Supplement 1 for Table 4 . 79 highly cited biomedical text mining papers

No Title Author Country Source of LiteratureYear of

publication

Time

s

Annual

Average

Times

Cited

1 Systematic and integrative

analysis of large gene lists

using DAVID

bioinformatics resources

Huang, Da Wei; Sherman,

Brad T.; Lempicki, Richard A.

USA NATURE PROTOCOLS 2009 3177 529.50

2 The Gene Ontology

Annotation (GOA)

Database: sharing

knowledge in Uniprot with

Gene Ontology

Camon, E; Magrane, M;

Barrell, D,ect

UK NUCLEIC ACIDS

RESEARCH

2004 366 33.27

3 RegulonDB (version 6.0):

gene regulation model of

Escherichia coli K-12

Gama-Castro, Socorro;

Jimenez-Jacinto, Veronica;

Peralta-Gil, Martin,ect

Morelos NUCLEIC ACIDS

RESEARCH

2008 274 39.14

beyond transcription, active

(experimental) annotated

promoters and Textpresso

navigation

4 Cluster analysis for gene

expression data: A survey

Jiang, DX; Tang, C; Zhang,

AD

USA IEEE TRANSACTIONS

ON KNOWLEDGE AND

DATA ENGINEERING

2004 269 24.45

5 Literature mining for the

biologist: from information

retrieval to biological

discovery

Jensen, LJ; Saric, J; Bork, P Germany NATURE REVIEWS

GENETICS

2006 237 26.33

6 Computational cluster

validation in post-genomic

data analysis

Handl, J; Knowles, J; Kell, DB  UK BIOINFORMATICS 2005 236 23.60

7 Clustering by compression Cilibrasi, R; Vitanyi, PMB Netherlands IEEE TRANSACTIONS

ON INFORMATION

THEORY

2005 228 22.80

8 The Mouse Genome

Database (MGD): mouse

biology and model systems

Bult, Carol J.; Eppig, Janan T.;

Kadin, James A. ,ect

USA. NUCLEIC ACIDS

RESEARCH

2008 222 31.71

9 Textpresso: An ontology-

based information retrieval

and extraction system for

biological literature

Muller, HM; Kenny, EE;

Sternberg, PW

USA. PLOS BIOLOGY 2004 201 18.27

10 A survey of current work in

biomedical text mining

Cohen, AM; Hersh, WR USA. BRIEFINGS IN

BIOINFORMATICS

2005 177 17.70

11

Textpresso: An ontology-based information retrieval and extraction system for biological literature

Muller, HM; Kenny, EE; Sternberg, PW USA PLOS BIOLOGY 2004

171 19

12

BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments

Al-Shahrour, Fatima; Minguez, Pablo; Tarraga, Joaquin; Montaner, David; Alloza, Eva; Vaquerizas, Juan M.; Conde, Lucia; Blaschke, Christian; Vera, Javier; Dopazo, Joaquin Spain

NUCLEIC ACIDS RESEARCH 2006

168 24

13 Overview of BioCreAtIvE: Hirschman, L; Yeh, A; USA,Spain BMC BIOINFORMATICS 2005 151 16.8

critical assessment of information extraction for biology Blaschke, C; Valencia, A

14A text-mining analysis of the human phenome

van Driel, MA; Bruggeman, J; Vriend, G; Brunner, HG; Leunissen, JA Netherlands

EUROPEAN JOURNAL OF HUMAN GENETICS 2006

150 18.8

15

A systematic review of modafinil: Potential clinical uses and mechanisms of action Ballon, JS; Feifel, D USA

JOURNAL OF CLINICAL PSYCHIATRY 2006

144 18

16BRENDA, the enzyme information system in 2011

Scheer, Maurice; Grote, Andreas; Chang, Antje; Schomburg, Ida; Munaretto, Cornelia; Rother, Michael; Soehngen, Carola; Stelzer, Michael; Thiele, Juliane; Schomburg, Dietmar Germany

NUCLEIC ACIDS RESEARCH 2011

135 45

17

FatiGO+: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments

Al-Shahrour, Fatima; Minguez, Pablo; Tarraga, Joaquin; Medina, Ignacio; Alloza, Eva; Montaner, David; Dopazo, Joaquin Spain

