ISMB/ECCB 2017 TALKS

The full listing of talks can be found below.

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

Type Title Presenter Keywords
3Dsig Large-scale structure prediction by improved contact predictions and model quality assessment Mirco Michel ,
3Dsig Proteins from Peptides Andrei Lupas ,
3Dsig Deep learning based subdivision approach for large scale macromolecules structure recovery from electron cryo tomograms Min Xu ,
BD2K Track Going FAIR: where are we? Susanna-Assunta Sansone ,
BD2K Track Omics Discovery Index: Supporting multi-omics analysis with public data Henning Hermjakob ,
BD2K Track Opportunities for Data Intensive Research in Infectious Diseases Maria Giovanni ,
BD2K Track CEDAR: Technology for using metadata standards to ease sharing, integration, and reuse of biomedical data Mark Musen ,
BD2K Track Inferring and explaining gene-disease associations through implicit knowledge Kristina Hettne ,
BD2K Track The NCI Cancer Research Data Commons Tony Kerlavage ,
BD2K Track Aztec: A machine learning empowered platform for FAIR biomedical software Wei Wang ,
BD2K Track To be FAIR, we should give Ontologies and Data Visualization a try Nils Gehlenborg ,
BD2K Track Introduction and Overview of BD2K Susan Gregurick ,
BD2K Track Open Neuroimaging Laboratory and BrainBox Roberto Toro ,
BioVis BioVis Reconstruction and visualization of large-scale volumetric models of neocortical circuits for physically-plausible in silico optical studies Marwan Abdellah ,
BioVis BioVis BrainScope: interactive visual exploration of the spatial and temporal human brain transcriptome Sjoerd M. H. Huisman ,
BioVis BioVis AnimoAminoMiner: exploration of protein tunnes ald their properties in molecular dynamics Jan Byška ,
BioVis BioVis CellNetVis: a web tool for visualization of biological networks using force-directed layout constrained by cellular components Henry Heberle ,
BioVis BioVis Rondo: interactive visual exploration of genome spatial connectivity Benedetta Frida Baldi ,
BioVis BioVis Visualization and creation of biochemical networks with Escher Andreas Dräger ,
BioVis BioVis MUTAFRAME - a data visualization platform for mutation effect prediction Ibrahim Tanyalcin ,
BioVis BioVis RPAN: rice pan-genome browser for ~3,000 rice genomes Chaochun Wei ,
BioVis BioVis Systems-level interactive data exploration (SLIDE): user-driven visualization of large-scale omics data on a web browser with flexible customized graphics Soumita Ghosh ,
BioVis BioVis Bayesian unidimensional scaling for visualizing uncertainty in high dimensional datasets with latent ordering of observations Lan Huong Nguyen ,
BioVis BioVis MediSyn: uncertanty-aware visualization of multiple biomedical datasets to support drug treatment selection Chen He ,
BioVis BioVis Overcoming the visualization challenges of pE-MAP results John H Morris ,
BioVis BioVis Extending R gplots Venn diagrams with polyominoes for 6 and 7 dimensions and an unconstrained graph representation Sarah O Fisher ,
BOSC BOSC Introduction and welcome Nomi Harris ,
BOSC The Open Bioinformatics Foundation Hilmar Lapp ,
BOSC OBF in the Google Summer of Code. Wrapping up 2016 and presenting the 2017 projects Kai Blin ,
BOSC Codefest 2017 summary Brad Chapman ,
BOSC Rabix Executor: an open-source executor supporting recomputability and interoperability of workflow descriptions Janko Simonovic ,
BOSC Rabix Composer: an open-source integrated development environment for the Common Workflow Language Ivan Batic ,
BOSC The GA4GH Tool Registry Service (TRS) and Dockstore - Year One Denis Yuen ,
BOSC The GA4GH Task Execution System (TES) and Funnel Server Brian O'Connor ,
BOSC The GA4GH Workflow Execution Schema (WES) Peter Amstutz ,
BOSC The GA4GH/DREAM Infrastructure Challenges Brian O'Connor ,
BOSC Workflows interoperability with Nextflow and Common WL Kevin Sayers ,
