ISMB 2012 TALKS

The full listing of talks can be found below.

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

Type Title Presenter Keywords
Keynote Seeing forward by looking back Richard H. Lathrop, Lawrence Hunter ,
Keynote Data integration for understanding dynamic biological systems Ziv Bar-Joseph ,
Keynote Analysis of transcriptome structure and chromatin landscapes Barbara Wold ,
Keynote Progress, challenges and opportunities in population genome sequencing Richard Durbin ,
Keynote Integrative Structural Biology Andrej Sali ,
Keynote The other Third: Coming to grips with membrane proteins Gunnar von Heijne ,
PP01 (PT) GenomeRing: alignment visualization based on SuperGenome coordinates Alexander Herbig Bioimaging,
PP02 (HT) Enriching the human apoptosis pathway by predicting the structures of protein-protein complexes Saliha Ece Acuner Ozbabacan Protein Interactions and Molecular Networks, Protein Structure & Function
PP03 (HT) Prediction by promoter logic in bacterial quorum sensing Mukund Thattai Gene Regulation and Transcriptomics, Protein Interactions & Molecular Networks
PP04 (PT) Joint Stage Recognition and Anatomical Annotation of Drosophila Gene Expression Patterns Xiao Cai Bioimaging,
PP05 (HT) Understanding human disease through 3D protein interactome network Haiyuan Yu Protein Interactions and Molecular Networks, Disease Models & Epidemiology
PP06 (HT) An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways Pavel Sumazin Gene Regulation and Transcriptomics, Applied Bioinformatics
PP07 (PT) Improved synapse detection for mGRASP-asssisted brain connectivity mapping Linqing Feng Bioimaging,
PP08 (HT) Guilt by association is the exception rather than the rule in gene networks Jesse Gillis Protein Interactions and Molecular Networks, Protein Interactions & Molecular Networks
PP09 (PT) Nonparametric Bayesian Inference for Perturbed and Orthologous Gene Regulatory Networks Christopher A. Penfold Gene Regulation and Transcriptomics,
PP10 (PT) Protein Subcellular Location Pattern Classification in Cellular Images Using Latent Discriminative Models Jieyue Li Bioimaging,
PP11 (HT) Putting genetic interactions in context through a global modular decomposition Chad Myers Protein Interactions and Molecular Networks, Gene Regulation & Transcriptomics
PP12 (PT) NOrMAL: Accurate Nucleosome Positioning using a Modified Gaussian Mixture Model Anton Polishko Gene Regulation and Transcriptomics,
PP13 (HT) Disrupting human pathways by minimal miRNA sets Ohad Balaga Protein Interactions and Molecular Networks, Gene Regulation & Transcriptomics
PP14 (HT) cn.MOPS: mixture of Poissons for discovering copy number variations in next generation sequencing data with a low false discovery rate Guenter Klambauer Population Genomics, Evolution & Comparative Genomics
PP15 (HT) RNA secondary structure mediates alternative 3’ss selection in Saccharomyces cerevisiae Eduardo Eyras Gene Regulation and Transcriptomics, Sequence Analysis
PP16 (HT) Identification of a Novel Class of Farnesylation Targets by Structure-Based Modeling of Binding Specificity Ora Schueler-Furman Protein Interactions and Molecular Networks, Protein Structure & Function
PP17 (HT) Systematic Detection of Epistatic Interactions Based on Allele Pair Frequencies Marit Ackermann Population Genomics,
PP18 (HT) Deciphering the Gene Translation Code and its Modeling Tamir Tuller Gene Regulation and Transcriptomics, Applied Bioinformatics
PP19 (PT) How networks change with time Yongjin Park Protein Interactions and Molecular Networks,
PP20 (PT) Leveraging Input and Output Structures For Joint Mapping of Epistatic and Marginal eQTLs Seunghak Lee Population Genomics,
PP21 (PT) Lineage based identification of cellular states and expression programs Tatsunori Hashimoto Gene Regulation and Transcriptomics,
PP22 (PT) A single-source k shortest paths algorithm to infer regulatory pathways in a gene network Yu-Keng Shih Protein Interactions and Molecular Networks,
PP23 (PT) Incorporating Prior Information into Association Studies Gregory Darnell Population Genomics,
PP24 (PT) Matching experiments across species using expression values and textual information Aaron Wise Gene Regulation and Transcriptomics,
PP25 (HT) HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment Johannes Soeding Applied Bioinformatics, Applied Bioinformatics
