ISMB 2014 TALKS

The full listing of talks can be found below.

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

Type Title Presenter Keywords
awards Awards ,
Keynote Good Things Come in Small Packages – Replicators and Innovators Michal Linial ,
Keynote DNA Assembly: Past, Present, and Future Eugene Myers ,
Keynote Biomedical Quants of the World Unite! We only have our disease burden to lose Isaac Kohane ,
Keynote A multidimensional single cell approach to understand cellular behavior Dana Pe'er ,
Keynote Biomaterials and biotechnology: From the discovery of the first angiogenesis inhibitors to the development of controlled drug delivery systems and the foundation of tissue engineering. Robert Langer ,
Keynote Informatics for understanding drug response at all scales. Russ Altman ,
PP01 Simultaneous Identification of Multiple Driver Pathways in Cancer Mark Leiserson Applied Bioinformatics, Protein Interactions & Molecular Networks
PP02 Ragout - A reference-assisted assembly tool for bacterial genomes Son Pham Sequence Analysis,
PP03 Linking hypothetical patterns to disease molecular signatures in Alzheimer's disease Ashutosh Malhotra Text Mining, Databases & Ontologies
PP04 AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references Ergude Bao Sequence Analysis,
PP05 Cross-study validation for assessment of prediction models and algorithms Christoph Bernau Gene Regulation and Transcriptomics,
PP06 Constructing module maps for integrated analysis of heterogeneous biological networks David Amar Protein Interactions & Molecular Networks, Gene Regulation & Transcriptomics
PP07 ExSPAnder: a Universal Repeat Resolver for DNA Fragment Assembly Andrey D. Prjibelski Sequence Analysis,
PP08 Large scale analysis of signal reachability Andrei Todor Gene Regulation and Transcriptomics,
PP09 Complete Genome Assembly with Long Reads Adam Phillippy Sequence Analysis, Applied Bioinformatics
PP10 GRASP: Analysis of genotype-phenotype results from 1,390 genome-wide association studies and corresponding open access database Richard Leslie Population Genomics,
PP11 Capturing short tandem repeat variation from paired-end sequencing data Mikael Boden Sequence Analysis, Population Genomics
PP12 How antibodies chase antigens, how Antigens try to escape and how we can use this to predict antibody specificity Inbal Sela-Culang Protein Structure & Function, Protein Interactions & Molecular Networks
PP13 A comparative meta-analysis of prognostic gene signatures for late-stage ovarian cancer Levi Waldron Applied Bioinformatics, Disease Models & Epidemiology
PP14 BlockClust: efficient clustering and classification of non-coding RNAs from short read profiles Fabrizio Costa RNA Bioinformatics,
PP15 Tertiary structure-based prediction for conformational B-cell epitopes through B factors Jing Ren Protein Structure and Function,
PP16 Dissecting Cancer Heterogeneity with network based approach Teresa Przytycka Protein Interactions & Molecular Networks, Disease Models & Epidemiology
PP17 WISECONDOR detects small fetal chromosomal aberrations in low-coverage NGS data of maternal plasma. Roy Straver Applied Bioinformatics, Sequence Analysis
PP18 An Efficient Parallel Algorithm for Accelerating Computational Protein Design Yichao Zhou Protein Structure and Function,
PP19 Inductive Matrix Completion for Predicting Gene-Disease Associations Nagarajan Natarajan Disease Models and Epidemiology,
PP20 Probabilistic Method for Detecting Copy Number Variation in a Fetal Genome using Maternal Plasma Sequencing Ladislav Rampášek Population Genomics,
PP21 BioC: a minimalist approach to interoperability for biomedical text processing Donald C. Comeau Text Mining, Databases & Ontologies
PP22 Country-specific antibiotic use practices impact the human gut resistome Kristoffer Forslund Disease Models & Epidemiology, Evolution & Comparative Genomics
PP23 RNA-Skim: a rapid method for RNA-Seq quantification at transcript level Zhaojun Zhang RNA Bioinformatics,
PP24 Metabolite Identification through Multiple Kernel Learning on Fragmentation Trees Huibin Shen Mass Spectrometry and Proteomics,
PP25 Methods for time series analysis of RNA-seq data with application to human Th17 cell differentiation Tarmo Äijö Gene Regulation and Transcriptomics,
PP26 Relating the metatranscriptome and metagenome of the human gut Eric Franzosa Gene Regulation & Transcriptomics, Applied Bioinformatics
PP27 Power and Limitations of RNA-Seq: findings from the SEQC (MAQC-III) consortium David Kreil Gene Regulation & Transcriptomics, other
PP28 Computational Biology in Medicine: Novel Targets and Drug Repositioning Use Cases Pankaj Agarwal Applied Bioinformatics, other
PP29 Cell-selective labeling using amino acid precursors for proteomic studies of multicellular environments Nicholas Gauthier Mass Spectrometry & Proteomics, Protein Interactions & Molecular Networks
