ISMB/ECCB 2013 TALKS

The full listing of talks can be found below.

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

Type Title Presenter Keywords
Keynote How Chromatin organization and epigenetics talk with alternative splicing Gil Ast ,
Keynote Sequencing based functional genomics (analysis) Lior Pachter ,
Keynote Searching for Signals in Sequences Gary Stormo ,
Keynote Results may vary: what is reproducible? why do open science and who gets the credit? Carole Goble ,
Keynote Protein Interactions in Health and Disease David Eisenberg ,
PP01 (PT) Simple Topological Properties Predict Functional Misannotations in a Metabolic Network Rodrigo Liberal Metabolic networks, Network topology, Enzyme function
PP02 (HT) Heart Attacks: Leveraging A Cardiovascular Systems Biology Strategy To Predict Future Outcomes Carlo Vittorio Cannistraci Applied Bioinformatics, Applied Bioinformatics
PP03 (HT) Computational identification of a transiently open L1/S3 pocket for reactivation of mutant p53. Richard Lathrop Applied Bioinformatics, Disease Models & Epidemiology
PP04 (PT) Stability selection for regression-based models of transcription factor-DNA binding specificity Fantine Mordelet DNA binding specificity, Regression models, LASSO, Protein binding microarr
PP05 (HT) Of Men and Not Mice: Comparative Genomic Analysis of Human Diseases and Mouse Models Wenzhong Xiao Disease Models & Epidemiology, Evolution & Comparative Genomics
PP06 (HT) Virtual ligand screening against comparative structural models of membrane transporters Avner Schlessinger Protein Structure & Function, Applied Bioinformatics
PP07 (PT) A Graph Kernel Approach for Alignment-Free Domain-Peptide Interaction Prediction with an Application to Human SH3 Domains Kousik Kundu PRM: Protein Recognition module, SVM: Support Vector Machine, PWM: Position Weight
PP08 (HT) Impact of genetic dynamics and single-cell heterogeneity on development of nonstandard personalized medicine strategies for cancer Chen-Hsiang Yeang Applied Bioinformatics, Disease Models & Epidemiology
PP09 (HT) Extensive changes in DNA methylation are associated with expression of mutant huntingtin Christopher Ng Gene Regulation & Transcriptomics, Applied Bioinformatics
PP10 (HT) Systems-based metatranscriptomic analysis Xuejian Xiong Sequence Analysis, Applied Bioinformatics
PP11 (HT) Metabolic phenotypic analysis uncovers reduced proliferation associated with oxidative stress in progressed breast cancer Livnat Jerby Arnon Applied Bioinformatics, Disease Models & Epidemiology
PP12 (HT) Mapping the Strategies of Viruses Hijacking Human Host Cells – An Experimental and Computational Comparative Study Jacques Colinge Protein Interactions & Molecular Networks, Mass Spectrometry & Proteomics
PP13 (HT) Ultrashort and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution Caroline Friedel Gene Regulation & Transcriptomics, other
PP14 (HT) Identifying differentially expressed transcripts from RNA-seq data with biological variation Peter Glaus Gene Regulation & Transcriptomics, Sequence Analysis
PP15 (PT) Multi-task learning for Host-Pathogen protein interactions Meghana Kshirsagar Host-pathogen protein interaction, multi-task learning, machine learning, bacteria hu
PP16 (HT) Gene expression anti-profiles as a basis for accurate universal cancer signatures Hector Corrada Bravo Applied Bioinformatics, Gene Regulation & Transcriptomics
PP17 (PT) GeneScissors: a comprehensive approach to detecting and correcting spurious transcriptome inference due to RNAseq reads misalignment Zhaojun Zhang Pseudogene, RNA-seq, RNA-seq Alignment, RNA-seq Assembling
PP18 (HT) A Conserved Map of Genetic Interactions Induced by DNA Damage Rohith Srivas Protein Interactions & Molecular Networks, Disease Models & Epidemiology
PP19 (HT) Newborn screening for SCID identifies patients with ataxia telangiectasia Steven Brenner Sequence Analysis, Disease Models & Epidemiology