PP26 (PT) Toward 3D structure prediction of large RNA molecules: An integer programming framework to insert local 3D motifs in RNA secondary structure Vladimir Reinharz Sequence Analysis,
PP27 (HT) Differential oestrogen receptor binding is associated with clinical outcome in breast cancer Rory Stark Gene Regulation and Transcriptomics, Sequence Analysis
PP28 (HT) A structural systems biology approach to polypharmacological drug discovery Lei Xie Protein Structure and Function, Protein Interactions & Molecular Networks
PP29 (PT) Identification of Sequence-Structure RNA Binding Motifs for SELEX Derived Aptamers Jan Hoinka Sequence Analysis / RNA,
PP30 (HT) Construction of regulatory networks using expression time-series data of a genotyped population Ka Yee Yeung Gene Regulation and Transcriptomics, Applied Bioinformatics
PP31 (HT) Integrating energy calculations with functional assays to decipher the specificity of G-protein inactivation by RGS proteins Mickey Kosloff Protein Structure and Function, Protein Structure & Function
PP32 (PT) GraphClust: alignment-free structural clustering of local RNA secondary structures Fabrizio Costa Sequence Analysis / RNA,
PP33 (HT) A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information Xiaotu Ma Ma Gene Regulation and Transcriptomics, Sequence Analysis
PP34 (HT) Text Mining Improves Prediction of Protein Functional Sites Karin Verspoor Protein Structure and Function, Text Mining
PP35 (PT) Detection of Allele-Specific Methylations through a Generalized Heterogeneous Epigenome Model Qian Peng Sequence Analysis / RNA,
PP36 (HT) Functional conservation of enhancers without sequence conservation Ivan Ovcharenko Gene Regulation and Transcriptomics, Evolution & Comparative Genomics
PP37 (HT) Why CDRs are not what you think they are or How to identify the real antigen binding sites Vered Kunik Protein Structure and Function,
PP38 (HT) Putative amino acid determinants of the emergence of the 2009 influenza A (H1N1) virus in the human population Nir Ben-Tal Sequence Analysis, Protein Structure & Function
PP39 (HT) Mapping and analysis of chromatin state dynamics in nine human cell types Jason Ernst Gene Regulation and Transcriptomics,
PP40 (HT) Image-derived, Three-dimensional Generative Models of Cellular Organization Robert Murphy Bioimaging & Data Visualization, other
PP41 (HT) Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach Keren Lasker Protein Structure and Function, Protein Interactions & Molecular Networks
PP42 (HT) Oases: Robust de novo RNA-seq assembly across the dynamic range of expression levels Marcel Schulz Sequence Analysis, Gene Regulation & Transcriptomics
PP43 (HT) Proteomics Signature Profiling (PSP): A novel contextualization approach applied towards cancer proteomics Wilson Wen Bin Goh Mass Spectrometry and Proteomics, Mass Spectrometry & Proteomics
PP44 (HT) Toward interoperable bioscience data Susanna-Assunta Sansone Databases and Ontologies, Applied Bioinformatics
PP45 (PT) A Conditional Neural Fields model for protein threading Jianzhu Ma Protein Structure and Function,
PP46 (HT) Multiple reference genomes and transcriptomes for Arabidopsis thaliana Gunnar Ratsch Sequence Analysis, Population Genomics
PP47 (HT) Identifying the unknowns by aligning fragmentation trees Sebastian Böcker Mass Spectrometry and Proteomics, Applied Bioinformatics
PP48 (HT) The Three-Dimensional Architecture of a Bacterial Genome and Its Alteration by Genetic Perturbation Davide Bau other, Applied Bioinformatics
PP49 (PT) Novel domain combinations in proteins encoded by chimeric transcripts Milana Frenkel-Morgenstern Protein Structure and Function,
PP50 (PT) Xenome - A Tool for Classifying Reads from Xenograft Samples Thomas Conway Sequence Analysis,
PP51 (PT) Fast alignment of fragmentation trees Franziska Hufsky Mass Spectrometry and Proteomics,
PP52 (PT) Dissect: Detection and Characterization of Novel Structural Alterations in Transcribed Sequences Deniz Yorukoglu Sequence Analysis,
PP53 (PT) MoRFpred, a computational tool for sequence-based prediction and characterization of disorder-to-order transitioning binding sites in proteins Fatemeh Miri Disfani Protein Structure and Function,