NUCLEIC ACIDS RESEARCH 2007

132 18.9

18 GeneWays: a system for Rzhetsky, A; Iossifov, I; USA,Japan JOURNAL OF 2004 123 12.3

extracting, analyzing, visualizing, and integrating molecular pathway data

Koike, T; Krauthammer, M; Kra, P; Morris, M; Yu, H; Duboue, PA; Weng, WB; Wilbur, WJ; Hatzivassiloglou, V; Friedman, C

BIOMEDICAL INFORMATICS

19

ABNER: an open source tool for automatically tagging genes, proteins and other entity names in text Settles, B USA BIOINFORMATICS 2005

117 14.6

20

Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome

Ramani, AK; Bunescu, RC; Mooney, RJ; Marcotte, EM USA GENOME BIOLOGY 2005

116 12.9

21

Discovering disease-genes by topological features in human protein-protein interaction network Xu, Jianzhen; Li, Yongjin Peoples R China BIOINFORMATICS 2006

115 16.4

22

Multilabel neural networks with applications to functional genomics and text categorization

Zhang, Min-Ling; Zhou, Zhi-Hua Peoples R China

IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING 2006

113 16.1

23 Integration of text- and data-mining using ontologies

Tiffin, N; Kelso, JF; Powell, AR; Pan, H; Bajic, VB; Hide,

South Africa,Singapore

NUCLEIC ACIDS RESEARCH

2005 109 15.6

successfully selects disease gene candidates WA

24

Molecular characterization of pediatric gastrointestinal stromal tumors

Agaram, Narasimhan P.; Laquaglia, Michael P.; Ustun, Berrin; Guo, Tianhua; Wong, Grace C.; Socci, Nicholas D.; Maki, Robert G.; DeMatteo, Ronald P.; Besmer, Peter; Antonescu, Cristina R. USA

CLINICAL CANCER RESEARCH 2008

108 18

25The Human Serum Metabolome

Psychogios, Nikolaos; Hau, David D.; Peng, Jun; Guo, An Chi; Mandal, Rupasri; Bouatra, Souhaila; Sinelnikov, Igor; Krishnamurthy, Ramanarayan; Eisner, Roman; Gautam, Bijaya; Young, Nelson; Xia, Jianguo; Knox, Craig; Dong, Edison; Huang, Paul; Hollander, Zsuzsanna; Pedersen, Theresa L.; Smith, Steven R.; Bamforth, Fiona; Greiner, Russ; McManus, Bruce; Newman, John W.; Goodfriend, Theodore; Wishart, David S. Canada,USA PLOS ONE 2011

105 35

26

Discovery of drug mode of action and drug repositioning from transcriptional responses

Iorio, Francesco; Bosotti, Roberta; Scacheri, Emanuela; Belcastro, Vincenzo; Mithbaokar, Pratibha; Ferriero, Rosa; Murino, Loredana; Tagliaferri, Roberto; Brunetti-Pierri, Nicola; Isacchi, Antonella; di Bernardo, Diego Italy

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 2010

102 25.5

27

Text mining and its potential applications in systems biology

Ananiadou, Sophia; Kell, Douglas B.; Tsujii, Jun-ichi UK,JAPAN

TRENDS IN BIOTECHNOLOGY 2006 102

14.6

28Machine learning in bioinformatics

Larranaga, Pedro; Calvo, Borja; Santana, Roberto; Bielza, Concha; Galdiano, Josu; Inza, Inaki; Lozano, Jose A.; Armananzas, Ruben; Santafe, Guzman; Perez, Aritz; Robles, Victor Spain,USA

BRIEFINGS IN BIOINFORMATICS 2006

97 13.9

29 Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila

Bergman, CM; Carlson, JW; Celniker, SE

UK,USA BIOINFORMATICS 2005 93 10.3

melanogaster

30

Text mining and ontologies in biomedicine: Making sense of raw text

Spasic, I; Ananiadou, S; McNaught, J; Kumar, A UK

BRIEFINGS IN BIOINFORMATICS 2005

88 9.78

31

Experiencing SAX: a novel symbolic representation of time series

Lin, Jessica; Keogh, Eamonn; Wei, Li; Lonardi, Stefano USA

DATA MINING AND KNOWLEDGE DISCOVERY 2007

87 14.5

32

Alternative splicing in cancer: Noise, functional, or systematic?