BOSC CWL Viewer: The Common Workflow Language Viewer Stian Soiland-Reyes ,
BOSC Screw: tools for building reproducible single-cell epigenomics workflows Kieran O'Neill ,
BOSC BioThings Explorer: Utilizing JSON-LD for Linking Biological APIs to Facilitate Knowledge Discovery Jiwen Xin ,
BOSC Discovery and visualisation of homologous genes and gene families using Galaxy Anil Thanki ,
BOSC YAMP : Yet Another Metagenomic Pipeline Alessia Visconti ,
BOSC MultiQC: Visualising results from common bioinformatics tools Philip Ewels ,
BOSC NGL - a molecular graphics library for the web Alexander Rose ,
BOSC GRAPHSPACE: Stimulating interdisciplinary collaborations in network biology Aditya Bharadwaj ,
BOSC Efficient detection of well-hopping duplicate reads on Illumina patterned flowcells Timothy Booth ,
BOSC An ensemble approach for gene set testing analysis with reporting capabilities Monther Alhamdoosh ,
BOSC Interoperable, collaborative multi-platform variant calling with bcbio Brad Chapman ,
BOSC Gene Set Variation Analysis in cBioPortal Kees Bochove ,
BOSC The backbone of research reproducibility: sustainable and flexible tool deployment Bjoern Gruening ,
BOSC Reproducible and user-controlled software management in HPC with GNU Guix Ricardo Wurmus ,
BOSC A Ubiquitous Approach to Reproducible Bioinformatics across Computational Platforms John Chilton ,
BOSC Revitalizing a classic bioinformatics tool using modern technologies: the case of the Cytoscape Project Keiichiro Ono ,
BOSC The SPOT ontology toolkit : semantics as a service Olga Vrousgou ,
BOSC Biopython Project Update 2017 Sourav Singh ,
BOSC Open Sourcing Ourselves Madeleine Ball ,
BOSC BeerDeCoded: exploring the beer metagenome Jonathan Sobel ,
BOSC Supporting curation communities & collecting technical dividends Monica Munoz-Torres ,
BOSC Journal of Open Source Software (JOSS) Pjotr Prins ,
BOSC Building an open, collaborative, online infrastructure for bioinformatics training Berenice Batut ,
BOSC Software and social strategies for community sourced biological networks and ontologies Dexter Pratt ,
BOSC Distance-based, online bioinformatics training in Africa: the H3ABioNet experience Nicola Mulder ,
BOSC Recent object formation in the core of Galaxy Martin Cech ,
BOSC Reproducibility of computational workflows is automated using continuous analysis Brett Beaulieu-Jones ,
BOSC Full-stack genomics pipelining with GATK4 + WDL + Cromwell Kate Voss ,
BOSC ToolDog - generating tool descriptors from the ELIXIR tool registry Kenzo-Hugo Hillion ,
BOSC BioThings SDK: a toolkit for building high-performance data APIs in biology Chunlei Wu ,
BOSC Integrating cloud storage providers for genomic analyses Ted Liefeld ,
BOSC Fighting Superbugs with Open Source Software Kai Blin ,
BOSC RADAR-CNS - Research Infrastructure for processing wearable data to improve health Nivethika Mahasivam ,
BOSC Using Wikidata as an open, community-maintained database of biomedical knowledge Andrew Su ,
BOSC Emerging public databases of clinical genetic test results: Implications for large scale deployment of precision medicine Stephen Lincoln ,
BOSC Discovering datasets with DATS in DataMed Philippe Rocca-Serra ,
BOSC Bioschemas for life science data Carole Goble ,
BOSC Introducing the Brassica Information Portal: Towards integrating genotypic and phenotypic Brassica crop data Annemarie Eckes ,
CAMDA Molecular networks as determinants of response and outcome Lodewyk Wessels ,
CAMDA The CAMDA Challenges David P. Kreil ,
CAMDA Predicting clinical outcome of neuroblastoma patients using an integrative network-based approach Léon-Charles Tranchevent ,
CAMDA Predicting clinical outcomes in neuroblastoma with genomic data integration Hilal Kazan ,
CAMDA Accumulation of Potential Driver Genes with Genomic Alterations Predicts Survival in High-Risk Neuroblastoma Chen Suo ,
