Broad Institute Fifth Annual Retreat November 2ND – 3RD | 2009 New Research Building Harvard Medical School
INFORMATION
Information Information Fifth Annual Retreat Wireless Access
Click on your web browser and agree to the terms of November 2ND - 3RD use for Harvard wireless. No username or password 2009 is required.
HMS New Research Overflow Building 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 - 3 320 Charles and 7 Cambridge Center 8:00AM – 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. Broad LaptopSleeves Tomato Bisque Soup Station water bottled and soda, chips, cookie, a include lunches All Assorted sandwichesfromRubin’s Deli,Brookline Kosher Tote Lunch Tomatoes, hard-boiledeggs,crumbledbluecheese Turkey CobbSalad Oven-roasted peppers,mixedgreens,balsamicdressing Roasted Portobello Mushroom Salad bread Lettuce, tomato,7-grain Albacore Tuna Sandwich basil wrap tomato arugula, provolone, spread, bean white and Herb Roast BeefWrap Roasted poblanopeppers Chicken SaladWrap Grilled vegetables,pesto,ciabattabread Vegetable Sandwich November 2 Lunch Offerings ground flooratregistration. the on sleeve laptop Broad own very your up Pick
5 Broad Institute | Fifth Annual Retreat Fifth Annual Lunch Offerings Retreat November 3
November 2ND - 3RD Vegetable Wrap Grilled vegetables, hummus, feta 2009
HMS Santa Fe Chicken Wrap New Research Building 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 MAP
Map Floor Plans | New Research Building
Plenary Session | Registration
Bray Room Bray
Mother’s Room
Pechet Room
Plenary Session | Reception Elements Café Floor Plans|NewResearch Building Poster |Reception Session Poster |Reception Session 216 214 217
9 Broad Institute | Fifth Annual Retreat
AGENDA I
Agenda | Monday November 2ND 2009 Agenda | Monday November 2ND 2009 Fifth Annual Retreat 8:15 AM – 9:00 AM Registration and Poster Session I Set‐Up November 2ND Breakfast 2009
HMS 9:00 AM – 9:15 AM New Research Building 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 Psychiatric Disease|EdScolnick Session Plenary Third 1:45 and BroadMedley Psychiatric Disease,Cancer, EmergingTechnologies, Medical andPopulation Genetics,Metabolism, Poster Session IandLunch 11:50 Emerging Technologies |Wendy Winckler Session Plenary Second 11:00 Closing comments 2:40 EdScolnick formation Chromatin remodeling, HDACs, andmemory 2:25 Li-HueiTsai compulsive disorder Identifying amajorgeneforcanineobsessive- 2:10 ElinorKarlsson diseases are confoundedbygenesize neuropsychiatric in analyses Pathway 2:00 SoumyaRaychaudhuri Overview Quantitative biologywithoutimmunoassays Carr 11:35 SteveA. throughput mammaliangeneticscreens cellmicroarraysforhigh- Lentivirus-infected 11:20 KrisWood initio ab transcriptome characterization for assembly and sequencing RNA 11:05 MoranYassour Overview 1:45 Pamela Sklar 11:00 Aviv Regev PM AM AM –2:45 –1:45 – 11:50 PM PM AM
13 Broad Institute | Fifth Annual Retreat 2:45 PM – 3:00 PM Fifth Annual Break Retreat
3:00 PM – 4:30 PM November 2ND Fourth Plenary Session Cancer | Todd Golub 2009 3:00 Todd Golub HMS Overview New Research Building 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 5:30 Reception andInformalPoster Viewing 5:30 New AssociateMemberOrientation PM PM –6:00 –7:00 PM PM (Concurrent) 15 Broad Institute | Fifth Annual Retreat
POSTER SESSION 1
Poster Session I and Lunch Medical and Population Genetics, Metabolism, Psychiatric Disease, Cancer, Emerging Technologies, and Broad Medley ND poster Poster Session I November 2 2009 session I Medical and Population Genetics
