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All events in Fairmont Hotel Vancouver.
Sunday March 27
17:00-19:00 |
Registration
Opens |
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19:00-21:00 |
Welcome Reception |
Monday March 28
8:45-9:00 |
Opening
Remarks |
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9:00-10:40 |
Session Chair: Cenk
Sahinalp (SFU) |
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9:00-10:00 |
KEYNOTE:
Dr. Elaine Mardis (WUSTL) |
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10:00-10:20 |
Hapsembler:
An assembler for highly polymorphic
genomes
Nilgun Donmez (U. Toronto) and Michael
Brudno |
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10:20-10:40 |
Opera: Reconstructing
optimal genomic scaffolds with high-throughput
paired-end sequences
Gao Song (NUS), Niranjan Nagarajan and
Wing-Kin Sung |
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10:40-11:00 |
BREAK |
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11:00-12:00 |
Session Chair: Cenk
Sahinalp (SFU) |
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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 |
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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 |
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11:40-12:00 |
HIGHLIGHT:
Discovery and characterization of
chromatin states for systematic annotation
of the human genome
Jason Ernst and Manolis Kellis (MIT) |
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12:00-13:30 |
LUNCH |
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13:30-14:10 |
Session Chair: Michael
Brudno (U. Toronto) |
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13:30-13:50 |
IsoLasso: A
LASSO Regression Approach to RNA-Seq
Based Transcriptome Assembly
Wei Li (UC Riverside), Jianxing Feng
and Tao Jiang |
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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 |
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14:10-14:30 |
BREAK |
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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)
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16:30-16:50 |
BREAK |
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16:50-18:10 |
Session Chair: Michal
Linial (Hebrew University of Jerusalem) |
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16:50-17:10 |
Blocked Pattern
Matching Problem and its Applications
in Proteomics
Julio Ng (UCSD), Amihood Amir and Pavel
Pevzner |
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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 |
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17:30-17:50 |
Computing Fragmentation
Trees from Metabolite Multiple Mass
Spectrometry Data
Kerstin Scheubert (U. Jena), Franziska
Hufsky, Florian Rasche and Sebastian
Bocker |
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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 |
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18:10-19:40 |
Poster Session |
Tuesday March 29
9:00-10:00 |
Session
Chair: Teresa Przytycka (NCBI) |
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9:00-9:20 |
Disease Gene
Prioritization Based on Topological
Similarity in Protein-Protein Interaction
Networks
Sinan Erten (CWRU), Gurkan Bebek and
Mehmet Koyuturk |
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9:20-9:40 |
Optimally Orienting
Physical Networks
Dana Silverbush (Tel Aviv U.), Michael
Elberfeld and Roded Sharan |
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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 |
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10:00-10:20 |
BREAK |
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10:20-12:00 |
Session Chair: Eleazar
Eskin (UCLA) |
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10:20-11:20 |
KEYNOTE:
Dr. Daphne Koller (Stanford) |
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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 |
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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 |
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12:00-13:30 |
LUNCH |
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13:30-15:30 |
Session Chair: Michael
Brent (WUSTL) |
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13:30-14:30 |
KEYNOTE:
Dr. Karen Nelson (Craig Venter Inst.) |
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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 |
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15:10-15:30 |
Identifying
Branched Metabolic Pathways by Merging
Linear Metabolic Pathways
Allison Heath (Rice), George Bennett
and Lydia Kavraki |
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15:30-15:50 |
BREAK |
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15:50-17:10 |
Session Chair: Ron
Shamir (Tel Aviv U.) |
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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) |
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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 |
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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 |
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16:50-17:10 |
Experiment Specific
Expression Patterns
Tobias Petri (L.M. U. Munich), Robert
Kuffner and Ralf Zimmer |
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17:10-17:30 |
BREAK |
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17:30-18:45 |
