ISMB/ECCB 2015 TALKS

Video Recording sponsored in part by:

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The full listing of talks can be found below.

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

Type Title Presenter Keywords
3D Sig Birth and Future of Multiscale Modeling of Macromolecules Michael Levitt ,
3D Sig-Intro A Multiscale Introduction of Michael Levitt Ilan Samish ,
AKES 03 - Giannoulatou How to implement quality assurance in clinical diagnostic laboratories? Eleni Giannoulatou ,
AKES 03 - Ho Bioinformatics Software Testing and Quality Assurance Joshua Ho ,
AKES 06 -Goble A grant reviewers perspective Carole Goble ,
AKES 06 -Rodgers Being judged: an editor’s view Peter Rodgers ,
AKES 06 -Winhide Win Hide's 2015: A career odyssey Winston Hide ,
Awards Awards and Closing ,
ISCB Award ISCB Award - ,
Keynote Fun With Large Structures and Masses of Sequence Michael Levitt ,
Keynote Understanding microbial community function and the human microbiome in health and disease Curtis Huttenhower ,
Keynote Genome regulation during embryonic development Eileen Furlong ,
Keynote Reversible DNA rearrangement as a switch for cell type in yeasts Kenneth Wolfe ,
Keynote How Lucky I Have Been
*Nature Publication Group has provided a journal cover photo used in this presentation
http://www.nature.com/nature/journal/v302/n5908/index.html
Cyrus Chothia ,
Keynote neXtProt 2015 highlights: SPARQL endpoint and biocuration efforts around the human protein variome Amos Bairoch ,
SP01 James Joyce's Ulysses: A Bioinformatics Perspective David Searls ,
SS01-Part A Translational Medicine: the current landscape and future directions Winston Hide ,
SS01-Part B Standards and ontologies in harmonisation efforts of clinical data Philippe Rocca-Serra ,
SS01-Part C eTRIKS, European Translational Information and Knowledge Management Services David Henderson ,
SS02-Part A Chromosome organization & polymer entanglements: Insights from computer simulations Angelo Rosa ,
SS02-Part D Assessing the limits of restraint-based 3D modeling of genomes and genomic domains. Marc A. Marti-Renom ,
SS02-Part E Mining chromatin interactions: challenges in data integration and classification Yoli Shavit ,
SS04-Part A Crowd-Sourced Benchmarking of Somatic Single Nucleotide Variant Detection Paul Boutros ,
SS04-Part B Structural Variant Detection in DNA Anna Lee ,
SS04-Part C novoBreak: robust characterization of structural breakpoints in cancer genomes Ken Chen ,
TP001 Synthetic long read technologies in genome phasing and beyond Volodymyr Kuleshov Genes,
TP002 PAGER: Constructing PAGs and new PAG-PAG Relationships for Network Biology Zongliang Yue Systems,
TP003 MSProGene - Integrative proteogenomics beyond six-frames and single nucleotide polymorphisms Franziska Zickmann Proteins,
TP004 Computational dissection of transcriptional heterogeneity in single-cell RNA-Seq studies Oliver Stegle Genes,
TP005 Metabolome-scale de novo pathway reconstruction using regioisomer-sensitive graph alignments Yoshihiro Yamanishi Systems,
TP006 Revising human protein coding gene numbers Michael Tress Proteins,
TP007 Scaffolding Draft Genomes with Nanopore Reads Rene Warren ,
TP008 Unbiased Metabolic Pathway Analysis of Large Networks by Metabolomics Integration Christian Jungreuthmayer Systems,
TP009 IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis Yana Safonova Proteins,
TP011 Refined elasticity sampling for Monte Carlo-based identification of stabilizing network patterns Dorothee Childs Systems,
TP012 Bumps and traffic lights along the translation of secretory proteins Michal Linial Proteins,
TP013 De Novo Meta-Assembly of Ultra-deep Sequencing Data Timothy J. Close Genes,
TP014 Dynamic networks reveal key players in aging Tijana Milenkovic Systems,
TP015 Protein (Multi-) Location Prediction: Utilizing Interdependencies via a Generative Model Ramanuja Simha Proteins,