PP30 Pipasic: Similarity and Expression Correction for Strain-Level Identification and Quantification in Metaproteomics Anke Penzlin Mass Spectrometry and Proteomics,
PP31 Deep learning of the tissue-regulated splicing code Michael Leung Gene Regulation and Transcriptomics,
PP32 DrugComboRanker: Drug Combination Discovery Based on Target Network Analysis Lei Huang Protein Interactions and Molecular Networks,
PP33 Automated detection and tracking of many cells by using 4D live-cell imaging data Terumasa Tokunaga Bioimaging and Data Visualization,
PP34 Primate Transcript and Protein Expression Levels Evolve under Compensatory Selection Pressures Zia Khan Mass Spectrometry & Proteomics, Gene Regulation & Transcriptomics
PP35 Systematically Differentiating Functions for Alternatively Spliced Isoforms through Integrating RNA-seq Data Yuanfang Guan Protein Structure & Function, Gene Regulation & Transcriptomics
PP36 Drug synergy screen and network modeling in dedifferentiated liposarcoma identifies CDK4 and IGF1R as synergistic drug targets Martin Miller Protein Interactions & Molecular Networks, Disease Models & Epidemiology
PP37 NaviCell: a web-based environment for navigation, curation, maintenance and data analysis in the context of large molecular interaction maps Emmanuel Barillot Protein Interactions & Molecular Networks, Gene Regulation & Transcriptomics
PP38 Efficient Modeling and Active Learning Discovery of Biological Responses Armaghan Naik Applied Bioinformatics, other
PP39 Analyzing DNase I biases reveals a novel DNA methylation readout mechanism Harmen Bussemaker Gene Regulation & Transcriptomics, Protein Interactions & Molecular Networks
PP40 Statistical challenges in whole-exome sequencing of 7000 individuals with schizophrenia and controls Menachem Fromer Sequence Analysis, Disease Models & Epidemiology
PP41 Pareto-Optimal Phylogenetic Tree Reconciliation Ran Libeskind-Hadas Evolution and Comparative Genomics,
PP42 Stochastic EM-based TFBS motif discovery with MITSU Alastair Kilpatrick Sequence Analysis,
PP43 Constructing Hepitypes:Phasing Local Genotyping and DNA Methylation Wen-Yu Chung Sequence Analysis, Gene Regulation & Transcriptomics
PP44 Genome leaks Steven Brenner other, Population Genomics
PP45 Human disease locus discovery and mapping to molecular pathways through phylogenetic profiling Yuval Tabach Evolution & Comparative Genomics, Disease Models & Epidemiology
PP46 Gene network inference by probabilistic scoring of relationships from a factorized model of interactions Marinka Zitnik Protein Interactions and Molecular Networks,
PP47 A-to-I RNA editing occurs at over a hundred million genomic sites, located in a majority of human genes Erez Levanon Gene Regulation & Transcriptomics, Evolution & Comparative Genomics
PP48 Privacy Preserving Protocol for Detecting Genetic Relatives Using Rare Variants Farhad Hormozdiari Population Genomics,
PP49 Arboretum: reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules Sushmita Roy Evolution & Comparative Genomics, Gene Regulation & Transcriptomics
PP50 Functional Association Networks as Priors for Gene Regulatory Network Inference Matthew Studham Gene Regulation and Transcriptomics,
PP51 Ubiquitously transcribed genes use alternative polyadenylation to achieve tissue-specific expression Steve Lianoglou Gene Regulation & Transcriptomics, Applied Bioinformatics
PP52 Detecting chromatin modifications in cancer samples: challenges and solutions Valentina Boeva Gene Regulation & Transcriptomics, Applied Bioinformatics
PP53 Proteomic Universal Correlate of Evolution David Horn Evolution & Comparative Genomics, Sequence Analysis
PP54 Novel Burkholderia mallei Virulence Factors Linked to Specific Host-Pathogen Protein Interactions Jaques Reifman Protein Interactions & Molecular Networks,
PP55 Mapping Functional Transcription Factor Networks from Gene Expression Data Michael Brent Gene Regulation & Transcriptomics,
PP56 Protein Expansion Is Primarily due to Indels in Intrinsically Disordered Regions. Arne Elofsson Evolution & Comparative Genomics, Protein Structure & Function
PP57 Graph Regularized Dual Lasso for Robust eQTL Mapping Wei Cheng Gene Regulation and Transcriptomics,
PP58 Mathematical Modeling of Virus-Host Interactions Lars Kaderali Disease Models & Epidemiology, Applied Bioinformatics
PP59 Chromatin landscapes and long-range interactions of retroviral and transposon integrations Jeroen de Ridder Gene Regulation & Transcriptomics, Disease Models & Epidemiology
PP60 Characterizing changes in the rate of protein-protein dissociation upon interface mutation using hotspot energy and organization Rudi Agius Protein Structure & Function, Protein Interactions & Molecular Networks
PP61 EPIQ - Efficient detection of SNP-SNP epistatic interactions for quantitative traits Yaara Arkin Applied Bioinformatics,
PP62 Accurate viral population assembly from ultra-deep sequencing data Serghei Mangul Sequence Analysis,
