algorithms for Kemeny scores. In: Proceedings of algorithmic aspects in Information and Management, 4th International Conference (aaIM 2008), Shanghai, China, 23-25 June 2008. Lecture Notes in Computer Science 5034:60-71 (R. Fleischer & J. Xu, Eds) .Springer. ISBn 978-3-540-68865-5.

Betzler, n., Fellows, M.R., Komusiewicz, C. & niedermeier, R. (2008) Parameterized algorithms and hardness results for some graph motif problems. In: Proceedings of the 19th annual Symposium on Combinatorial Pattern Matching (CPM 2008), Pisa, Italy, 18-20 June 2008. Lecture Notes in Computer Science 5029:31-43 (P. Ferragina & g.M. landau, Eds). Springer-verlag. ISBn 978-3-540-69066-5.

Bodén, M. (2008) Predicting nucleolar proteins using support-vector machines. In: Proceedings of the 6th asia-Pacific Bioinfomatics Conference (aPBC 2008), Kyoto, Japan, 14-17 January 2008. Advances in Bioinformatics and Computational Biology 6:19-28 (a. Brazma, S. Miyano & t. akutsu, Eds). Imperial College Press. ISBn 978-1-84816-108-5

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Bodlaender, h.l, Fellows, M.R., heggernes, P., Mancini, F., Papadopoulos, C. & Rosamond, F.A. (2008) Clustering with partial information. In: Proceedings of Mathematical Foundations of Computer Science 2008, 33rd International Symposium (MFCS 2008), torun, Poland, 25-29 august 2008. Lecture Notes in Computer Science 5162:144-155 (E.Ochmanski & J. tyszkiewicz, Eds). Springer. ISBn 978-3-540-85237-7.

Bodlaender, h.l., downey, R.g., Fellows, M.R. & hermelin, d. (2008) On problems without polynomial kernels (extended abstract). In: Proceedings of automata, languages and Programming, 35th International Colloquium (ICalP 2008) Reykjavik, Iceland, 7-11 July 2008. Part I: tack a: algorithms, automata, Complexity, and games. Lecture Notes in Computer Science 5125:563-574. (l. aceto, I. damagård, l.a. goldberg, M.M. halldórsson, a. Ingólfsdóttir & I. walukiewicz, Eds). Springer. ISBn 978-3-540-70574-1.

Davis, M.J., Newman, A., Khan, I., hunter, J. & Ragan, M.A. (2008) Integrating hierarchical controlled vocabularies with Owl ontology: a case study from the domain of molecular interactions. In: Proceedings of the 6th asia-Pacific Bioinfomatics Conference (aPBC 2008), Kyoto, Japan, 14-17 January 2008. Advances in Bioinformatics and Computational Biology 6:145-154 (a. Brazma, S. Miyano, t. akutsu, Eds). Imperial College Press. ISBn 978-1-84816-108-5

ding, Z. & Zhou, X. (2008) location update strategies for network-constrained moving objects. In: Proceedings of the 13th International Conference on database Systems for advanced applications (daSFaa 2008), new delhi, India, 19-21 March 2008. Lecture Notes in Computer Science 4947:644-652. Springer. ISBn978-3-540-78567-5.

Fellows, M.R. & Fermau, h. (2008) Facility location problems: a parameterized view. In: Proceedings of algorithmic aspects in Information and Management, 4th International Conference (aaIM 2008), Shanghai, China, 23-25 June 2008. Lecture Notes in Computer Science 5034:188-199 (R. Fleischer & J. Xu, Eds). Springer. ISBn 978-3-540-68865-5.

Fellows, M.R., hermelin, d., Müller, M. & Rosamond, F.A. (2008) a purely democratic characterization of w[1]. In: Proceedings of Parameterized and Exact Computation, third International workshop (IwPEC 2008), victoria, Canadia, 14-16 May 2008. Lecture Notes in Computer Science 5108:103-114 (M. grohe & R. niedermeier, Eds). Springer. ISBn 978-3-540-79722-7.

Fellows, M.R., lokshtanov, d., Misra, n., Rosamond, F.A. & Saurabh, S. (2008) graph layout problems parameterized by vertex cover. In: Proceedings of 19th International Symposium of algorithms and Computation (ISaaC 2008), gold Coast, australia 15-17 december 2008. Lecture Notes in Computer Science 5369:294-305 (S.-h. hong, h. nagamochi & t. Fukunaga, Eds). Springer. ISBn 978-3-540-92181-3.

Fellows, M.R., Meister d., Rosamond, F.A., Sritharan, R. & telle, J.a. (2008) leaf powers and their properties: Using the trees. In: Proceedings of 19th International Symposium of algorithms and Computation (ISaaC 2008), gold Coast, australia 15-17 december 2008. Lecture Notes in Computer Science 5369:402-413 (S.-h. hong, h. nagamochi & t. Fukunaga, Eds). Springer. ISBn 978-3-540-92181-3.

garcke, J. & Hegland, M. (2008) Modeling, simulation and optimisation of complex processes. In: Proceedings of the 3rd International Conference on high Performance Scientific Computing, hanoi, vietnam, 6-10 March 2006, XII:235-248 (h.g. Bock, E. Ekostina, h.X. Phu & R. Rannacher, Eds). Springer. ISBn 978-3-540-79408-0.

goode, M., guindon, S. & Rodrigo, A., (2008) Modelling the evolution of protein coding sequences sampled from measurably evolving populations. In: genome Informatics 2008. Proceedings of the 19th International Conference, gold Coast, Queensland, australia, 1-3 december 2008 (J. arthur & S.-K. ng, Eds). Genome Informatics Series 21: 150-164. Imperial College Press, london. ISBn 978-1-84816-331-7.