Medical and The limit of population genetic inference from Population resequencing data: How much information can we Genetics Rotunda, 3rd Floor gain? Hua Chen, Nick Patterson, David Reich
11:50 AM - 1:45 PM 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 origin Zofia 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 approach Cynthia Morton, Robin Williamson, Kerry Kocher Brown
From DNA sequence variant to lipoprotein phenotype at a novel cholesterol and myocardial infarction locus Kiran 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 locus locus susceptibility alleleintheTNFRSF1A Exploring thefunctionalconsequencesofMS in Drosophila Intermediate phenotypesandfunctionalvalidation disease:Enhancing GWAS powerinAlzheimer’s loci associated among interconnectivity significant Crohn’s in reveals disease networking interaction Protein-protein new and fingerprinting assaydevelopment MassARRAY with genotyping Targeted blood lipids Pooled sequencingofexonsatlocimappedfor genome scans sclerosis multiple of meta-analysis A Whole genomeplatformoverview Philip De Jager De Philip Feany, Mel Patricia Bennett, David Leurgans, Kramer, Sue Tran, Dong Aubin, Cristin Shulman, Joshua Xavier, Daly Mark Ramnik Raychaudhuri, Soumya Lage, Kasper Cotsapas, Chris Rossin, Elizabeth Winkler Wendy Crenshaw, Andrew Larkin, Katie Camargo, Amy Redman, Michelle Smith, Cherylyn Tony Rachupka, Ziaugra, Liuda Kathiresan Sekar Altshuler, Stacey David Gabriel, Daly, Mark Melander, Olle Orho-Melander, Marju Burtt, Noel Voight, Keebler, Benjamin Mary Surti, Aarti Gonzalez, Elena Neale, Benjamin Rivas, Manuel James Pirruccello, Kiran Musunuru, Candace Guiducci, DeJager Bakker, Hafler,de Paul Philip David Pohl, Christoph Reischl, Joachim Patsopoulos, Nikolaos Winckler Wendy Crenshaw, Andrew Sullivan, Jordan Rooney, Katie Parkin, Melissa McGinty, Ryan Teni Pei Lin, Minnetyan, Johnson, Charles Gyaltsen, Kunsang Grant, George Gage, Diane DaSilva, Carey, Jay Michael Camarata, Jody Brodeur, Wendy Jager De Hafler, Philip David Severson, Christopher Briskin, Rebeccah Ottoboni, Linda
19 Broad Institute | Fifth Annual Retreat Role of APOE E2/E4 in ICH: A large-scale multi- poster center study session I Akshata Sonni, Alessandro Biffi, Jeremiasz Jagiella, Lynelle Cortellini, Alexandra Oleinik, Maureen Skehan, Aaron Gilson, Amy Halpin, Alison Ayres, Andrew Medical and Simmons, Karol Juchniewicz, Andrzej Urbanik, Kristin Population Schwab, Anand Viswanathan, Natalia Rost, Joshua Genetics Rotunda, 3rd Floor Goldstein, Chelsea Kidwell, Devin Brown, James Meschia, Magdy Selim, Scott Silliman, Bradford Metabolism Worrall, Steven M. Greenberg, Agnieszka Slowik, 2nd Floor Jonathan Rosand Cancer 2nd Floor Identifying protective breast cancer alleles through GWAS
11:50 AM - 1:45 PM Brian 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 genomes Jeremy Zucker, Michael Koehrsen, Ed Freedman, Matt Pearson
Expanding the functional network of IMP2 using CLIP-Seq Diedra Wrighting, Ning Dai, Joseph Avruch, David Altshuler
Metabolism
Discovery of rare variants in the type 2 diabetes gene SLC30A8 in a multiethnic cohort Jose Florez, Jarred McAteer, Rebecca Fanelli, Andrew Taylor, Liana Billings, Rachel Ackerman, The Diabetes Prevention Program Research Group
Cancer