CAMDA Multi-omics integration for neuroblastoma clinical endpoint prediction Margherita Francescatto ,
CAMDA Integration of Molecular Features with Clinical Information for Predicting Outcome for Neuroblastoma Patients Kun Huang ,
CAMDA Integration analysis based on survial associated co-expression gene modules for predicing neuroblastom patients survival times Kun Huang ,
CAMDA A multi-layer network approach to data integration for patient stratification Maciej Kandula ,
CAMDA Predicting survival times for neuroblastoma patients using RNA-Seq expression profiles Tyler Grimes ,
CAMDA Integration of CNV and RNA-seq data can increase the predictive power of Neuroblastoma endpoint Tieliu Shi ,
CAMDA Analysis of CAMDA RNA-seq data with the knowlegde of protein domains in genes Michał Okoniewski ,
CAMDA Microbiome Diversity on Materials Chandrima Bhattacharya ,
CAMDA Codon usage diversity in city microbiomes Haruo Suzuki ,
CAMDA Unraveling bacterial fingerprints of city subways from microbiome 16S gene profiles Susmita Datta ,
CAMDA Assessing reproducibility of metagenomics studies and diversity of public transport systems microbiome profiles of New York, Boston and Sacramento cities Alina Frolova ,
CAMDA CAMDA Welcome and opening remarks Pawel Labaj ,
CAMDA Strain-level bacterial and viral diversity in the MetaSUB dataset Moreno Zolfo ,
CAMDA Viral and eukaryotic communities of urban ecosystems across US metropolitan areas Serghei Mangul ,
CAMDA Assessment of urban microbiome assemblies with the help of targeted mock communities Samuel Gerner ,
CAMDA MetaBinG2: a fast and accurate metagenomics sequence classification method for samples with many unknown organisms Yuyang Qiao ,
CAMDA LAST + MEGAN-LR Approach to the Oxford Nanopore Wiggle Space Challenge Caner Bagci ,
CAMDA Towards a scientific blockchain framework for reproducible data analysis Cesare Furlanello ,
CAMDA CAMDA Award announcements, Panel Discussion and closing remarks David P. Kreil ,
Elixir Special Industry Engagement: ELIXIR and Open Innovation Pablo Roman-Garcia ,
Elixir Special ELIXIR Compute Platform: Access, exchange and storage Ludek Matyska ,
Elixir Special ELIXIR Data Platform: Sustaining Europe's life science data infrastructure Johanna McEntyre ,
Elixir Special ELIXIR Training - Professional skills for managing and exploiting data Patricia Palagi ,
Function fusionDB: assessing microbial diversity and environmental preference via functional similarity networks Yannick Mahlich ,
Function Region-specific Function Prediction: automatically inferring function labels for protein regions Da Chen Emily Koo ,
Function Investigation of Multi-task Deep Neural Networks in Automated Protein Function Prediction Ahmet Süreyya Rifaioğlu ,
Function Reasoning on Gene Ontology Networks Predicts Novel Protein Annotations Ilya Novikov ,
Function Predicting Protein Function Directly from STRING Network Topology using Deep Learning Techniques Cen Wan ,
Function Automatic Generation of Functional Annotation Rules Using Inferred GO-Domain Associations Seyed Ziaeddin Alborzi ,
Function Protein Function Prediction by COFACTOR in CAFA3 Peter Freddolino ,
Function Proceedings: DextMP: Deep dive into Text for predicting Moonlighting Proteins Daisuke Kihara ,
Function Phylogenetic- based gene function prediction in the Gene Ontology Consortium Huaiyu Mi ,
Function BAR 3.0: going beyond protein function annotation Giuseppe Profiti ,
Function Predicting Novel Abnormal Circadian Phenotypes in Mouse John Williams ,
Function Automating Genomic Context Analysis with a Probabilistic Model of Protein Function and Relatedness Jeffrey Yunes ,
HiTSeq Integrating Diverse Transcriptomic Alterations to Identify Cancer-Relevant Genes and Signatures Natalie Davidson ,
HiTSeq Deconvolution of heterogeneous bulk tumor genomic data via structured mixed membership models Russell Schwartz ,
