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Broad Institute Fifth Annual Retreat
November 2ND – 3RD | 2009
New Research Building Harvard Medical School
INFO
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ATIO
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Information
November 2ND - 3RD
2009
HMSNew Research
Building
Fifth Annual Retreat
Information
Wireless Access
Click on your web browser and agree to the terms of use for Harvard wireless. No username or password is required.
Overflow
The Bray Room, Pechet Room, 216 and 217 are available for overflow during the retreat (see map for room locations).
Note: The Bray Room will be unavailable from 12:30-3:00PM on November 3.
Mother’s Room
A Mother’s Room is located within the first floor women’s restroom, just outside the Pechet Room (see map). Room 214 on the second floor may also be used as a Mother’s Room. Both rooms are available on a first-come, first-served basis.
Free Shuttle Service
November 2 - 3320 Charles and 7 Cambridge Center8:00AM – 7:00PM
Shuttle buses will run continuously between 320 Charles Street, 7 Cambridge Center and the conference venue on both days of the retreat. Buses will arrive in approximately 10-15 min. intervals with the last bus leaving the conference venue at 7PM.
Shuttle buses will pick up and drop off at the main entrance of the conference center and both Broad buildings.
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Broad Laptop Sleeves
Pick up your very own Broad laptop sleeve on the ground floor at registration.
Lunch Offerings
November 2
Vegetable Sandwich Grilled vegetables, pesto, ciabatta bread
Chicken Salad Wrap Roasted poblano peppers
Roast Beef Wrap Herb and white bean spread, provolone, arugula, tomato basil wrap
Albacore Tuna Sandwich Lettuce, tomato, 7-grain bread
Roasted Portobello Mushroom Salad Oven-roasted peppers, mixed greens, balsamic dressing
Turkey Cobb Salad Tomatoes, hard-boiled eggs, crumbled blue cheese
Kosher Tote Lunch Assorted sandwiches from Rubin’s Deli, Brookline
All lunches include a cookie, chips, soda, and bottled water
Soup Station Tomato Bisque
November 2ND - 3RD
2009
HMSNew Research
Building
Fifth Annual Retreat
Lunch Offerings
November 3
Vegetable Wrap Grilled vegetables, hummus, feta
Santa Fe Chicken Wrap Sweet corn, black beans, romaine lettuce, chipotle lime mayo
Roast Beef Wrap Herb and white bean spread, provolone, arugula, tomato basil wrap
Roasted Turkey Sandwich St. Andre pears, baguette
Roasted Portobello Mushroom Salad Oven-roasted peppers, mixed greens, balsamic dressing
Kosher Tote Lunch Assorted sandwiches from Rubin’s Deli, Brookline
All lunches include a cookie, chips, soda, and bottled water
Soup Station Minestrone
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Floor Plans | New Research Building
Bray Roo
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Mother’s Room
Elements Café
Plenary Session | Registration
Plenary Session | Reception
Pechet Room
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Floor Plans | New Research Building
Poster Session | Reception
Poster Session | Reception
216 217
214
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Agenda | Monday November 2ND 2009
Fifth Annual Retreat
November 2ND
2009
HMSNew Research
Building
Agenda | Monday November 2ND 2009
8:15 AM – 9:00 AM
Registration and Poster Session I Set‐Up
Breakfast
9:00 AM – 9:15 AM
Welcome David Altshuler
9:15 AM – 10:45 AM
First Plenary Session Medical and Population Genetics | Stacey Gabriel
9:15 David Altshuler Overview
9:30 Stuart Orkin GWAS to the hemoglobin switch
9:45 Kiran Musunuru From DNA sequence variant to lipoprotein phenotype at a novel cholesterol and myocardial infarction locus
10:00 Mark DePristo A more detailed picture of common human genetic variation from the 1000 Genomes Project
10:15 Tim Yu Next-generation sequencing for neurologic disease in consanguineous pedigrees
10:30 Vamsi Mootha The Mito 10K and beyond
10:45 AM – 11:00 AM
Break
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11:00 AM – 11:50 AM
Second Plenary Session Emerging Technologies | Wendy Winckler
11:00 Aviv Regev Overview
11:05 Moran Yassour RNA sequencing and assembly for ab initio transcriptome characterization
11:20 Kris Wood Lentivirus-infected cell microarrays for high-throughput mammalian genetic screens
11:35 Steve A. Carr Quantitative biology without immunoassays
11:50 AM – 1:45 PM
Poster Session I and Lunch Medical and Population Genetics, Metabolism, Psychiatric Disease, Cancer, Emerging Technologies, and Broad Medley
1:45 PM – 2:45 PM
Third Plenary Session Psychiatric Disease | Ed Scolnick
1:45 Pamela Sklar Overview
2:00 Soumya Raychaudhuri Pathway analyses in neuropsychiatric diseases are confounded by gene size
2:10 Elinor Karlsson Identifying a major gene for canine obsessive-compulsive disorder
2:25 Li-Huei Tsai Chromatin remodeling, HDACs, and memory formation
2:40 Ed Scolnick Closing comments
Fifth Annual Retreat
November 2ND
2009
HMSNew Research
Building
2:45 PM – 3:00 PM
Break
3:00 PM – 4:30 PM
Fourth Plenary Session Cancer | Todd Golub
3:00 Todd Golub Overview
3:15 Adam Bass Genomic characterization of gastrointestinal cancers