Hawkins, J. & Bailey, T.L. (2008) the statistical power of phylogenetic motif models. In: Proceedings of twelfth annual International Conference on Research in Computational Molecular Biology (RECOMB 2008), Singapore, 30 March-2 april 2008. Lecture Notes in Computer Science 4955:112-126 (M. vingron & l. wong, Eds). Springer-verlag. ISBn 978-3-540-78838-6.

Hegland, M., Burden, C. & Santoso, l. (2008) Modeling, simulation and optimisation of complex processes. In: Proceedings of the 3rd International Conference on high Performance Scientific Computing, hanoi, vietnam, 6-10 March 2006, XII:259-272 (h.g. Bock, E. Ekostina, h.X. Phu & R. Rannacher, Eds). Springer. ISBn 978-3-540-79408-0.

huang, h., liu, C. & Zhou, X. (2008) Computing relaxed answers on RdF databases. In: Proceedings of the 9th International Conference on web Information Systems Engineering (wISE 2008), auckland, new Zealand, 1-3 September 2008. Lectures Notes in Computer Science 5175:163-175 (J. Bailey, d. Maier, K.-d. Schewe, B. thalheim, X.S. wang, Eds). Springers. ISBn 978-3-540-85480-7.

huang, Z., li, y., Shao, J., Shen, t., wang, l., Zhang, d., Zhou, X.M. & Zhou, X. (2008) Content-based video search: is there a need, and is it possible? In: Proceedings of International workshop on Information-explosion and next generation search (IngS), Shenyang, China, 26-27 april 2008 (a. nadamoto, y. Ishikawa, M. Kitsuregawa & K. tanaka, Eds), pp. 12-19. IEEE Computer Society. ISBn 978-0-7695-3300-1. (Keynote).

huang, Z., Shen, h.t., Shao, J., Rueger, S. & Zhou, X. (2008) locality condensation: a new dimensionality reduction method for image retrieval. In: Proceedings of the 16th International Conference on Multimedia, vancouver, Canada, 26-31 October 2008. a. El-Saddik, S. vuong, C. griwodz, a.d. Bimbo, K.S. Candan & a. Jaimes, Eds), pp. 219-228. aCM 2008. ISBn 978-1-60558-303-7.

lukman, S., Sim, K., li, J. & Chen, Y.-P.P. (2008) Interacting amino acid preferences of 3d pattern pairs at the binding sites of transient and obligate protein complexes. In: Proceedings of the Sixth asia Pacific Bioinformatics Conference (aPBC 2008), Kyoto, Japan, 14-17 January 2008, pp. 69-78 (a. Brazma, S. Miyano & t. akutsu, Eds). Imperial College Press. ISBn 978-1-84816-108-5.

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McLachlan, G.J., ng, S.K. & wang, K. (2008) Clustering via mixture regression models with random effects. In: Proceedings of Computational Statistics (COMPStat 2008), Porto, Portugal, 24-29 august 2008. Part XI::397-407 (P. Brito, Ed.) Springer. ISBn 978-3-7908-2083-6.

Montera, l.; do Carmo nicoletti, M.; da Silva, F.h. & Moscato, P. (2008) an effective mutation-based measure for evaluating the suitability of parental sequences to undergo dna shuffling experiments. In: Proceedings of IEEE Congress on Evolutionary Computation (CEC 2008) (IEEE world Congress on Computational Intelligence), hong Kong, 1-6 June 2008. (Z. Michalewicz & R.g. Reynolds, eds), pp. 765-772. IEEE. ISBn 978-1-4244-1823-7

Mujuni, E. & Rosamond, F.(2008) Parameterized complexity of the clique partition problem. In: Proceedings of the 14th Computing: the australasian theory Symposium (CatS 2008), wollongong, nSw, australia, 1 January 2008. Conferences in Research and Practice in Information Technology Series 316:77:75-78 (J. harland & P. Manyem, Eds). australian Computer Society. ISBn 978-1-920682-58-3.

Newman, A., hunter, J., li., y.F., Bouton, C. & Davis, M.J. (2008) BioManta Ontology: the integration of proein-protein interaction data. In: Proceedings of the Interdisciplinary Ontology Conference (InterOntology08), tokyo, 26-27 February 2008. (M. Okada & B. Smith, Eds), pp. 105-110. Keio University. ISBn 978-4-904239-00-1.

Newman, A., li, y.-F. & hunter, J. (2008) Scalable semantics – the silver lining of cloud computing. In: Proceedings of IEEE Fourth International Conference on eScience 2008 (eScience’08), Indiana, USa, 7-12 december 2008. (R. van Engelen, M. govindaraju & M. Cafaro, Eds), pp.111-118. IEEE. ISBn 978-1-4244-3380-3.

