ISMB 2008 ISCB

16th Annual
International Conference
Intelligent Systems
for Molecular Biology


Metro Toronto Convention Centre (South Building)
Toronto, Canada


 




Highlights Track
(as of June 16, 2008)

Highlights Track: HL01
Automated learning of generative models for subcellular location
Sunday, July 20 - 10:45 a.m. - 11:10 a.m.
Room: 718A
Presented by: Robert F Murphy, Carnegie Mellon University, US
Session Chair: Jaap Heringa
↑ TOP

Highlights Track: HL03
Automatic derivation of function prediction from de novo structure prediction for whole genomes
Sunday, July 20 - 11:15 a.m. - 11:40 a.m.
Room: 718A
Presented by: Richard Bonneau, New York University, US
Session Chair: Jaap Heringa
↑ TOP

Highlights Track: HL04
A Systems Biology Approach for Steady State Analysis of Signaling Pathways
Wednesday, July 23 - 11:15 a.m. - 11:40 a.m.
Room: 718B
Presented by: Sorin Draghici, Wayne State University, US
Session Chair: Burkhard Rost
↑ TOP

Highlights Track: HL05
Alternative Splicing and Protein Structure Evolution
Sunday, July 20 - 11:45 a.m. - 12:10 p.m.
Room: 718A
Presented by: Fabian Birzele, Ludwig Maximilians Universitt Mnchen, DE
Session Chair: Jaap Heringa
↑ TOP

Highlights Track: HL06
A network-based signaling mechanism of cancer developement and progression
Sunday, July 20 - 11:45 a.m. - 12:10 p.m.
Room: 718B
Presented by: Edwin Wang, National Research Council Canada, CA
Session Chair: Burkhard Rost
↑ TOP

Highlights Track: HL07
Local pairwise structural RNA alignments by pruning the dynamical programming matrix
Sunday, July 20 - 12:15 p.m. - 12:40 p.m.
Room: 718A
Presented by: Jan Gorodkin, University of Copenhagen, DK
Session Chair: Jaap Heringa
↑ TOP

Highlights Track: HL08
Universally Sloppy Parameter Sensitivities in Systems Biology
Sunday, July 20 - 12:15 p.m. - 12:40 p.m.
Room: 718B
Presented by: Christopher R. Myers, Cornell University, US
Session Chair: Burkhard Rost
↑ TOP

Highlights Track: HL09
Computational Approaches for the Analysis of Immunoglobulin Gene Rearrangement
Sunday, July 20 - 2:15 p.m. - 2:40 p.m.
Room: 718A
Presented by: Bruno A Gaeta, The University of New South Wales, AU
Session Chair: Nir Ben-Tal
↑ TOP

Highlights Track: HL10
Heat Shock Response in CHO Mammalian Cells Is Controlled by a Nonlinear Stochastic Process
Sunday, July 20 - 2:15 p.m. - 2:40 p.m.
Room: 718B
Presented by: Ovidiu Lipan, University of Richmond, US
Session Chair: Jill Mesirov
↑ TOP

Highlights Track: HL11
Predicting Protein Function with Hierarchical Phylogenetic Profiles.
Sunday, July 20 - 2:45 p.m. - 3:10 p.m.
Room: 718A
Presented by: Corin Yeats, University College London, UK
Session Chair: Nir Ben-Tal
↑ TOP

Highlights Track: HL13
Automated Protein Subfamily Identification and Classification
Sunday, July 20 - 3:15 p.m.- 3:40 p.m.
Room: 718A
Presented by: Kimmen Sjolander, University of California Berkeley, US
Session Chair: Nir Ben-Tal
↑ TOP

Highlights Track: HL14
De Novo identification of in Vivo Binding Sites from ChIP-chip Data
Sunday, July 20 - 3:15 p.m.- 3:40 p.m.
Room: 718B
Presented by: Victor X Jin, University of Memphis, US
Session Chair: Jill Mesirov
↑ TOP

Highlights Track: HL16
SherLoc: High-accuracy Prediction of Protein Subcellular Localization by Integrating Text and Protein Sequence Data
Sunday, July 20 - 3:45 p.m. - 4:10 p.m.
Room: 718B
Presented by: Hagit Shatkay, School of Computing, Queen's University, CA
Session Chair:
↑ TOP

Highlights Track: HL17
Towards Ontology-driven Navigation of the Lipid Bibliosphere and Mutation Literature
Monday, July 21 - 10:45 a.m. - 11:10 a.m.
Room: 718A
Presented by: Christopher J. O. Baker, Institute for Infocomm Research, SG
Session Chair: Andrey Rzhetsky
↑ TOP

