ISMB/ECCB 2011 TALKS

The full listing of talks can be found below.

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

Type Title Presenter Keywords
HL01 Analysis and design of RNA sequencing experiments for identifying isoform regulation Yarden Katz Methods, RNA modeling
HL02 The Central Human Proteome Jacques Colinge Systems biology, Networks
HL03 From revealing new insights into Human Tissue Development to Minimum Curvineality Carlo Cannistraci Systems biology, Machine learning
HL04 Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding Benoit Ballester Evolution, Regulation
HL05 Protein Complexes are Central in the Yeast Genetic Landscape Magali Michaut Networks, Interactions
HL06 Comparative Genomics Reveals Birth and Death of Fragile Regions in Mammalian Evolution Max Alekseyev Evolution, Genome comparisons
HL07 Survival of the Friendly - the Importance of Protein-Protein Interactions in the Evolution of Bacterial Genomes Yanay Ofran Interactions, Evolution
HL08 Universal epitope prediction for class II MHC Andrew Bordner Interactions, Structure prediction
HL09 Topological network alignment uncovers biological function and phylogeny Natasa Przulj Networks, Interactions
HL10 Systematic planning of genome-scale experiments in poorly studied species. Casey Greene Function prediction, Genome annotation
HL11 A survey of genomic traces reveals a common sequencing error, RNA editing, and DNA editing. Erez Levanon Sequence analysis, Genome annotation
HL12 Pi Release From Myosin: A Simulation Analysis of Possible Pathways Marco Cecchini Simulations,
HL13 Initial steps towards a production platform for DNA sequence analysis on the grid Barbera Van Schaik Sequence analysis, other
HL14 The imprint of codons on protein structure Charlotte Deane Structure prediction, Evolution
HL15 SlideSort: Fast and exact algorithm for Next Generation Sequencing data analysis Kana Shimizu Sequence analysis, Methods
HL16 Predicting genetic modifier loci using functional gene networks Insuk Lee Networks, Interactions
HL17 Genome3D: a viewer-model framework for integrating and visualizing multi-scale epigenomic information within a three-dimensional genome W Zheng Genome annotation, Integration
HL18 The Impact of Multifunctional Genes on "Guilt by Association" Analysis Jesse Gillis Function prediction, Networks
HL19 Structure determination of genomes and genomic domains by satisfaction of spatial restraints. Marc A. Marti-Renom Genome annotation, Structural genomics
HL20 Bringing order to protein disorder through comparative genomics and genetic interactions Philip Kim Systems biology, Proteomics
HL21 A Unifying Theory for GC3 Biology in Plants and Animals Tatiana TATARINOVA Systems biology, Sequence analysis
HL22 Model-Based Learning for All SCOP Families Stefan Kramer Machine learning, Function prediction
HL23 Strengths and limitations of the federal guidance on synthetic DNA Jean Peccoud Alignment, Methods
HL24 Next-generation genome alignment with LAST Paul Horton Alignment, Genome comparison
HL25 A scalable approach for discovering conserved active subnetworks across species Raamesh Deshpande Networks, Genome comparisons
HL26 Benchmarking Ontologies: Bigger or Better? Lixia Yao Ontologies, Text mining
HL27 Network Modeling Identifies Molecular Functions Targeted by miR-204 to Suppress Head and Neck Tumor Metastasis and Mechanisms of Therapeutic Resistance Yves Lussier Function prediction, Medical biology
HL28 miRGator v2.0 and the construction of miRNA-disease network Wankyu Kim Databases, Integration
HL29 Mutation Impact Mining using SADI Semantic Web Services Christopher Baker Semantics, Integration
HL30 Fast and Efficient Dynamic Nested Effects Models Holger Fröhlich Systems biology, Machine learning
HL31 The chicken or the egg problem in epidemiology: untangling the mutual impact of transmission network dynamic and epidemic spread. Christel Kamp Networks, Human disease
HL32 C(alpha)-trace model of the transmembrane domain of human copper transporter 1, motion and functional implications Nir Ben-Tal Structure prediction,
HL33 Organization of mammalian genomes with respect to the nuclear lamina Wouter Meuleman Regulation, Transcription
HL34 Multi-species integrative biclustering Peter Waltman Evolution, Systems biology