Rosso, O.A., larrondo, h.a., Martín, M.t. & Plastino, a. (2008) generalized Statistical Complexity Measure: a new tool for dynamical systems. In: Proceedings of International Conference “Modelling and Computation on Complex networks and Related topics (net-works 2008) Pamplona, Spain, 9-11 June 2008. (R. Criado, w. gonzales viñas, h. Mancini, R. Romance, Eds), pp. 149 – 156. Universiad Rey Juan Carlos, Spain. ISBn 978-84-691-3819-9

Sadiq, S., Zhou, X. & deng, K. (2008) Research and practice in data quality. In: Proceedings of the 10th asia-Pacific web Conference on Progress in www Research and development (aPweb 2008), Shenyang, China, 26-28 april 2008. Lecture Notes in Computer Science 4976:41-42 (y.Zhang, g. yu, E. Bertino & g, Xu, Eds). Springer. ISBn 978-3-540-78848-5.

Saedi, S., yang, g., Zhou, X., Shi, y., Zhai, B. & Jiang, w.w.-R. (2008) Pattern-based extraction of addresses from web page content. In: Proceedings of the 10th asia-Pacific web Conference on Progress in www Research and development (aPweb 2008), Shenyang, Chaina, 26-28 april 2008. Lecture Notes in Computer Science 4976:407-418 (y.Zhang, g. yu, E. Bertino & g, Xu, Eds). Springer. ISBn 978-3-540-78848-5.

Sajjanhar, S., lu, g., Zhang, d., Zhou, w. & Chen, Y.-P.P. (2008) Image retrieval based on semantics of intra-region color properties. In: Proceedings of 2008 IEEE 8th International Conference on Computer and Information technology, Sydney, australia, 8-11 July 2008, pp. 338-343 (Q. wu, X.he, Q.v. nguyen, w. Jia & M. huang, Eds). IEEE. ISBn 978-1-4244-2358-3.

Schmidt, S., li, g. & Chen, Y.-P.P. (2008) Medical knowledge discovery from a regional asthma dataset. In: Proceedings of 4th International Conference on Intelligent Computing (ICIC 2008), Shanghai, China, 15-18 September 2008. Lecture Notes in Computer Science 5227:888-895 (d.-S. huang, d.C. wunsch II, d.S. levine, K.-h. Jo, Eds), pp. 69-78. Springer. ISBn 978-3-540-85983-3.

Shao, J., huang, Z., Shen, h.t., Shen, J. & Zhou, X. (2008) distribution-based similarity measures for multi-dimensional point set retrieval applications. In: Proceedings of the 16th International Conference on Multimedia, vancouver, Canada, 26-31 October 2008. (a. El-Saddik, S. vuong, C. griwodz, a.d. Bimbo, K.S. Candan & a. Jaimes, Eds), pp. 429-438. aCM 2008. ISBn 978-1-60558-303-7.

wu, d., Fung, G., yu, J. & liu, Z. (2008) Integrating multiple data sources for stock prediction. In: Proceedings of the 9th International Conference web Information Systems Engineering (wISE 2008), auckland, new Zealand, 1-3 September 2008. Lectures Notes in Computer Science 5175:77-89 (J. Bailey, d. Maier, K.-d. Schewe, B. thalheim, X.S. wang, Eds). Springers. ISBn 978-3-540-85480-7.

wu, d., Fung, G., yu, J. & liu, Z. (2008) Mining multiple time series co-movements. In: Proceedings of the 10th asia-Pacific web Conference on Progress in www Research and development (aPweb 2008). Sheng, China, 26-28 april 2008. Lecture Notes in Computer Science 4976:572–583 (y. Zhang, g. yu, E. Bertino & g. Zu Eds). Springer. ISBn 978-3-540-78848-5.

Xu, Q., Shen, t.t., dai, y., Cui, B. & Zhou, X. (2008) achieving effect multi-term queries for fast dht information retrieval. In: Proceedings of the 9th International Conference on web Information Systems Engineering (wISE 2008), auckland, new Zealand, 1-3 September 2008. Lectures Notes in Computer Science 5175:20-35 (J. Bailey, d. Maier, K.-d. Schewe, B. thalheim, X.S. wang, Eds). Springer. ISBn 978-3-540-85480-7.

Zhang, y., Chesler, E.J. & Langston, M.A. (2008) On finding bicliques in bipartite graphs: a novel algorithm with application to the integration of diverse biological data types. Proceedings of the 41st annual hawaii International Conference on System Sciences (hICSS 2008), pp. 473-481. ISBn 0-7695-3075-3.

Zhou, X., Sadiq, S. & deng, K. (2008) data quality in web information systems. In: Proceedings of the 9th International Conference on web Information Systems Engineering (wISE 2008), auckland, new Zealand, 1-3 September 2008. Lectures Notes in Computer Science 5175:1 (J. Bailey, d. Maier, K.-d. Schewe, B. thalheim, X.S. wang, Eds). Springers. ISBn 978-3-540-85480-7.

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E2. Conference – full written paper – non-refereed proceedingsJeng, h., liu, Q., Shen, h.t. & Zhou, X. (2008) a hybrid prediction model for moving objects. In: Proceedings of the 24th International Conference on data Engineering (ICdE 2008), Cancun, Mexico, 7-12 april 2008. pp. 70-79. IEEE Computer Society. ISBn 978-1-4244-1837-4.

