Abstracts of papers, posters and talks presented at the 2009 Joint RECOMB Satellite Conference on REGULATORY GENOMICS - REGULATORYSYSTEMS BIOLOGY GENOMICS - DREAM4 Wed Dec 2-Sun Dec 6, 2009 YDL051W YKR057W MIT / Broad Institute / CSAIL YNL232W YLR179C YER060WA YNL277W YPL206C YJR139C YJR010W YPR167C YNR051C YDR502C YFR030W YDR253C YOR038C YPL038W YIR017C YNL103W YER114C YOL064C YJR138W YER092W YOR344C YJR137C YGR204W YLR157C YAL012W YBR144C YER091C YLR158C YLR303W YJR060W Asparagine catabolism Cysteine biosynthetic process Methionine metabolism Sulfur acid metabolism YLR155C YBR145W Other or unknown function Conference Chairs: Manolis Kellis, MIT Ziv Bar-Joseph, CMU Andrea Califano, Columbia Gustavo Stolovitzky, IBM REGULATORY GENOMICS - SYSTEMS BIOLOGY - DREAM4 2009 Abstracts of papers, posters and talks presented at the 2009 Joint RECOMB Satellite Conference on REGULATORY GENOMICS - REGULATORYSYSTEMS BIOLOGY GENOMICS - DREAM4 Wed Dec 2-Sun Dec 6, 2009 MIT / Broad Institute / CSAIL Conference Chairs: Manolis Kellis, MIT Ziv Bar-Joseph, CMU Andrea Califano, Columbia Gustavo Stolovitzky, IBM Conference Chairs: Manolis Kellis ..................................................... Associate Professor, MIT Ziv Bar-Joseph ................................................ Associate Professor, CMU Andrea Califano ........................................ Professor, Columbia University Gustavo Stolovitzky.......................................Systems Biology Group, IBM In Partnership With: PLoS Computational Biology .........................editor: Catherine Nancarrow PLos ONE .................................................................. editor: Peter Binfield Associate Editor, PLoS Computational Biology Uwe Ohler Session Chairs: Regulatory Genomics: DREAM4: Systems Biology: Nitin Baliga Fritz Roth Diego di Bernardo Panayiotis (Takis) Benos Peter Sorger James Collins Michael Brent Yuval Kluger Christina Leslie Avi Ma'ayan Uwe Ohler Franziska Michor Ron Shamir Roded Sharan Pablo Tamayo Dennis Vitkup Program Committee: Regulatory Genomics: Hao Li Eleazar Eskin Manolis Kellis, chair Eran Segal Igor Jurisica Ziv Bar-Joseph, chair Ron Shamir Pascal Kahlem Orly Alter Saurabh Sinha Andre Levchenko Nitin S Baliga Mona Singh Avi Ma'ayan Panayiotis (Takis) Christopher Workman Adam Margolin Benos Satoru Miyano Mathieu Blanchette Systems Biology and Dana Pe'er Michael R. Brent DREAM: Theodore Perkins Albert Erives Andrea Califano, chair Timothy Ravasi Eleazar Eskin Gustavo Stolovitzky, Frederick Roth Ernest Fraenkel chair Michael Samoilov Nir Friedman M. Madan Babu Roded Sharan Mikhail Gelfand Gary Bader Mona Singh Sridhar Hannenhalli Joel Bader Pavel Sumazin Tim Hughes Diego di Bernardo Denis Thieffry Uri Keich Jim Collins Ioannis Xenarios Christina Leslie Joaquin Dopazo Local Organization and Student Volunteers: Local organization Matt Edwards CMU Monica Concepcion Chuck Epstein Anthony Gitter Sally Lee Sudeshna Fisch Peter Huggins Pia Handsom Taran Gujral Hai-Son Le Karen Shirer Christina Harview Henry Lin Eliana Hechter Shan Zhong Local Volunteers: Yan Meng Guy Zinman Loyal Goff Michal Rabani Charlie Frogner Erroll Rueckert Other Patrycja Missiuro Mark Sevecka Betty Chang Yang Ding Tal Shay Antonina Mitrofanova Mary Addonizio Eboney Smith Yeison Rodriguez Adam Callahan Li Wang Cover art credit: Yeast functional modules in amino-acid metabolism, Daniel Marbach Gene expression atlas for Drosophila Blastoderm. Fowlkes, DePace, Malik. Human membrane receptor interactions, Yanjun Qi, Judith Klein-Seetharaman. Special thanks for booklet assembly to: Michelle Martin Online material: All talks will be videotaped and shared freely online with presenter’s permission. All papers accepted and published will be available freely online from PLoS. All videos of accepted papers will be linked to the papers through the PLoS site. Photos from the meeting will be made available through the conference website. All invited talks will be sync’ed with slides in an interactive site by the New York Academy of Sciences. All these materials can be accessed at any time from: http://compbio.mit.edu/recombsat/ For any inquiries, please contact the conference chairs at: [email protected] Industry and Government Sponsors: The organizers wish to thank the following industrial and government sponsors for their generous support of this conference. The NIH National Centers for Biomedical Computing and the MAGNet Center at Columbia University The New York Academy of Sciences IBM Research Scientific Partners The organizers also wish to thank the following journals for their invaluable support in publishing conference manuscripts. PLoS Computational Biology PLoS ONE Local Hosts and Organization Many thanks also go to our local hosts for making this meeting