RECOMB 2011 Program Brochure

RECOMB 2011

15th Annual International Conference on Research in Computational Molecular Biology

Vancouver, BC | March 28-31, 2011

Conference Program

RECOMB 2011 |

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Contents Welcome ...................................................................... 2 RECOMB 2011 Organization ........................................ 3 General Information ....................................................5 Keynote Speakers ........................................................9 Conference Schedule ...............................................12 Posters Index .............................................................. 20 Sponsors & Exhibitors ................................................. 30 Notes ........................................................................... 32

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| RECOMB 2011

Welcome Dear RECOMB 2011 attendee, On behalf of the RECOMB 2011 organizing committee, it is a pleasure to welcome you in Vancouver, to the premier meeting in theoretical foundations of computational biology, the 15th Annual International Symposium on Computational Molecular Biology, along with two RECOMB Satellite Meetings on Massively Parallel Sequencing and Computational Cancer Biology.

This year we will have 43 papers presented in RECOMB selected out of more than 150 submissions. RECOMB will also feature 6 distinguished keynote speakers as well as 5 highlight presentations, selected among more than 58 submissions, and an industry panel on the future of high throughput sequencing that will contribute to the high quality of the program. With more than 120 posters in the main conference, together with several oral presentations, invited speakers and an additional poster session in the satellite meetings, we are expecting an exciting and lively conference.

We hope that the high quality of the technical program coupled with the attractions of beautiful Vancouver will help make this RECOMB a memorable meeting.

RECOMB 2011 benefited from the voluntary contributions of many members of the computational biology and bioinformatics community in Vancouver and Simon Fraser University, the host institution. Special thanks to Vineet Bafna, the Program Committee Chair, Martin Vingron, the Steering Committee Chair, Cedric Chauve, the Organizing Committee and Finances Chair, Inanc Birol, Industry Relations and Panels Chair and Martin Ester, the Sponsorship Chair.

We also thank all members of the Program, Steering and the Organization Committees, as well as our event coordinators.

The conference would not be financially viable without our Canadian and International sponsors, namely, Genome BC, Canadian Institutes of Health Research, Natural Sciences and Engineering Research Council of Canada, Simon Fraser University, the Pacific Institute for the Mathematical Sciences, International Society for Computational Biology, Mathematics of Information Technology and Computer Science Inc., Ion Torrent, BC Cancer Foundation and Pacific Biosciences.

We wish you all a great meeting, Sincerely, S. Cenk Sahinalp Conference Chair

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RECOMB 2011 Organization Conference Chair

• Cenk Sahinalp, SFU, Canada

Steering Committee Chair • Martin Vingron, Max Planck Institute for Molecular Genetics, Germany Members • Serafim Batzoglou, Stanford University, USA • Bonnie Berger, MIT, USA • Sorin Istrail, Brown University, USA • Thomas Lengauer, Max Planck Institute for Informatics, Germany • Michal Linial, The Hebrew University of Jerusalem, Israel • Pavel Pevzner, University of California, San Diego, USA • Terry Speed, University of California, Berkeley, USA

Organizing Committee Chairs • Cedric Chauve, SFU, Canada Organization and Finances Chair • Martin Ester, SFU, Canada Sponsorship Chair • Inanc Birol, BCGSC, Canada Industry Relations and Panels Chair Members • Fiona Brinkman, SFU, Canada • Steven Jones, BCGSC, Canada • Anne Condon, UBC, Canada • Jack Chen, SFU, Canada • Artem Cherkasov, Prostate Centre, VGH, Canada

• Colin Collins, Prostate Centre, VGH, Canada • Tamon Stephen, SFU, Canada • Stas Volik, Prostate Centre, VGH) • Wyeth Wasserman, UBC, Canada • Kay Wiese, SFU, Canada

Program Committee Chair • Vineet Bafna, UCSD, USA Members • Tatsuya Akutsu, U. Kyoto, Japan • Can Alkan, U. Washington, USA • Nancy Amato, Texas A&M U., USA • Rolf Backofen U. Freiburg, Germany • Joel Bader, Johns Hopkins U., USA • Nuno Bandeira UCSD, USA • Vikas Bansal Scripps Institute, USA • Ziv Bar-Joseph, Carnegie Mellon U., USA • Bonnie Berger, MIT, USA • Jadwiga Bienkowska, Boston U., USA • Mathieu Blanchette McGill U., Canada • Philip Bradley, Fred Hutchinson Center, USA • Michael Brent, Wash. U. St Louis, USA • Michael Brudno U. Toronto, Canada • Lenore Cowen, Tufts U., USA • Colin Dewey, U. WisconsinMadison, USA • Dannie Durand, Carnegie Mellon U., USA • Eleazar Eskin, UCLA, USA • David Gifford, MIT, USA • Bjarni Halldorsson, Reykjavik U., Iceland

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| RECOMB 2011

• Eran Halperin, Tel Aviv U., Israel • Alexander Hartemink, Duke U., USA • Trey Ideker, UCSD, USA • Sorin Istrail, Brown U., USA • Tao Jiang, U. Riverside, USA • Simon Kasif, Boston U., USA • Mehmet Koyuturk, Case Western Reserve U., USA • Jens Lagergren, KTH, Sweden • Thomas Lengauer, MPISaarbrucken, Germany • Michal Linial Hebrew U., Israel • Satoru Miyano, U. Tokyo, Japan • Bernard Moret EPFL, Switzerland • William Noble, U. Washington, USA • Lior Pachter, UC Berkeley, USA • Ron Pinter, Technion, Israel • Teresa Przytycka, NCBI, NIH, USA • Predrag Radivojac, U. Indiana, USA • Ben Raphael, Brown U., USA • Knut Reinert, Freie U. Berlin, Germany

• Marie-France Sagot, Inria RhoneAlpes, France • S. Cenk Sahinalp, SFU, Canada • David Sankoff, U. Ottawa, Canada • Russell Schwartz, Carnegie Mellon U., USA • Roded Sharan, Tel Aviv U., Israel • Adam Siepel, Cornell U., USA • Mona Singh, Princeton U., USA • Donna Slonim, Tufts U., USA • Terence Speed, Walter+Eliza Hall Institute, Australia • Haixu Tang, U. Indiana, USA • Anna Tramontano, U. RomeSapienza, Italy • Alfonso Valencia, U. Autonoma Madrid, Spain • Martin Vingron, MPI-Berlin, Germany • Tandy Warnow, U. Texas-Austin, USA • Eric Xing, Carnegie Mellon U., USA • Jinbo Xu, TTI Chicago, USA • Michal Ziv-Ukelson, Ben Gurion U., Israel

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General Information Conference Venue THE FAIRMONT HOTEL VANCOUVER 900 West Georgia Street Vancouver, British Columbia Canada V6C2W6 TEL: (604) 684-3131 FAX: (604) 662-1929 E-MAIL: hvc.concierge@fairmont.com URL: http://www.fairmont.com/hotelvancouver

Centrally located in the heart of the city is The Fairmont Hotel Vancouver.