Newman, A., hunter, J., li. y.F., Bouton, C. & Davis, M.J. (2008) a scale-out RdF molecule store for distributed processing of biomedical data. Semantic web for health Care and life Sciences workshop, the 17th International world wide web Conference (www 2008), Beijing, China. 21-25 april 2008. ISBn 978-1-60558-085-2.

E4. Conference – unpublished presentationThis listing does not include presentations at the 2008 Winter School in Mathematics and Computational Biology.

Carpi, l., Rosso, O.A. & P. Saco (2008) analysis of australian stream flow rivers using quantifiers based on Information theory. XvI non-Equilibrium Statistical Mechanics and non-linear Physics, MEdyFInOl’08, Punta del Este, Uruguay, 1-5 december 2008.

de Micco, l., Rosso, O.A. & larrondo, h. (2008) Medidas de mixing de mapas caóticos. 93 Reunión nacional de la asociacion de Física argentina, XI Reunión de la Sociedad Uruguaya de Física, Buenos aires, argentina, 15-19 September 2008.

Fung, G. & Zhou, X. (2008) Biolism – a system for searching and mining bio-literatures. 19th International Conference on genome Informatics, gold Coast, australia, 1-3 december 2008.

Gaikwad, J. (2008) CMKb - integrating australian customary medicinal plant knowledge with the framework of atlas of living australia. Biodiversity Information Standards (tdwg) annual Conference 2008, Perth, australia, 19-25 October 2008.

Khoo, C.F. (2008) the total quasi-steady state assumption: its justification by singular perturbation theory and its application to the chemical master equation. Computational techniques and applications Conference (CtaC 2008), Canberra, australia, 13-16 July 2008.

larrondo, h., de Micco, l., Rosso, O.A. & Plastino a. (2008) Quantifiers for stochasticity of chaotic pseudo random number generators. XvI non-Equilibrium Statistical Mechanics and non-linear Physics, MEdyFInOl’08, Punta del Este, Uruguay, 1-5 december 2008.

Noske, A.(2008) 3d Reconstructions and analysis of whole mammalian cells by new tomographic and computational approaches. Systems Biology Symposium, Queenstown Molecular Biology Meeting, Queenstown, new Zealand, 2-4 September 2008.

Ranganathan, S. (2008) needles in the ESt haystack: in silico approaches to analyse expressed sequence tags (ESts) from parasitic nematodes. Seventh International Conference in Bioinformatics (InCoB) 2008, taipei, taiwan, 20-23 October 2008 (keynote).

E4i. Conference – edited volume of conference proceedingshartmann, S., Zhou, X. & Kirchberg, M., Eds (2008) Proceedings of web Information Systems Engineering (wISE2008) International workshops, auckland, new Zealand, 1-4 September 2008. Lectures Notes in Computer Science 5176. Springer. ISBn 978-3-540-85199-8.

tang, C., ling, C. Zhou, X., Cercone, n. & li, X., Eds (2008) Proceedings of the 4th International Conference on advanced data Mining and applications (adMa 2008), Chengdu, China, 8-10 October 2008. Lecture Notes in Computer Science 5139. Springer. ISBn 978-3-540-88191-9.

g. COMPUtER SOFtwaRE Bauer, D. & Bailey, T.L. (2008) StREaM: modeling, visualizing, and predicting the regulation of the transcription rate of a target gene. available online at http://research1t.imb.uq.edu.au/stream.

Frith, M.C. & Bailey, T.L. (2008) glaM2: discovering gapped motifs in dna and protein sequences. available online at http://bioinformatics.org.au/glam2.

McComb, T., Cairncross, O., Noske, A.B., wood, d.l.a., Marsh, B.J. & Ragan, M.A. (2008) Illoura™: a software tool for analysis, visualization and semantic querying of cellular and other spatial biological data. available online at http://www.visiblecell.com/illoura/

OthER aCadEMIC OUtPUt

demosding, Z., guo, l., liu, K., wu, h. & Zhou, X. (2008) MOIR: a prototype for managing moving objects in road networks. 9th International Conference on Mobile data Management (MdM’08), Beijing, China, 27-30 april 2008.

newsletterRosamond, F. (2008) FPt news: the Parameterized Complexity newsletter, Editor. at: http://fpt.wikidot.com, volume 3, april 2008.

PostersAmaral, P.P., Dinger, M.E., Mercer, T.R., Bruce, S.J., Askarian-Amiri, M., wilkins, S.J., neyt, C., Soldà, g.M.E., Sunkin, S.M., Perkins, a.C. & Mattick, J.S. (2008) Characterization of long noncoding Rnas associated with developmental genes in vertebrates. the 29th lorne genome Conference, lorne, australia, 17-21 Februar7y 2008.

Amaral, P.P., Dinger, M.E., Mercer, T.R., Pang, K.C., Askarian-Amiri, M., Bruce, S.J., wilkins, S.J., neyt, C., Soldà, g.M., Sunkin, S.M., Perkins, a.C. & Mattick, J.S. (2008) Characterization of long noncoding Rnas in mouse embryonic stem cell differentiation and vertebrate development (P478, p. 319). the XX International Congress of genetics, Berlin, germany, 12-17 July 2008.