HiTSeq Profiling immunoglobulin repertoires across multiple human tissues by RNA Sequencing Serghei Mangul ,
HiTSeq Outlier detection for improved differential splicing quantification from RNA-Seq experiments with replicates Yoseph Barash ,
HiTSeq Improved Data-Driven Likelihood Factorizations for Transcript Abundance Estimation Rob Patro ,
HiTSeq Computing Optimal Flow Decompositions for Assembly Philipp Kuinke ,
HiTSeq deBGR: An Efficient and Near-Exact Representation of the Weighted de Bruijn Graph Prashant Pandey ,
Keynote KEYNOTE: Christoph Bock - Bioinformatics for Personalized Medicine: Looking Beyond the Ge-nome Christoph Bock ,
Keynote KEYNOTE: Pavel Pevzner - Bioinformatics: a Servant or the Queen of Molecular Biology? Pavel Pevzner ,
SST04 Lineage estimation from single-cell RNAseq time-series Fabian Theis ,
SST04 Transcriptome-wide splicing quantification in single cells Yuanhua Huang ,
SST04 Gaussian processes for identifying branching dynamics in single cell data Alexis Boukouvalas ,
SST04 Modeling Post-treatment Gene Expression Change with a Deep Generative Model Ladislav Rampášek ,
SST04 Generative Learning of Dynamic Structures using Spanning Arborescence Sets Anthony Coutant ,
SST04 Understanding and predicting drug efficacy in cancer: from machine learning to biochemical models Julio Saez-Rodriguez ,
SST04 Kernelized Rank Learning for Personalized Drug Recommendation Xiao He ,
SST04 Ask the doctor - Improving drug sensitivity predictions through active expert knowledge elicitation Iiris Sundin ,
NetBio Predicting multicellular function through multi-layer tissue networks Marinka Zitnik ,
NetBio Incorporating Interaction Networks into the Determination of Functionally Related Hit Genes in Genomic Experiments with Markov Random Fields Sean Robinson ,
NetBio Active Interaction Mapping reveals the hierarchical organization of autophagy Michael Kramer ,
NetBio PathSys: Integrating pathway curation, profiling methods, and public repositories: An infrastructure for functional molecular data sharing Sokratis Kariotis ,
NetBio A novel method for network crosstalk analysis that improves accuracy of pathway annotation Christoph Ogris ,
NetBio Drug Response Prediction as a Link Prediction Problem Zachary Stanfield ,
NetBio NetProphet 2.0: Mapping Transcription Factor Networks by Exploiting Scalable Data Resources Michael R. Brent ,
NetBio Multiple network-constrained regressions expand insights into influenza vaccination responses Stefan Avey ,
NetBio Genome-wide competing endogenous RNA networks highlight biomarkers in cancer Markus List ,
NetBio Using network analysis to identify a new key set of Parkinson’s Disease associated gene Katharina F Heil ,
NetBio NetRep: a scalable permutation approach for assessing replication and preservation of network modules in large datasets Scott Ritchie ,
NetBio An R package for diffusion algorithms in biological networks Sergio Picart-Armada ,
NetBio The STRING app: bringing quality-controlled protein-protein and protein-chemical networks into Cytoscape Nadezhda T. Doncheva ,
NetBio Pathways on demand: automated reconstruction of human signaling networks T. M. Murali ,
NetBio Predicting Novel Metabolic Pathways through Subgraph Mining Karthik Raman ,
Abstracts Nonlinear Mixed-Effects Modeling of Proteomics Antibody-Based Multiplex Assays: A Bioinformatics Post-Hoc Approach to Improve Signal-to-Noise Ratios Julián Candia ,
Abstracts Ultra-sensitive n-plexed protein quantification by a model-based reconstruction method Kyowon Jeong ,
Abstracts A Drug-Centric View of Drug Development: How Drugs Spread from Disease to Disease Raul Rodriguez-Esteban ,
Abstracts On the feasibility of mining CD8+ T-cell receptor patterns underlying immunogenic peptide recognition Nicolas De Neuter ,
Abstracts Misleading arrows? Fitness landscapes and cancer progression models Ramon Diaz-Uriarte ,