The hotel is a Vancouver landmark, rich in history, vibrant and cosmopolitan.

Within the Hotel Vancouver, you will find the exclusive Fairmont Gold floor, a state-of-the-art health club and indoor pool, Absolute Spa facility and many designer shops, including the flagship Louis Vuitton boutique

Location and Access

TRANSPORTATION The following transportation options are available from the Vancouver International Airport to The Fairmont Hotel Vancouver: Canada Line Skytrain The Canada Line Skytrain (light rapid transit system) departs every 12 minutes (every 6 minutes during peak periods) to downtown Vancouver. The current fare is $8.75 per person and will take you to Vancouver City Centre Station which is 2 blocks away from the hotel. The trip will take 30 minutes and is recommended for guests with little luggage.

Taxi Taxis are readily available at the Arrivals Level. The trip will take 30 minutes and the cost is a metered rate of approximately $30.00 - $35.00. There is also an “Aerocar� limousine stand in the same area which offers sedan cars to our hotel for approximately $45.00 - $50.00 but they do not take advance reservations.

Private Car The concierge desk at the hotel can arrange a private car and driver for a cost of approximately $145.00. For the private transfer, the driver will be inside the airport with a sign and will assist with luggage. The concierge would simply require the flight information and a credit card to confirm the car. There would be a 24 hour cancellation for this service.

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Registration and Information

Desk (opening hours): • Sunday, March 27th, 15:00-20:00; • Monday, March 28th – Thursday, March 31st, 8:00-17:00

Conference proceedings

All Conference delegates will receive one copy of the RECOMB 2010 Proceedings, which are included in the delegate bag. The poster abstracts will also be available in a CD.

Conference badge

You must wear your name badge at all RECOMB 2011 conference events.

Coat check and baggage storage Please note there are no rooms for holding baggage or clothing.

Lunches and coffee breaks

All meals will be provided in the foyer and poster session room (Columbia Room)

Speaker presentation uploads

Speakers will be assisted at the Speaker Registration Desk to upload their presentations to the main presentation computer. Please ask about uploading your presentation upon registering.

Poster sessions

The poster sessions will take place in the Columbia Room. All posters will be displaying until 15:30 Thursday afternoon. The authors are required to be available for presentation of their poster during the scheduled poster sessions.

Internet access

Complimentary internet can be received through the venue.

Poster session times: • Monday, 18:10-19:40 • Tuesday, 18:45-20:15

Mobile phones

Social events

Please ensure that your mobile phones are turned off during all sessions of the conference.

Lost and found

More information at the Information Desk.

Sunday, March 27, 17:00-20:00 • Welcome Reception in the Pacific Ballroom Wednesday, March 30, 18:00-21:00 • Conference Banquet in the Rooftop Room (located on the 15th Floor of the hotel)

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Tourist information

For tourism information please visit: http://www.tourismvancouver.com/visitors/ Local Attractions: • Science World (http://www.scienceworld.ca/) • Vancouver Aquarium (http://www.vanaqua.org/) • Stanley Park (http://vancouver.ca/parks/parks/stanley/) • Granville Island (http://www.granvilleisland.com/) • Vancouver Lookout at Harbour Centre (http://www.vancouverlookout. com/) • Space Centre (http://www.spacecentre.ca/) • Chinatown (http://www.vancouver-chinatown.com/)

Emergency assistance/Medical

Care Pharmacy The emergency number in Canada is 911.

Hospitals provide round the clock emergency service.

The nearest pharmacy from the conference venue is Rexall Drugstore, address: 1055 West Georgia #122, phone: 604-684-8204 and the closest hospital is St. Paul’s Hospital, address: 1081 Burrard Street, phone: 604-682-2344.

Post office

The nearest post office is located at 1014 Robson Street and is open Mon. to Fri. Phone: 604-684-4011.

Credit card, ATM cash machines

The most common accepted credit cards in local hotels restaurants and shops are Visa, MasterCard and American Express. ATM cash machines are widely available.

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Conference Floor

Columbia Room British Columbia Foyer

British Columbia Ballroom

Banquet Service Kitchen

Auto Elevator

British Room

Vancouver Island Room

Escalator

Coat Check Burrard Street

Garabaldi Room

Elevators

Hornby Street

Lions Room

Stairs

Tweedsmuir Room

Grand Staircase

Pacific Foyer

Office

Stage

Pacific Ballroom Waddington Room

Boardroom

Georgia Street

Discovery Floor Saturna Galiano

Coat Check

Georgia Street

N

Cortes

Foyer

Elevators

Service Pantry

Gabriola

Moresby

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Keynote Speakers Evan Eichler Evan Eichler is a Professor and Howard Hughes Medical Institute Investigator in the Department of Genome Sciences, University of Washington School of Medicine. He graduated with a B.Sc. Honours degree in Biology from the University of Saskatchewan, Canada in 1990. He received his Ph.D. in 1995 from the Department of Molecular and Human Genetics at Baylor College of Medicine, Houston. After a Hollaender post-doctoral fellowship at Lawrence Livermore National Laboratory, he joined the faculty of Case Western Reserve University in 1997 and later the Department of Genome Sciences in 2004. He was a March of Dimes Basil O’Connor Scholar (1998-2001), was appointed as an HHMI Investigator (2005), and awarded an AAAS Fellowship (2006) and the American Society of Human Genetics Curt Stern Award (2008). He is an editor of Genome Research and has served on various scientific advisory boards for both NIH and NSF. His research group provided the first genome-wide view of segmental duplications within human and other primate genomes and he is a leader in an effort to identify and sequence normal and disease-causing structural variation in the human genome. The long-term goal of his research is to understand the evolution and mechanisms of recent gene duplication and its relationship to copy-number variation and human disease.

Daphne Koller Daphne Koller is a Professor of Computer Science at Stanford University. Her main research focus is in developing and using machine learning and probabilistic methods to model and analyze complex systems, and she is particularly interested in using these techniques to help us understand biological systems and to help computers perceive the world around us. Professor Koller is the author of over 150 refereed publications, which have appeared in venues that include Science, Nature Genetics, and the Journal of Games and Economic Behavior. She is a fellow of the American Association for Artificial Intelligence, and has received numerous awards, including the Sloan Foundation Faculty Fellowship in 1996, the ONR Young Investigator Award in 1998, the Presidential Early Career Award for Scientists and Engineers (PECASE) from President Clinton in 1999, the IJCAI Computers and Thought Award in 2001, the Cox Medal for excellence in fostering undergraduate research at Stanford in 2003, the MacArthur Foundation Fellowship in 2004 and the first-ever ACM/Infosys award in 2008.