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Arieshanti, I., Bodén, M., Maetschke, S. & Buske, F.A. (2008) Similar sequence or structure: a kernel function that brings together the best of two worlds. 19th International Conference on genome Informatics (gIw–2008), gold Coast, australia, 1-3 december 2008.

Bauer, D.C. & Bailey, T.L. (2008) StREaM: a Practical workbench for the Quantitative Modeling of transcription. 19th International Conference on genome Informatics (gIw–2008), gold Coast, australia, 1-3 december 2008.

Buske, F.A., Bodén, M. & Bailey, T.L. (2008) Using comparative genomics to associate transcription factors with their roles. 19th International Conference on genome Informatics (gIw–2008), gold Coast, australia, 1-3 december 2008.

Bustaman, A., Sehgal, M.S., Wong, S., Ragan, M.A. & Burrage, K. (2008) Parallel Markov clustering for large-scale protein-protein interaction networks using MPI. 19th International Conference on genome Informatics (gIw–2008), gold Coast, australia, 1-3 december 2008.

Chacko, E. & Ranganathan, S. (2008) alternative splicing in bovine compared to human and mouse. 16th annual International Conference on Intelligent Systems for Molecular Biology (ISMB) 2008, toronto, Canada, 19-23 July 2008.

Choi, J.-Y., Davis, M.J. & Ragan, M.A. (2008) Evaluation and expression of “drug-likeness” of small molecules using semantic web technologies. 19th International Conference on genome Informatics (gIw–2008), gold Coast, australia, 1-3 december 2008.

Cootes, A.P., Sternberg, M.J.E., Muggleton, S.h. & Ranganathan, S. (2008) the identification of similarities between biological networks. 7th European Conference on Computational Biology (ECCB) 2008, Cagliari, Italy, 22-26 September 2008.

david, S., Mann, y.-P. & Chen, Y.-P.P. (2008) Modeling the bacterial transcription regulatory jigsaw. 19th International Conference on genome Informatics (gIw–2008), gold Coast, australia, 1-3 december 2008.

Dinger, M.E., Mercer, T.R., Amaral, P.P., Pang, K.C., Sunkin, S.M., Mehler, M.F. & Mattick, J.S. (2008) long noncoding Rnas in the central nervous system. Keystone Symposium: Rnai, MicroRna, and non-Coding Rna, abstract #162, whistler, Canada, 25-30 March 2008.

Fung, G. & Zhou, X. (2008) Biolism – a System for Searching and Mining Bio-literatures. 19th International Conference on genome Informatics, gold Coast, australia, 1-3 december 2008.

gorse, d., Wood, D., Marshall, M. & Barker, J. (2008) a web service framework for advanced bioinformatics. 19th International Conference on genome Informatics (gIw–2008), gold Coast, australia, 1-3 december 2008.

Hamilton, N.A., wang, J., Kerr, M. & Teasdale, R.D. (2008) visualising and testing for difference in high throughput bio-imaging. 19th International Conference on genome Informatics (gIw–2008), gold Coast, australia, 1-3 december 2008.

Kassahn, K.S. & Ragan, M.A. (2008) Inferring deep duplication nodes in vertebrate protein families. 19th International Conference on genome Informatics (gIw–2008), gold Coast, australia, 1-3 december 2008.

Kassahn, K.S. & Ragan, M.A. (2008) Retention and functional divergence of duplicate gene loci following whole-genome duplication in teleost fishes. SMBE 08. annual Meeting of the Society for Molecular Biology and Evolution. Barcelona, Spain, 5-8 June 2008.

Khan, J. & Ranganathan, S. (2008) a multi-species comparative structural bioinformatic analysis of inherited mutations in a-d-mannosidase. 12th annual International Research in Computational Molecular Biology (RECOMB) Conference 2008, Singapore, 30 March – 2 april 2008.

Khanna, V., Gaikwad, J., Jamie, J. & Ranganathan, S. (2008) Chemoinformatics module for CMKb, a customary medicinal database. Strasbourg Summer School on Chemoinformatics 2008, Obernai, France, 22-25 June 2008

Khanna, V., Gaikwad, J., Jamie, J. & Ranganathan, S. (2008) Chemoinformatics module for CMKb, a customary medicinal database. International Conference on new developments in drug discovery from natural Products and traditional Medicines 2008, Mohali, India, 16-20 november 2008.

Kumar, G., Cootes, A.P., nevalainen, h. & Ranganathan, S. (2008) Integration of protein interaction and metabolic data for subcellular localisation prediction.19th International Conference on genome Informatics (gIw–2008), gold Coast, australia, 1-3 december 2008.

MacNamara, S., Bersani, a.M., Burrage, K. & Sidje, R.B. (2008) the total quasi-steady-state approximation for the mitogen-activated protein kianse cascade. 19th International Conference on genome Informatics (gIw–2008), gold Coast, australia, 1-3 december 2008.

Maruyama, O. & Bailey, T.L. (2008) Predicting transcription factors binding sistes through parsimonious composite patterns. the Sixth asia Pacific Bioinformatics Conference (aPBC 2008), Kyoto, Japan, 14-17 January 2008.

Mercer, T.R., Dinger, M.E., Amaral, P.P. & Mattick, J.S. (2008) Rna control of epigenetic processes. Queenstown Epigenetics Meeting, Queenstown, new Zealand, 31 august – 2 September 2008.

