 |
|
| 17:00-19:00 |
Registration |
Reception desks - Floor 0 |
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|
| 8:00-18:00 |
Registration |
Reception desks - Floor 0 |
|
| 8:45-9:00 |
Conference Welcome |
Auditorium I - Floor 0 |
| 9:00-10:40 |
Session Chair: Simon Kasif
|
| 9:00-10:00 |
KEYNOTE: Isaac Kohane
Preventing the incidentalome and personalizing medicine through instrumentation of the healthcare enterprise
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| 10:00-10:20 |
Paper Presentation
HLA type inference via haplotypes identical by descent
Manu Setty, Alexander Gusev and Itsik Pe'er |
| 10:20-10:40 |
Paper Presentation
The Clark Phase-able Sample Size Problem: Long-range Phasing and Loss of Heterozygosity in GWAS
Bjarni Halldorsson, Derek Aguiar, Ryan Tarpine and Sorin Istrail
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|
| 10:40-11:00 |
Break |
Main Hall - Floor 1 |
|
| 11:00-12:00 |
Session Chair: Roded Sharan
|
Auditorium I - Floor 0 |
| 11:00-11:20 |
Highlights Presentation
Deciphering the Swine-flu pandemics of 1918 and 2009
Richard Goldstein, Mario dos Reis, Asif Tamuri and Alan Hay
|
| 11:20-11:40 |
Paper Presentation
Admixture Aberration Analysis: Application to mapping in admixed population using pooled DNA
Sivan Bercovici and Dan Geiger |
| 11:40-12:00 |
Paper Presentation
Subnetwork State Functions Define Dysregulated Subnetworks in Cancer
Salim A. Chowdhury, Rod K. Nibbe, Mark R. Chance and Mehmet Koyuturk |
|
| 12:00-13:30 |
Lunch |
Espaço Tejo Restaurant |
|
| 13:30-15:30 |
Session Chair: Sorin Istrail
| Auditorium I - Floor 0 |
| 13:30-14:30 |
KEYNOTE: Mona Singh
Towards the dynamic interactome |
| 14:30-14:50 |
Paper Presentation
An Algorithmic Framework for Predicting Side-Effects of Drugs
Nir Atias and Roded Sharan
|
| 14:50-15:10 |
Paper Presentation
Algorithms for Detecting Significantly Mutated Pathways in Cancer
Fabio Vandin, Eli Upfal and Benjamin Raphael |
| 15:10-15:30 |
Paper Presentation
Extracting between-pathway models from E-MAP interactions using expected graph compression
David Kelley and Carl Kingsford
|
|
| 15:30-15:50 |
Break |
Main Hall - Floor 1 |
|
| 15:50-18:30 |
Session Chair: Serafim Batzoglou
| Auditorium I - Floor 0 |
| 15:50-16:10 |
Paper Presentation
Incremental Signaling Pathway Modeling by Data Integration
Geoffrey Koh, David Hsu and P. S. Thiagarajan |
| 16:10-16:30 |
Paper Presentation
Simultaneous Identification of Causal Genes and Dys-regulated Pathways in Complex Diseases
Yoo-Ah Kim, Stefan Wuchty and Teresa Przytycka |
| 16:35-18:30 |
SPECIAL PANEL
Genomics in Medicine (Isaac Kohane - Moderator)
Confirmed participants: Chris Bakal, Simon Kasif, David Gifford, Doron Lancet, Klaus Lindpainter and Eitan Rubin |
|
| 18:30-20:00 |
Reception |
Main Hall - Floor 1 |
|
| 19:00-20:30 |
Poster Session A |
Poster Area - Floors 0 and 1 |
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| Top |
|
|
| 9:00-10:00 |
Session Chair: Michael Brudno
|
Auditorium I - Floor 0 |
| 9:00-9:20 |
Paper Presentation
Gapped Spectral Dictionaries and Their Applications for Databases Searches of Tandem Mass Spectra
Kyowon Jeong, Sangtae Kim, Nuno Bandeira and Pavel Pevzner |
| 9:20-9:40 |
Paper Presentation
Proteome Coverage Prediction for Integrated Proteomics Datasets
Manfred Claassen, Ruedi Aebersold and Joachim M. Buhmann |
| 9:40-10:00 |
Paper Presentation
Hierarchical Generative Biclustering for MicroRNA Expression Analysis
José Caldas and Samuel Kaski |
|
| 10:00-10:20 |
Break |
Main Hall - Floor 1 |
|
| 10:20-12:00 |
Session Chair: Martin Vingron
|
Auditorium I - Floor 0 |
| 10:20-11:20 |
KEYNOTE: David Bartel
MicroRNAs and other small regulatory RNAs |
| 11:20-11:40 |
Paper Presentation
Discovering Regulatory Overlapping RNA Transcripts
Timothy Danford, Robin Dowell and David Gifford
|
| 11:40-12:00 |
Paper Presentation
Time and space efficient RNA-RNA interaction prediction via sparse folding
Raheleh Salari, Mathias Mohl, Sebastian Will, S. Cenk Sahinalp and Rolf Backofen |
|
| 12:00-13:30 |
Lunch |
Espaço Tejo Restaurant |
|
| 13:30-15:30 |
Session Chair: David Gifford
|
Auditorium I - Floor 0 |
