ISMB/ECCB 2009 TALKS

The full listing of talks can be found below.

**Not all presenters provided permission to make talks available.

Type Title Presenter Keywords
HL01 The Plurality of Prognostic Gene Signatures for Cancer Paul Boutros Human disease, Medical biology
HL02 Modeling Ecological and Genetic Diversity in Bacteria Eric Alm Evolution, other
HL03 Whole genome analysis of mtDNA natural evolution in human and in cancer Eitan Rubin Human disease, Genome comparisons
HL04 The role of the RNA folding free energy in the evolution of the influenza virus Panayiotis Benos Evolution, Genome comparisons
HL05 Proteomics first approach for discovering sub-network targets in cancer Rod Nibbe Proteomics, Systems biology
HL06 Bayesian Inference of Selection Histories in Six Mammalian Genomes Tomas Vinar Evolution, Methods
HL07 Computational approach to model peptide antigenicity Carlos Camacho Interactions, Simulations
HL08 Insights into corn genes derived from large-scale cDNA sequencing Nickolai Alexandrov ,
HL09 Inferring pathway activity toward precise disease classification Eunjung Lee Human disease, Systems biology
HL10 Evolution of genome structure: what statistics can tell us about the biology of chromosomes Aaron Darling Evolution, Genome comparisons
HL11 Using side effects of medicines to identify drug targets Michael Kuhn Medical biology, Pharmaceutical informatics
HL12 Gene Loss Under Neighbourhood Selection Following Whole Genome Duplication And The Reconstruction Of The Ancestral Diploid David Sankoff Evolution, Genome comparisons
HL13 The Human Phenotype Ontology Peter Robinson Ontologies, Human disease
HL14 Visualizing Genomic Dark Matter: Repeat Probability Clouds in the Human Genome David Pollock Genome comparisons, Evolution
HL15 Analyzing risk factor of heart disease by a computational lipidology approach Katrin Huebner Systems biology, Medical biology
HL16 MotifMap: a human genome-wide map of candidate regulatory motif sites. Xiaohui Xie Sequence analysis, Genome comparison
HL17 Learning from Resequencing Data: What To Do When the $1000 Genome Arrives? Gregory Kryukov Human disease, Evolution
HL18 Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods Christophe Dessimoz Evolution, Function prediction
HL19 A Mathematical Framework for the Selection of an Optimal Set of Peptides for Epitope-Based Vaccines Oliver Kohlbacher Pharmaceutical informatics, Human disease
HL20 Prediction of Binding Sites on Proteins Using the Gaussian Network Model Burak Erman Function prediction, Structure prediction
HL21 The miRNA/siRNA saturation effect - transfection of small RNAs compromise gene regulation by endogenous microRNAs Debora Marks Regulation,
HL22 Sequence Similarity Network Reveals Common Ancestry of Multidomain Proteins Dannie Durand Genome comparisons, Evolution
HL23 Models from experiments: combinatorial perturbations of cancer cells Sven Nelander Systems biology, Networks
HL24 Discovery of a hidden sequence motif conserved in the bacterial type III secretion signal: implications for structure, drug discovery and host-pathogen systems models. Jason McDermott Machine learning, Medical biology
HL25 Re-examining the connection between the network topology and essentiality Teresa Przytycka Systems biology, Networks
HL26 Built-in loops allow versatility in domain-domain interactions: Lessons from self-interacting domains Eyal Akiva ,
HL27 Regulatory networks define phenotypic classes of human stem cell lines Igor Ulitsky Systems biology, Arrays
HL28 Confirming alternative protein isoforms in Drosophila Michael Tress Proteomics, Genome annotation
HL29 Biomedical Discovery Acceleration Lawrence Hunter Systems biology, Integration
HL30 Automated Analysis of Patterns in Human Protein Atlas Images Robert Murphy Proteomics, Machine learning
HL31 Toward Automated, Practical Provision of Need-Based, High-Utility Text to Diverse Biomedical Users and Database Curators Hagit Shatkay Text mining, Machine learning
HL32 Network modeling of human interactome and phenome Rui Jiang Systems biology, Networks
HL33 Mitochondrial beta-barrel Outer Membrane Proteins, All Accounted For? Paul Horton ,
HL34 Network-based prediction of human tissue-specific metabolism Tomer Shlomi Systems biology, Networks
HL35 Context-specific BLAST detects twice as many homologous proteins as BLAST Johannes Soeding Sequence analysis, Alignment
HL36 Leveraging the context-specific coordination of transcript and metabolite concentrations to discover gene-metabolite interactions. Patrick Bradley Systems biology, Integration
HL37 Classification, Evolution, and Assembly of Protein Complexes Emmanuel Levy Structural genomics, Evolution
HL38 MeltDB: A software platform for the analysis and integration of Metabolomics Experiment Data Heiko Neuweger Systems biology, Integration