PP63 Large-scale reconstruction of 3D structures of human chromosomes from chromosomal contact data Jianlin Cheng Evolution & Comparative Genomics,
PP64 Why N-Terminal domains tend to be shorter than C-Terminal domains? Ron Unger Protein Structure & Function, Sequence Analysis
PP65 A combinatorial approach for analyzing intra-tumor heterogeneity from high-throughput sequencing data Iman Hajirasouliha Evolution and Comparative Genomics,
PP66 Deciphering human disease mutations through the atomic-resolution protein interactome network Haiyuan Yu Protein Interactions & Molecular Networks, Disease Models & Epidemiology
PP67 A statistical approach for inferring the 3D structure of the genome Nelle Varoquaux Applied Bioinformatics,
PP68 New Directions for Diffusion-Based Network Prediction of Protein Function: Incorporating Pathways with Confidence Mengfei Cao Protein Interactions and Molecular Networks,
PP69 Reconstructing tumor evolution using simple somatic mutation frequencies Quaid Morris Evolution & Comparative Genomics, Disease Models & Epidemiology
PP70 Genomic underpinnings for network patterns and evolution Luay Nakhleh Protein Interactions & Molecular Networks, Gene Regulation & Transcriptomics
PP71 Inferring Gene Ontologies from Pairwise Similarity Data Michael Kramer Applied Bioinformatics,
PP72 Evaluating Synteny for Improved Comparative Studies Cristina G. Ghiurcuta Applied Bioinformatics,
PP73 Network-based stratification of tumor mutations Matan Hofree Applied Bioinformatics, Disease Models & Epidemiology
PP74 Scale-space measures for graph topology link protein network architecture to function Marc Hulsman Protein Interactions and Molecular Networks,
PP75 Using association rule mining to determine promising secondary phenotyping hypotheses Anika Oellrich Databases, Ontologies and Text Mining,
PP76 Robust Clinical Outcome Prediction based on Bayesian Analysis of Transcriptional Profiles and Prior Causal Networks Kourosh Zarringhalam Disease Models and Epidemiology,
PP77 Detecting independent and recurrent copy number aberrations using interval graphs Hsin-Ta Wu Population Genomics,
PP78 GraphProt: How to make sense out of CLIP-seq data Rolf Backofen Sequence Analysis, Protein Interactions & Molecular Networks
PP79 Improved exome prioritization of disease genes through cross-species phenotype comparison Peter Robinson Databases & Ontologies, Sequence Analysis
PP80 MIRA: Mutual Information-Based Reporter Algorithm for Metabolic Networks A. Ercument Cicek Metabolomic Networks,
PP81 Emerging landscape of oncogenic signatures across human cancers Giovanni Ciriello Applied Bioinformatics, Disease Models & Epidemiology
PP82 From 1D to 3D and back: Genome scaffolding from DNA interaction frequency Noam Kaplan other, other
PP83 A community effort to assess drug sensitivity prediction algorithms identifies approaches for improved performance James Costello Applied Bioinformatics, Disease Models & Epidemiology
PP84 Metabolome-scale prediction of intermediate compounds in multi-step metabolic pathways with a recursive supervised approach Masaaki Kotera Metabolomic Networks,
PP85 MicroRNA-gene association as a prognostic biomarker in cancer exposes disease mechanisms Rotem Ben-Hamo Applied Bioinformatics, Applied Bioinformatics
Sig1 A quality control system for the certification of ChIP-seq and enrichment-related NGS-generated datasets Marco Mendoza Parra ,
Sig2 Using ChIP-seq and DNase-seq to identify TF binding and their target genes Xiaole Shirley Liu ,
Sig2_10 Transcriptional (dis)regulation in cancer genomes Carl Herrmann ,
Sig2_5 Characterizing context-dependent transcription factor activity Shaun Mahony ,
Sig2_6 Mapping transcription factor networks that govern specific physiological processes with NetProphet and PhenoProphet Michael Brent ,
Sig2_8 Evolution of a transcription factor co-expression network active in the primate prefrontal cortex Katja Nowick ,
Sig3 Computational analysis of chromatin-state plasticity provides insights into cell identity Guo-Cheng Yuan ,
Sig6 Improved Computational and Experimental Methods for Motif Determination Gary Stormo ,
Sig7 The use of HT-SELEX to infer TF binding models: comparison to PBM and an improved algorithm Yaron Orenstein ,
SS01-B Experimental approaches for elucidating interactions between drugs and gut microbes Peter Turnbaugh ,
SS04-A Human Genome Analysis Mark Gerstein ,
SS04-B1 Interatomics: Computational Analysis of Novel Drug Opportunities Ram Samudrala ,
SS04-B2 Natural Modeling in Structural Biology Peter Minary ,
SS05-B Evaluating Tumor Exome Sequencing in the Oncology Clinic: Lessons from the BASIC3 study Will Parsons ,
SS05-C Guiding clinical decision-making with omics data Josh Stuart ,
SS06-B Partitioning heritability across functional categories Alkes Price ,
ST01 Nobel Prize Celebration: Arieh Warshel’s Legacy Lynn Kamerlin ,