possible. Massachusetts Broad Institute of Computer Science Institute of MIT and Harvard and Artificial Technology Intelligence Lab Wednesday December 2nd, 2009 Dear attendees, Welcome to the 6th Annual RECOMB Satellite on Regulatory Genomics, the 5th Annual RECOMB Satellite on Systems Biology, and the 4th Annual DREAM reverse engineering challenges. The goal of this meeting is to bring together computational and experimental scientists in the area of regulatory genomics and systems biology, to discuss current research directions, latest findings, and establish new collaborations towards a systems-level understanding of activities in the cell. The next 5 days will consist of keynote presentations, oral presentations selected from submitted full length papers and 1-page abstracts, and posters presentations also selected from submitted abstracts. But most importantly, it’s an opportunity to connect, discuss, exchange ideas, think together, and plan ahead. For the second year in a row this meeting has been sold out, this year more than a month in advance. We have also received a record number of more than 50 full length papers and more than 250 abstracts, resulting in a scientific program of outmost quality. All submitted full length papers were fully reviewed by the program committee and 17 were accepted to the conference and by our partner journals, with 8 papers going to PLoS Computational Biology and 9 papers to PLoS ONE. These papers should appear online by the time the meeting starts, and will be ultimately linked together with the corresponding talks on the PLoS website, providing a new means for science dissemination. All abstracts were reviewed by the conference chairs and 16 additional session chairs, resulting in 50 abstracts selected for oral presentation, and most remaining abstracts for poster presentation. Welcome to Boston, for what promises to be a very exciting meeting! The conference chairs: Regulatory Genomics: Manolis Kellis (MIT), Ziv Bar-Joseph (CMU). Systems/DREAM: Andrea Califano (Columbia), Gustavo Stolovitzky (IBM). RECOMB Regulatory Genomics 2009 ( Full length manuscript; ► Invited talk; Accepted abstract) Wednesday, Dec. 2, 2009 3pm Conference check-in open, Poster session I set-up 5pm Welcome Remarks 5:15► Mark Biggin: Evidence for Quantitative Transcription Networks ...1 5:45 Sarah E. Calvo: Widespread translational repression...................2 6pm Hilal Kazan: Learning binding preferences....................................3 6:15 Igor Ulitsky: Towards prediction of MicroRNA function..………… 4 Light snacks – 6:30-6:45pm 6:45 Clifford A. Meyer: Inferring key transcriptional regulators .............5 7pm Jason Ernst: Genome-wide discovery of chromatin states……….6 7:15 Mattia Pelizzola: Human DNA methylomes at base resolution .....7 7:30 Leonid Mirny: Different strategies for gene regulation……………8 7:45► Bob Waterston: Deciphering C. Elegans embryonic network.......9 Regulatory Genomics Welcome Reception/Poster Session I 8:15pm-9:45pm Hors d’oeuvres, snacks, refreshments, cash bar Thursday, Dec. 3, 2009 Breakfast – 8am 9am► Rick Young: Programming cell state ...........................................10 9:30 Jesse M. Gray: Widespread RNA polymerase II recruitment......11 9:45 Yue Zhao: Inferring binding energies ..........................................12 10am Guillaume Bourque: Binding site turnover in stem cells ………..13 Coffee / Snacks / Fruit Break – 10:15-10:45am 10:45 Michael Brodsky: Identification and analysis of regulatory regions14 11am Yang Ding: Exact calculation of partition function ………………15 11:15 Sheng Zhong: A analysis of transcription factor interactions….16 11:30 Pouya Kheradpour: Regulatory motifs associated with TF........17 11:45 Quan Zhong: Edgetic perturbation models of human ................18 Lunch Break / Networking Opportunities – 12-1pm 1pm► Naama Barkai: Evolution of nucleosome positioning .................19 1:30 Pieter Meysman: Structural DNA for the prediction of binding....20 1:45 Claes Wadelius: Nucleosomes are positioned in exons..............21 2pm Eugene Bolotin: Identification of human HNF4 target genes….. 22 Coffee / Snacks / Fruit Break – 2:15-2:45pm Poster set-up for Session II 2:45 Damian Wójtowicz: Mapping of non-B DNA structures ...............23 3pm Elizabeth A. Rach: The landscape of transcription initiation .......24 3:15 Julia Lasserre: TSS detection......................................................25 3:30 Ron Shamir : Signaling pathways analysis tool...........................26 Regulatory Genomics Poster Session II – 3:45pm-5:15pm Hors d’oeuvres, snacks, refreshments 5:15► Nikolaus Rajewsky: Post-transcriptional gene regulation............27 5:45 Stein Aerts : Regulatory network for retinal differentiation ..........28 6pm Raja Jothi: A link