HL39 Evolutionary potentials for protein structure and function prediction Francisco Melo Structure prediction, Function prediction
HL40 Histone modifications at human enhancers reflect global cell-type-specific gene expression Gary Hon Transcription, Systems biology
HL41 Comparative analysis of crystal interfaces of homologous proteins Roland Dunbrack Structure prediction, Interactions
HL42 Exploring the human genome with functional maps Curtis Huttenhower Integration, Systems biology
HL43 Disordered flanks prevent peptide aggregation Sanne Abeln Simulations, Dynamics
HL44 Benchmarking tools in Metabolic Pathway Analysis Luis de Figueiredo Systems biology, Networks
HL45 From the detection of functional regions towards function annotation in proteins Nir Ben-Tal Structural genomics, Function prediction
HL46 Prioritizing functional modules mediating genetic perturbations and phenotypic effects Li Wang Systems biology, Methods
HL47 Fitting multiple components into a cryoEM map of their assembly Keren Lasker Structure prediction, Integration
HL48 Architecture of CpG methylation in the human genome Israel Steinfeld Regulation, Arrays
HL49 Robust simplifications of multiscale biochemical networks Andrei Zinovyev Systems biology, Dynamics
HL50 Rapid sampling of molecular motion with prior information constraints: Insights into channel gating and domain swapping Ora Schueler-Furman Structure prediction, Simulations
HL51 GraphWeb: functional analysis of genomic networks Jüri Reimand Networks, Integration
HL52 Characterizing transcriptome plasticity using whole-genome tiling arrays and machine learning Georg Zeller Transcription, Arrays
HL53 Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project Chris Taylor Methods, Integration
HL54 Search and discovery of recurring patterns with interactomes Mona Singh Networks, Interactions
HL55 The Computational Exploration of (Alternative) Splicing Mechanisms Michael Sammeth Transcription, Regulation
HL56 Nominalization and alternations in the language of molecular biology: Implications for text mining Kevin Cohen Text mining,
HL57 FunCoup: global networks of functional coupling in eukaryotes Erik Sonnhammer Networks, Interactions
HL58 A new method for high-resolution gene expression analysis Caroline Friedel Transcription, Regulation
HL59 Comparative community assessments for applied biomedical text mining: BioCreative II challenge and metaservices. Florian Leitner Text mining, Integration
HL60 Studying alternative splicing regulatory networks through partial correlation analysis Liang Chen Networks, Arrays
HL61 Global Measures of Uncertainty: Long Overdue in Computational Molecular Biology Lee Newberg Methods, Sequence analysis
HL62 A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing Richard Green ,
Keynote New Challenges and Opportunities in Network Biology Trey Ideker ,
Keynote Bioinformatics Methods to Study Species Extinctions Webb Miller ,
Keynote Information and Biology Pierre-Henri Gouyon ,
Keynote Individual Genetic Variation: From Networks to Mechanisms Daphne Koller ,
Keynote Chasing the AIDS Virus Thomas Lengauer ,
Keynote The comparative analysis reveals independence of developmental processes during early development in frogs Eugenia del Pino ,
Keynote Computational Neuroscience: Models of the Visual System Tomaso Poggio ,
Keynote A global view on protein expression based on the Human Protein Atlas Mathias Uhlen ,
PT01 PICKY: A Novel SVD-Based NMR Spectra Peak Picking Method Babak Alipanahi Ramandi Protein Structure and Function,
PT02 From Disease Ontology (DO) to Disease-Ontology Lite (DOLite): Statistical Methods to Adapt a General-Purpose Ontology for the Test of Gene-Disease Associations Warren Kibbe Databases and Ontologies,
PT03 Prediction of Sub-Cavity Binding Preferences Using an Adaptive Physicochemical Structure Representation Izhar Wallach Protein Structure and Function,
PT04 Alignment of the UMLS Semantic Network with BioTop Methodology and Assessment Stefan Schulz Databases and Ontologies,
PT05 Pokefind: A Novel Topological Filter for use With Protein Structure Prediction Firas Khatib Protein Structure and Function,
PT06 Ontology Quality Assurance Through Analysis of Term Transformations Karin Verspoor Databases and Ontologies,
PT07 REPETITA: Detection and Discrimination of the Periodicity of Protein Solenoid Repeats by Discrete Fourier Transform Silvio Tosatto Protein Structure and Function,
PT08 Modeling Stochasticity and Robustness in Gene Regulatory Networks Abhishek Garg Gene Regulation and Transcriptomics,
PT09 A Framework to Refine Particle Clusters Produced by EMAN Liya Fan Protein Structure and Function,
PT10 Clustered Alignments of Gene-Expression Time Series Data Adam Smith Gene Regulation and Transcriptomics,