PP20 (PT) Poly(A) motif prediction using spectral latent features from human DNA sequences Bo Xie Poly(A) motif, classification, generative learning, discriminativ
PP21 (HT) Synthetic lethality between gene defects affecting a single non-essential molecular pathway with reversible steps Inna Kuperstein Protein Interactions & Molecular Networks, Disease Models & Epidemiology
PP22 (HT) BioJS: An Open Source JavaScript Framework for Biological Data Visualization. Bioinformatics Manuel Corpas Bioimaging & Data Visualization, Databases & Ontologies
PP23 (PT) Genome-wide identification and predictive modeling of tissue-specific alternative polyadenylation Dina Hafez Alternative polyadenylation, tissue-specific regulation, RNA-seq, predictive mo
PP24 (HT) Efficient Computation of Gene Tree Probability based on Coalescent Theory under Incomplete Lineage Sorting Yufeng Wu Population Genomics, Evolution & Comparative Genomics
PP25 (PT) Predicting protein contact map using evolutionary and physical constraints by integer programming Jinbo Xu Protein contact map prediction, integer programming, physical constraint, evolutio
PP26 (HT) Interpreting Personal Transcriptomes: Personalized Mechanism-Scale Profiling Predicts Survival in Oral, Prostate, Lung and Gastric Cancers Yves Lussier Applied Bioinformatics, Databases & Ontologies
PP27 (HT) Deconvolution of targeted protein-protein interaction maps Alexey Stukalov Protein Interactions & Molecular Networks, Mass Spectrometry & Proteomics
PP28 (PT) IBD-Groupon : An Efficient Method for Detecting Group-wise Identity-by-Descent regions simultaneously in Multiple Individuals based on Pairwise IBD relationships Dan He Identity-by-Descent, HMM, MCMC, group-wise IBD
PP29 (PT) ThreaDom: Extracting Protein Domain Boundary Information from Multiple Threading Alignments Zhidong Xue Protein structure prediction, Protein domain prediction, Threading, CASP experim
PP30 (HT) Compressive Genomics Michael Baym Sequence Analysis, Databases & Ontologies
PP31 (PT) Minimum curvilinearity to enhance topological prediction of protein interactions by network embedding Carlo Vittorio Cannistraci Network topology, network embedding, topological prediction, nonline
PP32 (PT) Inference of historical migration rates via haplotype sharing Pier Francesco Palamara Population genetics, Demographic inference, Identity by descent, Haplot
PP33 (PT) Protein Threading Using Context-Specific Alignment Potential Jianzhu Ma Protein Threading, Alignment Potential, Protein Pairwise Information
PP34 (PT) Predicting Drug-Target Interactions Using Restricted Boltzmann Machines Yuhao Wang Drug-Target Interaction, Drug Repositioning, Restricted Boltzmann Machine,
PP35 (PT) Supervised de novo reconstruction of metabolic pathways from metabolome-scale compound sets Masaaki Kotera Metabolic network, de novo metabolic pathway reconstruction, enzymati
PP36 (PT) Efficient network-guided multi-locus association mapping with graph cuts Chloé-Agathe Azencott Feature selection, statistical genetics, network biology, graph minin
PP37 (HT) The role of proteins encoded by chimeric RNAs in eukaryotes Milana Frenkel-Morgenstern Evolution & Comparative Genomics, Sequence Analysis
PP38 (HT) Navigating chemical and biological space – in the search of novel pharmaceuticals Paula Petrone Protein Interactions & Molecular Networks, other
PP39 (PT) A framework for scalable parameter estimation of gene circuit models using structural information Xin Gao Parameter estimation, gene circuits, systems biology, synthetic biology
PP40 (PT) Identifying proteins controlling key disease signaling pathways Anthony Gitter Pathway inference, viral infection, RNAi screens, genetic interaction
PP41 (PT) Automated Cellular Annotation for High Resolution Images of Adult C. elegans Sarah Aerni Bioinformatics, Gene expression, Image analysis, Machine learning