Characterization of melanoma transcriptomes by RNA-Seq Michael 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 influence tumor progression? A proteomics-based proteomics-based approach A progression? tumor influence How doestheextracellularmatrixcomposition The IntegrativeGenomicsViewer Molecular SignaturesDatabase(MSigDB) sequencing-based methods Pathogen discoverybynext-generation Wnt signalingnetwork A system-wideinvestigationofthedynamics and functional structural annotationofthecancergenome systematic a Towards II: Achilles and factors GTPases usingRNAi transcription Targeting differentiate: Forcing glioblastomatumorinitiatingcellsto Alexandra Naba, Karl Clauser, Steve Carr, Richard Hynes Carr, Steve KarlClauser, Richard Naba, Alexandra Michael Reich, Cameron Brennan, Jill Mesirov Robinson, Jim Gao, Qing Nedzel, Jared Ted Liefeld, Mesirov Tamayo, Pablo Jill Thorvaldsdottir, Helga Kuehn, Heidi Wrobel, Matt Subramanian, Aravind Liberzon, Arthur Meyerson Matthew Ojesina, Akinyemi Kostic, Aleksandar MacBeath Gavin Taran Gujral, Root David Hahn, Garraway, Levi William Meyerson, Matthew Barbie, David Cheung, Tamayo, Pablo Wing Tsherniak, Hiu Aviad Derr, Alan Gopal, Shuba Terence Wong, Barretina, Jordi Weir, Barbara Patrick Boehm, S. Jesse Hsiao, Jessica Lizotte, Scott, Justine Rusin, Scott Cowley, Glenn David Hahn William Sabatini, David Root, Carpenter, Anne Fine, Howard Silver, Serena Lee, Bray, Mark Jeongwu Chudnovsky, Jacob Chheda, Milan LeviGarraway Nusbaum, Chad Gnirke, Andreas Dummer, Reinhard Gabriel, Stacey Jaffe, David Meyerson, Lander, Matthew Eric Getz, Gad Winckler, 21 Broad Institute | Fifth Annual Retreat GenePattern poster session I Peter Carr, Marc-Danie Nazaire, Michael Reich, Ted Liefeld, Josh Gould, Helga Thorvaldsdottir, Heidi Kuehn, Barbara Hill, Jared Nedzel, Jim Robinson, Pablo Cancer Tamayo, Jill Mesirov 2nd Floor Emerging GeneCruiser: A web service for microarray Technology annotation 2nd Floor Jared Nedzel, Jussin Paananen, Helga Thorvaldsdottir, Michael Reich, Ted Liefeld, Jill Mesirov
11:50 AM - 1:45 PM Unraveling the prostate cancer metabolome Carmen Priolo, Massimo Loda
Next-gen visualization with the Integrative Genomics Viewer James Robinson, Helga Thorvaldsdottir, Gad Getz, Marc-Danie Nazaire, Michael Reich, Jill Mesirov
Mining the Broad-Novartis Cell Line Encyclopedia Nicolas 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 data Aviad Tsherniak, Pablo Tamayo, Wiliam Hahn, David Root, Jill Mesirov
Genomics and chemical genomics of cancer apoptosis Guo Wei, Adam Margolin, Rameen Beroukhim, Marina Ramirez, Leila Haery, Emily Brown, Bina Julian, Jinyan Machine learning enables microbiome-based diagnostics microbiome-based enables learning Machine of strategy pooling sequencing PCR productsfornext-gen multiplex a of Implementation Quantifying challengingphenotypesinimages GE-HTS inGAPusingLuminextechnology SSF finance:EvolutionoffundingscienceatBroad2.0 sequencing screening methods ofFFPEtissuesforhybridselection and amplification genome Whole sequencingdata Visualization ofnext-generation TechnologyEmerging for riskstratificationinmedulloblastoma BayesiannetworkapproachA knowledge-based Jason Carey, Andrew Crenshaw, George Grant George Crenshaw, Carey, Andrew Jason Houde, Nathan Donovan, Scott Mittelman, Rachel Carpenter. Wahlby, Anne Carolina Logan, David Ljosa, Vebjorn Kamentsky, Lee (Ray) Jones, Thouis Fraser, Bray, Mark Adam Anthony, Peggy Madden, Kate Winckler Wendy Crenshaw, Andrew Peck, David Howard Walzer, Gil Grant, Carey, George Jason Gupta, Pei Lin, Rafal, Supriya Houde, Nathan Leslie, Jessica Rushton Howard Gregory Rafal, Azer, Marc O’Brien, Joseph Kemble, Colin Gabriel Stacey Cibulskis, Kristian Ardlie, Kristin Ziaugra, Wendy Liuda