| 13:30-14:30 |
KEYNOTE: Norbert Perrimon
Global analyses of signal transduction pathways |
| 14:30-14:50 |
Highlights Presentation
Allegro: Analyzing expression and sequence in concert to discover regulatory programs
Ron Shamir, Yonit Halperin, Chaim Linhart and Igor Ulitsky
|
| 14:50-15:10 |
Highlights Presentation
A Self-Regulatory System of Interlinked Signaling Feedback Loops Controls Mouse Limb Patterning
Felix Naef, Rolf Zeller, Jean-Denis Benazet and Mirko Bischofberger
|
| 15:10-15:30 |
Highlights Presentation
Automated High-Dimensional Flow Cytometric Data Analysis
Saumyadipta Pyne, Xinli Hu, Kui Wang, Elizabeth Rossin, Tsung-I Lin, Lisa Maier, Clare Baecher-Allan, Geoffrey McLachlan, Pablo Tamayo, David Hafler, Philip De Jager and Jill Mesirov
|
|
| 15:30-15:50 |
Break |
Main Hall - Floor 1 |
|
| 15:50-18:00 |
Session Chair: Bonnie Berger
| Auditorium I - Floor 0 |
| 15:50-16:10 |
Paper Presentation
Predicting nucleosome positioning using multiple evidence tracks
Sheila Reynolds, Zhiping Weng, Jeff Bilmes and William Stafford Noble
|
| 16:10-16:30 |
Paper Presentation
SubMAP: Aligning metabolic pathways with subnetwork mappings
Ferhat Ay and Tamer Kahveci
|
| 16:35-18:00 |
SPECIAL PANEL
Regulatory RNAs (David Bartel - Moderator)
Confirmed Participants: Cecília Arraiano, Jan Gorodkin, Philipp Kapranov and Norbert Perrimon |
|
| 18:00-19:00 |
Business Meeting |
Room 1 - Floor 0 |
|
| 18:30-20:00 |
Poster Session B |
Poster Area - Floors 0 and 1 |
|
| Top |
|
|
| 9:00-10:40 |
Session Chair: Michal Linial
| Auditorium I - Floor 0 |
| 9:00-10:00 |
KEYNOTE: Philipp Kapranov
Direct sequencing of DNA and RNA using Helicos Single Molecule Sequencing to unravel biological questions |
| 10:00-10:20 |
Paper Presentation
naiveBayesCall: An efficient model-based base-calling algorithm for high-throughput sequencing
Wei-Chun Kao and Yun S. Song |
| 10:20-10:40 |
Paper Presentation
Poisson Margin Test for Normalisation Free Significance Analysis of NGS Data
Adam Kowalczyk, Justin Bedo, Thomas Conway and Bryan Beresford-Smith |
|
| 10:40-11:00 |
Break |
Main Hall - Floor 1 |
|
| 11:00-12:00 |
Session Chair: Vineet Bafna
| Auditorium I - Floor 0 |
| 11:00-11:20 |
Paper Presentation
A novel abundance-based algorithm for binning metagenomic sequences using l-tuples
Yu-Wei Wu and Yuzhen Ye |
| 11:20-11:40 |
Paper Presentation
Genovo: De Novo Assembly For Metagenomics
Jonathan Laserson, Vladimir Jojic and Daphne Koller |
| 11:40-12:00 |
Paper Presentation
Pathway-Based Functional Analysis of Metagenomes
Sivan Bercovici, Itai Sharon, Ron Pinter and Tomer Shlomi |
|
| 12:00-13:30 |
Lunch |
Espaço Tejo Restaurant |
|
| 13:30-15:30 |
Session Chair: Russell Schwartz
| Auditorium I - Floor 0 |
| 13:30-13:50 |
Paper Presentation
Accurate estimation of expression levels of homologous genes in RNA-seq experiments
Bogdan Pasaniuc, Noah Zaitlen and Eran Halperin
|
| 13:50-14:10 |
Paper Presentation
Inference of Isoforms from Short Sequence Reads
Jianxing Feng, Wei Li and Tao Jiang
|
| 14:10-14:30 |
Paper Presentation
IDBA - A Practical Iterative de Bruijn Graph De Novo Assembler
Yu Peng, Henry C.M. Leung, SM Yiu and Francis Chin |
| 14:30-14:50 |
Paper Presentation
Seed design framework for mapping AB SOLiD reads
Laurent Noé, Marta Gîrdea and Gregory Kucherov |
| 14:50-15:10 |
Paper Presentation
Compressing genomic sequence fragments using SlimGene
Christos Kozanitis, Chris Saunders, Semyon Kruglyak, Vineet Bafna and George Varghese |
| 15:10-15:30 |
Paper Presentation
MoGUL: Detecting Common Insertions and Deletions in a Population
Seunghak Lee, Eric Xing and Michael Brudno
|
|
| 15:30-15:50 |
Break |
Main Hall - Floor 1 |
|
| 15:50-16:50 |
Session Chairs: Arlindo Oliveira and Jadwiga Bienkowska
| Auditorium I - Floor 0 |
| 15:50-16:50 |
Selected Poster Presentations
Prioritizing Candidate Genes by Network Analysis of
Differential Expression using Machine Learning Approaches
Daniela Nitsch, Joana P. Gonçalves, Fabian Ojeda and Yves
Moreau
Autoimmune Disease Classification by
Inverse Association with SNP Alleles
Marina Sirota, Marc A. Schaub, Serafim Batzoglou, William H.