Highlights Track: HL18
The Utilization of Redundancy by Genetic Networks
Monday, July 21 - 10:45 a.m. - 11:10 a.m.
Room: 718B
Presented by: Ran Kafri, Harvard Medical School, US
Session Chair: Trey Ideker
↑ TOP

Highlights Track: HL19
Toward the Demise of the Highest Scoring Paradigm
Monday, July 21 - 11:15 a.m. - 11:40 a.m.
Room: 718A
Presented by: Charles E. Lawrence, Brown University, US
Session Chair: Andrey Rzhetsky
↑ TOP

Highlights Track: HL20
Casting a Net for Kinases - Systematic Discovery of Cellular Phosphorylation Networks
Monday, July 21 - 11:15 a.m. - 11:40 a.m.
Room: 718B
Presented by: Rune Linding, Institute of Cancer Research, UK
Session Chair: Trey Ideker
↑ TOP

Highlights Track: HL21
Modelling Ion Channel Kinetics Using Voltage-Clamp Recordings and a Genetic Algorithm
Monday, July 21 - 11:45 a.m. - 12:10 p.m.
Room: 718A
Presented by: Meron Gurkiewicz, Bar-Ilan University, IL
Session Chair: Andrey Rzhetsky
↑ TOP

Highlights Track: HL22
A Systems Biology Analysis of the Drosophila Phagosome
Monday, July 21 - 11:45 a.m. - 12:10 p.m.
Room: 718B
Presented by: Joel Bader, Johns Hopkins University, US
Session Chair: Trey Ideker
↑ TOP

Highlights Track: HL23
Qualitative Biological Ontologies
Monday, July 21 - 12:15 p.m. - 12:40 p.m.
Room: 718A
Presented by: Thomas Bittner, State University of New York at Buffalo, US
Session Chair: Andrey Rzhetsky
↑ TOP

Highlights Track: HL24
eQED: an Efficient Method for Interpreting eQTL Associations Using Protein Networks
Monday, July 21 - 12:15 p.m. - 12:40 p.m.
Room: 718B
Presented by: Andreas Beyer, TU Dresden, Germany, DE
Session Chair: Trey Ideker
↑ TOP

Highlights Track: HL25
High-confidence Prediction of Global Interactomes Based on Genome-wide Coevolutionary Networks
Monday, July 21 - 2:15 p.m. - 2:40 p.m.
Room: 718A
Presented by: David Juan, Spanish National Cancer Research Centre, ES
Session Chair: Ivet Bahar
↑ TOP

Highlights Track: HL26
Growth-specific Programs of Gene Expression
Monday, July 21 - 2:15 p.m. - 2:40 p.m.
Room: 718B
Presented by: Curtis Huttenhower, Princeton University, US
Session Chair: Terry Gaasterland
↑ TOP

Highlights Track: HL27
Using Conserved Protein Interactions Across Eukaryotes to Construct a Predicted Plant Interactome
Monday, July 21 - 2:45 p.m. - 3:10 p.m.
Room: 718A
Presented by: Matt Geisler, Southern Illinois University Carbondale, US
Session Chair: Ivet Bahar
↑ TOP

Highlights Track: HL28
Allostery: Absence of a Change in Shape Does not Imply That Allostery is Not at Play
Monday, July 21 - 2:45 p.m. - 3:10 p.m.
Room: 718B
Presented by: Antonio del Sol, Fujirebio Inc., JP
Session Chair: Terry Gaasterland
↑ TOP

Highlights Track: HL29
Off Targets for Some Major Pharmaceuticals and Their Implications
Monday, July 21 - 3:15 p.m.- 3:40 p.m.
Room: 718A
Presented by: Philip Bourne, University fo California San Diego, US
Session Chair: Ivet Bahar
↑ TOP

Highlights Track: HL30
Binding Site Sequence Does not Determine Function - but Position Can Help
Monday, July 21 - 3:15 p.m.- 3:40 p.m.
Room: 718B
Presented by: John L Spouge, National Center for Biotechnology Information, US
Session Chair: Terry Gaasterland
↑ TOP

Highlights Track: HL31
Evolution of Cellular Interaction Networks
Monday, July 21 - 3:45 p.m. - 4:10 p.m.
Room: 718A
Presented by: Pedro Beltrao, Lim Lab at UCSF, US
Session Chair: Ivet Bahar
↑ TOP