Freedman, Matthew Winckler, Blumenstiel, Brendan Defelice, Matthew Galagan James Van Parys, Thomas Abeel, Thomas Mesirov Pomeroy, Jill Scott Tsherniak, Aviad Cho, Tamayo,Pablo Yoon-Jae Todd Golub Meyerson, Matthew Loda, Massimo Kung, Andrew Flavin, Richard Tanaka, Kumiko Shehata, Shyemaa Mermel, H. Craig Du, Athos Bousvaros, Eric Alm Eric Bousvaros, Athos Ward, Doyle Feldgarden, Mike Gevers, Dirk Papa, Eliseo 23 Broad Institute | Fifth Annual Retreat Tracing the evolution of gene regulatory networks poster in yeast: Applying Agilent microarray technology session I at the Broad Jenna Pfiffner, Courtney French, Michelle Chan, Mark Emerging Styczynksi Dawn Thompson, Aviv Regev Technology 2nd Floor Whole-genome RNA profiling in the Genetic Psychiatric Analysis Platform Disease 3rd Floor Bradley Taylor, Supriya Gupta, Jody Camarata, Kunsang Gyaltsen, Diane Gage, Pei Lin, Jason Carey, George Grant, Andrew Crenshaw, Wendy Winckler 11:50 AM - 1:45 PM Psychiatric Disease
Data comparison: Saliva- vs. blood-derived DNA on both Affy and Illumina platforms Kimberly 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 deacetylases Krista 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 agents Stephen 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 disorders Michael Lewis, Elizabeth Clore, Erin Berry, Misha Riley, Tracey Petryshen acetylation andbehaviorinmousemodels Histone deacetylaseinhibitorsdifferentiallyaffect Chromatin modificationinpsychiatricdisease: elegans) screeningtechnologies High-throughput microfluidicsmall-animal(C. Quality controlinPsychiatric GWAS Consortium involved indopaminoceptiveneurons neuroplasticity chromatin-mediated Targeting schizophrenia Toward iPScellmodelsofbipolardisorderand Krista Hennig, Daniel Fass, Stephen Haggarty, Tracey Tracey Petryshen Haggarty, Stephen Fass, Daniel Hennig, Krista Clore, Elizabeth Lewis, Michael Schroeder, Frederick Yanik Fatih M. Haggarty, Steve Norton, Stephanie Christopher Rohde, Cody Gilleland, Chrysanthi Samara, Daly Mark Neale, Benjamin Ripke, Stephan Haggarty Stephen Ed Holson, Tracey Lewis, Petryshen, Mike Schroeder, Al Hennig, Krista Fass, Daniel Reis, Surya Chad Daheron, Cowan, Pamela Sklar, Stephen Haggarty Laurence Sheridan, Steve Reis, Surya Theriault, Kraig Rueckert, Erroll Zhou, Fen Madison, Jon 25 Broad Institute | Fifth Annual Retreat
AGENDA II
Agenda | Tuesday November 3RD 2009 Agenda | Tuesday November 3RD 2009 Fifth Annual Retreat 8:15 AM – 9:00 AM Registration and Poster Session II Set Up November 3rd 2009 Breakfast
HMS 9:00 AM – 10:00 AM New Research Building 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 Break 3:00 Yaffe Mike | RNAi and Circuits Cell Session Plenary Eighth 2:00 Disease, CellCircuitsandRNAi,GenomeBiology Infectious Therapeutics, Novel and Biology Chemical Poster Session IIandLunch 12:00 Eric Lander State oftheBroad 11:45 11:30 JoshBittker 11:00 SaraBuhrlage profiling andRNAiscreening in pathways osteoblasts throughintegrationofmolecular regulatory novel of Identification 2:45 DallasJones the in thymus expression AIRE-driven of analysis RNAi 2:30 MatthieuGiraud responses transcriptional networkmediatingpathogenmammalian a of reconstruction Unbiased 2:15 IdoAmit Overview novel screeningcollection Building successforthefuture:Theneeda controlling proliferation andepigeneticmemor molecules Small chromatin: Targeting 11:15 StefanKubicek Macrocyclic inhibitorsofthehedgehogpathway 2:00 NirHacohen PM PM PM AM – 3:15 – 3:00 – 2:00 – 12:00 PM PM PM PM