HL35 Model-based method for transcription factor target identification with limited data Magnus Rattray Systems biology, Regulation
HL36 Inference of Signaling Network Architecture and Dynamics from High-throughput Combinatorial RNAi Screens Chris Bakal Networks, Systems biology
HL37 Quantitative analysis of the Drosophila segmentation regulatory network using pattern generating potentials Saurabh Sinha Transcription, Sequence analysis
Keynote Computational biology in the 21st century: making sense out of massive data Bonnie Berger ,
Keynote Integrating computation and experiments for a molecular-level understanding of human disease Olga Troyanskaya ,
Keynote The Evolution of Enzyme Mechanisms and Functional Diversity Janet Thornton ,
Keynote Challenges for Bioinformatics in Personalized Cancer Medicine Alfonso Valencia ,
Keynote M pneumoniae (Towards a full quantitive understanding of a free-living system) Luis Serrano ,
Keynote From sequences to ontologies - adventures in informatics Michael Ashburner ,
PT01 Sorting the nuclear proteome Mikael Boden Protein Structure and Function,
PT02 vipR: Variant identification in pooled DNA using R Andre Altmann Sequence Analysis,
PT03 Environment specific substitution tables improve membrane protein alignment Jamie R. Hill Protein Structure and Function,
PT04 IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming Kengo Sato Sequence Analysis,
PT05 Sequence-based prediction of protein crystallization, purification, and production propensity Marcin J. Mizianty Protein Structure and Function,
PT06 Meta-IDBA: De Novo Assembler for Mixed Species in Metagenomic Data Yu Peng Sequence Analysis,
PT07 A method for probing the mutational landscape of amyloid structure Charles W. O'Donnell Protein Structure and Function,
PT08 A Conditional Random Fields Method for RNA Sequence-Structure Relationship Modeling and Conformation Sampling Zhiyong Wang Sequence Analysis,
PT09 Piecewise Linear Approximation of Protein Structures using the Principle of Minimum Message Length Arun Konagurthu Protein Structure and Function,
PT10 Discovering and visualising indirect associations between biomedical concepts Sophia Ananiadou Text Mining,
PT11 QAARM: Quasi-anharmonic auto-regressive model reveals molecular recognition pathways in ubiquitin Andrej Savol Protein Structure and Function,
PT12 MeSH: A Window into Full-Text for Document Summarization Sanmitra Bhattacharya Text Mining,
PT13 Multi-view Methods for Protein Structure Comparison using Latent Dirichlet Allocation Ashish Tendulkar Protein Structure and Function,
PT14 A Folding Algorithm for Extended RNA Secondary Structures Christian Hoener Zu Siederdissen Sequence Analysis,
PT15 Template-free detection of macromolecular complexes in cryo electron tomograms Min Xu Protein Structure and Function,
PT16 Error correction of high-throughput sequencing datasets with non-uniform coverage Paul Medvedev Sequence Analysis,
PT17 Generative Probabilistic Models for Protein-Protein Interaction Networks – The Biclique Perspective Regev Schweiger Protein Interactions and Molecular Networks,
PT18 Epistasis detection on quantitative phenotypes by exhaustive enumeration using GPUs Tony Kam-Thong Disease Models and Epidemiology,
PT19 RINQ: Reference-based Indexing for Network Queries Gunhan Gulsoy Protein Interactions and Molecular Networks,
PT20 Detecting epistatic effect in association studies at a genomic level based on an ensemble approach Jing Li Disease Models and Epidemiology,
PT21 Construction of Co-complex Score Matrix for Protein Complex Prediction from AP-MS Data Xiaoli Li Protein Interactions and Molecular Networks,
PT22 Efficient spatial segmentation of large imaging mass spectrometry data sets with spatially-aware clustering Theodore Alexandrov Mass Spectrometry and Proteomics,
PT23 Uncover disease genes by maximizing information flow in the phenome-interactome network Rui Jiang Protein Interactions and Molecular Networks,
PT24 Automatic Tracing of 3D Neuron Structures Using All-Path Pruning Hanchuan Peng Bioimaging,
PT25 Physical Module Networks: an Integrative Approach for Reconstructing Transcription Regulation Noa Novershtern Protein Interactions and Molecular Networks,