3:30 Mike Chapman Whole genome sequencing of multiple myeloma reveals novel therapeutic targets
3:45 Jordi Barretina The Cancer Cell Line Encyclopedia Project
4:00 David Barbie Identification of synthetic lethal targets of oncogenic KRAS using systematic RNA interference
4:15 Andy Stern Strategies for targeting KRAS-dependent tumors
4:30 PM – 5:30 PM
Fifth Plenary Session Metabolism | Monty Krieger
4:30 Vamsi Mootha Overview
4:45 Roland Nilsson Expanding biochemical pathways through large-scale integration of gene expression data
5:00 Eugene Rhee Metabolomic predictors of diabetes
5:15 Matthew Vander Heiden Understanding cancer cell metabolism
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5:30 PM – 6:00 PM
New Associate Member Orientation
5:30 PM – 7:00 PM (Concurrent)
Reception and Informal Poster Viewing
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Poster Session I and LunchMedical and Population Genetics, Metabolism,
Psychiatric Disease, Cancer, Emerging Technologies, and Broad Medley
postersession I
11:50 AM - 1:45 PM
Medical and Population
GeneticsRotunda, 3rd Floor
Poster Session I November 2ND 2009
Medical and Population Genetics
The limit of population genetic inference from resequencing data: How much information can we gain?Hua Chen, Nick Patterson, David Reich
Integrating genetic risk factors into a clinical algorithm for multiple sclerosis susceptibility Philip De Jager, Lori Chibnik, Jing Cui, Joachim Reischl, Stephan Lehr, Claire Simon, Cristin Aubin, David Bauer, Jurgen Heubach, Rupert Sandbrink, Michaela Tyblova, Petra Lelkova, the steering committees of studies evaluating IFNB-1b and a CCR1-antagonist, Eva Havrdova, Christoph Pohl, Dana Horakova, Alberto Ascherio, David Hafler, Elizabeth Karlson
IL12A, MPHOSPH9/CDK2AP1, and RGS1 are multiple sclerosis susceptibility loci International Multiple Sclerosis Genetics Consortium
Genome-wide genotyping of pooled samples for ancestry assessment of populations of unknown originZofia Gajdos, Charleston Chiang, Josh Korn, Finny Kuruvilla, Johannah Butler, Rachel Hackett, Candace Guiducci, Thutrang Nguyen, Helen Lyon, Katherine Henderson, Chris Haiman, Loic Le Marchand, Brian Henderson, Mark Palmert, Rainford Wilks, Terrence Forrester, Colin McKenzie, Richard Cooper, Xiaofeng Zhu, Joel Hirschhorn
DGAP: Disease gene discovery in deafness using a cytogenetic approachCynthia Morton, Robin Williamson, Kerry Kocher Brown
From DNA sequence variant to lipoprotein phenotype at a novel cholesterol and myocardial infarction locusKiran Musunuru, Alanna Strong, Maria Frank-Kamenetsky, Jamie Wong, Will Cantley, Hui Li, Kenechi Ejebe, Eric Schadt, Marju Orho-Melander, Olle Melander, Chad Cowan, Victor Kotelianski, Kevin Fitzgerald, Ronald Krauss, Daniel Rader, Sekar Kathiresan
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Exploring the functional consequences of the MS susceptibility allele in the TNFRSF1A locus Linda Ottoboni, Rebeccah Briskin, Christopher Severson, David Hafler, Philip De Jager
Whole genome platform overviewWendy Brodeur, Jody Camarata, Jay Carey, Michael DaSilva, Diane Gage, George Grant, Kunsang Gyaltsen, Charles Johnson, Pei Lin, Teni Minnetyan, Ryan McGinty, Melissa Parkin, Katie Rooney, Jordan Sullivan, Andrew Crenshaw, Wendy Winckler
A meta-analysis of multiple sclerosis genome scans Nikolaos Patsopoulos, Joachim Reischl, Christoph Pohl, David Hafler, Paul de Bakker, Philip DeJager
Pooled sequencing of exons at loci mapped for blood lipidsJames Pirruccello, Kiran Musunuru, Candace Guiducci, Manuel Rivas, Benjamin Neale, Elena Gonzalez, Aarti Surti, Mary Keebler, Benjamin Voight, Noel Burtt, Marju Orho-Melander, Olle Melander, Mark Daly, Stacey Gabriel, David Altshuler, Sekar Kathiresan
Targeted genotyping with MassARRAY and new fingerprinting assay developmentLiuda Ziaugra, Tony Rachupka, Cherylyn Smith, Michelle Redman, Amy Camargo, Katie Larkin, Andrew Crenshaw, Wendy Winkler
Protein-protein interaction networking in Crohn’s disease reveals significant interconnectivity among associated loci Elizabeth Rossin, Chris Cotsapas, Kasper Lage, Soumya Raychaudhuri, Ramnik Xavier, Mark Daly
Enhancing GWAS power in Alzheimer’s disease: Intermediate phenotypes and functional validation in Drosophila Joshua Shulman, Cristin Aubin, Dong Tran, Patricia Kramer, Sue Leurgans, David Bennett, Mel Feany, Philip De Jager
postersession I
11:50 AM - 1:45 PM
Role of APOE E2/E4 in ICH: A large-scale multi-center studyAkshata Sonni, Alessandro Biffi, Jeremiasz Jagiella, Lynelle Cortellini, Alexandra Oleinik, Maureen Skehan, Aaron Gilson, Amy Halpin, Alison Ayres, Andrew Simmons, Karol Juchniewicz, Andrzej Urbanik, Kristin Schwab, Anand Viswanathan, Natalia Rost, Joshua Goldstein, Chelsea Kidwell, Devin Brown, James Meschia, Magdy Selim, Scott Silliman, Bradford Worrall, Steven M. Greenberg, Agnieszka Slowik, Jonathan Rosand
Identifying protective breast cancer alleles through GWASBrian Thomson, Candace Guiducci, Todd Green, Josh Korn, Mia Gaudet, Vijai Joseph, Tomas Kirchoff, Robert Klein, Bert Gold, Noel Burtt, Mark Daly, Kenneth Offit, David Altshuler
