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All events in Fairmont Hotel Vancouver.

 

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 high-throughput 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

   

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:
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: Michal Linial (Hebrew University of Jerusalem)

   

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

 

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 (Pfizer), 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

   

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

 

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

   

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

 

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

Optimization of combinatorial mutagenesis
Andrew Parker (Dartmouth), Karl Griswold and Chris Bailey-Kellogg

   

9:40-10:00

HIGHLIGHT: Seeing More Is Knowing More: V3D Enables Real-time 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 paired-end sequenced genomes
Fereydoun Hormozdiari (SFU), Iman Hajirasouliha, Andrew McPherson, Evan Eichler and S. Cenk Sahinalp

   

11:40-12:00

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

   

14:10-14:30

A Probabilistic Model For Sequence Alignment with Context-Sensitive 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 Ensemble-Based 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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