Proceedings Track: PT01

Estimating True Evolutionary Distances under the DCJ Model

Sunday, July 20 - 10:45 a.m. - 11:10 a.m.

Room: Hall G

Presented by: Yu Lin, Ecole Polytechnique Federale de Lausanne

Session Chair: TBD

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Proceedings Track: PT02

Differential variability analysis of gene expression and its application to human diseases

Sunday, July 20 - 10:45 a.m. - 11:10 a.m.

Room: 801

Presented by: Joshua Ho, The University of Sydney

Session Chair: Igor Jurisica

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Proceedings Track: PT03

Efficient Inference of Bacterial Strain Trees From Genome-scale Multi-locus Data

Sunday, July 20 - 11:15 a.m. - 11:40 a.m.

Room: Hall G

Presented by: Cuong Than, Rice University

Session Chair: TBD

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Proceedings Track: PT04

Selecting anti-HIV Therapies Based on a Variety of Genomic and Clinical Factors

Sunday, July 20 - 11:15 a.m. - 11:40 a.m.

Room: 801

Presented by: Michal Rosen-Zvi, IBM

Session Chair: Igor Jurisica

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Proceedings Track: PT05

The Multiple Gene Duplication Problem Revisited

Sunday, July 20 - 11:45 a.m. - 12:10 p.m.

Room: Hall G

Presented by: Mukul S. Bansal, Iowa State University

Session Chair: TBD

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Proceedings Track: PT06

Reversible Jump MCMC Approach for Peak identification for Stroke SELDI Mass Spectrometry Using Mixture Model

Sunday, July 20 - 11:45 a.m. - 12:10 p.m.

Room: 801

Presented by: Yuan Wang, The Methodist Hospital, Weill Cornell Medical College

Session Chair: Igor Jurisica

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Proceedings Track: PT07

Assessment and Improvement of Plasmodium yoelii yoelii Genome Annotation through Comparative Analysis

Sunday, July 20 - 12:15 p.m. - 12:40 p.m.

Room: Hall G

Presented by: Xinxia Peng, Seattle Biomedical Research Institute

Session Chair: Roderic Guigo

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Proceedings Track: PT08

Assessing the Functional Structure of Genomic Data

Sunday, July 20 - 12:15 p.m. - 12:40 p.m.

Room: 801

Presented by: Curtis Huttenhower,

Session Chair: Alfonso Valencia

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Proceedings Track: PT09

MACHOS: Markov Clusters of Homologous Subsequences

Sunday, July 20 - 2:15 p.m. - 2:40 p.m.

Room: Hall G

Presented by: Simon Wong, The University of Queensland

Session Chair: Roderic Guigo

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Proceedings Track: PT10

Identifying Functional Modules in Protein-Protein Interaction Networks: An Integrated Exact Approach

Sunday, July 20 - 2:15 p.m. - 2:40 p.m.

Room: 801

Presented by: Gunnar W. Klau, University of Wrzburg

Session Chair: Joel Bader

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Proceedings Track: PT11

Classification and Feature Selection Algorithms for Multi-class CGH Data

Sunday, July 20 - 2:45 p.m. - 3:10 p.m.

Room: Hall G

Presented by: Jun Liu, PhD student

Session Chair: Roderic Guigo

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Proceedings Track: PT12

Prediction of Drug-target Interaction Networks from the Integration of Chemical and Genomic Spaces

Sunday, July 20 - 2:45 p.m. - 3:10 p.m.

Room: 801

Presented by: Yoshihiro Yamanishi, Centre for Computational Biology, Ecole des Mines de Paris

Session Chair: Joel Bader

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Proceedings Track: PT13

A High Accurate Model of the Individual Haplotyping Problem Based on Weighted SNP Fragments and Genotype with Errors

Sunday, July 20 - 3:15 p.m.- 3:40 p.m.

Room: Hall G

Presented by: Minzhu Xie, Central South University

Session Chair: Roderic Guigo

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Proceedings Track: PT14

Biomolecular Network Motif Counting and Discovery by Color Coding

Sunday, July 20 - 3:15 p.m.- 3:40 p.m.

Room: 801

Presented by: Iman Hajirasouliha, Simon Fraser University

Session Chair: Joel Bader

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Proceedings Track: PT15

Guided Genome Halving: Hardness, Heuristics and the History of the Hemiascomycetes

Sunday, July 20 - 3:45 p.m. - 4:10 p.m.

Room: Hall G

Presented by: Chunfang Zheng, University of Ottawa

Session Chair: Roderic Guigo

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Proceedings Track: PT16

Protein Complex Identification by Supervised Graph Local Clustering

Sunday, July 20 - 3:45 p.m. - 4:10 p.m.