Functional annotation and metabolic reconstruction of 1000 genomesJeremy Zucker, Michael Koehrsen, Ed Freedman, Matt Pearson
Expanding the functional network of IMP2 using CLIP-SeqDiedra Wrighting, Ning Dai, Joseph Avruch, David Altshuler
Metabolism
Discovery of rare variants in the type 2 diabetes gene SLC30A8 in a multiethnic cohortJose Florez, Jarred McAteer, Rebecca Fanelli, Andrew Taylor, Liana Billings, Rachel Ackerman, The Diabetes Prevention Program Research Group
Cancer
Characterization of melanoma transcriptomes by RNA-SeqMichael Berger, Joshua Levin, Krishna Vijayendran, Andrey Sivachenko, Xian Adiconis, Jared Maguire, Laura Johnson, James Robinson, Roel Verhaak, Carrie Sougnez, Robert Onofrio, Liuda Ziaugra, Kristian Cibulskis, Elisabeth Laine, Jordi Barretina, Wendy
Medical and Population
GeneticsRotunda, 3rd Floor
Metabolism2nd Floor
Cancer2nd Floor
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Winckler, Gad Getz, Eric Lander, Matthew Meyerson, David Jaffe, Stacey Gabriel, Reinhard Dummer, Andreas Gnirke, Chad Nusbaum, Levi Garraway
Forcing glioblastoma tumor initiating cells to differentiate: Targeting transcription factors and GTPases using RNAiMilan Chheda, Jacob Chudnovsky, Mark Bray, Jeongwu Lee, Serena Silver, Howard Fine, Anne Carpenter, David Root, David Sabatini, William Hahn
Achilles II: Towards a systematic functional and structural annotation of the cancer genomeGlenn Cowley, Scott Rusin, Justine Scott, Patrick Lizotte, Jessica Hsiao, Jesse S. Boehm, Barbara Weir, Jordi Barretina, Terence Wong, Shuba Gopal, Alan Derr, Aviad Tsherniak, Pablo Tamayo, Hiu Wing Cheung, David Barbie, Matthew Meyerson, Levi Garraway, William Hahn, David Root
A system-wide investigation of the dynamics of Wnt signaling networkTaran Gujral, Gavin MacBeath
Pathogen discovery by next-generation sequencing-based methodsAleksandar Kostic, Akinyemi Ojesina, Matthew Meyerson
Molecular Signatures Database (MSigDB)Arthur Liberzon, Aravind Subramanian, Matt Wrobel, Heidi Kuehn, Helga Thorvaldsdottir, Pablo Tamayo, Jill Mesirov
The Integrative Genomics ViewerTed Liefeld, Jared Nedzel, Qing Gao, Jim Robinson, Michael Reich, Cameron Brennan, Jill Mesirov
How does the extracellular matrix composition influence tumor progression? A proteomics-based approachAlexandra Naba, Karl Clauser, Steve Carr, Richard Hynes
GenePatternPeter Carr, Marc-Danie Nazaire, Michael Reich, Ted Liefeld, Josh Gould, Helga Thorvaldsdottir, Heidi Kuehn, Barbara Hill, Jared Nedzel, Jim Robinson, Pablo Tamayo, Jill Mesirov
GeneCruiser: A web service for microarray annotationJared Nedzel, Jussin Paananen, Helga Thorvaldsdottir, Michael Reich, Ted Liefeld, Jill Mesirov
Unraveling the prostate cancer metabolomeCarmen Priolo, Massimo Loda
Next-gen visualization with the Integrative Genomics ViewerJames Robinson, Helga Thorvaldsdottir, Gad Getz, Marc-Danie Nazaire, Michael Reich, Jill Mesirov
Mining the Broad-Novartis Cell Line EncyclopediaNicolas Stransky, Jordi Barretina, Gaddy Getz, Mike Berger, Cory Johannessen, Yan Ding, Paula Morais, Scott Mahan, Supriya Gupta, Robb Onofrio, Carrie Sougnez, Wendy Winckler, Lili Niu, Sarah Kehoe, Charlie Hatton, Ted Liefeld, Mike Morrissey, Kavitha Venkhatesan, Dmitriy Sonkin, Mike Jones, Giordiano Caponigro, Chris Wilson, Sungjoon Kim, John Che, Andrew Su, Laura MacConaill, Stacey Gabriel, Kristin Ardlie, Michael Reich, Markus Warmuth, Matthew Meyerson, William Sellers, Todd Golub, Jennifer Harris, Bob Schlegel, Levi Garraway
Oncogenic and drug-sensitive ERBB2 mutations in GBM Kumiko Tanaka, Tzu-Hsiu Chen, Milan Chheda, Amit Dutt, Kwok Wong, William Hahn, Heidi Greulich, Matthew Meyerson
MSRI: Making sense out of RNAi dataAviad Tsherniak, Pablo Tamayo, Wiliam Hahn, David Root, Jill Mesirov
Genomics and chemical genomics of cancer apoptosisGuo Wei, Adam Margolin, Rameen Beroukhim, Marina Ramirez, Leila Haery, Emily Brown, Bina Julian, Jinyan
postersession I
11:50 AM - 1:45 PM
Cancer2nd Floor
Emerging Technology
2nd Floor
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Du, Craig H. Mermel, Shyemaa Shehata, Kumiko Tanaka, Richard Flavin, Andrew Kung, Massimo Loda, Matthew Meyerson, Todd Golub
A knowledge-based Bayesian network approach for risk stratification in medulloblastomaPablo Tamayo, Yoon-Jae Cho, Aviad Tsherniak, Scott Pomeroy, Jill Mesirov
Emerging Technology
Visualization of next-generation sequencing dataThomas Abeel, Thomas Van Parys, James Galagan
Whole genome amplification and screening methods of FFPE tissues for hybrid selection sequencingMatthew Defelice, Brendan Blumenstiel, Wendy Winckler, Matthew Freedman, Liuda Ziaugra, Kristin Ardlie, Kristian Cibulskis, Stacey Gabriel
SSF finance: Evolution of funding science at Broad 2.0Colin Kemble, Joseph O’Brien, Marc Azer, Howard Rafal, Gregory Rushton
GE-HTS in GAP using Luminex technologyJessica Leslie, Nathan Houde, Supriya Gupta, Howard Rafal, Pei Lin, Jason Carey, George Grant, Gil Walzer, David Peck, Andrew Crenshaw, Wendy Winckler
Quantifying challenging phenotypes in imagesKate Madden, Peggy Anthony, Mark Bray, Adam Fraser, Thouis (Ray) Jones, Lee Kamentsky, Vebjorn Ljosa, David Logan, Carolina Wahlby, Anne Carpenter.