PT26 Tanglegrams for Rooted Phylogenetic Trees and Networks Celine Scornavacca Evolution and Comparative Genomics,
PT27 Identification of metabolic network models from incomplete high-throughput datasets Sara Berthoumieux Protein Interactions and Molecular Networks,
PT28 Mapping ancestral genomes with massive gene loss: a matrix sandwich problem Eric Tannier Evolution and Comparative Genomics,
PT29 TREEGL: Reverse Engineering Tree-Evolving Gene Networks Underlying Developing Biological Lineages Ankur Parikh Protein Interactions and Molecular Networks,
PT30 Predicting site-specific human selective pressure using evolutionary signatures Javad Sadri Evolution and Comparative Genomics,
PT31 Optimal Discriminating Subnetwork Markers Predict Responses To Cancer Treatments Phuong Dao Protein Interactions and Molecular Networks,
PT32 PhyloCSF: a comparative genomics method to distinguish protein-coding and non-coding regions Michael Lin Evolution and Comparative Genomics,
PT33 The role of proteosome-mediated proteolysis in modulating the activity of potentially harmful transcription factor activity in Saccharomyces cerevisiae Jasmin Fisher Applied Bioinformatics,
PT34 ccSVM: Correcting Support Vector Machines for confounding factors in biological data classification Limin Li Databases and Ontologies,
PT35 Mixed Model Coexpression (MMC): calculating gene coexpression while accounting for expression heterogeneity Nicholas Furlotte Applied Bioinformatics,
PT36 Ontology Patterns for Tabular Representations of Knowledge on Neglected Tropical Diseases Filipe Santana da Silva Databases and Ontologies,
PT37 A generalized model for multi-marker analysis of cell-cycle progression in synchrony experiments Michael B. Mayhew Applied Bioinformatics,
PT38 Detection and interpretation of metabolite-transcript co-responses using combined profiling data Henning Redestig Gene Regulation and Transcriptomics,
PT39 Systematic exploration of error sources in pyrosequencing flowgram data Susanne Balzer Applied Bioinformatics,
PT40 From Sets to Graphs: Towards a Realistic Enrichment Analysis of Transcriptomic Systems Ludwig Geistlinger Gene Regulation and Transcriptomics,
PT41 An enhanced Petri-net model to predict synergistic effects of pairwise drug combinations from gene microarray data Stephen Wong Applied Bioinformatics,
PT42 Small sets of interacting proteins suggest functional linkage mechanisms via Bayesian analogical reasoning Katherine A. Heller Gene Regulation and Transcriptomics,
PT43 Accurate Estimation of Heritability in Genome Wide Studies using Random Effects Models David Golan Population Genomics,
PT44 Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling Paweł P. Łabaj Gene Regulation and Transcriptomics,
PT45 StructHDP: Automatic inference of number of clusters from admixed genotype data Suyash Shringarpure Population Genomics,
PT46 An Integrative Clustering and Modeling Algorithm for Dynamical Gene Expression Data Julia Sivriver Gene Regulation and Transcriptomics,
PT47 Reconstruction of genealogical relationships with applications to Phase III of HapMap Sofia Kyriazopoulou-Panagiotopoulou Population Genomics,
PT48 A novel computational framework for simultaneous integration of multiple functional genomic data to identify microRNA-gene regulatory modules Shihua Zhang Gene Regulation and Transcriptomics,
SS01 BioLINK: Issues in Annotating Whole-Genome Data with Clinically Relevant Pharmacogenomics Knowledge Russ Altman ,
SS02 Results from CAGI 2010: successes and challenges Pauline Ng ,
SS02 Methods to predict individuals’ medical phenotypes from genomic data Sean Mooney, Rachel Karchin, Hannah Carter ,
SS02 Future directions for CAGI and Genome Interpretation
(Russ Altman, Rita Casadio, Iddo Friedberg, Mauno Vihinen, Moderator: John Moult)
Panel Discussion ,
SS03 Atomic accuracy and blind predictions through enumerative 3D RNA modeling Rhiju Das ,
SS03 Bacterial small RNAs in regulatory networks Susan Gottesman ,
SS04 Building ELIXIR Janet Thornton ,
SS04 ELIXIR and the other ESFRI BMS Projects Andrew Lyall ,
SS04 ELIXIR and Industry Dominic Clark ,
SS05 Synthetic biology: from parts to modules to therapeutic systems Ron Weiss ,
SS05 Managing the "BRICKS" of synthetic biology C. Forbes Dewey ,