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Elaine R Mardis Elaine R Mardis is an Associate Professor of Genetics, with an adjunct appointment in the Department of Molecular microbiology at Washington University in St. Louis and Co-Director of The Genome Center. Dr. Mardis is also the Director of The Genome Center’s Technology Development group, a group that researches, tests and implements new sequencing technologies. Using next-generation sequencing technology, her group is developing applications and processes for use in The Genome Center’s sequencing projects. Dr. Mardis also helped lead the group that sequenced the first whole cancer genome and has since gone on to sequence many other cancer genomes to determine the genetic changes that may lead to cancer. Other research Dr. Mardis participates in includes human genetic variation and genomics education. Prior to joining the Washington University faculty, she was Senior Research Scientist at Bio-Rad Laboratories in Hercules, California. She received her B.S. degree in 1984 and her Ph.D. in 1989 from the University of Oklahoma.

Marco Marra Marco Marra is the Director of Michael Smith Genome Sciences Centre, BC Cancer Agency and a Professor and Canada Research Chair in Medical Genetics at the University of British Columbia. Marra received his PhD from Simon Fraser University, and postdoctoral training at the Washington University Genome Sequence Center. When Nobel Laureate Michael Smith set out in 1998 to establish the Genome Science Centre (GSC) in Vancouver, Dr. Marra was appointed to head the Mapping and Sequencing division. He later became GSC director, leading more than 200 staff and an annual grant funding level averaging more than $20 million per year. During his tenure at GSC Dr. Marra and his team succeeded to map the human genome, and sequence the SARS virus, putting Canada on the world map in the genome era. Dr. Marra has received numerous honours recognizing his scientific contributions and leadership including the Order of British Columbia, the Royal Society of Canada Fellowship and the 2010 Genome BC Award of Scientific Excellence.

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Joseph Nadeau Joseph Nadeau is the Director of Research and Academic Affairs and a Professor at the Institute for Systems Biology. Formerly he was the James H. Jewel Professor and Chair of Genetics Department at Case Western Reserve University.

Dr. Nadeau received his Ph.D. in population biology from Boston University in 1978. He was a postdoctoral fellow with Jan Klein in the Max Planck Institute for Biology, Tubingen (1978-1980) and with Eva Eicher at the Jackson Laboratory (1980-1981). He was with Jackson Laboratory between 1981 and 1994 as a senior staff scientist and later with McGill University, as a Professor of Human Genetics (1994-1996). He was a founding member of the International Mammalian Genome Society and a founding editor of Mammalian Genome and of Systems Biology and Medicine. He was founder and director of the Mouse Genome Informatics Project and founder of the Mouse Gene Expression Database Project. He has served on review panels and advisory groups at the National Institutes of Health, the National Science Foundation and the Human Genome Database, and has consulted for several biotech and major pharmaceutical companies. He has won several awards for his work and is an Elected Fellow of the American Association for the Advancement of Science.

Karen Nelson Karen Nelson is the Director of the Rockville Campus of the J. Craig Venter Institute (JCVI). She was formerly the Director of Human Microbiology and Metagenomics in the Department of Human Genomic Medicine at the JCVI. Dr. Nelson has extensive experience in microbial ecology, genomics and metagenomics as well as in microbial physiology. Since joining the JCVI legacy institutes, Dr. Nelson has led several genomic and metagenomic efforts. She has also been involved in the analysis of the microbiota of the human stomach and gastrointestinal tract, and led the 2006 metagenomics study on fecal material derived from three individuals. Additional ongoing studies in her group include metagenomic approaches to study the ecology of the rumen and corals. Dr. Nelson received her undergraduate degree from the University of the West Indies, and her Ph.D. from Cornell University. She has authored or co-authored over 100 publications, and is currently Editor-in-Chief of the journal Microbial Ecology. She is also a standing member of the NRC Committee on Biodefense, and a member of the American Society for Microbiology Communications Committee.

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Conference Schedule Sunday March 27 17:00-19:00

Registration Opens

19:00-21:00

Welcome Reception

Monday March 28 8:45-9:00

Opening Remarks

9:00-10:40

Session Chair: Cenk Sahinalp (SFU)

9:00-10:00

KEYNOTE: Dr. Elaine Mardis (WUSTL)

10:00-10:20

Hapsembler: An assembler for highly polymorphic genomes Nilgun Donmez (U. Toronto) and Michael Brudno

10:20-10:40

Opera: Reconstructing optimal genomic scaffolds with highthroughput paired-end sequences Gao Song (NUS), Niranjan Nagarajan and Wing-Kin Sung

10:40-11:00

BREAK

11:00-12:00

Session Chair: Cenk Sahinalp (SFU)

11:00-11:20

Paired de Bruijn graphs: a novel approach for incorporating mate pair information into genome assemblers Paul Medvedev (UCSD), Son Pham, Mark Chaisson, Glenn Tesler and Pavel Pevzner

11:20-11:40

AREM: aligning short reads from ChIP-sequencing by expectation maximization Daniel Newkirk (UC Irvine), Alvin Chon, Jacob Biesinger, Kyoko Yokomori and Xiaohui Xie

11:40-12:00

HIGHLIGHT: Discovery and characterization of chromatin states for systematic annotation of the human genome Jason Ernst and Manolis Kellis (MIT)

12:00-13:30

LUNCH

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13:30-14:10

Session Chair: Michael Brudno (U. Toronto)

13:30-13:50

IsoLasso: A LASSO Regression Approach to RNA-Seq Based Transcriptome Assembly Wei Li (UC Riverside), Jianxing Feng and Tao Jiang

13:50-14:10

T-IDBA: A de novo Iterative de Bruijn Graph Assembler for Transcriptome Yu Peng (HKU), Henry C.M. Leung, S.M. Yiu and Francis Chin

14:10-14:30

BREAK

14:30-16:30

PANEL: High Throughput Sequencing: Data Types and Applications Session Chair: Inanc Birol (BC Genome Sciences Centre) Participants (tentative): Steve Lincoln (Complete Genomics), Jordan Stockton (Illumina), Mike Lelivelt (Life Technologies for the Ion Torrent platform), Daryl Thomas (Life Techologies for the SOLiD platform), Jon Sorenson (Pacific Biosciences)

16:30-16:50

BREAK

16:50-18:10

Session Chair: Vineet Bafna (UCSD)

16:50-17:10

Blocked Pattern Matching Problem and its Applications in Proteomics Julio Ng (UCSD), Amihood Amir and Pavel Pevzner

17:10-17:30

Multiplex De Novo Sequencing of Peptide Antibiotics Hosein Mohimani (UCSD), Wei ting Liu, Yu Liang Yang, Susana Gaudencio, William Fenical, Pieter Dorrestein and Pavel Pevzner

17:30-17:50

Computing Fragmentation Trees from Metabolite Multiple Mass Spectrometry Data Kerstin Scheubert (U. Jena), Franziska Hufsky, Florian Rasche and Sebastian Bocker