Implementation of a multiplex pooling strategy of PCR products for next-gen sequencingRachel Mittelman, Scott Donovan, Nathan Houde, Jason Carey, Andrew Crenshaw, George Grant
Machine learning enables microbiome-based diagnosticsEliseo Papa, Dirk Gevers, Mike Feldgarden, Doyle Ward, Athos Bousvaros, Eric Alm
Tracing the evolution of gene regulatory networks in yeast: Applying Agilent microarray technology at the BroadJenna Pfiffner, Courtney French, Michelle Chan, Mark Styczynksi Dawn Thompson, Aviv Regev
Whole-genome RNA profiling in the Genetic Analysis PlatformBradley Taylor, Supriya Gupta, Jody Camarata, Kunsang Gyaltsen, Diane Gage, Pei Lin, Jason Carey, George Grant, Andrew Crenshaw, Wendy Winckler
Psychiatric Disease
Data comparison: Saliva- vs. blood-derived DNA on both Affy and Illumina platformsKimberly Chambert, Doug Ruderfer, Jennifer Moran, Melissa Parkin, Shannon Power, Hugh Gurling, Pamela Sklar
Discovery of novel chemical probes of chromatin remodeling relevant to nervous system diseases: Histone deacetylasesKrista Hennig, Daniel Fass, Surya Reis, Al Schroeder, Iren Kurtser, Ralph Mazitschek, Tracey Petryshen, Ed Holson, Stephen Haggarty
Identifying multivariant biomarkers in primary neuronal cultures treated with mood stabilizers: A potential strategy for screening novel therapeutic agentsStephen Haggarty, Thomas Nieland, David Logan, Jennifer Pan
RNAi-mediated knockdown of the Ankyrin 3 bipolar disorder risk gene in mice Melanie Leussis, Erin Berry, Georgius De Haan, Misha Riley, Keenan Richards, Tracey Petryshen
Targeting of GSK3B for the treatment of mood disordersMichael Lewis, Elizabeth Clore, Erin Berry, Misha Riley, Tracey Petryshen
postersession I
11:50 AM - 1:45 PM
Emerging Technology
2nd Floor
Psychiatric Disease3rd Floor
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Toward iPS cell models of bipolar disorder and schizophreniaJon Madison, Fen Zhou, Erroll Rueckert, Kraig Theriault, Surya Reis, Steve Sheridan, Laurence Daheron, Chad Cowan, Pamela Sklar, Stephen Haggarty
Targeting chromatin-mediated neuroplasticity involved in dopaminoceptive neuronsSurya Reis, Daniel Fass, Krista Hennig, Al Schroeder, Mike Lewis, Tracey Petryshen, Ed Holson, Stephen Haggarty
Quality control in Psychiatric GWAS ConsortiumStephan Ripke, Benjamin Neale, Mark Daly
High-throughput microfluidic small-animal (C. elegans) screening technologiesChristopher Rohde, Cody Gilleland, Chrysanthi Samara, Stephanie Norton, Steve Haggarty, M. Fatih Yanik
Chromatin modification in psychiatric disease: Histone deacetylase inhibitors differentially affect acetylation and behavior in mouse modelsFrederick Schroeder, Michael Lewis, Elizabeth Clore, Krista Hennig, Daniel Fass, Stephen Haggarty, Tracey Petryshen
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Agenda | Tuesday November 3RD 2009
November 3rd
2009
HMSNew Research
Building
Fifth Annual Retreat
Agenda | Tuesday November 3RD 2009
8:15 AM – 9:00 AM
Registration and Poster Session II Set Up
Breakfast
9:00 AM – 10:00 AM
Sixth Plenary Session Infectious Disease | Bruce Birren
9:00 Deb Hung Overview
9:15 Todd M. Allen Viral sequence evolution: Identifying correlates of immune control of HIV
9:30 Ralph Mazitschek Malaria drug discovery at the Broad Institute: From HTS to POC
9:45 Jun Rong Wei Crunching tiger, hidden dragon: Proteolysis as a tool to uncover function
10:00 AM – 10:15 AM
Break
10:15 AM – 11:45 AM
Seventh Plenary Session Chemical Biology and Novel Therapeutics | José Perez
10:15 Robert Gould Overview
10:30 Bridget Wagner Chemical strategies to increase human beta-cell mass
10:45 Shrikanta Chattopadhyay Small-molecule studies of blood cancer within the bone marrow niche
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11:00 Sara Buhrlage Macrocyclic inhibitors of the hedgehog pathway
11:15 Stefan Kubicek Targeting chromatin: Small molecules controlling proliferation and epigenetic memory
11:30 Josh Bittker Building success for the future: The need for a novel screening collection
11:45 AM – 12:00 PM
State of the Broad Eric Lander
12:00 PM – 2:00 PM
Poster Session II and Lunch Chemical Biology and Novel Therapeutics, Infectious Disease, Cell Circuits and RNAi, Genome Biology
2:00 PM – 3:00 PM
Eighth Plenary Session Cell Circuits and RNAi | Mike Yaffe