PP42 (PT) Haplotype assembly in polyploid genomes and identical by descent shared tracts Derek Aguiar Haplotype, haplotype assembly, single individual haplotyping,
PP43 (HT) Emerging methods in protein co‐evolution David Juan Evolution & Comparative Genomics, Sequence Analysis
PP44 (PT) Compressive genomics for protein databases Noah Daniels Sequence Analysis, protein search,BLAST
PP45 (PT) FuncISH: Learning a functional representation of neural ISH images Noa Liscovitch PCA, censored data, censoring, single-cell qPCR, Gaussi
PP46 (PT) Using State Machines to Model the IonTorrent Sequencing Process and Improve Read Error-Rates David Golan Sequencing, Viterbi, IonTorrent, Flowgram, Base calling
PP47 (HT) Short Toxin-like Proteins Abound in Cnidaria Genomes Michal Linial Evolution & Comparative Genomics, Sequence Analysis
PP48 (HT) Predicting the molecular complexity of sequencing libraries Andrew Smith Applied Bioinformatics, other
PP49 (PT) Automated annotation of gene expression image sequences via nonparametric factor analysis and conditional random fields Iulian Pruteanu-Malinici Nonparametric sparse Bayesian factor analysis, undirected graphical models, gene annotation, miss
PP50 (HT) A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis Mathieu Clément-Ziza Mass Spectrometry & Proteomics, Gene Regulation & Transcriptomics
PP51 (PT) Predicting protein interactions via parsimonious network history inference Robert Patro Protein interaction evolution, ancestral network reconstruction, interaction pred
PP52 (HT) Interpreting genomic data via entropic dissection Rajeev Azad Sequence Analysis, Applied Bioinformatics
PP53 (PT) A High-Throughput Framework to Detect Synapses in Electron Microscopy Images Saket Navlakha Image processing, Machine learning, Semi-supervised, Synapses, Elect
PP54 (HT) A probabilistic histone modification map of the human genome and its implications for gene regulation Misook Ha Sequence Analysis, Gene Regulation & Transcriptomics
PP55 (HT) Identification of small RNA pathway genes using patterns of phylogenetic conservation and divergence. Yuval Tabach Evolution & Comparative Genomics, other
PP56 (PT) IDBA-Tran: A More Robust de novo de Bruijn Graph Assembler for Transcriptomes with Uneven Expression Levels Yu Peng Transcriptome assembling, paired-end reads, isoforms, RNA-Seq, de Bruijn gra
PP57 (HT) Visual Exploration for Cancer Subtype Analysis Nils Gehlenborg Bioimaging & Data Visualization, Applied Bioinformatics
PP58 (HT) Simulating Delta/Notch Signaling in Somitogenesis and Pancreas Development Hendrik Tiedemann Gene Regulation & Transcriptomics, Protein Interactions & Molecular Networks
PP59 (HT) From sequence co-evolution to protein (complex) structure prediction Martin Weigt Sequence Analysis, Protein Structure & Function
PP60 (PT) Short Read Alignment with Populations of Genomes Victoria Popic Short read alignment, genome collection, burrows-wheeler transform
PP61 (HT) The cBio Portal for Cancer Genomics Nikolaus Schultz Bioimaging & Data Visualization, Databases & Ontologies
PP62 (HT) ATARiS: Computational quantification of gene suppression phenotypes from multisample RNAi screens Aviad Tsherniak Gene Regulation & Transcriptomics, Gene Regulation & Transcriptomics
PP63 (HT) Accurate prediction of peptide-induced dynamical changes within the second PDZ domain of PTP1e Elisa Cilia Protein Structure & Function,
PP64 (PT) Design of Shortest Double-Stranded DNA Sequences Covering All K-mers with Applications to Protein Binding Microarrays and Synthetic Enhancers Yaron Orenstein de Bruijn sequence, de Bruijn graph, protein binding microarray, oligo
PP65 (HT) Visualizing and Mining Chemical-Biological Space Stefan Kramer Applied Bioinformatics, Protein Structure & Function