17:50-18:10

Constrained De Novo Sequencing of Peptides with Application to Conotoxins Swapnil Bhatia (Boston U.), Yong Kil, Beatrix Ueberheide, Brian Chait, Lemmuel Tayo, Bingwen Lu, John Yates III and Marshall Bern

18:10-19:40

Poster Session

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Tuesday March 29 9:00-10:00

Session Chair: Teresa Przytycka (NCBI)

9:00-9:20

Disease Gene Prioritization Based on Topological Similarity in Protein-Protein Interaction Networks Sinan Erten (CWRU), Gurkan Bebek and Mehmet Koyuturk

9:20-9:40

Optimally Orienting Physical Networks Dana Silverbush (Tel Aviv U.), Michael Elberfeld and Roded Sharan

9:40-10:00

HIGHLIGHT: Understanding gene sequence variation in the context of transcription regulation in yeast Irit Gat-Viks (Broad Inst.), Renana Meller, Martin Kupiec and Ron Shamir

10:00-10:20

BREAK

10:20-12:00

Session Chair: Eleazar Eskin (UCLA)

10:20-11:20

KEYNOTE: Dr. Daphne Koller (Stanford)

11:20-11:40

Recovering Key Biological Constituents through Sparse Representation of Gene Expression Yosef Prat (Hebrew U.), Menachem Fromer, Michal Linial and Nathan Linial

11:40-12:00

Causal reasoning on biological networks: Interpreting transcriptional changes Leonid Chindelevitch (MIT), Daniel Ziemek, Ahmed Enayetallah, Ranjit Randhawa, Ben Sidders, Christoph Brockel and Enoch Huang

12:00-13:30

LUNCH

13:30-15:30

Session Chair: Michael Brent (WUSTL)

13:30-14:30

KEYNOTE: Dr. Karen Nelson (Craig Venter Inst.)

14:30-14:50

Bacterial Community Reconstruction Using Compressed Sensing Amnon Amir (Weizmann Inst.) and Or Zuk

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14:50-15:10

Metabolic Network Analysis Demystified Leonid Chindelevitch (MIT), Aviv Regev and Bonnie Berger

15:10-15:30

Identifying Branched Metabolic Pathways by Merging Linear Metabolic Pathways Allison Heath (Rice), George Bennett and Lydia Kavraki

15:30-15:50

BREAK

15:50-17:10

Session Chair: Ron Shamir (Tel Aviv U.)

15:50-16:10

HIGHLIGHT: A quantitative model of glucose signaling in yeast reveals an incoherent feed forward loop leading to a specific, transient pulse of transcription Sooraj KuttyKrishnan, Jeffrey Sabina, Laura Langton, Mark Johnston and Michael R. Brent (WUSTL)

16:10-16:30

Inferring Mechanisms of Compensation from E-MAP and SGA Data Using Local Search Algorithms for Max Cut Mark Leiserson (Tufts), Diana Tatar, Lenore Cowen and Benjamin Hescott

16:30-16:50

Learning Cellular Sorting Pathways Using Protein Interactions and Sequence Motifs Tien-ho Lin (CMU), Ziv Bar-Joseph and Robert F. Murphy

16:50-17:10

Experiment Specific Expression Patterns Tobias Petri (L.M. U. Munich), Robert Kuffner and Ralf Zimmer

17:10-17:30

BREAK

17:30-18:45

Business Meeting

18:45-20:15

Poster Session

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Wednesday March 30 9:00-10:00

Session Chair: Bonnie Berger (MIT) & Mona Singh (Princeton)

9:00-9:20

A geometric arrangement algorithm for structure determination of symmetric protein homo-oligomers from NOEs and RDCs Jeffrey Martin (Duke), Anthony Yan, Chris Bailey-Kellogg, Pei Zhou and Bruce Donald

9:20-9:40

Protein Loop Closure using Orientational Restraints from NMR Data Chittaranjan Tripathy (Duke), Jianyang Zeng, Pei Zhou and Bruce Donald

9:40-10:00

Efficient traversal of protein folding pathways using ensemble models Solomon Shenker (Cornell), Charles O’Donnell, Srinivas Devadas, Bonnie Berger and Jerome Waldispuhl

10:00-10:20

BREAK

10:20-12:00

Session Chair: Can Alkan (U. Washington)

10:20-11:20

KEYNOTE: Dr. Marco Marra (BC Genome Sciences Centre)

11:20-11:40

De novo Discovery of Mutated Driver Pathways in Cancer Fabio Vandin (Brown), Eli Upfal and Ben Raphael

11:40-12:00

Increasing Power of Groupwise Association Test with Likelihood Ratio Test Jae Hoon Sul (UCLA), Buhm Han and Eleazar Eskin

12:00-13:30

LUNCH

13:30-15:30

Session Chair: Sorin Istrail (Brown)

13:30-14:30

KEYNOTE: Dr. Joe Nadeau (Inst. Systems Biology)

14:30-14:50

Weighted genomic distance can hardly impose a bound on the proportion of transpositions Shuai Jiang (U. South Carolina) and Max Alekseyev

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14:50-15:10

Conservative Extensions of Linkage Disequilibrium Measures from Pairwise to Multi-Loci and Algorithms for Optimal Tagging SNP Selection Ryan Tarpine (Brown), Fumei Lam and Sorin Istrail

15:10-15:30

Nonparametric combinatorial sequence models Fabian Wauthier (UC Berkeley), Michael Jordan and Nebojsa Jojic

15:30-15:50

BREAK

15:50-17:10

Session Chairs: Ben Raphael (Brown)

15:50-16:10

Haplotype Reconstruction in Large Pedigrees with Many Untyped Individuals Xin Li (CWRU) and Jing Li

16:10-16:30

Pedigree Reconstruction using Identity by Descent Bonnie Kirkpatrick (UC Berkeley), Shuai Cheng Li, Richard M. Karp and Eran Halperin

16:30-16:50

Algorithms for MDC-based Multi-locus Phylogeny Inference Yun Yu (Rice), Tandy Warnow and Luay Nakhleh

16:50-17:10

An optimization-based sampling scheme for phylogenetic trees Navodit Misra (MPI MG), Guy Blelloch, R. Ravi and Russell Schwartz

17:10

Conference Banquet

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Thursday March 31 9:00-10:00

Session Chair: William Noble (U. Washington)

9:00-9:20

Variable selection through correlation sifting Jim Huang (Microsoft Research) and Nebojsa Jojic

9:20-9:40

Variable selection through correlation sifting Jim Huang (Microsoft Research) and Nebojsa Jojic

9:40-10:00

HIGHLIGHT: Seeing More Is Knowing More: V3D Enables Realtime 3D Visualization and Quantitative Analysis of Large-scale Biological Image Data Sets Hanchuan Peng, Fuhui Long (HHMI, Janelia Farm), Zongcai Ruan, Julie H Simpson and Eugene W Myers