2:00 Nir Hacohen Overview
2:15 Ido Amit Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses
2:30 Matthieu Giraud RNAi analysis of AIRE-driven expression in the thymus
2:45 Dallas Jones Identification of novel regulatory pathways in osteoblasts through integration of molecular profiling and RNAi screening
3:00 PM – 3:15 PM
Break
November 3rd
2009
HMSNew Research
Building
Fifth Annual Retreat
3:15 PM – 4:45 PM
Ninth Plenary Session Genome Biology | John Rinn
3:15 Eric Lander Overview
3:30 Erez Lieberman-Aiden Mapping the three-dimensional architecture of the genome
3:45 Daniel E. Neafsey Genomic diversity in Anopheles vector mosquitoes
4:00 Federica DiPalma and Michael C. Zody Selective sweeps in the chicken and stickleback genomes
4:15 Andy Barry Towards single-lane whole exome sequencing: Production scale in-solution hybrid selection
4:30 Alex Tsankov The role of nucleosome positioning in the evolution of gene regulation in fungi
4:45 PM – 5:00 PM
Closing Remarks Eric Lander
5:00 PM – 6:30 PM
Reception and Informal Poster Viewing
POST
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Poster Session II and LunchChemical Biology and Novel Therapeutics,
Infectious Disease, Cell Circuits and RNAi, Genome Biology
postersession II
12:00 PM - 2:00 PM
Chemical Biology and Novel
TherapeuticsRotunda, 3rd Floor
Poster Session II November 3RD 2009
Chemical Biology and Novel Therapeutics Discovery of small molecules that directly bind to NF-κB and modulate transcription in cellsRakhee Busanelli, Katie Doud, Edgar Ibarra, Michel Weiwer, Hyman Carrinski, Paul Clemons, Larry MacPherson, Alain Viel, Nicola Tolliday, Angela Koehler
Small-molecule approaches to preventing cytokine-induced beta-cell apoptosisDanny Chou, Patrick Faloon, Nicole Bodycombe, Deepika Walpita, Paul Clemons, Stuart Schreiber, Bridget Wagner
Utilization of a linear amine scaffold for the production of a library of macrocyclesMark Fitzgerald, Carol Mulrooney, Jingqiang Wei, Byung-Chul Suh, Jeremy Duvall, Lisa Marcaurelle
Altering pancreatic cell fate with small moleculesDina Fomina, Stefan Kubicek, Jacob Hecksher-Sorensen, Deepika Walpita, Bridget Wagner, Stuart Schreiber
Unbiased analysis methods integrating gene-expression experiments exposed to a common set of chromatin-modulating small moleculesJoshua Gilbert, Nicole Bodycombe, Joshiawa Paulk, Kenneth Ross, Jianping Cui, Stefan Kubicek, Alykhan Shamji, Stuart Schreiber, Paul Clemons
Search for small molecule inhibitors of histone demethylase JMJD2CJennifer Goodhart, Qiu Wang, Stuart Schreiber
Development of an LC-MS method for compound collection purity assessmentStephen Johnston, Christopher Johnson, Kachichola Agu , Michael Lewandowski
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Screening for possible class I histone deacetylase inhibitorsMelissa Kemp, Nathan West, Elizabeth Morse, Jason Fuller, Qiu Wang, Nicole Martinez, Hy Carrinski, Paul Clemons, Stuart Schreiber, James Bradner, Angela Koehler
Development of solubility, logD, plasma protein binding and plasma stability assays for early drug discovery characterization Stephen Johnston, Michael Lewandowski
A fragment-based domain shuffling DOS libraryAlexandre Clabault, Eamon Comer, Haibo Liu, Lisa Marcaurelle
How to make doxorubicin a better chemotherapy drugYan Liu, Randall Peterson
Identifying chemical regulators of hematopoiesis and hepatocyte proliferation via image-based screens of co-cultured cellsDavid Logan, Kimberly Hartwell, Peter Miller, Jing Meghan Shan, Alison Stewart, Todd Golub, Ben Ebert, Stuart Schreiber, Sangeeta Bhatia, Anne Carpenter
A DOS approach to access a full stereochemical matrix of complex heterocycles via SNAr: Solid-phase library synthesis and preliminary biological evaluationJeremy Duvall, Baudouin Gerard, Haibo Liu, Jason Lowe, Tiffanie Murillo, Bhaumik Pandya, Byung-Chul Suh, Jingqiang Wei, Damian Young, Lisa Marcaurelle
Pharmacodynamic measurement of protein acetylationElizabeth Morse, Nathan West, Edward Greenberg, Melissa Kemp, James Bradner
Diversity-oriented synthesis of a library of biaryl- and indole-containing macrocyclesCarol Mulrooney, Mark Fitzgerald, Lisa Marcaurelle
postersession II
12:00 PM - 2:00 PM
Chemical Biology and Novel
TherapeuticsRotunda, 3rd Floor
Infectious Disease3rd Floor