Mercer, T.R., Dinger, M.E., wilhelm, d., Soldà, g.M., Simons, C., glazov, E.a., Koopman P. & Mattick, J.S. (2008) Regulated independent expression of 3’ untranslated regions in mammals. Queenstown Molecular Biology Meeting, Queenstown, new Zealand, 2-4 September 2008.

Nahkuri, S., Taft, R.J. & Mattick, J.S. (2008) Evolution of a snoRna cluster by duplication. First International EURaSnEt Conference on alternative Splicing: abstract 63. Krakow, Poland. 21-23 May 2008.

Pang, K.C., Dinger, M.E., Mercer, T.R., Amaral, P.P., Soldà, g.M., Bruce, S., gardiner, g., Crowe, M.l., Perkins, a.C., grimmond, S.M. & Mattick, J.S. (2008) long noncoding Rnas in mouse embryonic stem cell differentiation. Keystone Symposium: Rnai, MicroRna, and non-Coding Rna, abstract #355, whistler, Canada.





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Pheasant, M., Bryant, M., Simons, C., Brris, w., Miotto, a., Stephen, S., Korn, O., gorse, d., Barker, J., Brusic, v., dalrymple, B., degnan, B.M., griffiths, l., hogan, J., Ragan, M.A., Roe, P., timms, P., wells, C.a. & Mattick, J.S. (2008) australian mirror of the UCSC genome browser. 19th International Conference on genome Informatics (gIw–2008), gold Coast, australia, 1-3 december 2008.

Whitington, T., Perkins, a. & Bailey, T.L. (2008) Predicting tissue-specific transcription factor binding sites with chromatin modification information. 19th International Conference on genome Informatics (gIw–2008), gold Coast, australia, 1-3 december 2008.

wilhelm, d., Soldà, g.M., Dinger, M.E., Mercer, T.R., Simons, C., Koopman, P. & Mattick, J.S. (2008) Identification of a new class of non-coding Rnas associated with 3’ untranslated regions. Keystone Symposium: Rnai, MicroRna, and non-Coding Rna, whistler, Canada.

Postgraduate thesesBoskovitz, A. (2008) data editing and logic: the covering set method from the perspective of logic. the australian national University. 259 pp.

Hawkins, J. (2008) Machine architectures for biological sequence classification. Phd thesis, the University of Queensland. 178 pp.

MacNamara, S. (2008) Krylov and finite space projection methods for simulating stochastic biochemical kinetics via the Chemical Master Equation. Phd thesis, the University of Queensland.

Mortimer, d. (2008) a Bayesian model of axon guidance. Phd thesis, the University of Queensland.

Nagaraj, S.H. (2008) Improved in silico approaches for the analysis of expressed sequence tags (ESts): validation and application to parasitic nematodes. Phd thesis, Macquarie University. 182 pp.

Pantelic, S. (2008) Enhanced filter algorithms and application of single particle analysis to the study of ovine atadenovirus. Phd thesis, the University of Queensland, 155 pp.

Simons, C. (2008) transposon-free regions in vertebrate genomes. Phd thesis, the University of Queensland, 193 pp.

Stephen, S. (2008) Ultraconserved elements and noncoding Rnas in mammals. Phd thesis, the University of Queensland, 212 pp.

Zhou, E.X. (2008) Similarity search in large video database. Phd thesis, School of Information technology and Electrical Engineering, the University of Queensland. 239 pp.



gIw-2008 Roundtable workshops

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Round table 1 Monday 1 december 2008

Forum on innovation and commercialisation in genome-scale bioinformatics

Chair/Moderator:

dr Mervyn thomas, CEO, Emphron Informatics Pty ltd, australia

Expert Panel:

Mr Jeremy Barker, CEO, Queensland Facility for advanced Bioinformatics (QFaB)

dr Jill gray, Manager, technology & Commercialisation, department of tourism, Regional development & Innovation, Queensland government

Professor Ming li, Founder, Bioinformatics Solutions ltd (Canada)

Professor limsoon wong, Founder, geneticXchange (USa) and Molecular Connections (India)

Bioinformatics grew out of the early genome-sequencing projects, and has now developed into an enabling platform essential for life science research. advances in technology make it possible to deeper questions, but also present challenges arising from the large volumes of data that must be captured, managed, integrated, analysed and visualised. addressing these challenges demand innovative bioinformatics and information technology solutions. Organisations are tackling these challenges in a variety of ways, and have applied a range of commercialisation models with varying degrees of short- and long-term success. this forum on innovation and commercialization in bioinformatics brought together representatives from industry, government and academia with experience in the commercialisation of bioinformatics to share their thoughts and experience, and to answer questions from conference delegates.

the panellists first shared with gIw delegates their own diverse experiences with bioinformatics commercialisation and innovation. Mervyn, limsoon and Ming described their experiences with commercialisation of bioinformatics research and services and various start-up companies, highlighting commercial strategies that were or were not successful. Jill then presented Queensland government policies supporting innovation and commercialisation, and Jeremy concluded the opening addresses with a description of his key findings from a Churchill Fellowship-supported international study tour of bioinformatics services provision, and the QFaB experience.