Skotheim, Rolf I.; Nees, Matthias Finland,Norway

INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY 2007

86 14.3

33Hedgehog signaling pathway and gastric cancer Katoh, Y; Katoh, M Japan

CANCER BIOLOGY & THERAPY 2005

85 10.6

34The human cerebrospinal fluid metabolome

Wishart, David S.; Lewis, Michael J.; Morrissey, Joshua A.; Flegel, Mitchel D.; Jeroncic, Kevin; Xiong, Yeping; Cheng, Dean; Eisner, Roman; Gautam, Bijaya; Tzur, Dan; Sawhney, Summit; Bamforth, Fiona; Greiner, Russ; Li, Liang Canada

JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES 2008

81 16.2

35 Babelomics: an integrative platform for the analysis of transcriptomics, proteomics

Medina, Ignacio; Carbonell, Jose; Pulido, Luis; Madeira, Sara C.; Goetz, Stefan;

Spain,Portugal NUCLEIC ACIDS RESEARCH

2010 80 20

and genomic data with advanced functional profiling

Conesa, Ana; Tarraga, Joaquin; Pascual-Montano, Alberto; Nogales-Cadenas, Ruben; Santoyo, Javier; Garcia, Francisco; Marba, Martina; Montaner, David; Dopazo, Joaquin

36

Understanding ZHENG in traditional Chinese medicine in the context of neuro-endocrine-immune network

Li, S.; Zhang, Z. Q.; Wu, L. J.; Zhang, X. G.; Li, Y. D.; Wang, Y. Y. Peoples R China IET SYSTEMS BIOLOGY 2007

79 11.3

37

A human functional protein interaction network and its application to cancer data analysis

Wu, Guanming; Feng, Xin; Stein, Lincoln Canada,USA GENOME BIOLOGY 2010

73 18.3

38Frontiers of biomedical text mining: current progress

Zweigenbaum, Pierre; Demner-Fushman, Dina; Yu, Hong; Cohen, Kevin B. France,USA

BRIEFINGS IN BIOINFORMATICS 2007

73 12.2

39

Metabolomics, modelling and machine learning in systems biology - towards an understanding of the languages of cells Kell, DB UK FEBS JOURNAL 2006

73 9.13

40 Corpus annotation for mining biomedical events

Kim, Jin-Dong; Ohta, Tomoko; Tsujii, Jun'ichi

Japan,UK BMC BIOINFORMATICS 2008 73 12.2

from literature

41

HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms

Persico, M; Ceol, A; Gavrila, C; Hoffmann, R; Florio, A; Cesareni, G Italy,USA BMC BIOINFORMATICS 2005

73 8.11

42

Linking genes to literature: text mining, information extraction, and retrieval applications for biology

Krallinger, Martin; Valencia, Alfonso; Hirschman, Lynette Spain GENOME BIOLOGY 2008

73 12.2

43

Identification and characterization of human HES2, HES3, and HES5 genes in silico Katoh, M; Katoh, M Japan

INTERNATIONAL JOURNAL OF ONCOLOGY 2004

73 12.2

44

Text-mining and information-retrieval services for molecular biology Krallinger, M; Valencia, A Spain GENOME BIOLOGY 2005

72 8

45

PolySearch: a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites

Cheng, Dean; Knox, Craig; Young, Nelson; Stothard, Paul; Damaraju, Sambasivarao; Wishart, David S. Canada

NUCLEIC ACIDS RESEARCH 2008

70 11.7

46

Systematic association of genes to phenotypes by genome and literature mining

Korbel, JO; Doerks, T; Jensen, LJ; Perez-Iratxeta, C; Kaczanowski, S; Hooper, SD; Andrade, MA; Bork, P

Germany,Canada, Poland PLOS BIOLOGY 2005

70 7.78

47

Evaluation of text-mining systems for biology: overview of the Second BioCreative community challenge

Krallinger, Martin; Morgan, Alexander; Smith, Larry; Leitner, Florian; Tanabe, Lorraine; Wilbur, John; Hirschman, Lynette; Valencia, Alfonso USA,Spain GENOME BIOLOGY 2008