Stereochemical and skeletal diversity by coupling Petasis reaction to 1,3-dipolar cycloadditionGiovanni Muncipinto, Stuart Schreiber
A novel DOS pathway targeting stereochemical and skeletal diversityDaniela Pizzirani, Stuart Schreiber
In situ oxidation of new TADs and Diels-Alder tandem reactions as a powerful strategy for biasing element introductionManuela Rodriquez, Daniela Pizzirani, Cinzia Botta, Stuart Schreiber
The Chemical Biology/Novel Therapeutics Outreach LabNicola Tolliday
Chemical phylogenetics of histone deacetylasesNathan West, Melissa Grachan, Edward Greenberg, Stephen Haggarty, Ralph Mazitschek, James Bradner
Diversity-oriented synthesis of a library of tricyclic pyran-containing compounds via an intramolecular SNAr reactionSivaraman Dandapani, Jean-Charles Marie, Diane Hamann, Tiffanie Murillo, Lisa Marcaurelle
A chemical screen for biological small molecule-RNA conjugates reveals CoA-linked RNAWalter Kowtoniuk, Y. Grace Chen, Yinghua Shen, Isha Agarwal, Aaron Leconte, David Liu
An effective way to synthesize cyclic α-Silyl carbonyl compounds based on modified RCM and silapinacol rearrangementYikai Wang, Miguel Jimenez, Damian Young, Stuart Schreiber
Identification of chemical probes for the study of platelet granule secretionLynn VerPlank, Joseph Negri, Jason Burbank, Gil Walzer, Tyler Aldredge, Chris Dockendorff, Lawrence MacPherson, James Dilks, Robert Flamenhaft, Michelle Palmer, Stuart Schreiber
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Infectious Disease
Next-generation sequencing for HLA typingRachel Erlich, Xiaoming Jia, Niall Lennon, Scott Anderson, Matthew Henn, Tim Fennell, Eric Banks, Mark DePristo, Paul de Bakker
A 100 genome-based investigation into the evolution of antibiotic resistance and virulence in Escherichia coliMichael Feldgarden, David Gordon, James Johnson, Leigh Aird, Michael Fitzgerald, Dirk Gevers, Paul Godfrey, Theresa Hepburn, Rosie Levine, Sakina Saif, Doyle Ward, Sarah Young, Qiandong Zeng, Bruce Birren, Broad Sequencing Platform
A new strategy for detecting rare HIV+ cells using high-throughput single-cell RT-PCRYuan Gong, Xu Yu, J. Christopher Love
The HIV Elite Controllers StudyNicole Beattie, Noel Burtt, Amy Camargo, Andrew Crenshaw, Leela Davies, Paul de Bakker, Stacey Gabriel, Casey Gates, Lauren Gianniny, Candace Guiducci, Robert Graham, Jamie Moore, Robert Plenge, Cherylyn Smith, Liuda Ziaugra, David Altshuler, Marylyn Addo, Todd Allen, Marcus Altfeld, Marina Boyarina, Mark Brockman, Zabrina Brumme, David Heckerman, Daniel Kaufmann, Daniel Kuritzkes, Sylvie LeGall, Toshi Miura, Florencia Pereyra, Alicia Piechocka-Trocha, Alissa Rothchild, Bruce Walker, Elena Gonzalez, Jordan Sullivan
Single-cell multidimensional cytokine profiles using quantitative microengravingQing Han, Elizabeth Bradshaw, Bjorn Nilsson, David Hafler, J. Christopher Love
Comparative analysis of secreted proteins in apicomplexan parasitesRays Jiang, Matthias Marti, Daniel Neafsey
A novel approach for B-cell repertoire analysisAdebola Ogunniyi, Douglas Kwon, Navin Varadarajan, Pascal Poignard, Dennis Burton, Bruce Walker, J. Christopher Love
Measuring the human microbiomeBruce Birren, Dawn Ciulla, Ashlee Earl, Mike Feldgarden, Dirk Gevers, Georgia Giannoukos, Brian Haas, Diana Tabbaa, Doyle Ward
Comparative analysis of Mycobacterium tuberculosisAbigail McGuire, Brian Weiner, Robert Riley, Matthew Peterson, Jeremy Zucker, Jared White, James Galagan
Genome-wide silencing screen to identify regulators of Trypanosoma cruzi: Invasion and intracellular growthKacey Caradonna, David Ndegwa, Barbara Burleigh
Cell Circuits and RNAi
Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responsesIdo Amit, Manuel Garber, Nicolas Chevrier, Ana Paula Leite, Yoni Donner, Thomas Eisenhaure, Mitchell Guttman, Jennifer K. Grenier, Weibo Li, Or Zuk, Lisa A. Schubert, Brian Birditt, Tal Shay, Alon Goren, Xiaolan Zhang, Zachary Smith, Raquel Deering, Rebecca C. McDonald, Moran Cabili, Bradley E Bernstein, John L. Rinn, Alex Meissner, David E. Root, Nir Hacohen, Aviv Regev
Construction of a genome scale ORF libraryJesse Boehm, Xiaoping Yang, Kourosh Salehi-Ashtiani, Bruno Piqani, Rakela Lubonja, Sapana Thomas, Cory Johannessen, So Young Kim, Serena Silver, Ozan Alkan, Tashfeen Bhimdi, Thomas Green, Carsten Russ, Jim Bochicchio, Todd Golub, Mike Yaffe, David Sabatini, David Hill, Marc Vidal, David Root, William Hahn