a common theme from these presentations involved the commercial challenges faced in the commercial sector for bioinformatics products, including the nature of the product (e.g. software, data or hardware) or service (e.g. data curation or provision of skills-based solutions) to be commercialised. a strength highlighted by the discussions was the sustainability provided by commercial bioinformatics solutions: whereas open-source or in-house bioinformatics can be derailed by loss of key personnel, commercial services can guarantee continuity and quality. It was also noted, however, that open-source solutions can be adequate for some intended uses, and companies have successfully commercialised software in this arena.

the panellists presented a variety of models for bioinformatics commercialisation which had met varying degrees of success. limsoon contrasted pricing strategies actually used by two different companies: in one, a full product was packaged with a single, expensive price, whereas the second was incremental, with an entry-level price for a basic product and many small increases for additional features; the latter was more successful. Mervyn highlighted the importance of offering cutting-edge products and services in a field such as bioinformatics that changes so rapidly. a skill or technique may be “cutting-edge today, but in six months a commodity”; it is, therefore, imperative for providers to stay at the crest of the wave in order to survive. Ming characterised his company’s strategy as providing cutting-edge services to the more-discerning sector of the market.

discussions initiated by questions from the floor covered difficulties in assessing the value of research and knowledge-based products to justify government investment in innovation and commercialisation; the importance of preserving commercial value through intellectual property management; managing the potentially competing interests of science and commercialisation; the difficulties in determining an appropriate business model for bioinformatics; and the important role of governments in linking R&d with domestic and international markets. the animated discussion around these and other topics of interest reflect the level of interest in innovation and commercialisation in bioinformatics across a broad sector of the australian and international community.

the overarching conclusion was that each commercialisation strategy demands a careful assessment of the presented opportunity; no single solution is the absolute answer in every instance, and opportunities can appear, evolve and disappear on a dynamic basis. astute business judgment determines the blend of nature of the products and/or services that can successfully be commercialised in each case.

the workshop was very well-attended, with no shortage of questions and comments from the audience. Informal discussion continued well after the close of the session.




Round table 2 tuesday 2 december 2008

Forum on the development of genome-scale bioinformatics in China and India

Chair/Moderator:

Professor Shoba Ranganathan, Macquarie University (australia)

Participants:

Professor ashok Kolaskar (national Knowledge Commission and University of Pune, India)

Professor Ming li (University of waterloo, Canada)

Professor yi-xue li (Shanghai Jiaotong University and academia Sinica, China)

Professor Shoba Ranganathan (Macquarie University, australia)

genome-scale biology is generating unprecedented quantities of data relevant to most fundamental and applied areas of the life sciences including agriculture, fisheries and forestry, ecological sciences and biodiversity, human health and disease, and molecular and cellular biotechnology. Existing and new technologies for automated dna sequencing, gene expression analysis, proteomics, systems analysis, imaging and high-content screening are widely available, adding locally produced data sources to the wealth of information available on-line from international data facilities such as EBI or nCBI. the quantity and complexity of these data requires researchers, institutions and countries to apply information technologies of corresponding scale and sophistication. Bioinformatics encompasses the management and analysis of these data, and development and provision of software tools, and immediately proximate areas of mathematics, statistics and algorithmics.

In asia, the economically developing countries China and India have been deeply involved in bioinformatics for several decades. with the emergence of these countries as economic superpowers, this is an opportune moment to discuss where these countries are currently poised; what challenges they face; what strategies they have developed or are developing in research, development, infrastructure, education and training for bioinformatics; what the prognosis might be for their future development in this important area; what opportunities are available for international coordination and collaboration; and not least, what broader lessons can be learnt from their development and success in genome informatics.

“Rising bioinformatic stars”

Chinathe article “Bioinformatics in China: a personal perspective” by liping wei and Jun yu (PLoS Computational Biology 4(4):e1000020, april 2008) is absolutely essential reading in this context. the authors present statistics on the growth of publications, and information on online databases, web tools and software developed and maintained in China and on bioinformatics training programs offered by institutions in China.

Specific issues discussed in this workshop included:

• TherecruitmentofoverseasChineseback to China• Diversityandflexibilityof

arrangements, e.g. appointment as guest professors

• Widerangeofsalaries,start-uppackages across institutions

• Thepossibilityof“reverseculture shock”

• R&Dinvestmentplans• MultiplenationalMinistriesand

bodies are involved • MinistryofScience&Technology:

2001-2010 US$3.8B in biological & biomedical research

• PhaseI(2001-05):mainfieldsarebioengineering, gene manipulation, Bioinformation technologies, biomedical technologies

• PhaseII(2006-10):mainfieldsare industrial technologies, gene manipulation, biomedical technologies, bioinformation & biocomputingtechnologies(*)

(*)National“863”programinbioinformatics, 2006-2010 increasing focus on neuro-informatics

• Inaddition,thereisongoinginvestmentby other national ministries (health, Education) and by local governments.

• Newnationalprograms(November2008): • Newdrugs(US$1B)–note

that China doesn’t have a large pharmaceutical industry, although international pharmaceutical companies have recently located R&d facilities in China and graduates are finding jobs there.

• Infectiousdisease(US$800M)• 3%-5%ofthesefundssetasidefor

bioinformatics • Fundsmustbespentinnexttwo

years• Heavyinvestmentnationallyindata

production (genome sequencing, metagenomics, microbial genomics, functional genomics, proteomics, metabolomics).