68 11.3

48

The mouse genome database (MGD): new features facilitating a model system

Eppig, Janan T.; Blake, Judith A.; Bult, Carol J.; Kadin, James A.; Richardson, Joel E. USA

NUCLEIC ACIDS RESEARCH 2007

68 9.71

49

Recognizing names in biomedical texts: a machine learning approach

Zhou, GD; Zhang, J; Su, J; Shen, D; Tan, CL Singapore BIOINFORMATICS 2004

67 6.7

50HAGR: the human ageing genomic resources

de Magalhaes, JP; Costa, J; Toussaint, O USA

NUCLEIC ACIDS RESEARCH 2005

67 7.44

51

Text processing through web services: calling Whatizit

Rebholz-Schuhmann, Dietrich; Arregui, Miguel; Gaudan, Sylvain; Kirsch, Harald; Jimeno, Antonio UK BIOINFORMATICS 2008

66 11

52 An evaluation of GO annotation retrieval for BioCreAtIvE and GOA

Camon, EB; Barrell, DG; Dimmer, EC; Lee, V; Magrane, M; Maslen, J; Binns,

UK BMC BIOINFORMATICS 2005 63 7

D; Apweiler, R

53

Knowledge discovery in traditional Chinese medicine: State of the art and perspectives

Feng, Yi; Wu, Zhaohui; Zhou, Xuezhong; Zhou, Zhongmei; Fan, Weiyu Peoples R China

ARTIFICIAL INTELLIGENCE IN MEDICINE 2006

62 8.86

54The edaphic factor in the origin of plant species Rajakaruna, N USA

INTERNATIONAL GEOLOGY REVIEW 2004

61 6.78

55Target discovery from data mining approaches

Yang, Yongliang; Adelstein, S. James; Kassis, Amin I. USA

DRUG DISCOVERY TODAY 2009

60 12

56

Expression and genomic profiling of colorectal cancer

Cardoso, J.; Boer, J.; Morreau, H.; Fodde, R. Netherlands

BIOCHIMICA ET BIOPHYSICA ACTA-REVIEWS ON CANCER 2007

59 8.43

57WNT antagonist, SFRP1, is Hedgehog signaling target Katoh, Y; Katoh, M Japan

INTERNATIONAL JOURNAL OF MOLECULAR MEDICINE 2006

58 7.25

58

The Mouse Genome Database genotypes::phenotypes

Blake, Judith A.; Bult, Carol J.; Eppig, Janan T.; Kadin, James A.; Richardson, Joel E. USA

NUCLEIC ACIDS RESEARCH 2009

57 11.4

59BioCreAtIvE task IA: gene mention finding evaluation

Yeh, A; Morgan, A; Colosimo, M; Hirschman, L USA BMC BIOINFORMATICS 2005

56 6.22

60The application of systems biology to drug discovery

Cho, Carolyn R.; Labow, Mark; Reinhardt, Mischa; van Oostrum, Jan; Peitsch, Manuel C. USA

CURRENT OPINION IN CHEMICAL BIOLOGY 2006

55 6.88

61 Evidence-Based Annotation Zhou, Yingyao; USA PLOS ONE 2008 54 9

of the Malaria Parasite's Genome Using Comparative Expression Profiling

Ramachandran, Vandana; Kumar, Kota Arun; Westenberger, Scott; Refour, Phillippe; Zhou, Bin; Li, Fengwu; Young, Jason A.; Chen, Kaisheng; Plouffe, David; Henson, Kerstin; Nussenzweig, Victor; Carlton, Jane; Vinetz, Joseph M.; Duraisingh, Manoj T.; Winzeler, Elizabeth A.

62

Integrating high-throughput technologies in the quest for effective biomarkers for ovarian cancer

Kulasingam, Vathany; Pavlou, Maria P.; Diamandis, Eleftherios P. Canada

NATURE REVIEWS CANCER 2010

53 13.3

63Evaluation of BioCreAtIvE assessment of task 2

Blaschke, C; Leon, EA; Krallinger, M; Valencia, A Spain BMC BIOINFORMATICS 2005

52 5.78

64

Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments

Al-Shahrour, Fatima; Carbonell, Jose; Minguez, Pablo; Goetz, Stefan; Conesa, Ana; Tarrraga, Joaquin; Medina, Ignacio; Alloza, Eva; Montaner, David; Dopazo, Joaquin Spain

NUCLEIC ACIDS RESEARCH 2008

50 8.33

65 Networks Inferred from Alexopoulos, Leonidas G.; USA MOLECULAR & 2010 50 12.5

Biochemical Data Reveal Profound Differences in Toll-like Receptor and Inflammatory Signaling between Normal and Transformed Hepatocytes

Saez-Rodriguez, Julio; Cosgrove, Benjamin D.; Lauffenburger, Douglas A.; Sorger, Peter K.