Highlights Track: HL32
A Nucleosome-Guided Map of Transcription Factor Binding Sites in Yeast
Monday, July 21 - 3:45 p.m. - 4:10 p.m.
Room: 718B
Presented by: Raluca M Gordan, Duke University, US
Session Chair: Terry Gaasterland
↑ TOP

Highlights Track: HL33
Structural Reorganisation and Potential Toxicity of Oligomeric Species Formed during the Assembly of Amyloid Fibrils
Tuesday, July 22 - 10:45 a.m. - 11:10 a.m.
Room: 718A
Presented by: Giorgio Favrin, University of Cambridge, UK
Session Chair: Yanay Ofran
↑ TOP

Highlights Track: HL35
Pathway-based Diagnosis of Cancer and Metastasis
Tuesday, July 22 - 11:15 a.m. - 11:40 a.m.
Room: 718A
Presented by: Han-Yu Chuang, University of California San Diego, US
Session Chair: Yanay Ofran
↑ TOP

Highlights Track: HL36
Association Analysis-based Transformations for Protein Interaction Networks: A Function Prediction Case Study
Tuesday, July 22 - 11:15 a.m. - 11:40 a.m.
Room: 718B
Presented by: Gaurav Pandey, University of Minnesota, Twin Cities, IN
Session Chair: Alfonso Valencia
↑ TOP

Highlights Track: HL37
Integration of Genome-wide Experiments to Find Genes Associated with Complex Polygenic Disorders: Fighting Back Against the Limitations of GWAS
Tuesday, July 22 - 11:45 a.m. - 12:10 p.m.
Room: 718A
Presented by: Atul Butte, Stanford University School of Medicine, US
Session Chair: Yanay Ofran
↑ TOP

Highlights Track: HL38
Unraveling Protein Networks with Power Graph Analysis
Tuesday, July 22 - 11:45 a.m. - 12:10 p.m.
Room: 718B
Presented by: Loic Royer, Biotec, TU Dresden, DE
Session Chair: Alfonso Valencia
↑ TOP

Highlights Track: HL39
Combined Analysis Reveals a Core Set of Cycling Genes
Tuesday, July 22 - 12:15 p.m. - 12:40 p.m.
Room: 718A
Presented by: Yong Lu, Carnegie Mellon University, US
Session Chair: Yanay Ofran
↑ TOP

Highlights Track: HL40
A Global Analysis of Genetic Interactions in Caenorhabditis Elegans
Tuesday, July 22 - 12:15 p.m. - 12:40 p.m.
Room: 718B
Presented by: Matthew T. Weirauch, UCSC, US
Session Chair: Alfonso Valencia
↑ TOP

Highlights Track: HL41
Organization and Evolution of Primate Centromeric DNA from Whole Genome Shotgun Sequence Data
Tuesday, July 22 - 2:15 p.m. - 2:40 p.m.
Room: 718A
Presented by: Can Alkan, University of Washington, US
Session Chair: William Noble
↑ TOP

Highlights Track: HL42
Life Works on AC Power
Tuesday, July 22 - 2:15 p.m. - 2:40 p.m.
Room: 718B
Presented by: Andrey Ptitsyn, Colorado State University, US
Session Chair: Michal Linial
↑ TOP

Highlights Track: HL43
Graph-theory Meets Evolutionary Biology: Reticulate Classification of Prokaryotic Mobile Genetic Elements
Tuesday, July 22 - 2:45 p.m. - 3:10 p.m.
Room: 718A
Presented by: Gipsi Lima-Mendez, Université Libre de Bruxelles, BE
Session Chair: William Noble
↑ TOP

Highlights Track: HL44
A Systems Approach to Delineate Functions of Paralogous Transcription Factors
Tuesday, July 22 - 2:45 p.m. - 3:10 p.m.
Room: 718B
Presented by: Kai Tan, University of California at San Diego, US
Session Chair: Michal Linial
↑ TOP

Highlights Track: HL45
Discovering Common Sequence Variation in Arabidopsis thaliana
Tuesday, July 22 - 3:15 p.m.- 3:40 p.m.
Room: 718A
Presented by: Ratsch Gunnar, Friedrich Miescher Laboratory, Max Planck Society, DE
Session Chair: William Noble
↑ TOP

Highlights Track: HL46
Genome-wide Transcriptional Analysis of the Human Cell Cycle Identifies Genes Differentially Regulated in Normal and Cancer Cells
Tuesday, July 22 - 3:15 p.m.- 3:40 p.m.
Room: 718B
Presented by: Ziv Bar-Joseph, Carnegie Mellon University, US
Session Chair: Michal Linial
↑ TOP