10:00-10:20

BREAK

10:20-12:00

Session Chair: Vineet Bafna (UCSD)

10:20-11:20

KEYNOTE: Dr. Evan Eichler (U. Washington)

11:20-11:40

Simultaneous structural variation discovery in multiple pairedend sequenced genomes Fereydoun Hormozdiari (SFU), Iman Hajirasouliha, Andrew McPherson, Evan Eichler and S. Cenk Sahinalp

1:40-12:00

HIGHLIGHT: A three-dimensional model of the yeast genome William Noble (U. Washington), Zhi-jun Duan, Mirela Andronescu, Kevin Schutz, Sean McIlwain, Yoo Jung Kim, Choli Lee, Jay Shendure, Stanley Fields and C. Anthony Blau

12:00-13:30

LUNCH

13:30-15:10

Session Chair: Martin Vingron (CMB)

13:30-13:50

Rich Parameterization Improves RNA Structure Prediction Shay Zakov (BGU), Yoav Goldberg, Michael Elhadad and Michal Ziv-Ukelson

13:50-14:10

An unbiased adaptive sampling algorithm for the exploration of RNA mutational landscapes under evolutionary pressure Jerome Waldispuhl (McGill) and Yann Ponty

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14:10-14:30

A Probabilistic Model For Sequence Alignment with ContextSensitive Indels Glenn Hickey (McGill) and Mathieu Blanchette

14:30-14:50

PSAR: Measuring Multiple Sequence Alignment Reliability by Probabilistic Sampling Jaebum Kim (UIUC) and Jian Ma

14:50-15:10

Genome-Scale Analysis of Translation Elongation with a Ribosome Flow Model Shlomi Reuveni (Tel Aviv U.), Isaac Meilijson, Martin Kupiec, Eytan Ruppin and Tamir Tuller

15:10-15:30

BREAK

15:30-16:30

Session Chairs: Rolf Backofen (U. Freiburg)

15:30-15:50

Metric Labeling and Semi-metric Embedding for Protein Annotation Prediction Emre Sefer (U. Maryland) and Carl Kingsford

15:50-16:10

Design of Protein-Protein Interactions with a Novel EnsembleBased Scoring Algorithm Kyle E. Roberts (Duke), Patrick R. Cushing, Prisca Boisguerin, Dean R. Madden and Bruce R. Donald

16:10-16:30

A Bayesian Approach for Determining Protein Side-Chain Rotamer Conformations Using Unassigned NOE Data Jianyang Zeng (Duke), Kyle Roberts, Pei Zhou and Bruce Donald

16:30-16:45

Closing Remarks

16:45

Conference Adjourns

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Posters Index #

Authors, Title

P1

Mahmoud Elhefnawi, Mohamed Ahmed and Jon Garibaldi. MysiRNADesigner: A workflow for Efficient siRNA Design Considering splicevariants, Multi-score filtration, Target Accessibility and both perfect and seed-matching off-targets

P2

Kiyeol Kim and In-Ho Cha. Significance of molecular markers in survival prediction of oral squamous cell carcinoma

P3

Franziska Hufsky, Kerstin Scheubert, Florian Rasche and Sebastian Böcker. Fragmentation Trees from MSn Data

P4

Meng-Ru Ho, Kuo-Wang Tsai and Wen-Chang Lin. Pseudo? Regulation of Young Duplicated Genes in Human

P5

Vindyashree C. Sequence and conformational analysis of AgrD peptides. Implications: bacterial studies in Staphylococcus aureus

P6

Ahmad Mahmoody-Ghaidary, Cedric Chauve and Ladislav Stacho.

Theoretical advances on multichromosomal median computation

P7

Bruno Zeitouni, Valentina Boeva, Andrei Zinovyev, Kevin Bleakley, Isabelle Janoueix-Lerosey, Sophie Loeillet, Patricia Legoix-Ne, Alain Nicolas, Olivier Delattre and Emmanuel Barillot. SVDetect - FREEC: two complementary tools for the detection of genomic structural variants from deep sequencing data

P8

Magdalena Stock, Antje Burse and Wilhelm Boland. Annotation of Phaedon cochleariae’s transcriptome and establishment of BLAST servers and genome browser

P9

Sudeep Srivastava and Liang Chen. A two parameter generalized Poisson model to improve the analysis of RNA-seq data

P10

John Reid and Lorenz Wernisch. STEME: Efficient EM for motif search using suffix trees

P11

Xiaolin Hao, Rui Jiang and Ting Chen. CROP: Clustering 16S rRNA for OTU Prediction

P12

Florian Schatz, Sascha Möller and Manfred Schimmler. Smarti - A fast short read alignment algorithm Florian Schatz, Sascha Möller and Manfred Schimmler. Smarti - A fast short read alignment algorithm

P13

Matthew D. Whiteside, Matthew R. Laird and Fiona S. L. Brinkman.

Ortholuge: a tool for precise, high-throughput prediction of orthologs

P14

Daron Standley, Taeho Kim, Takashi Mino, Alexis Vandenbon, Yutaka Suzuki and Osamu Takeuchi. An Integrated Approach to RNA Regulatory Motif Discovery

P15

Ho-Lin Chen, Anne Condon and Hosna Jabbari. An O(n^5) Algorithm for MFE Prediction of Kissing Hairpins and 4-Chains in Nucleic Acids

RECOMB 2011 | 23

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Authors, Title

P16

Samart Wanchana, Sarah Covshoff, Rowan Sage, Gane Wong, Julian Hibberd and Richard Bruskiewich. Cloud-Based High-Throughput Comparative Analysis of Plant Species Genomes

P17

Dennis Wang, Augusto Rendon and Lorenz Wernisch. Cis-regulatory binding predicts gene expression across human tissues.

P18

Shatavia Morrison, Aurora Cain and Cynthia Gibas. Genosets: Pangenomic view of Vibrio vulnificus Biotype 1 E-genotypes strains through use of next gen sequencing

P19

Christian Frech and Nansheng Chen. Computational comparison of six Plasmodium genomes identifies putative human virulence genes

P20

Yaron Butterfield, Olena Morozova, Alexandra Maslova, Michael Blough, Suganthi Chittaranjan, Jennifer Chan, Nina Thiessen, Richard Varhol, Yongjun Zhao, Martin Hirst, Richard Corbett, Stephen Yip, Gregory Cairncross and Marco Marra. Integrative genomic and transcriptome analysis of oligodendroglioma using next generation sequencing technology

P21

Uri Weingart, Erez Persi and David Horn. Specific Peptides Facilitate Metagenomic Analysis

P22

Leonid Zaslavsky, Boris Fedorov, Azat Badretdin, Yiming Bao, James Brister, Stacy Ciufo, William Klimke, Kathleen O’Neill, Alexandre Souvorov and Tatiana Tatusova. Visualizing Multiscale Complexity and Features of Biological Sequence Datasets