PP54 (HT) Uncovering Ancient Networks from Present-Day Interactions Carl Kingsford Protein Interactions and Molecular Networks, Evolution & Comparative Genomics
PP55 (HT) An effective statistical evaluation of ChIPseq dataset similarity Maria Chikina Applied Bioinformatics,
PP56 (PT) Extending ontologies by finding siblings using set expansion techniques Götz Fabian Databases and Ontologies / Disease Models and Epid,
PP57 (PT) Recognition Models to Predict DNA-binding Specificities of Homeodomain Proteins Ryan Christensen Protein Structure and Function,
PP58 (HT) A three-dimensional map of protein networks within and between species Yu Xia Protein Interactions and Molecular Networks, Protein Structure & Function
PP59 (PT) DELISHUS: An Efficient and Exact Algorithm for Genome-Wide Detection of Deletion Polymorphism in Autism Derek Aguiar Population Genomics,
PP60 (PT) Ranking of Multidimensional Drug Profiling Data by Fractional Adjusted Bi-Partitional Scores Dorit Hochbaum Disease Models and Epidemiology,
PP61 (PT) TMBMODEL: Toward 3D modeling of transmembrane beta barrel proteins based on z-coordinate and topology prediction Sikander Hayat Protein Structure and Function,
PP62 (HT) Network-Based Prediction and Analysis of HIV Dependency Factors T. Murali Protein Interactions and Molecular Networks,
PP63 (PT) SEQuel: Improving the Accuracy of Genome Assemblies Roy Ronen Sequence Analysis,
PP64 (PT) DACTAL: divide-and-conquer trees (almost) without alignments Serita Nelesen Evolution and Comparative Genomics,
PP65 (PT) Minimum Message Length Inference of Secondary Structure from Protein Coordinate Data. Arun Konagurthu Protein Structure and Function,
PP66 (PT) Weighted Pooling - Practical and Cost Effective Techniques for Pooled High Throughput Sequencing David Golan Sequence Analysis,
PP67 (HT) Predicting relapse in medulloblastoma patients by integrating evidence from clinical and genomic features Pablo Tamayo Disease Models and Epidemiology,
PP68 (HT) Chemical-Protein Interactome and its Application in Personalized Medicine and Drug Repositioning Lun Yang Applied Bioinformatics,
PP69 (HT) Large-scale DNA editing of retrotransposons accelerates mammalian genome evolution. Erez Levanon Evolution and Comparative Genomics,
PP70 (HT) Interpreting human disease associations using comparative genomic and epigenomic signatures Manolis Kellis Disease Models and Epidemiology, Evolution & Comparative Genomics
PP71 (HT) A data integration approach illustrates evolutionary mechanisms of ligand selectivity between related protein targets Felix Kruger Applied Bioinformatics, Evolution & Comparative Genomics
PP72 (HT) Domain architecture conservation in orthologs Erik Sonnhammer Evolution and Comparative Genomics, Protein Structure & Function
PP73 (PT) Statistical model-based testing to evaluate the recurrence of genomic aberrations Atsushi Niida Disease Models and Epidemiology,
PP74 (HT) Materiomics: instructing cell fate using topographical biomaterials Marc Hulsman Applied Bioinformatics, Applied Bioinformatics
PP75 (HT) Viral-host coevolution: Playing 'seek and hide' Michal Linial Evolution and Comparative Genomics, Sequence Analysis
PP76 (PT) Data-Driven Integration Of Epidemiological And Toxicological Data To Select Candidate Interacting Genes And Environmental Factors In Association With Disease Chirag Patel Disease Models and Epidemiology,
PP77 (PT) Identifying Disease Sensitive and Quantitative Trait Relevant Biomarkers from Heterogeneous Imaging Genetics Data via Sparse Multi-Modal Multi-Task Learning Hua Wang Applied Bioinformatics / Disease Models,
PP78 (PT) Efficient Algorithms for the Reconciliation Problem with Gene Duplication, Horizontal Transfer, and Loss Mukul S. Bansal Evolution and Comparative Genomics,
SS2_partB Reconstructing the Regulatory Network of TB: Deconstruction of the Hypoxic Response Elham Azizi ,
SS2_partD Systems Biology of Infectious Disease Jason McDermott ,
SS7_partA Assessing the contribution of scientists to Wikipedia for Pfam and Rfam annotation Alex Bateman ,
SS7_partB WikiPathways and How to Change the World (or at least your small corner of the world) Alexander Pico ,
SS7_partC The Gene Wiki: Crowdsourcing the annotation of human gene function Andrew Su ,
SS7_partD Distributed Community Intelligence through the Scientific Discovery Game Foldit Firas Khatib ,