Job prospects for bioinformatics graduates in China are good. Some graduates go overseas, e.g. for further training. Many others are finding jobs within China.

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IndiaMuch information is available at the following two websites:

http://www.btisnet.gov.in (Biotechnology Information System network)

http://bioinfo.ernet.in (Bioinformatics Centre at University of Pune)

Bioinformatics in India started in 1981 Bioinformatics task force – 1983

• Recommendsadistributednetworkapproach: Biogrid

• Triggeredinternetconnectivityforscientific research across India

• Morerecently,developmentofathree-tiered system: • CentresofExcellence(6nationally)• Distributedinformationcentres(10)

and sub-centres (51) • Infrastructurefacilities(76)

Main components of national strategy (for further detail, see below):

• Advancedresearch• Developmentofhumanresources• Academia-industryinterface• Internationallinkages• AdvancedResearch

• About1050bioinformaticsresearch papers, plus >3000 that use bioinformatics

• Developmentofhumanresources• Goalistotrain>2000

bioinformaticians per year at all levels

• Centralgovernmentsupportfor7undergraduate, 28 postgraduate, 12 certificate / diploma, 9 Phd and 9 other training programs; many other programs funded by private institutions. Quality, especially of the latter, is variable. hence BInC, Bioinformatics national Certification Examination. the BInC is open to anyone, including self-taught candidates, but is (intentionally) very difficult and the pass rate is “very, very low”. the BInC is implemented in three steps: short-answer questions, long-answer questions, and a practical; >50% correct answers is needed to proceed to each successive step. website: http://bioinfo.ernet.in/BInC

• DiscussionsareunderwaywithMalaysia about adopting the BInC there.

• BioGridasa“virtualclassroom”• Marketis(sofar)imperfectin

matching graduates to jobs. there is difficulty in finding qualified teachers. Some graduates have trouble finding jobs, although these are mostly from the programs of questionable quality. there was much discussion in the workshop about how to match graduates to jobs lies: Professor Kolaskar advised that the principal approach must be through improvement in quality.

• Academia-industryinterface• Since1982,centralgovernment

support of the bioinformation industry has been about US$ 25M in total, of which >$5M is being spent this year.

• ThereisaveryactiveICTindustryin India, including large and small companies in bioinformatics (e.g. Molecular Connections, mentioned in the Innovation and Commercialisation forum).

• Notethatthereisalargedrugindustry in India. this has attracted bioinformatics and software companies from overseas, e.g. accelrys, to invest in India.

• Internationallinkages• Themainpartnersinbioinformatics

at this point are Japan, australia, and others in the asia-Pacific region; and Europe, particularly Italy.

IBIN – Indian Bioresource Information Network• Inthreeregionallanguages• Pictorial,common-languagefocusto

facilitate broad public impact• Developmentofdatabasesinhighly

relevant: rice, tuberculosis

the Indian government and institutions have noted China’s success in attracting overseas Chinese back to China, and are considering how to emulate this vis-à-vis overseas Indians, whether for permanent relocation or on a part-time basis. One possibility being discussed is that overseas Indians might be made eligible to apply for government research grants.




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InCOME

Balance carry forward 440,763aRC 1,144,719host institution support 525,000TOTAL INCOME 2,110,482

EXPEndItURESalaries 1,215,982Scholarships 20,325Student programming/research experience/workshops Interns 6,320 workshops/conferences 23,571 29,891Strategic visitors/sponsorship program/director strategic discretionary 15,047Equipment 14,016accommodation 2,730travel 1,892Maintenance/consumables annual report 14,575 Computer consumables/maintenance 738 laboratory consumables 12,268 Photography/slides/posters 315 Postage & freight 1,076 Stationery 304 transport - local & overseas 2,787 Meetings - advisory Board, Research Programs, annual all hands 2,206 Printing - books/journals/reprints 4,422 Relocation 3,483 Recruitment 207 telephone & fax 251 Registration: trademark, domain name 512 43,143Other (bank charges, payroll tax, FBt, cost recoveries/journal adjustments etc.) -17,083TOTAL EXPENDITURE 1,325,944

BalanCE 784,539

appendix 2: Financial statement




Acknowledgements:Cover image courtesy of Mr Oliver Cairncross, aRC Centre of Excellence in Bioinformatics, dr Brad Marsh and Mr andrew noske, Institute for Molecular Bioscience, the University of Queensland.

Other images courtesy of Ms denis Bauer, Mr Fabian Buske and dr timothy Bailey (page 25); dr nicholas hamilton (page 21), and dr Brad Marsh and Mr andrew noske (page 23), Institute for Molecular Bioscience, the University of Queensland.

Page 29 image reproduced from Mercer et al. (2008) with permission from Proceedings of the National Academy of Sciences of the United States of America and supplied courtesy of Prof. John Mattick, Institute for Molecular Bioscience, the University of Queensland.

ARC Centre of Excellence in Bioinformatics Institute for Molecular Bioscience The University of Queensland Brisbane Qld 4072

Telephone: (07) 3346 2617

Facsimile: (07) 3346 2101

Email: [email protected]

Website: http://bioinformatics.org.au

Design by: PROdesign Australia

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