TP016 Misassembly Detection using Paired-End Sequence Reads and Optical Mapping Data Martin Muggli Genes,
TP018 Global view of the protein universe Rachel Kolodny Proteins,
TP019 Developments to the Combined Annotation Dependent Depletion (CADD) framework for estimating deleteriousness of human genetic variation Martin Kircher Disease,
TP020 Structural features of the 5-colors Drosophila chromatin types Davide Bau ,
TP021 Genome-wide detection of intervals of genetic heterogeneity associated with complex traits Felipe Llinares-Lopez Systems,
TP022 Inferring mechanism of DNA double-strand break formation using sequencing data Maga Rowicka ,
TP023 Big Data, AI, and Evolution: Towards a Calculus for Precision Medicine Olivier Lichtarge Disease,
TP024 A comparative encyclopedia of DNAelements in the mouse genome Feng Yue Genes,
TP025 Identification of causal genes for complex traits Farhad Hormozdiari Systems,
TP026 Comparing Genomes with Rearrangements and Segmental Duplications Mingfu Shao Genes, Disease
TP027 Optimizing cancer genome sequencing and analysis Malachi Griffith ,
TP028 Cypiripi: exact genotyping of CYP2D6 using High Throughput Sequencing Data Salem Malikic Genes,
TP029 Exploring disease etiology through a large-scale mapping of deleterious genes to cell types Alex Cornish ,
TP030 3D hotspots of recurrent retroviral insertions reveal long-range interactions with cancer genes Jeroen de Ridder Genes, Disease
TP031 Dynamic changes of RNA-sequencing expression for precision medicine: N-of-1-pathways Mahalanobis distance within pathways of single subjects predicts breast cancer survival A. Grant Schissler Disease,
TP032 Insights into Secondary Metabolism from a Global Analysis of Prokaryotic Biosynthetic Gene Clusters Marnix Medema Genes, Proteins
TP033 Integrative Random Forest for Gene Regulatory Network Inference Zhidong Tu Systems,
TP034 In silico phenotyping via co-training for improved phenotype prediction from genotype Damian Roqueiro Genes, Disease
TP035 FERAL: Network Based Classifier with Application to Breast Cancer Outcome Prediction Amin Allahyar Disease,
TP036 Understanding operon evolution using an event-driven model and phylogenetic visualizatons Iddo Friedberg Genes, Proteins
TP037 Gene network inference by fusing data from diverse distributions Marinka Zitnik Systems,
TP038 The human splicing code reveals new insights into the genetic determinants of disease Brendan Frey Genes, Disease
TP039 Integrating Different Data Types by Regularized Unsupervised Multiple Kernel Learning with Application to Cancer Subtype Discovery Nora Katharina Speicher Disease,
TP040 Deconvolving Molecular Signatures of Interactions Between Microbial Colonies Yeu-Chern Harn Genes, Proteins
TP041 Inferring orthologous gene regulatory networks using interspecies data fusion Christopher Penfold Systems,
TP042 Associating enhancers with TH2 memory differentiation and asthma susceptibility Lukas Chavez Genese, Disease
TP043 Reconstructing 16S rRNA genes in metagenomic data Cheng Yuan Genes,
TP044 Inferring parental genomic ancestries using pooled semi-Markov processes James Zou Systems,
TP045 A hierarchical Bayesian model for flexible module discovery in three-way time series data David Amar Disease, Other
TP046 A genome-wide map of hyper-edited RNA reveals numerous new sites Erez Levanon Genes,
TP047 Adapt-Mix: Learning local genetic correlation structure improves summary statistics based analyses Danny Park Systems,
TP048 CANDL: Coarsely Aligning Networks with Diffusion and Landmarks Benjamin Hescott ,
TP050 Natural genetic variation impacts expression levels of coding, non-coding, and antisense transcripts in fission yeast Mathieu Clément-Ziza Systems,
TP051 Bayesian inference of viral fitness landscapes in the quasispecies model David Seifert Disease, Other
TP052 NGS-Logistics: federated analysis of NGS sequence variants across multiple locations. Amin Ardeshirdavani Genes,