PP66 (PT) Learning Subgroup-Specific Regulatory Interactions and Regulator Independence with PARADIGM Andrew J. Sedgewick Cancer, pathway, gene expression, copy number, probabilist
PP67 (HT) A large‐scale evaluation of computational protein function prediction Predrag Radivojac Protein Structure & Function,
PP68 (HT) Combinatorial Pooling Enables Selective Sequencing of the Barley Gene Space Denisa Duma Sequence Analysis, Applied Bioinformatics
PP69 (HT) Designing with the user in mind: how UCD can work for bioinformatics Jennifer Cham other, other
PP70 (PT) Hard-wired heterogeneity in blood stem cells revealed using a dynamic regulatory network model Nicola Bonzanni Haematopoietic stem cell, cis-regulatory elements, transcription factor netw
PP71 (HT) Comparative proteomics reveals a significant bias toward alternative protein isoforms with conserved structure and functioncc Michael Liam Tress Mass Spectrometry & Proteomics, Evolution & Comparative Genomics
PP72 (HT) Genetic variants in the next generation: detection, reprioritizing and function annotation Junwen Wang Databases & Ontologies, Sequence Analysis
PP73 (HT) Metagenomic inference and biomarker discovery for the gut microbiome in inflammatory bowel disease Timothy Tickle Disease Models & Epidemiology, Applied Bioinformatics
PP74 (HT) Interplay of microRNAs, transcription factors and target genes: linking dynamic expression changes to function Petr Nazarov Gene Regulation & Transcriptomics,
PP75 (HT) Systematic Computational Drug Repositioning Philippe Sanseau Applied Bioinformatics, Disease Models & Epidemiology
PP76 (PT) Information-theoretic evaluation of predicted ontological annotations Wyatt Clark Gene Ontology, Bayesian Network, Information Content, Protein Fun
PP77 (PT) CAMPways: Constrained Alignment Framework for the Comparative Analysis of a Pair of Metabolic Pathways Gamze Abaka Metabolic pathways, Network alignment, Graph matching, Algorithms
PP78 (PT) Integrating sequence, expression and interaction data to determine condition-specific miRNA regulation Hai-Son Le microRNA, gene regulation, transcriptomics, regulatory netwo
PP79 (PT) Phylogenetic analysis of multiprobe fluorescence in situ hybridization data from tumor cell populations Salim Akhter Chowdhury dose-response analysis, antioxidant mechanisms of interactions, simulation
PP80 (HT) Turning networks into ontologies of gene function Janusz Dutkowski Protein Interactions & Molecular Networks, Applied Bioinformatics
PP81 (HT) Along Signal Paths: Connecting Pathway Annotation to Topological Analyses Gabriele Sales Protein Interactions & Molecular Networks, Gene Regulation & Transcriptomics
PP82 (PT) The RNA Newton Polytope and Learnability of Energy Parameters Elmirasadat Forouzmand RNA structure prediction, Energy parameter estimation, Computational algebra
PP83 (PT) Automated target segmentation and fast alignment methods for high-throughput classification and averaging of crowded cryo-electron subtomograms Min Xu Cryo-electron tomography, Subtomogram alignment, Subtomogram classification
PP84 (PT) A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text Makoto Miwa Text mining, Pathway, Ranking
PP85 (PT) A Context-Sensitive Framework for the Analysis of Human Signalling Pathways in Molecular Interaction Networks Alex Lan PPI-Network, Context-Sensitive-Path, Systems-Biology
PP86 (PT) A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotides distribution Vladimir Reinharz RNA, secondary structure, design, weighted sampling, GC
SS03_PartB Inference, visualization and evaluation of signaling networks: A literature based framework Hayssam Soueidan ,
SS03_PartD Using the rxncon framework for network definition, visualisation and modelling Marcus Krantz ,
SS06_PartA1 ELIXIR Niklas Blomberg ,
SS06_PartA2 BioMedBridges - providing data and services bridges between the biomedical sciences infrastructures Janet Thornton ,
SS06_PartC3 ELIXIR Swedish Node Bengt Persson ,