Robinson and Atul J. Butte
Gene regulation re-wired upon DNA damage
Ewa Szczurek, Florian Markowetz, Irit Gat-Viks, Przemyslaw Biecek, Jerzy Tiuryn and Martin Vingron
Evidence for Widespread microRNA Targeting in Drosophila Coding Regions
Michael Schnall-levin, Yong Zhao, Norbert Perrimon and Bonnie Berger
CRAVELA: a framework to identify and evaluate miRNA regulatory modules
Nuno Mendes, Ana Freitas, Ana Vasconcelos, Marie-France Sagot
Mutational pathways to reverse transcriptase inhibitor resistance in HIV
Glenn Lawyer, Andre Altmann, Alexander Thielen and Thomas Lengauer
|
|
| 16:50-17:00 |
Leave for Activities and Banquet (Oceanarium) |
|
| Top |
|
|
| 9:00-10:40 |
Session Chair: Ana Teresa Freitas
| Auditorium I - Floor 0 |
| 9:00-10:00 |
KEYNOTE: Cecília Arraiano
Post-transcriptional control of gene expression: RNA dictates the rules! |
| 10:00-10:20 |
Paper Presentation
On the Genealogy of Asexual Diploids
Fumei Lam, Charles H. Langley and Yun S. Song
|
| 10:20-10:40 |
Paper Presentation
Generalized Buneman pruning for inferring the most parsimonious multi-state phylogeny
Navodit Misra, Guy Blelloch, R Ravi and Russell Schwartz |
|
| 10:40-11:00 |
Break |
Main Hall - Floor 1 |
|
| 11:00-12:00 |
Session Chair: Cenk Sahinalp
| Auditorium I - Floor 0 |
| 11:00-11:20 |
Paper Presentation
Alignment-Free Phylogenetic Reconstruction
Constantinos Daskalakis and Sebastien Roch
|
| 11:20-11:40 |
Highlights Presentation
Genomic DNA k-mer spectra: Models and modalities
Benny Chor, David Horn, Yaron Levy, Nick Goldman and Tim Massingham
|
| 11:40-12:00 |
Highlights Presentation
Distinguishing direct versus indirect transcription factor-DNA interactions
Raluca Gordan, Alexander Hartemink and Martha Bulyk
|
|
| 12:00-13:30 |
Lunch |
Free choice (click for some suggestions) |
|
| 13:30-14:30 |
Session Chair: Teresa Przytycka
| Auditorium I - Floor 0 |
| 13:30-13:50 |
Paper Presentation
A new algorithm for improving the resolution of cryo-EM density maps
Michael Hirsch, Bernhard Schoelkopf and Michael Habeck |
| 13:50-14:10 |
Paper Presentation
Towards Automated Structure-based NMR Assignment
Richard Jang, Xin Gao and Ming Li
|
| 14:10-14:30 |
Paper Presentation
A Markov Random Field Framework for Protein Side-Chain Resonance Assignment
Jianyang Zeng, Pei Zhou and Bruce Donald |
|
| 14:30-14:50 |
Break |
Main Hall - Floor 1 |
|
| 14:50-16:20 |
Session Chairs: Serafim Batzoglou and Sorin Istrail
| Auditorium I - Floor 0 |
| 14:50-15:10 |
Paper Presentation
Cactus Graphs for Genome Comparisons
Benedict Paten, Mark Diekhans, Jian Ma, Bernard Suh and David Haussler |
| 15:10-15:30 |
Paper Presentation
Leveraging Sequence Classification by Taxonomy-based Multitask Learning
Christian Widmer, Jose Miguel Leiva-Murillo, Yasemin Altun and Gunnar Rätsch |
| 15:30-15:50 |
Paper Presentation
Dense Subgraphs with Restrictions and Applications to Gene Annotation Graphs
Barna Saha, Allison Hoch, Samir Khuller, Louiqa Raschid and Xiao-Ning Zhang |
| 15:50-16:20 |
Awards Ceremony |
| 16:20 |
Conference Adjourns |
|
| Top |