P23

Sandra Smieszek, Paul Devlin and Alberto Paccana. Towards a programming code of circadian clock in plants

P24

Murray Patterson. The Gapped Consecutive-Ones Property

P25

Jung Eun Shim and Insuk Lee. Network-guided prediction of functiondriven domains

P26

Annika Kreuchwig, Gunnar Kleinau, Franziska Kreuchwig, Catherine L. Worth and Gerd Krause. Interactive online toolbox for sequencestructure-function analysis based on comprehensive mutation data

P27

Kevin Silverstein, Kenneth Beckman, Matthew Bower, Kari Bunjer, Matthew Schomaker, Teresa Kemmer, Lisa Schimmenti, Sophia Yohe, Randolph Peterson, Amy Karger, Monika Roychowdhury and Bharat Thyagarajan. Optimization of Bait Selection for Sequence Capture Arrays

P28

Ting Gong, Nicole Hartmann, Isaac Kohane, Volker Brinkmann, Bolan Linghu, Frank Staedtler, Martin Letzkus and Joseph Szustakowski.

Computational Deconvolution of Complex Transcriptomics Data from Clinical Trials

24 | RECOMB 2011

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Authors, Title

P29

Shailesh Tripathi and Frank Emmert-Streib. Comparing the influence of the sample size on the differential expression of pathways on univariate and multivariate methods

P29

Francesca Cordero, Daniele Manini, Andras Horvath and Gianfranco Balbo. Simplification of a complex signal transduction model by the application of invariants and flow equivalent server

P30

Elena Rivas and Sean Eddy. Probabilistic modeling improves RNA secondary structure prediction

P31

Ying Zhang, Mark Romanish and Dixie Mager. Finding TransposonSensitive Zones in Mammalian Introns

P32

Amin Emad, Wei Dai and Olgica Milenkovic. Protein-protein interaction prediction using non-linear matrix completion methods

P33

Jaeyoung Kim, Miyoung Shin, Munpyo Hong and Erkhembayar Jadamba. A SNP Ranking Method Using Gene Relation Network Derived from Literature for Genome-Wide Association Study

P34

Jianlin Cheng, Zheng Wang and Jesse Eickholt. Designing and Benchmarking the MULTICOM Protein Structure Prediction System

P35

Jea Woon Ryu, Byeol Na Park, Sung Jin Cho, Jun Ho Park, Jae Soo Yoo and Hak Yong Kim. Identification of putative domains that suppress cancer cell growth from cancer target proteins

P36

Tobias Petri, Robert K端ffner and Ralf Zimmer. Experiment Specific Expression Patterns

P37

Byeol Na Park, Sung Jin Cho, Jun Ho Park, Jae Soo Yoo and Hak Yong Kim. Transcriptional regulation of cancer-related target proteins based on microRNAs

P38

Jurgen F. Nijkamp, Marcel A. Van Den Broek, Marcel J.T. Reinders, Jean-Marc Daran and Dick De Ridder. Whole genome sequencing, assembly and annotation of the Saccharomyces cerevisiae strain CEN. PK 113-7D

P39

Louella Vasquez and Sach Mukherjee. Exploring early drivers of stemcell reprogramming by an integrative statistical approach

P40

Ratna Prabha, Dhananjaya Pratap Singh, Alok Srivastava and Dilip Arora. Codon selection pattern in Thermosynechococcus elongatus genome

P41

Yves Gagnon, Mathieu Blanchette and Nadia El-Mabrouk. Evolution by Whole Genome Duplication

P42

Babak Alipanahi Ramandi, Nathan Krislock, Ali Ghodsi, Henry Wolkowicz, Logan Donaldson and Ming Li. SPROS: An SDP-Based Protein Structure Determination from NMR Data

P43

Florian Hahne, Remi Terranova, Jonathan Moggs, Olivier Grenet and David Heard. Locus-specific DNA methylation analysis via amplicon deep sequencing

RECOMB 2011 | 25

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Authors, Title

P44

Andrew Parker, Karl Griswold and Chris Bailey-Kellogg. Functional deimmunization of therapeutic proteins by IP^2 (Integer Programming for Immunogenic Proteins)

P45

Ole Schulz-Trieglaff, Matthew Hims, Niall Gormley, Geoffrey Smith and Dirk Evers. Assembling whole genomes using Illumina mate pair reads

P46

Patrick Schmid, Nathan Palmer, Isaac Kohane and Bonnie Berger.

Building Large-Scale Gene Expression Classification Databases Using Active Learning

P47

Alex Pankov, Raymond Cavalcante, Daniel Dewoskin, Rob Scharein, Catherine Park, Mariel Vazquez and Javier Arsuaga. Using Computational Algebraic Topology to Characterize Chromosomal Instability in Cancer

P48

Meromit Singer, Alexander Engstroem, Alexander Schoenhuth and Lior Pachter. Determining coding CpG islands by identifying regions significant for pattern statistics on Markov chains

P49

Richard Varhol, Tina Wong, Irene Li, Margret Asgeirsdottir, Yaron Butterfield, Richard Corbett, Anthony Fejes, Greg Stazyk, Inanc Birol and Steven Jones. An I ntegrated Database And Viewer For Tracking Illumina and SOLiD Sequencing and Analysis

P50

Saman Vaisipour, Russell Greiner, David Wishart, Meysam Bastani and Chun-Nam Yu. Learning Predictors by Integrating Multiple Microarray Datasets

P51

Heesun Shin, Mandeep Takhar, Zsuzsanna Hollander, Janet WilsonMcmanus, Raymond Ng, Robert Balshaw, Paul Keown, Robert Mcmaster, Bruce Mcmanus and Scott Tebbutt. Exploratory multivariate analysis of peripheral whole blood gene expression data in organ transplantation

P52

Jesse Gillis and Paul Pavlidis. Multifunctionality drives gene characterization: A re-evaluation of hubs and promiscuity in gene function prediction

P53

Elena Peterson, Jeffrey Jensen, Hyunjoo Walker, Alexandra SchrimpeRutledge, Lee Ann Mccue, Samuel Payne, Joshua Adkins and BobbieJo Webb-Robertson. A Visualization and Evaluation Platform to Facilitate Prokaryotic Proteogenomic data analysis – VESPA

P54

Warren Cheung, Francis Ouellette and Wyeth Wasserman. MeSHOPs: Medical Subject Heading Overrepresentation Profiles

P55

Eugene Bolotin, Karthikeyani Chelappa, Wendy Hwang-Verslues, Chuhu Yang and Frances Sladek. HNF4A Transcription Factor Binding Sequences are Widespread in Alu Repeats

P56

Leon French and Paul Pavlidis. Relationships between gene expression and brain wiring in the adult rodent brain

26 | RECOMB 2011

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Authors, Title

P57

Jason Wong, Luke Hesson, Mathew Sloane, John Pimanda, Michael Bourke, Nicholas Hawkins and Robyn Ward. Computational identification of universal alterations in DNA methylation and nucleosome positioning in a matched normal/tumor sample

P58

Samuel Handelman, Js Verducci, Jj Kwiek, Sb Kumar and Da Janies.

