Wednesday, August 11, 2010
17:00-19:00 Registration Reception desks - Floor 0

Thursday, August 12, 2010
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
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

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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Friday, August 13, 2010
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
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Saturday, August 14, 2010
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)
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Sunday, August 15, 2010
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
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