Highlights Track: HL47
A Phylogenomic Study of Human, Dog and Mouse
Tuesday, July 22 - 3:45 p.m. - 4:10 p.m.
Room: 718A
Presented by: Gina M. Cannarozzi, Institue of Computational Science, CH
Session Chair: William Noble
↑ TOP

Highlights Track: HL48
High-resolution Timing of Cell Cycle-regulated Gene Expression
Tuesday, July 22 - 3:45 p.m. - 4:10 p.m.
Room: 718B
Presented by: Andrzej S. Kudlicki, University of Texas Southwestern Medical Center, US
Session Chair: Michal Linial
↑ TOP

Highlights Track: HL49
Transducers: a Unified Framework for Alignment, Phylogeny, Annotation, Reconstruction, Parameter Estimation and Simulating Evolution.
Wednesday, July 23 - 10:45 a.m. - 11:10 a.m.
Room: Hall G
Presented by: Ian Holmes, University of California at Berkeley, US
Session Chair: Reinhard Schneider
↑ TOP

Highlights Track: HL50
Accurate Multiple Sequence and Structural Alignment of Distantly Related Proteins
Wednesday, July 23 - 10:45 a.m. - 11:10 a.m.
Room: 801
Presented by: Jimin Pei, Howard Hughes Medical Institute, UT Southwestern Medical Center, US
Session Chair: Mona Singh
↑ TOP

Highlights Track: HL51
Signal Propagation in Proteins and Relation to Equilibrium Fluctuations
Wednesday, July 23 - 10:45 a.m. - 11:10 a.m.
Room: 718A
Presented by: Chakra S. Chennubhotla, University of Pittsburgh, US
Session Chair: Ivo Hofacker
↑ TOP

Highlights Track: HL52
Binding Site Graphs: A New Graph Theoretical Framework for Prediction of Transcription Factor Binding Sites.
Wednesday, July 23 - 10:45 a.m. - 11:10 a.m.
Room: 718B
Presented by: Boris E Shakhnovich, Harvard University, US
Session Chair: Reinhard Schneider
↑ TOP

Highlights Track: HL53
Detecting Coevolution in and Among Protein Domains
Wednesday, July 23 - 11:15 a.m. - 11:40 a.m.
Room: Hall G
Presented by: Chen-Hsiang Yeang, Institute for Advanced Study, US
Session Chair: Reinhard Schneider
↑ TOP

Highlights Track: HL54
Local Flexibility Aids Protein Multiple Structure Alignment
Wednesday, July 23 - 11:15 a.m. - 11:40 a.m.
Room: 801
Presented by: Lenore J Cowen, Tufts University, US
Session Chair: Mona Singh
↑ TOP

Highlights Track: HL55
Transient mediated fate-determination in HIV (why bistability in unnecessary)
Wednesday, July 23 - 11:15 a.m. - 11:40 a.m.
Room: 718A
Presented by: Leor S Weinberger, University of California, San Diego, US
Session Chair: Ivo Hofacker
↑ TOP

Highlights Track: HL56
Nucleosome Positioning Signals in Yeast and Human Genomic DNA
Wednesday, July 23 - 11:45 a.m. - 12:10 p.m.
Room: Hall G
Presented by: William S Noble, University of Washington, US
Session Chair: Reinhard Schneider
↑ TOP

Highlights Track: HL57
Directed Search of Large Microarray Compendia
Wednesday, July 23 - 11:45 a.m. - 12:10 p.m.
Room: 801
Presented by: Matthew A Hibbs, Princeton University, US
Session Chair: Mona Singh
↑ TOP

Highlights Track: HL58
Semi-supervised Learning for Peptide Identification from Shotgun Proteomics Datasets
Wednesday, July 23 - 11:45 a.m. - 12:10 p.m.
Room: 718A
Presented by: Lukas Kšll, University of Washington, US
Session Chair: Ivo Hofacker
↑ TOP

Highlights Track: HL59
Inferring Non-Coding RNA Families by Genome-Scale Structure-Based Clustering
Wednesday, July 23 - 12:15 p.m. - 12:40 p.m.
Room: Hall G
Presented by: Rolf Backofen, University of Freiburg, DE
Session Chair: Reinhard Schneider
↑ TOP

Highlights Track: HL60
Exploring Interaction Space of Multiple Retroviral Proteases and Their Substrates
Wednesday, July 23 - 12:15 p.m. - 12:40 p.m.
Room: 801
Presented by: Aleksejs Kontijevskis, Uppsala University, SE
Session Chair: Mona Singh
↑ TOP