GENPHEN: Genotype/Phenotype Association with Reference to Phylogeny

P59

Sharon Bruckner, Tim Conrad and Christof Schuette. Understanding biological networks with the random walker’s perspective

P60

Yasuhito Inoue. Proteome-wide classification and identification of transmembrane protein sequences in plant genomes

P61

Jocelyne Bruand, Theodore Alexandrov, Srinivas Sistla, Maxence Wisztorski, CĂŠline Meriaux, Michael Becker, Michel Salzet, Isabelle Fournier, Eduardo Macagno and Vineet Bafna. Exploring MS Imaging Data in a semi-supervised and interactive manner.

P62

Raheleh Salari and Teresa M Przytycka. The effect of SNPs on Boltzmann distribution for RNA secondary structure

P63

Mark Seligman and Chris Fraley. Model-averaged L1-penalized regression for biological data sets

P64

Raymond Lim and Paul Pavlidis. Wide-scale Comparison of Transcriptome Data

P65

Armando Solis. Optimal Use of Protein Structural Data for KnowledgeBased Potentials

P66

Andrew Roth, Samuel Aparicio and Sohrab Shah. Detecting Somatic Mutation In Tumour/Normal Paired Sample Sequence Data

P67

Richard Jang, Xin Gao and Ming Li. A Graph-based Peak Walking Algorithm for the Chemical Shift Mapping of Peaks in Serially Titrated 15N-HSQC NMR Spectra

P68

Tiffany J. Chen, Matthew R. Clutter, Nikesh Kotecha, Garry P. Nolan and Serafim Batzoglou. Automatically Finding Leukemic Cells that React Differently to Chemotherapeutics

P69

Seokjong Yu, Junho Park, Jihee Lee, Jongtae Lim, Weiwei Bao, Mikyoung Kim, Hyunju Kim, Mirim Jo, Jeawoon Ryu, Hakyong Kim and Jaesoo Yoo. ezBioNet: a Modeling and Simulation System for Biological Reaction Networks

P70

Kana Shimizu and Koji Tsuda. SlideSort: A fast and exact tool for finding all similar pairs from next-generation sequencing data

P71

Seokjong Yu, Junho Park, Jihee Lee, Jongtae Lim, Weiwei Bao, Mikyoung Kim, Hyunju Kim, Mirim Jo and Jaesoo Yoo. A Simulation for the G-Protein Coupled Receptor Signaling Model

RECOMB 2011 | 27

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Authors, Title

P72

Junho Park, Seokjong Yu, Jihee Lee, Jongtae Lim, Weiwei Bao, Mikyoung Kim, Hyunju Kim, Mirim Jo, Jeawoon Ryu, Hakyong Kim and Jaesoo Yoo. Design and Implementation of a Protein and Disease Retrieval Services System Based on Integrated Databases

P73

Chen Li, Masao Nagasaki, Chuan Hock Koh and Satoru Miyano.

Parameter estimation of a neuronal fate decision simulation model in C. elegans using online model checker: a high-level Petri net approach

P74

Yilong Li, Eevi Kaasinen, Miika Mehine, Taru Koski and Lauri A. Aaltonen.

Genetic changes associated with uterine leiomyoma

P75

Nitendra Sahu and Dv Kohli. Pharmacophore modeling and 3D-QSAR of novel chalcone derivatives as Plasmodium falciparum growth inhibitors

P76

Slim Fourati, Carolyn Nessim, Michael Hallett and Sylvie Mader. Geneexpression signatures predicting therapeutic response of breast tumors to tamoxifen

P77

Vicky Choi, Chunfang Zheng and David Sankoff. Maximal Strip Recovery based on Interval Graphs

P78

Markus Bauer, Anthony Cox and Dirk Evers. Comparison of BWT Construction Algorithms for Very Large Read Collections

P79

Aurora Cain, Adam Price, Shatavia Morrison, Robert Kosara and Cynthia Gibas. Visualization-Driven Analytical System for Comparative Microbial Genomics

P80

Charlotte Ng, Susanna Cooke, Kevin Howe, Scott Newman and James Brenton. Genomic instability and evolution in high-grade serous ovarian cancers

P81

Xianlong Wang, Dongqing Huang, Chenwei Lin, Brian Piening, Amanda Paulovich and Pei Wang. A DNA Copy Number Co-deletion Network Identifies Genetic Interactions

P82

Jonas Paulsen and Eivind Hovig. Computational aspects of threedimensional genomics

P83

Joseph Herman, Ádám Novák, Rune Lyngsø and Jotun Hein. Efficient calculation of a representative multiple sequence alignment from posterior samples

P84

Adam Sardar and Julian Gough. Horizontal Gene Transfer of Protein Domain Architectures

P85

Damian Wójtowicz, Fedor Kouzine, Arito Yamane, Craig J. Benham, Rafael Casellas, David Levens and Teresa M. Przytycka. Genome-wide mapping and computational analysis of non-B DNA structures in vivo

P86

Matt Oates, Julian Gough and Alistair Hetherington. An Exhaustive Search for the Inositol 1,4,5-triphosphate Receptor Protein in Plants

P87

Mahboubeh Ghoryshi. Elastin Polymorphism Associated With Increased Risk Thoracic Aortic Aneurysm and Dissection

28 | RECOMB 2011

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Authors, Title

P88

Oksana Korol and Marcel Turcotte. Module Inducer – a tool to automatically extract knowledge from biological sequences

P89

Steve Goldstein and David Schwartz. De Bruijn graph assembly for optical maps

P90

Stale Nygard, Trond Reitan, Trevor Clancy, Vegard Nygaard, Johannes Bjørnstad, Biljana Skrbic, Theis Tønnessen, Geir Christensen and Eivind Hovig. Identifying pathogenic signaling and regulatory networks by integrating microarray data with prior knowledge

P91

Allen Chen, Christopher Lin, Janet Luo, Jack Chen, Joy Chen, Eleanor Wong, Javier Arsuaga, Mariel Vazquez, Caoan Wang and Rainer Sachs. Neanderthal sharing haplotypes and gene flow in modern humans

P92

Erin E. Gill, Geoff L. Winsor, Matthew R. Laird, Karin Breuer, Shannan J. Ho Sui, Nancy Y. Yu, Raymond Lo, Robert E. Hancock, David J. Lynn and Fiona S. L. Brinkman. Computational Approaches and Tools for Infectious Disease Bioinformatics

P93

Bonnie Kirkpatrick and Kristian Stevens. Efficiently Constructing Phylogenies from Partial Characters