TRC RNAi Library 2.0: An expansion by performanceXiaoping Yang, Jennifer Grenier, Tom Green, Ozan Alkan, Amanda Allen, Nate Berkowitz, Tashfeen Bhimdi, Adam Brown, Quynh Dang, Matt Greene, Luke Hamm, Sabrina Hazelton, Son Hoang, Daniel Lam, Rakela Lubonja, Susan Ma, Glen Munson, Cindy Nguyen, Thu Nguyen, Tenchoe Nyima, Bruno Piqani, Pema Tenzin, Nancy Tran, David Root
postersession II
12:00 PM - 2:00 PM
Infectious Disease3rd Floor
Cell Circuits and RNAi
3rd Floor
Genome Biology 2nd Floor
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Functional interrogation of the genome: RNAi screening at the BroadSerena Silver, Thomas Nieland, Ozan Alkan, Glenn Cowley, Shuba Gopal, Alan Derr, John Sullivan, Douglas Alan, Biao Luo, Sridevi Ponduru, Jessica Hsiao, Michael Okamoto, David Root
Genome Biology
The epigenome(s) of pluripotent cells: variations of a common theme Christoph Bock, Konstantin Halachev, Tarjei Mikkelsen, Leon Ptaszek, Evangelos Kiskinis, Gabriella Boulting, Tim Ahfeldt, Hongcang Gu, Xiaolan Zhang, Mike Coyne, Thomas Lengauer, Brad Bernstein, Kevin Eggan, Chad Cowan, Thomas Lengauer, Alexander Meissner
Expression and structural analysis with mRNA-SeqDavid Borenstein, Chad Nusbaum, Nick Rhind, Manfred Grabherr, Joshua Levin, Andreas Gnirke, James Galagan, Bruce Birren, Brian Haas
Temporal dynamics of regulatory networks in Drosophila melanogaster embryogenesisRogerio Candeias, Manolis Kellis
Method development for sequencing of low copy viral RNA samplesMonica Casali, Christine Malboeuf, Elizabeth Ryan, Christian Boutwell, Karen Power, Andrew Berical , Rachel Erlich, Lisa Green, Chad Nusbaum, Molly OhAinle, Eva Harris, Niall Lennon, Joshua Levin, Bruce Walker, Todd Allen, Bruce Birren, Matthew Henn
Calling diversity and detecting low frequency variants in intra-host viral populations using 454 and IlluminaPatrick Charlebois, Aaron Berlin, Alexander Macalalad, Henry Bigelow, Sarah Young, Broad Genome Sequencing Platform, Bruce Birren, David Jaffe, Matthew Henn
Our microbes: A reference genome collection for the human microbiomeAshlee Earl, Doyle Ward, Dirk Gevers, Mike Feldgarden, Leigh Aird, Sarah Young, Theresa Hepburn, Sakina Saif, Broad 454 Sequencing Platform, Broad Genome Annotation Group, Bruce Birren
postersession II
12:00 PM - 2:00 PM
Genome Biology 2nd Floor
The Broad Institute Epigenomics InitiativeCharles Epstein, Li Wang, Xiaolan Zhang, Robbyn Issner, Mike Coyne, Noam Shoresh, Alon Goren, Tarjei Mikkelsen, Andi Gnirke, Hongcang Gu, Jason Ernst, Manolis Kellis, Chad Nusbaum, Alex Meissner, Bradley Bernstein, Eric Lander
Genome-wide discovery and characterization of chromatin states from combinatorial patterns of epigenetic marks Jason Ernst, Pouya Kheradpour, Tarjei Mikkelsen, Peter Kharchenko, Charles Epstein, Noam Shoresh, Peter Park, Gary Karpen, Brad Bernstein, Manolis Kellis
Kinonote: A method for the identification and classification of protein kinasesJonathan Goldberg, Allison Griggs, Qiandong Zeng, James Galagan, Bruce Birren, Brian Haas
Genome-scale DNA methylation analysisHongcang Gu, Christoph Bock, Tarjei Mikkelsen, Natalie Jaeger, Zack Smith, Eleni Tomazou, Eric Lander, Andreas Gnirke, Alexander Meissner
Hybrid assembly: Integrating the new with the oldDavid Heiman, Manfred Grabherr, Sarah Young, Assembly Computation and Development Core
Overview of the Affymetrix custom SNP array genotyping pipelineCharles Johnson, Melissa Parkin, Andrew Crenshaw, Wendy Winckler
Regulatory motifs associated with TF binding and chromatin dynamics in Drosophila and mammalian genomesPouya Kheradpour, Christopher Bristow, Jason Ernst, Rachel Sealfon, Manolis Kellis
The Genome Sequencing Sample Repository (GSSR): Procurement, preparation and storage of samples for sequencing whole genomesMarcia Lara, Kim Kanki, Susan Faro, Scott Nisbet, Louis Meneus, Pema Phunkhang, Helen Vassiliev, Tsamla
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Tsamla, Katie Hartfield, Ashley Ray, Desiree Hernandez, Keenan Ross, Danni Zhong, Daniel Ruan, Toby Bloom, Projects Team, Robert Nicol