Business Meeting |
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18:45-20:15 |
Poster Session |
Wednesday March 30
9:00-10:00 |
Session
Chair: Bonnie Berger (MIT) & Mona
Singh (Princeton) |
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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 |
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9:20-9:40 |
Protein Loop
Closure using Orientational Restraints
from NMR Data
Chittaranjan Tripathy (Duke), Jianyang
Zeng, Pei Zhou and Bruce Donald |
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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 |
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10:00-10:20 |
BREAK |
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10:20-12:00 |
Session Chair: Can
Alkan (U. Washington) |
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10:20-11:20 |
KEYNOTE:
Dr. Marco Marra (BC Genome Sciences
Centre) |
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11:20-11:40 |
De novo Discovery
of Mutated Driver Pathways in Cancer
Fabio Vandin (Brown), Eli Upfal and
Ben Raphael |
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11:40-12:00 |
Increasing Power
of Groupwise Association Test with Likelihood
Ratio Test
Jae Hoon Sul (UCLA), Buhm Han and Eleazar
Eskin |
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12:00-13:30 |
LUNCH |
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13:30-15:30 |
Session Chair: Sorin
Istrail (Brown) |
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13:30-14:30 |
KEYNOTE:
Dr. Joe Nadeau (Inst. Systems Biology) |
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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 |
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15:10-15:30 |
Nonparametric
combinatorial sequence models
Fabian Wauthier (UC Berkeley), Michael
Jordan and Nebojsa Jojic |
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15:30-15:50 |
BREAK |
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15:50-17:10 |
Session Chairs:
Ben Raphael (Brown) |
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15:50-16:10 |
Haplotype Reconstruction
in Large Pedigrees with Many Untyped
Individuals
Xin Li (CWRU) and Jing Li |
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16:10-16:30 |
Pedigree Reconstruction
using Identity by Descent
Bonnie Kirkpatrick (UC Berkeley), Shuai
Cheng Li, Richard M. Karp and Eran Halperin |
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16:30-16:50 |
Algorithms for
MDC-based Multi-locus Phylogeny Inference
Yun Yu (Rice), Tandy Warnow and Luay
Nakhleh |
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16:50-17:10 |
An optimization-based
sampling scheme for phylogenetic trees
Navodit Misra (MPI MG), Guy Blelloch,
R. Ravi and Russell Schwartz |
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17:10 |
Conference Banquet |
Thursday March 31
9:00-10:00 |
Session
Chair: William Noble (U. Washington) |
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9:00-9:20 |
Variable selection
through correlation sifting
Jim Huang (Microsoft Research) and Nebojsa
Jojic |
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9:20-9:40 |
Optimization
of combinatorial mutagenesis
Andrew Parker (Dartmouth), Karl Griswold
and Chris Bailey-Kellogg |
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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 |
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10:00-10:20 |
BREAK |
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10:20-12:00 |
Session Chair: Vineet
Bafna (UCSD) |
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10:20-11:20 |
KEYNOTE:
Dr. Evan Eichler (U. Washington) |
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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 |
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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 |
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12:00-13:30 |
LUNCH |
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13:30-15:10 |
Session Chair: Martin
Vingron (CMB) |
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13:30-13:50 |
Rich Parameterization
Improves RNA Structure Prediction
Shay Zakov (BGU), Yoav Goldberg, Michael
Elhadad and Michal Ziv-Ukelson |
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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 Context-Sensitive
Indels
Glenn Hickey (McGill) and Mathieu Blanchette |
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14:30-14:50 |
PSAR: Measuring
Multiple Sequence Alignment Reliability
by Probabilistic Sampling
Jaebum Kim (UIUC) and Jian Ma |
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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 |
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15:10-15:30 |
BREAK |
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15:30-16:30 |
Session Chairs:
Rolf Backofen (U. Freiburg) |
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15:30-15:50 |
Metric Labeling
and Semi-metric Embedding for Protein
Annotation Prediction
Emre Sefer (U. Maryland) and Carl Kingsford |
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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 |
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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 |
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16:30-16:45 |
Closing Remarks |
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16:45 |
Conference Adjourns |
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