PT11 Domain-oriented Edge-based Alignment of Protein Interaction Networks Xin Guo Protein Interactions and Molecular Networks,
PT12 KELLER: Estimating Time-Evolving Interactions Between Genes Le Song Gene Regulation and Transcriptomics,
PT13 Network-based Prediction of Metabolic Enzymes Subcellular Localization Shira Mintz-Oron Protein Interactions and Molecular Networks,
PT14 Predicting Functionality of Protein-DNA Interactions by Integrating Diverse Evidence Duygu Ucar Gene Regulation and Transcriptomics,
PT15 IsoRankN: Spectral Methods For Global Alignment of Multiple Protein Networks Michael Baym Protein Interactions and Molecular Networks,
PT16 Grouped Graphical Granger Modeling for Gene Expression Regulatory Networks Discovery Saharon Rosset Gene Regulation and Transcriptomics,
PT17 A Unified Statistical Model to Support Local Sequence Order Independent Similarity Searching for Ligand Binding Sites and its Application to Genome-Based Drug Discovery Lei Xie Protein Structure and Function,
PT18 Multi-Locus Match Probability in a Finite Population: A Fundamental Difference Between the Moran and Wright-Fisher Models Anand Bhaskar Population Genomics,
PT19 Global Alignment of Protein-Protein Interaction Networks by Graph Matching Methods Mikhail Zaslavskiy Protein Interactions and Molecular Networks,
PT20 Speeding Up HMM Algorithms for Genetic Linkage Analysis via Chain Reductions of the State Space Ydo Wexler Population Genomics,
PT21 Probabilistic retrieval and Visualization of Biologically Relevant Microarray Experiments Jose Caldas Other Bioinformatics Applications and Methods, Microarrays
PT22 A Multivariate Regression Approach to Association Analysis of Quantitative Trait Network Seyoung Kim Population Genomics,
PT23 Proteome Coverage Prediction with Infinite Markov Models Manfred Claassen Other Bioinformatics Applications and Methods,
PT24 Inference of Locus-Specific Ancestry in Closely Related Populations Sriram Sankararaman Population Genomics,
PT25 Fewer permutations, More Accurate P-values Theo Knijnenburg Other Bioinformatics Applications and Methods,
PT26 A Geometric Approach for Classification and Comparison of Structural Variants Suzanne Sindi Population Genomics,
PT27 A General Computational Method for Robustness Analysis with Applications to Synthetic Gene Networks Aurelien Rizk Other Bioinformatics Applications and Methods,
PT28 Joint Estimation of Gene Conversion Rates and Mean Conversion Tract Lengths from Population SNP Data Junming Yin Population Genomics,
PT29 E-zyme: Predicting Potential EC Numbers from the Chemical Transformation Pattern of Substrate-product Pairs Yoshihiro Yamanishi Other Bioinformatics Applications and Methods,
PT30 Computing Galled Networks from Real Data Daniel Huson Evolution and Phylogeny,
PT32 Genotype-Phenotype Associations: Substitution Models to Detect Evolutionary Associations Between Phenotypic Variables and Genotypic Evolutionary Rate Timothy O'Connor Evolution and Phylogeny,
PT33 Towards a Gold Standard for Promoter Prediction Evaluation Thomas Abeel Sequence Analysis and Alignment,
PT34 Constrained Mixture Estimation for Analysis and Robust Classification of Clinical Time Series Ivan Gesteira Costa Bioinformatics of Disease,
PT35 DISCOVER: A Feature-Based Discriminative Method for Motif Search in Complex Genomes Pradipta Ray Sequence Analysis and Alignment,
PT36 Graph Theoretical Approach To Study eQTL: A Case Study of Plasmodium Falciparum Yang Huang Bioinformatics of Disease,
PT37 Predictions of RNA Secondary Structure by Combining Homologous Sequence Information Michiaki Hamada Sequence Analysis and Alignment,
PT38 A Classifier-based Approach to Identify Genetic Similarities Between Diseases Marc Schaub Bioinformatics of Disease,
PT39 Assessing Phylogenetic Motif Models For Predicting Transcription Factor Binding Sites John Hawkins Sequence Analysis and Alignment,
PT40 Model Based Clustering of Array CGH Data Sohrab Shah Bioinformatics of Disease,
PT41 Modeling Interactions between Adjacent Nucleosomes Improves Genome-wide Predictions of Nucleosome Occupancy Shai Lubliner Sequence Analysis and Alignment,
PT42 Viruses Selectively Mutate Their Cd8 T Cell Epitopes - A Large Scale Immunomic Analysis Yoram Louzoun Bioinformatics of Disease,
PT43 Efficient Exact Motif Discovery Tobias Marschall Sequence Analysis and Alignment,
PT44 Family Classification Without Domain Chaining Jacob Joseph Comparative Genomics,
PT45 A Partition Function Algorithm for Interacting Nucleic Acid Strands HamidReza Chitsaz Sequence Analysis and Alignment,
PT46 Identifying Novel Constrained Elements by Exploiting Biased Substitution Patterns Xiaohui Xie Comparative Genomics,
PT47 Predicting and Understanding the Stability of G-Quadruplexes Oliver Stegle Sequence Analysis and Alignment,