Viral genome databases at the Broad: Data sharing, comparative visualization, and analysisLisa Larson, Dennis Jen, Michael Koehrsen, Christian Stolte, David Borenstein, Reinhard Engels, Edward Freedman, Marcel Gellesch, Ethan Heilman, Clint Howarth, Bil Lewis, Daniel Park, Matthew Pearson, Julian Richards, Andrew Roberts, Peter Sisk, Jared White, Lucia Alvarado, Bruce Birren, Qiandong Zeng, Matthew Henn
Computational approaches to accuracy in gene product namingSharvari Gujja, Narmada Shenoy, Qiandong Zeng, Clint Howarth, Matt Pearson, Bruce Birren, James Galagan, Brian Haas
Pidgin: A high-throughput tool for inferring accurate gene namesClint Howarth, Sharvari Gujja, Brian Haas, Michael Koehrsen, Matthew Pearson, Qiandong Zeng, Broad Genome Sequencing Platform
Large intergenic non-coding RNAs: From discovery to mechansimMaite Huarte, Mitch Guttman, Ahmad Khalil, Magda Koziol, Moran Cabili, Tal Shay, Aviv Regev, Eric Lander, John Rinn
Development and evaluation of RNA-Seq methodsJoshua Levin, Xian Adiconis, Lin Fan, Michael Berger, Dawn Thompson, Jenna Pfiffner, Moran Yassour, Mitchell Guttman, Sarah Young, Peter Rogov, Alexandre Melnikov, Timothy Fennell, Levi A. Garraway, Aviv Regev, Chad Nusbaum, Andreas Gnirke
Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium oxysporumLi-Jun Ma‚ Charlotte van der Does, Katherine Borkovich, Jeffrey Coleman, Marie-Jose Daboussi, Antonio Di Pietro, Marie Dufresne, Michael Freitag, Manfred Grabherr, Bernard Henrissat, Petra Houterman, Seogchan Kang,
postersession II
12:00 PM - 2:00 PM
Genome Biology 2nd Floor
Won-Bo Shim, Charles Woloshuk, Xiaohui Xie, Jin-Rong Xu, John Antoniw, Scott Baker, Burton Bluhm, Andrew Breakspear, Daren Brown, Robert Butchko, Sinead Chapman, Richard Coulson, Pedro Coutinho, Etienne Danchin, Andrew Diener, Liane Gale, Donald Gardiner, Stephen Goff , Kim Hammond-Kosack, Karen Hilburn, Aurlie Hua-Van, Wilfried Jonkers, Kemal Kazan, Chinnappa Kodira, Michael Koehrsen, Lokesh Kumar, Yong-Hwan Lee, Liande Li, John Manners, Diego Miranda-Saavedra, Mala Mukherjee, Gyungsoon Park, Jongsun Park, Sook-Young Park, Robert Proctor, Aviv Regev, Carmen Ruiz-Roldan, Divya Sain, Sharadha Sakthikumar, Sean Sykes, David Schwartz, Gillian Turgeon, Ilan Wapinski, Olen Yoder, Sarah Young, Qiandong Zeng, Shiguo Zhou, James Galagan, Christina Cuomo, Corby Kistler, Martijn Rep
Identifying point mutations in mouse mutants by hybrid capture and Illumina sequencingJennifer Moran, Evan Mauceli, Tim Fennell, Ross Swofford, Jeremy Johnson, Lauren Ambrogio, Miriam Meisler, John Schimenti, Kerstin Lindblad-Toh, Federica di Palma, David Beier, Stacey Gabriel
Genome-wide Bayesian reconstruction of phylogenetic treesMatthew Rasmussen, Manolis Kellis
Target-specific genotyping with Illumina’s VeraCode on the BeadXpress Reader systemMichelle Redman, Katie Larkin, Cherylyn Smith, Tony Rachupka, Amy Camargo, Liuda Ziaugra, Andrew Crenshaw, Wendy Winckler
Chromatin state dynamics during differentiationChristopher Reeder, Shaun Mahony, Esteban Mazzoni, Scott McCuine, Thomas Jessell, Richard Young, Hynek Wichterle, David Gifford
Keeping up with technology: Innovative, highly sensitive whole-genome alignment with Satsuma/SLAPPamela Russell, Evan Mauceli, Jessica Alfoldi, Federica Di Palma, Kerstin Lindblad-Toh, Manfred Grabherr
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Genomic signatures of speciation, sex, and selection in ocean bacteriaB. Jesse Shapiro, Eric Alm
Searching and visualizing polymorphisms in M. tuberculosis using next-generation sequencing Marcel Gellesch, Christian Stolte, Dennis Jen, Ethan Heilman, Thomas Abeel, Reinhard Engels, David Borenstein, Sean Sykes, Peter Sisk, Michael Koehrsen, James Galagan
Identification of Neurospora crassa differentially expressed genes within 10 EST librariesZehua Chen, Thomas Walk, Qiandong Zeng, Matthew Sachs, James Galagan, Bruce Birren, Brian Haas, Broad Genome Sequencing Platform
Fosill: Fosmid libraries for paired end Illumina sequencingLouise Williams, Na Li, Terrance Shea, Andreas Gnirke
Next-generation genome annotation at the Broad InstituteQiandong Zeng, Lucia Alvarado, Zehua Chen, Jonathan Goldberg, Allison Griggs, Sharvari Gujja, Teena Mehta, Narmada Shenoy, Tom Walk, Chandri Yandava, Matt Pearson, Clint Howarth, Michael Koehrsen, Bruce Birren, James Galagan, Brian Haas, Broad Genome Sequencing Platform
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