y 29 Broad Institute | Fifth Annual Retreat 3:15 PM – 4:45 PM Fifth Annual Ninth Plenary Session Retreat Genome Biology | John Rinn 3:15 Eric Lander November 3rd Overview 2009 3:30 Erez Lieberman-Aiden Mapping the three-dimensional architecture of HMS the genome New Research Building 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 POSTER SESSION II
Poster Session II and Lunch Chemical Biology and Novel Therapeutics, Infectious Disease, Cell Circuits and RNAi, Genome Biology RD poster Poster Session II November 3 2009 session II Chemical Biology and Novel Therapeutics
Chemical Biology Discovery of small molecules that directly bind to and Novel NF-κB and modulate transcription in cells Therapeutics Rotunda, 3rd Floor Rakhee Busanelli, Katie Doud, Edgar Ibarra, Michel Weiwer, Hyman Carrinski, Paul Clemons, Larry MacPherson, Alain Viel, Nicola Tolliday, Angela Koehler 12:00 PM - 2:00 PM Small-molecule approaches to preventing cytokine-induced beta-cell apoptosis Danny 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 macrocycles Mark Fitzgerald, Carol Mulrooney, Jingqiang Wei, Byung-Chul Suh, Jeremy Duvall, Lisa Marcaurelle
Altering pancreatic cell fate with small molecules Dina 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 molecules Joshua 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 JMJD2C Jennifer Goodhart, Qiu Wang, Stuart Schreiber
Development of an LC-MS method for compound collection purity assessment Stephen Johnston, Christopher Johnson, Kachichola Agu , Michael Lewandowski phase library synthesis and preliminary biological biological evaluation preliminary and synthesis library phase Screening for possible class I histone deacetylase deacetylase histone inhibitors I class possible for Screening and indole-containing macrocycles and indole-containing synthesisofalibrarybiaryl-Diversity-oriented acetylation Pharmacodynamic measurementofprotein matrix ofcomplexheterocyclesviaS A DOSapproachtoaccessafullstereochemical image-based cells screens ofco-cultured via proliferation hematopoiesis hepatocyte of and regulators chemical Identifying drug chemotherapy better a doxorubicin make to How A fragment-baseddomainshufflingDOSlibrary drug early for discovery characterizationassays stability plasma and binding Development ofsolubility, logD, plasmaprotein Carol Mulrooney, Mark Fitzgerald, Lisa Marcaurelle Marcaurelle Lisa Fitzgerald, Mark Mulrooney, Carol Melissa Kemp, James Bradner Greenberg, Edward West, Nathan Morse, Elizabeth Marcaurelle Young, Lisa Damian Wei, Jingqiang Suh, Byung-Chul Pandya, Bhaumik Murillo, Tiffanie Lowe, Jason Liu, Haibo Gerard, Baudouin Duvall, Jeremy Carpenter Anne Bhatia, Sangeeta Schreiber, Stuart Jing Ebert, Ben Todd Golub, Stewart, Alison Miller, Shan, Meghan Peter Hartwell, Kimberly Logan, David Peterson Yan Randall Liu, Marcaurelle Lisa Liu, Comer, Haibo Eamon Clabault, Alexandre Stephen Johnston, Michael Lewandowski Koehler Angela Bradner, James Schreiber, Stuart Clemons, Paul Carrinski, Hy Martinez, Nicole Wang, Fuller, Qiu Jason Morse, Elizabeth West, Kemp, Nathan Melissa N Ar: Solid- 33 Broad Institute | Fifth Annual Retreat Stereochemical and skeletal diversity by coupling poster Petasis reaction to 1,3-dipolar cycloaddition session II Giovanni Muncipinto, Stuart Schreiber
Chemical Biology A novel DOS pathway targeting stereochemical and Novel and skeletal diversity Therapeutics Daniela Pizzirani, Stuart Schreiber Rotunda, 3rd Floor