Room: 801

Presented by: Yanjun Qi, Carnegie Mellon University

Session Chair: Joel Bader

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Proceedings Track: PT17

Annotation-based Inference of Transporter Function

Monday, July 21 - 10:45 a.m. - 11:10 a.m.

Room: Hall G

Presented by: Peter Karp, SRI International

Session Chair: Hagit Shatkay

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Proceedings Track: PT18

The effectiveness of position - and composition - specific gap costs for protein homology search

Monday, July 21 - 10:45 a.m. - 11:10 a.m.

Room: 801

Presented by: Yi-Kuo Yu, NCBI/NLM/NIH

Session Chair: Des Higgins

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Proceedings Track: PT19

Detection of IUPAC and IUPAC-like Chemical Names

Monday, July 21 - 11:15 a.m. - 11:40 a.m.

Room: Hall G

Presented by: Roman Klinger, Fraunhofer Institute for Algorithms and Scientific Computing

Session Chair: Hagit Shatkay

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Proceedings Track: PT20

ProSOM: Core Promoter Prediction Based on Unsupervised Clustering of DNA Physical Profiles

Monday, July 21 - 11:15 a.m. - 11:40 a.m.

Room: 801

Presented by: Thomas Abeel, Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), Ghent University

Session Chair: Des Higgins

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Proceedings Track: PT21

Identifying Gene-Disease Associations Using Centrality on a Literature Mined Gene Interaction Network

Monday, July 21 - 11:45 a.m. - 12:10 p.m.

Room: Hall G

Presented by: Arzucan Ozgur, University of Michigan

Session Chair: Hagit Shatkay

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Proceedings Track: PT22

Optimal pooling for Genome Re-sequencing with Ultra-high-throughput Short-read Ttechnologies

Monday, July 21 - 11:45 a.m. - 12:10 p.m.

Room: 801

Presented by: Fereydoun Hormozdiari, Simon Fraser University

Session Chair: Des Higgins

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Proceedings Track: PT23

Integrating High Dimensional Bi-directional Parsing Models for Gene Mention Tagging

Monday, July 21 - 12:15 p.m. - 12:40 p.m.

Room: Hall G

Presented by: Chun-Nan Hsu, Institute of Information Science, Academia Sinica, Taiwan

Session Chair: Hagit Shatkay

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Proceedings Track: PT24

POIMs: Positional Oligomer Importance Matrices --- Understanding Support Vector Machine Based Signal Detectors Sequence Analysis and Alignment

Monday, July 21 - 12:15 p.m. - 12:40 p.m.

Room: 801

Presented by: Soeren Sonnenburg, 

Session Chair: Des Higgins

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Proceedings Track: PT25

The EXACT Description of Biomedical Protocols

Monday, July 21 - 2:15 p.m. - 2:40 p.m.

Room: Hall G

Presented by: Wayne Aubrey, Aberystwyth University

Session Chair: Robert Stevens

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Proceedings Track: PT26

Efficient Algorithms for Exact Hierarchical Clustering of Huge Datasets: Tackling the Entire Protein Space

Monday, July 21 - 2:15 p.m. - 2:40 p.m.

Room: 801

Presented by: Yaniv Loewenstein, HUJI

Session Chair: Alfonso Valencia

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Proceedings Track: PT27

Towards the use of Argumentation in Bioinformatics: A Gene Expression Case Study

Monday, July 21 - 2:45 p.m. - 3:10 p.m.

Room: Hall G

Presented by: Kenneth McLeod, Heriot-Watt University

Session Chair: Robert Stevens

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Proceedings Track: PT28

MiRNA Prediction with a Novel Ranking Algorithm Based on Random Walks

Monday, July 21 - 2:45 p.m. - 3:10 p.m.

Room: 801

Presented by: Xuefeng Zhou, Washington University in Saint Louis

Session Chair: Alfonso Valencia

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Proceedings Track: PT29

The Ontology of Biological Taxa

Monday, July 21 - 3:15 p.m.- 3:40 p.m.

Room: Hall G

Presented by: Stefan Schulz, Freiburg University Hospital

Session Chair: Robert Stevens

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Proceedings Track: PT30

A Robust Framework for Detecting Structural Variations in a Genome

Monday, July 21 - 3:15 p.m.- 3:40 p.m.

Room: 801

Presented by: Seunghak Lee, University of Toronto

Session Chair: Alfonso Valencia

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Proceedings Track: PT31

GenoQuery: A New Querying Module for Functional Annotation in a Genomic Warehouse

Monday, July 21 - 3:45 p.m. - 4:10 p.m.

Room: Hall G

Presented by: Frederic Lemoine, LRI

Session Chair: Robert Stevens

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Proceedings Track: PT32

A Max-margin Model for Efficient Simultaneous Alignment and Folding of RNA Sequences

Monday, July 21 - 3:45 p.m. - 4:10 p.m.