CELLULAR PROTEOMICS

66

Text mining approaches in molecular biology and biomedicine

Krallinger, M; Erhardt, RAA; Valencia, A Spain

DRUG DISCOVERY TODAY 2005

50 5.56

67

Techniques: Bioprospecting historical herbal texts by hunting for new leads in old tomes

Buenz, EJ; Schnepple, DJ; Bauer, BA; Elkin, PL; Riddle, JM; Motley, TJ USA

TRENDS IN PHARMACOLOGICAL SCIENCES 2004

47 4.7

68

Cancer systems biology: exploring cancer-associated genes on cellular networks

Wang, E.; Lenferink, A.; Connor-McCourt, M. O. Canada

CELLULAR AND MOLECULAR LIFE SCIENCES 2007

47 7.83

69

The next generation of literature analysis: Integration of genomic analysis into text mining

Scherf, M; Epple, A; Werner, T Germany

BRIEFINGS IN BIOINFORMATICS 2005

46 5.75

70

PROMISCUOUS: a database for network-based drug-repositioning

von Eichborn, Joachim; Murgueitio, Manuela S.; Dunkel, Mathias; Koerner, Soeren; Bourne, Philip E.; Preissner, Robert Germany,USA

NUCLEIC ACIDS RESEARCH 2011

46 15.3

71

Gene regulatory networks in lactation: identification of global principles using bioinformatics

Lemay, Danielle G.; Neville, Margaret C.; Rudolph, Michael C.; Pollard, Katherine S.; German, J. Bruce USA

BMC SYSTEMS BIOLOGY 2007

46 7.67

72

Event extraction for systems biology by text mining the literature

Ananiadou, Sophia; Pyysalo, Sampo; Tsujii, Jun'ichi; Kell, Douglas B. Japan

TRENDS IN BIOTECHNOLOGY 2010

45 11.3

73

Computational methods for Traditional Chinese Medicine: A survey

Lukman, Suryani; He, Yulan; Hui, Siu-Cheung UK

COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2007

45 7.5

74

2-Alkyl-4-hydroxymethylfuran-3-carboxylic acids, antibiotic production inducers discovered by Streptomyces coelicolor genome mining

Corre, Christophe; Song, Lijiang; O'Rourke, Sean; Chater, Keith F.; Challis, Gregory L. UK

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 2008

44 8.8

75

Dynamic interaction networks in a hierarchically organized tissue

Kirouac, Daniel C.; Ito, Caryn; Csaszar, Elizabeth; Roch, Aline; Yu, Mei; Sykes, Edward A.; Bader, Gary D.; Zandstra, Peter W. Canada

MOLECULAR SYSTEMS BIOLOGY 2010

43 10.8

76

LINNAEUS: A species name identification system for biomedical literature

Gerner, Martin; Nenadic, Goran; Bergman, Casey M. UK BMC BIOINFORMATICS 2010

43 10.8

77 A Pathway-Based View of Li, Yong; Agarwal, Pankaj USA PLOS ONE 2009 42 10.5

Human Diseases and Disease Relationships

78

Comparing Signaling Networks between Normal and Transformed Hepatocytes Using Discrete Logical Models

Saez-Rodriguez, Julio; Alexopoulos, Leonidas G.; Zhang, MingSheng; Morris, Melody K.; Lauffenburger, Douglas A.; Sorger, Peter K. USA CANCER RESEARCH 2011

42 21

79

Urine proteomics for profiling of human disease using high accuracy mass spectrometry

Kentsis, Alex; Monigatti, Flavio; Dorff, Kevin; Campagne, Fabien; Bachur, Richard; Steen, Hanno USA

PROTEOMICS CLINICAL APPLICATIONS 2009

42 10.5