Infectious In situ oxidation of new TADs and Diels-Alder Disease 3rd Floor tandem reactions as a powerful strategy for biasing element introduction Manuela Rodriquez, Daniela Pizzirani, Cinzia Botta, 12:00 PM - 2:00 PM Stuart Schreiber
The Chemical Biology/Novel Therapeutics Outreach Lab Nicola Tolliday
Chemical phylogenetics of histone deacetylases Nathan 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 reaction Sivaraman Dandapani, Jean-Charles Marie, Diane Hamann, Tiffanie Murillo, Lisa Marcaurelle
A chemical screen for biological small molecule- RNA conjugates reveals CoA-linked RNA Walter 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 rearrangement Yikai Wang, Miguel Jimenez, Damian Young, Stuart Schreiber
Identification of chemical probes for the study of platelet granule secretion Lynn VerPlank, Joseph Negri, Jason Burbank, Gil Walzer, Tyler Aldredge, Chris Dockendorff, Lawrence MacPherson, James Dilks, Robert Flamenhaft, Michelle Palmer, Stuart Schreiber Next-generation sequencingforHLAtyping Next-generation Disease Infectious A novel approach for B-cell repertoire analysis A novelapproachforB-cell apicomplexan parasites Comparative analysisofsecretedproteinsin using profiles cytokine quantitative microengraving multidimensional Single-cell The HIVEliteControllersStudy using cells HIV+ RT-PCRhigh-throughput single-cell rare detecting for strategy new A Escherichia coli the into evolution ofantibioticresistanceandvirulencein investigation genome-based 100 A Christopher Love Walker, J. Bruce Burton, Dennis Poignard, Pascal Varadarajan, Kwon, Navin Douglas Ogunniyi, Adebola Neafsey Daniel Marti, Matthias Jiang, Rays David Love Hafler, J. Christopher Nilsson, Bjorn Bradshaw, Elizabeth Han, Qing Sullivan Jordan Walker, Gonzalez, Elena Florencia Bruce Rothchild, Piechocka-Trocha, Alissa Alicia Pereyra, Miura, Toshi LeGall, Sylvie Kuritzkes, Daniel Kaufmann, Daniel Heckerman, David Brumme, Zabrina Brockman, Todd Mark Boyarina, Marina Addo, Altfeld, Marcus Allen, Marylyn Altshuler, David Ziaugra, Liuda Smith, Cherylyn Plenge, Robert Moore, Jamie Graham, Robert Guiducci, Candace Gianniny, Lauren Gates, Casey Gabriel, Bakker, de Paul Stacey Davies, Leela Crenshaw, Andrew Camargo, Amy Burtt, Noel Beattie, Nicole Love Xu Yu,Yuan J. Christopher Gong, Sequencing Platform Broad Birren, Bruce Zeng, Young, Qiandong Sarah Ward, Doyle Saif, Sakina Levine, Rosie Hepburn, Theresa Godfrey, Paul Gevers, Dirk Fitzgerald, Michael Aird, Leigh Johnson, James Gordon, David Feldgarden, Michael Bakker de Paul DePristo, Mark Banks, Eric Fennell, Tim Henn, Matthew Anderson, Scott Lennon, Niall Jia, Xiaoming Erlich, Rachel 35 Broad Institute | Fifth Annual Retreat Measuring the human microbiome poster session II Bruce Birren, Dawn Ciulla, Ashlee Earl, Mike Feldgarden, Dirk Gevers, Georgia Giannoukos, Brian Haas, Diana Tabbaa, Doyle Ward
Infectious Comparative analysis of Mycobacterium Disease 3rd Floor tuberculosis Abigail McGuire, Brian Weiner, Robert Riley, Matthew Cell Circuits Peterson, Jeremy Zucker, Jared White, James Galagan and RNAi 3rd Floor Genome Biology Genome-wide silencing screen to identify 2nd Floor regulators of Trypanosoma cruzi: Invasion and intracellular growth Kacey Caradonna, David Ndegwa, Barbara Burleigh
12:00 PM - 2:00 PM Cell Circuits and RNAi
Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses Ido 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 library Jesse 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 performance Xiaoping 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 Functional interrogation of the genome: RNAi RNAi genome: screening attheBroad the of interrogation Functional the humanmicrobiome Our microbes:Areferencegenome collectionfor and Illumina frequency low variants inintra-hostviralpopulationsusing454 detecting and diversity Calling copy low of viral RNAsamples sequencing for development Method Drosophila melanogasterembryogenesis Temporal dynamicsofregulatorynetworksin Expression andstructuralanalysiswithmRNA-Seq of variations theme cells: common a pluripotent of epigenome(s) The Biology Genome Annotation Group, Bruce Birren Bruce Group, Annotation Genome Broad Platform, Sequencing 454 Broad Saif, Sakina Hepburn, Young, Theresa Sarah Aird, Leigh Feldgarden, Mike Gevers, Dirk Ward, Doyle Earl, Ashlee Henn Matthew Jaffe, David Birren, Sequencing Bruce Platform, Genome Broad Young, Sarah Bigelow, Henry Patrick Charlebois, Aaron Berlin, Alexander Macalalad, Todd Henn Walker, Matthew Birren, Bruce Allen, Bruce Levin, Joshua Lennon, Eva Niall OhAinle, Harris, Molly Nusbaum, Chad Green, Lisa Erlich, ,Rachel Power,Berical Karen Andrew Boutwell, Christian Ryan, Elizabeth Malboeuf, Christine Casali, Monica Rogerio Candeias, Manolis Kellis Haas Brian Birren, Bruce Manfred Galagan, James Gnirke, Andreas Levin, Rhind, Joshua Grabherr, Nick Nusbaum, Chad Borenstein, David Chad Meissner Alexander Lengauer, Thomas Cowan, Eggan, Kevin Bernstein, Brad Lengauer, Thomas Coyne, Mike Zhang, Xiaolan Gu, Hongcang Ahfeldt, Tim Boulting, Gabriella Kiskinis, Evangelos Ptaszek, Leon Tarjei Halachev, Mikkelsen, Konstantin Bock, Christoph Root David Okamoto, Michael Douglas Hsiao, Jessica Ponduru, Sridevi Luo, Biao Alan, Sullivan, John Derr, Alan Gopal, Shuba Cowley, Glenn Alkan, Ozan Nieland, Silver, Thomas Serena 37 Broad Institute | Fifth Annual Retreat The Broad Institute Epigenomics Initiative poster session II Charles 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 Genome Biology Bernstein, Eric Lander 2nd Floor Genome-wide discovery and characterization of chromatin states from combinatorial patterns of 12:00 PM - 2:00 PM 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 kinases Jonathan Goldberg, Allison Griggs, Qiandong Zeng, James Galagan, Bruce Birren, Brian Haas
Genome-scale DNA methylation analysis Hongcang Gu, Christoph Bock, Tarjei Mikkelsen, Natalie Jaeger, Zack Smith, Eleni Tomazou, Eric Lander, Andreas Gnirke, Alexander Meissner
Hybrid assembly: Integrating the new with the old David Heiman, Manfred Grabherr, Sarah Young, Assembly Computation and Development Core
Overview of the Affymetrix custom SNP array genotyping pipeline Charles Johnson, Melissa Parkin, Andrew Crenshaw, Wendy Winckler
Regulatory motifs associated with TF binding and chromatin dynamics in Drosophila and mammalian genomes Pouya Kheradpour, Christopher Bristow, Jason Ernst, Rachel Sealfon, Manolis Kellis
The Genome Sequencing Sample Repository (GSSR): Procurement, preparation and storage of samples for sequencing whole genomes Marcia Lara, Kim Kanki, Susan Faro, Scott Nisbet, Louis Meneus, Pema Phunkhang, Helen Vassiliev, Tsamla Comparative genomics reveals mobile pathogenicity pathogenicity chromosomes inFusariummobile oxysporum reveals genomics Comparative methods Development andevaluationofRNA-Seq discovery From to mechansim RNAs: non-coding intergenic Large accurate inferring for gene names tool high-throughput A Pidgin: gene in product naming accuracy to approaches Computational comparative visualization,andanalysis Viral genomedatabasesattheBroad:Datasharing, Projects Team, Robert Nicol Nicol Team, Robert