P94

Jin Zhang and Yufeng Wu. Finding Deletions with Exact Break Points from Noisy Low Coverage Paired-end Short Sequence Reads

P95

Andrew T. Kwon, David J. Arenillas, Rebecca Hunt Newbury and Wyeth W. Wasserman. Evolutionarily Conserved Regulatory Programs

P96

Nitin Udpa, Dan Zhou, Gabriel Haddad and Vineet Bafna. Exploring Tests of Selection in Pooled Data

P97

Rebecca Hunt Newbury, David J. Arenillas, Andrew T. Kwon and Wyeth W. Wasserman. Beware of genomic nucleotide composition while hunting transcription factor binding sites in ChIP-based experiments

P98

Fong Chun Chan, Sanja Rogic and Randy Gascoyne. Detection of Differential Splicing Between Two Groups Using Gene Expression Arrays

P99

Sandhya Balasubramanian, Dinnanath Sulakhe, Eduardo Berrocal, Conrad Gilliam and Natalia Maltsev. Analysis of complex disorders from the systems biology perspective

P100

Andrew Mcpherson, Chunxiao Wu, Iman Hajirasouliha, Fereydoun Hormozdiari, Faraz Hach, Anna Lapuk, Stanislav Volik, Sohrab Shah, Colin Collins and S. Cenk Sahinalp. Comrad: a novel algorithmic framework for the integrated analysis of RNA-Seq and WGSS data

P101

Mahdi Belcaid, Guylaine Poisson, David Schanzenbach and Kyungim Baek. Inferring Hierarchical Population Structure through a Consensus of Significant Evolutionary Events

P102

Jiayin Wang, Li Wei and Yufeng Wu. A Graph Synchronization Model for Identifying SNP Interactions in Disease Association Studies

P103

Yaron Butterfield, Richard Corbett, Steven J.M. Jones and Inanc Birol.

Post analysis of SNV calls: Annotating, filtering and quality assessment

RECOMB 2011 | 29

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Authors, Title

P104

Elizabeth Permina, Julia Medvedeva and Vsevolod Makeev. Modulon Identification for Stress and Housekeeping Regulons Using Bacterial Gene Expression Array Data

P105

Christine Lo, Nitin Udpa and Vineet Bafna. Haplotype Phasing with Single Genome Amplification

P106

Bhavjinder K. Dhillon, Shannan J. Ho Sui, Jennifer L. Gardy, Robert C. Brunham, Patrick Tang and Fiona S.L. Brinkman. Bioinformatics Approaches for Analyzing Short-Read Illumina Sequences of Whole Mycobacterium tuberculosis Genomes from an Outbreak

P107

Adnan Sljoka. Predicting flexibility and motions of proteins using rigidity theory

P108

Matthew Ruffalo, Mehmet Koyuturk and Thomas Laframboise.

Comparative analysis of algorithms for next-generation sequencing read alignment

P109

Li Wei and Shaojie Jiao. Identifying SNP Interactions with Multiple Phenotypes using Fish-Agent Logic Regression

P110

Virginie Bernard, David J. Arenillas, Dimas Yusus and Wyeth W. Wasserman. Exome and genome analyses: Prioritizing the variant calling

P111

Virginie Bernard, David J. Arenillas, Dimas Yusus and Wyeth W. Wasserman. Exome and genome analyses: Prioritizing the variant calling

P112

Chen Yanover and Philip Bradley. Large-scale characterization of binding landscapes using structural simulations: application to C2H2 zinc-finger transcription factors and MHC proteins

P113

Chris Fjell, Jennifer Tan, Matt Mayer and Robert Hancock. MetaGEX: a systems biology meta-analysis toolkit and data repository with web server interface

P114

Dariusz Przybylski, Iain Maccallum, Sante Gnerre, Filipe J. Ribeiro, Joshua N. Burton, Bruce J. Walker, Ted Sharpe, Giles Hall, Terrance P. Shea, Sean Sykes, Aaron M. Berlin, Daniel Aird, Maura Costello, Riza Daza, Louise Williams, Robert Nicol, Andreas Gnirke, Chad Nusbaum, Eric S. Lander and David B. Jaffe. High-quality draft assemblies of large and small genomes from massively parallel DNA sequence data

P115

Shengsheng Zhang, Shib Basu, Mikyong Lee, David Acland, Judith Bowler, Kathryn Brocklehurst, Steve Elvidge, Philip Green, Peter Kilby, Elaine Mackay, Jo Mattocks, John Ray and Ravi Tailor. Protein Modeling and Engineering Increased Pepsin Susceptibility into a HeatTolerant Variant of Escherichia coli Phytase

P116

Hang He and Huangdong Meng. A Novel Data Mining Approach for Detecting the Mutated Peptides

P117

Christopher Bun and Catherine Putonti. Performing Phylogenomic Analysis on Unassembled Short-Read Genome Sequences

30 | RECOMB 2011

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Authors, Title

P118

Lin He, Xi Han and Bin Ma. An Efficient De Novo Sequencing Algorithm for the Identification of Modified Peptides from MS/MS spectra

P119

Layla Oesper, Sarah Aerni, Ryan Drebin and Benjamin J. Raphael.

Reconstructing Cancer Genome Organization from Paired End Sequencing

P120

Mai Hamdalla, David Grant, Sanguthevar Rajasekaran, Reda Ammar and Dennis Hill. Efficient Prediction of Biological Structures from Molecular Formulas

P121

Richard Morgan, Yvette Luyten and Geoffrey Wilson. RATIONAL ALTERATION OF DNA RECOGNITION: SIMPLE MUTATIONS THAT CHANGE TYPE IIG RESTRICTION ENZYME SPECIFICITY

P122

Lucas Swanson, Inanc Birol, S Cenk Sahinalp, Gordon Robertson, Karen Mungall, Readman Chiu, Shaun Jackman, Jenny Qian, Sam Lee, Deniz Yorukoglu, Rong She, Yongjun Zhao, Richard Moore, Marco Marra, Steven Jm Jones, Aly Karsan and Pamela Hoodless. Detecting Chimeric Transcripts in RNA-seq Data

P123

Leila Rahnama and Stephane Aris-Brosou. Dating the adaptation of H1N1 and H3N2 subtypes of Influenza A viruses in different hosts

The Chip is the Machine.

www.iontorrent.com

32 | RECOMB 2011

Sponsors & Exhibitors Platinum Sponsors Genome British Columbia

Canadian Institutes of Health Research

Gold Sponsors Natural Sciences and Engineering Research Council of Canada Simon Fraser University

Pacific Institute for the Mathematical Sciences

International Society for Computational Biology

MITACS

Ion Torrent

BC Cancer Foundation

Silver Sponsor Pacific Biosciences

RECOMB 2011 | 33

Exhibitors CRC Press/Taylor & Francis Group ISCB (International Society for Computational Biology) MITACS Inc. Springer

34 | RECOMB 2011

Notes