TP053 Co-analysis of transcriptome, exome, and protein interaction network information in cancers points to therapeutically targetable mutations Sarah-Jane Schramm ,
TP054 Finding Novel Molecular Connections between Developmental Processes and Disease Jisoo Park Disease, Other
TP055 The functional importance of synonymous mutations in cancer and microbes analyzed in massive genomic data sets Fran Supek Genes,
TP056 A multiscale statistical mechanical framework integrates biophysical and genomic data to assemble cancer networks. Mohammed AlQuraishi Systems, Disease
TP057 Uncovering the mechanisms modulating cardiac electrophysiology using systems genetics approaches in recombinant inbred rat strains Michiel Adriaens ,
TP058 Robust reconstruction of gene expression profiles from reporter gene data using linear inversion Valentin Zulkower Genes,
TP059 Biological network modeling helps finding genetic determinants of metastatic colon cancer Inna Kuperstein Systems, Disease
TP060 Relating Essential Proteins To Drug Side-Effects Using Canonical Component Analysis Tianyun Liu ,
TP061 Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes Benjamin Raphael Disease,
TP064 Using the Power of Big Data and Crowdsourcing for Catalyzing Breakthroughs in Amyotrophic Lateral Sclerosis (ALS) Robert Kueffner Systems, Disease
TP065 Statistical Assessment of Darwinian Selection for Mitochondrial Mutations in Cancer Thomas LaFramboise ,
TP066 Large-scale Imputation of Epigenomic Datasets for Systematic Annotation of Diverse Human Tissues Jason Ernst Genes,
TP068 A community computational challenge to predict the activity of pairs of compounds Gustavo Stolovitzky Systems, Disease
TP069 Identifying driver genomic alterations in cancers by searching minimum-weight, mutually exclusive sets Xinghua Lu ,
TP070 Correcting for sample heterogeneity in epigenome-wide association studies. James Zou Genes,
TP071 Widespread degradation of transcripts by splicing and nonsense-mediated mRNA decay (NMD) includes ultraconserved targets whose regulation by alternative splicing and NMD is conserved between kingdoms Steven Brenner Systems,
TP072 Improving compound-protein interaction prediction by building up highly credible negative samples Hui Liu Systems, Disease
TP073 An optimized chemical genomics pipeline for genome-wide discovery of new molecular probes from large compound collections Chad Myers ,
TP074 Histone variants delineate the transcription orientation at enhancers Kyoung-Jae Won ,
TP076 ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes Siavash Mirarab Genes, Other
TP077 Using collective expert judgements to evaluate quality measures of mass spectrometry images Andrew Palmer Data,
TP078 Phenome-driven Disease Genetics Prediction Towards Drug Discovery Yang Chen Disease,
TP079 Integrated reporters reveal distinct pathways of gene silencing in Drosophila Guillaume Filion ,
TP080 Alternatively spliced homologous exons have ancient origins and are highly expressed at the protein level Michael Liam Tress ,
TP081 Pooled Assembly of Metagenomic Data: Chimeric Contigs Enable Better Annotation and Discovery of New Marine Bacteria Dietlind Gerloff Genes, Other
TP082 Interactive and exploratory visual analytics of epigenome-wide data Hector Corrada Bravo Data,
TP083 Interactome based drug discovery Gaurav Chopra ,
TP084 Predicting the human epigenome from DNA motifs John Whitaker Genes,
TP086 Deciphering cocktail party of biological, technical and artefactual signals in tumoural transcriptomes Andrei Zinovyev Genes, Other
TP087 A generic methodological framework for studying single cell motility in high-throughput time-lapse data Alice Schoenauer Sebag Data,
TP088 A Study Of Common Disease Using The Human Phenotype Ontology Tudor Groza ,
TP089 Protein Structures in the PDB Show the Temperature Dependance of Hydrophobicity Sanne Abeln ,