Projects Toby Ruan, Bloom, Daniel Zhong, Danni Ross, Keenan Hernandez, Ray, Desiree Ashley Hartfield, Tsamla, Katie Bernard Henrissat, Petra Houterman, Seogchan Kang, Seogchan Houterman, Petra Henrissat, Bernard Grabherr, Manfred Freitag, Michael Dufresne, Marie Pietro, Di Antonio Daboussi, Marie-Jose Coleman, Jeffrey Borkovich, Katherine Does, der van Charlotte Ma‚ Li-Jun Gnirke Andreas Nusbaum, Chad Regev, Aviv Garraway, A. Levi Fennell, Timothy Melnikov, Rogov, Young, Alexandre Peter Sarah Guttman, Yassour, Mitchell Moran Pfiffner, Jenna Thompson, Dawn Berger, Michael Fan, Lin Adiconis, Xian Levin, Joshua Rinn John Magda Tal Cabili, Shay, Lander, Regev,Koziol, Eric Aviv Moran Khalil, Ahmad Guttman, Mitch Huarte, Maite Broad Platform Sequencing Zeng, Genome Qiandong Pearson, Matthew Koehrsen, Michael Haas, Brian Gujja, Sharvari Howarth, Clint Haas Brian Galagan, James Birren, Bruce Pearson, Matt Howarth, Clint Zeng, Shenoy, Qiandong Narmada Gujja, Sharvari Lucia Henn White, Matthew Zeng, Qiandong Jared Birren, Bruce Alvarado, Sisk, Peter Roberts, Andrew Richards, Julian Pearson, Matthew Park, Daniel Lewis, Bil Howarth, Edward Clint Heilman, Ethan Gellesch, Marcel Freedman, Engels, Reinhard Borenstein, David Stolte, Christian Koehrsen, Michael Jen, Dennis Larson, Lisa 39 Broad Institute | Fifth Annual Retreat Won-Bo Shim, Charles Woloshuk, Xiaohui Xie, Jin- poster Rong Xu, John Antoniw, Scott Baker, Burton Bluhm, session II Andrew Breakspear, Daren Brown, Robert Butchko, Sinead Chapman, Richard Coulson, Pedro Coutinho, Etienne Danchin, Andrew Diener, Liane Gale, Donald Genome Biology Gardiner, Stephen Goff , Kim Hammond-Kosack, Karen 2nd Floor 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, 12:00 PM - 2:00 PM 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 sequencing Jennifer 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 trees Matthew Rasmussen, Manolis Kellis
Target-specific genotyping with Illumina’s VeraCode on the BeadXpress Reader system Michelle Redman, Katie Larkin, Cherylyn Smith, Tony Rachupka, Amy Camargo, Liuda Ziaugra, Andrew Crenshaw, Wendy Winckler
Chromatin state dynamics during differentiation Christopher 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/ SLAP Pamela Russell, Evan Mauceli, Jessica Alfoldi, Federica Di Palma, Kerstin Lindblad-Toh, Manfred Grabherr Genomic signatures of speciation, sex, and and sex, selection inoceanbacteria speciation, of signatures Genomic Institute genomeannotationattheBroadNext-generation sequencing Fosill: FosmidlibrariesforpairedendIllumina expressed geneswithin10ESTlibraries differentially Identification ofNeurosporacrassa sequencing next-generation using tuberculosis Searching andvisualizingpolymorphismsinM. James Galagan, Brian Haas, Broad Genome Sequencing Platform Sequencing Genome Broad Haas, Brian Galagan, James Birren, Bruce Koehrsen, Michael Howarth, Clint Pearson, Yandava, Matt Shenoy, Tom Chandri Walk, Narmada Teena Mehta, Gujja, Sharvari Griggs, Allison Goldberg, Jonathan Chen, Zehua Alvarado, Lucia Zeng, Qiandong Gnirke Andreas Terrance Shea, Li, Na Williams, Louise Platform Broad Sequencing Genome Haas, Brian Birren, Bruce Galagan, James Sachs, Matthew Zeng, Qiandong Walk, Thomas Chen, Zehua James Galagan Koehrsen, Michael Sisk, Peter Sykes, Sean Borenstein, David Engels, Reinhard Abeel, Thomas Heilman, Ethan Jen, Dennis Stolte, Christian Gellesch, Marcel Alm Eric Shapiro, Jesse B. 41 Broad Institute | Fifth Annual Retreat
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