Room: 801

Presented by: Chuong Do, Stanford University

Session Chair: Alfonso Valencia

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Proceedings Track: PT33

Designing Succinct Structural Alphabets

Tuesday, July 22 - 10:45 a.m. - 11:10 a.m.

Room: Hall G

Presented by: Shuai Cheng Li, University of Waterloo

Session Chair: Nir Ben-Tal

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Proceedings Track: PT34

Alignment and Classification of Time Series Gene Expression in Clinical Studies

Tuesday, July 22 - 10:45 a.m. - 11:10 a.m.

Room: 801

Presented by: Tien-ho Lin, Carnegie Mellon University

Session Chair: Olga Troyanskaya

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Proceedings Track: PT35

Predicting Protein Thermostability Changes from Sequence Upon Multiple Mutations

Tuesday, July 22 - 11:15 a.m. - 11:40 a.m.

Room: Hall G

Presented by: Ludovica Montanucci, University of Bologna

Session Chair: Nir Ben-Tal

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Proceedings Track: PT36

Inferring Differentiation Pathways from Gene Expression

Tuesday, July 22 - 11:15 a.m. - 11:40 a.m.

Room: 801

Presented by: Ivan Gesteira Costa, Max Planck Institute for Molecular Genetics

Session Chair: Olga Troyanskaya

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Proceedings Track: PT37

Algorithm for Backrub Motions in Protein Design

Tuesday, July 22 - 11:45 a.m. - 12:10 p.m.

Room: Hall G

Presented by: Ivelin Georgiev, Duke University Computer Science Department

Session Chair: Nir Ben-Tal

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Proceedings Track: PT38

Predicting functional transcription factor binding through alignment-free, affinity-based analysis of orthologous promoter sequences

Tuesday, July 22 - 11:45 a.m. - 12:10 p.m.

Room: 801

Presented by: Lucas Ward, Columbia University

Session Chair: Olga Troyanskaya

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Proceedings Track: PT39

A Computational Framework to Empower Probabilistic Protein Design

Tuesday, July 22 - 12:15 p.m. - 12:40 p.m.

Room: Hall G

Presented by: Menachem Fromer, Hebew University, Jerusalem

Session Chair: Nir Ben-Tal

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Proceedings Track: PT40

Combinatorial Influence of Environmental Parameters on Transcription Factor Activity

Tuesday, July 22 - 12:15 p.m. - 12:40 p.m.

Room: 801

Presented by: Theo Knijnenburg, Delft Technical University

Session Chair: Olga Troyanskaya

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Proceedings Track: PT41

Nucleosome Positioning from Tiling Microarray Data

Tuesday, July 22 - 2:15 p.m. - 2:40 p.m.

Room: Hall G

Presented by: Moran Yossour, The Hebrew University of Jerusalem

Session Chair: Janice Glasgow

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Proceedings Track: PT42

A Maximum Common Substructure-Based Algorithm for Searching and Predicting Drug-Like Compounds

Tuesday, July 22 - 2:15 p.m. - 2:40 p.m.

Room: 801

Presented by: Yiqun Cao, University of California, Riverside

Session Chair: TBD

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Proceedings Track: PT43

Multi-Spectra Peptide Sequencing and its Applications to Multistage Mass Spectrometry

Tuesday, July 22 - 2:45 p.m. - 3:10 p.m.

Room: Hall G

Presented by: Nuno Bandeira, University of California, San Diego

Session Chair: Janice Glasgow

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Proceedings Track: PT44

Contact Replacement for NMR Resonance Assignment

Tuesday, July 22 - 2:45 p.m. - 3:10 p.m.

Room: 801

Presented by: Fei Xiong, Dartmouth College

Session Chair: TBD

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Proceedings Track: PT45

Modelling peptide fragmentation with dynamic Bayesian networks for peptide identification

Tuesday, July 22 - 3:15 p.m.- 3:40 p.m.

Room: Hall G

Presented by: Aaron Klammer, University of Washington

Session Chair: Janice Glasgow

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Proceedings Track: PT46

Classification of arrayCGH Data Using a Fused SVM

Tuesday, July 22 - 3:15 p.m.- 3:40 p.m.

Room: 801

Presented by: Franck Rapaport, Institut Curie / ENSMP

Session Chair: TBD

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Proceedings Track: PT47

BLASTing Small Molecules - Statistics and Extreme Statistics of Chemical Similarity Scores

Tuesday, July 22 - 3:45 p.m. - 4:10 p.m.

Room: Hall G

Presented by: Pierre Baldi, University of California, Irvine

Session Chair: Janice Glasgow

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Proceedings Track: PT48

Matching Isotopic Distributions from Metabolically Labeled Samples

Tuesday, July 22 - 3:45 p.m. - 4:10 p.m.

Room: 801

Presented by: Sean McIlwain, University of Wisconsin

Session Chair: TBD

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