TP090 Pancancer analysis of DNA methylation-driven genes using MethylMix Olivier Gevaert Disease,
TP091 Exploiting Ontology Graph for Predicting Sparsely Annotated Gene Function Sheng Wang Data,
TP092 Protein Structure Novelty has Regressed 20 Years John-Marc Chandonia ,
TP093 MEMCover: Integrated Analysis of Mutual Exclusivity and Functional Net-work Reveals Dysregulated Pathways Across Multiple Cancer Types Yoo-Ah Kim Disease,
TP094 SwissTargetPrediction: a web server for target prediction of bioactive small molecules David Gfeller Data,
TP095 Large-Scale Model Quality Assessment for Improving Protein Tertiary Structure Prediction Renzhi Cao Proteins,
TP096 Integrated exome and transcriptome sequencing reveals ZAK isoform usage in gastric cancer Jinfeng Liu Disease,
TP097 Inferring Models of Multiscale Copy Number Evolution for Single-Tumor Phylogenetics Salim Akhter Chowdhury Genes, Disease
TP098 Entropy-scaling search of massive biological data Noah Daniels ,
TP099 cNMA: A framework of encounter complex-based normal mode analysis to model conformational changes in protein interactions Yang Shen Proteins,
TP100 Reconstruction of clonal trees and tumor composition from multi-sample sequencing data Mohammed El-Kebir Genes, Disease
TP101 MeSHLabeler: Improving the Accuracy of Large-scale MeSH indexing by Integrating Diverse Evidence Ke Liu Data,
TP102 Sequence co-evolution gives 3D contacts and structures of protein complexes Debora Marks Proteins,
TP103 Reconstructing the Evolutionary History of Tumors Quaid Morris Genes, Disease
TP104 Knowledge-driven geospatial location resolution for phylogeographic models of virus migration Davy Weissenbacher Data,
TP105 Finding Optimal Interaction Interface Alignments between Biological Complexes Xuefeng Cui Proteins,
TP106 Importance of rare copy number alterations for personalized tumor characterization Andreas Beyer ,
TP107 An Integrated Mass Spectrometry-Computational Approach for Modelling Large Protein Assemblies Argyris Politis ,
TP108 Accurate phasing of allele-specific copy-numbers for inferring tumour evolution with probe-level resolution Roland Schwarz ,
TP109 In silico prediction of physical protein interactions and characterization of interactome orphans Igor Jurisica Proteins,
TP110 Inferring clonal evolution from single-cell sequencing data Edith Ross ,
TP111 Cereblon as a gateway for pharmacologically induced teratogenicity Andrei Lupas Proteins,
TP112 Exploring the structure and function of temporal networks with dynamic graphlets Yuriy Hulovatyy Systems,
TP113 Computational saturated mutagenesis for mapping protein binding landscapes and identifying affinity- and specificity-enhancing mutations Julia Shifman Proteins,
TP114 Data visualization and modeling using Atlas of Cancer Signaling Network predicts clinical outcome Inna Kuperstein ,
TP115 Using Kernelized Partial Canonical Correlation Analysis To Study Directly Coupled Side Chains and Allostery in Small G Proteins Mu Zhu Proteins,
TP116 Detecting Molecular Similarities Between Allergenic And Metazoan Parasitic Proteins: Allergy In The Light of Immunity Nicholas Furnham ,
VC03 The FATHMM Family of Predictors Colin Campbell ,
WK01_PartA Top Ten Tips for Setting up a Bioinformatics Course Gabriella Rustici ,
WK01_PartB Learn Bioinformatics by Doing Bioinformatics Myrto Kostadima ,
WK01_PartC Train-the-trainer: from bioinformatics turned to bioinformatics trainer Annette McGrath ,
WK01_PartD Experience Exchange: Focus on NGS Course Francis Ouellette, Gabriella Rustici, Dave Clements, Annette McGrath ,
WK02_PartAB Part A: The role of core facilities when everyone is a bioinformatician Part B: Bioinformatics core facilities as service providers Davide Cittaro and Sven Nahsen ,
WK02_PartCD Part C: Maintaining a Publicly Used Analysis Infrastructure Part D:The business of core services Madelaine Gogol and Jim Cavalcoli ,