Abstracts Using Ancestral Sequence Reconstruction to Characterize an Allosteric Bi-Enzyme Complex Kristina Heyn ,
Abstracts Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus Yuki Yoshida ,
Abstracts Reconstructing metastatic seeding patterns of human cancers Johannes G. Reiter ,
Abstracts PubSqueezer: a Text-Mining Tool to Discover Connections in Scientific Literature Alberto Calderone ,
RegGen Accurate prediction of in-vivo transcription factor binding across cell types Jan Grau ,
RegGen scTree: reconstructing complex cellular lineage trees from single-cell RNA-seq data R. Gonzalo Parra ,
RNA Capturing target-specific protein-RNA interaction footprints from iCLIP-seq data Sabrina Krakau ,
RNA Recurrent neural network models to quantitatively predict RNA-RNA interactions Michelle Wu ,
RNA Efficient approximations of RNA kinetics landscape using non-redundant sampling Juraj Michalik ,
RNA Genome-wide analysis for identification of lncRNAs that sponge RNA-binding proteins Hilal Kazan ,
RNA DeepBound: Accurate identification of transcript boundaries via deep convolutional neural fields Mingfu Shao ,
RNA Integrative Deep Models for Alternative Splicing Anupama Jha ,
SCS Christine Orengo - Student Council Keynote Christine Orengo ,
SCS The impact of native state switching on protein sequence evolution Avital Sharir-Ivry ,
SCS Differential network analysis hints at revealing mechanism of actions of combined drug applications Mohamed Hamed ,
SCS Logical modeling approaches as a proxy to analyze cardiovascular disease trajectories Amel Bekkar ,
SCS A comprehensive meta-analysis of the induced immediate early response reveals a conserved order of promoter activation Annalaura Vacca ,
SST01 Developing the new generation of bioinformatics engineers Bruno Gaeta ,
SST01 How to apply and improve curriculum and competency guidelines feedback Michelle Brazas ,
SST03 C: Optimizing the identification of immunogenic neoepitopes Bjoern Peters ,
SysMod Estimation of time-varying growth, uptake and excretion rates from dynamic metabolomics data Eugenio Cinquemani ,
SysMod Reversed dynamics to uncover basins of attraction of asynchronous logical models Claudine Chaouiya ,
SysMod Large Scale Mechanistic Modeling Enables Robust Prediction of Cancer Cell Drug Response Fabian Fröhlich ,
SysMod Incorporating patient-specific molecular data into a logic model of prostate cancer Pauline Traynard ,
SysMod popFBA: tackling intratumour heterogeneity with Flux Balance Analysis Chiara Damiani ,
Technology GenomeSpace: Open source interoperability platform with crowd-sourced analysis recipes Ted Liefeld ,
Technology Phyre2: Protein modeling and analysis made easy Michael Sternberg ,
Technology Using Online Classes to Flip Bioinformatics Classrooms Niema Moshiri ,
Technology The GenePattern Notebook Environment Michael Reich ,
Technology Pathway Studio Use Case: A disease-centric analysis of Pre-Eclampsia Chris Cheadle ,
Technology Recent Developments in the Pathway Tools Software and BioCyc Databases Peter Karp ,
TransMed Association testing of bisulfite sequencing methylation data via a Laplace approximation Omer Weissbrod ,
TransMed Identification of Associations between Genotypes and Longitudinal Phenotypes via Temporally-constrained Group Sparse Canonical Correlation Analysis Xiaoke Hao ,
TransMed Predicting phenotypes from microarrays using amplified, initially marginal, eigenvector regression Lei Ding ,
TransMed Epigenomic profiling of glioblastoma through treatment and progression Johanna Klughammer ,
TransMed Predicting cancer sequential treatments and drug repurposing with SATIE Héctor Tejero ,
TransMed canSAR: an integrated knowledgebase for cancer research and drug discovery Elizabeth Coker ,
TransMed Integrative analysis of personalized, multidimensional datasets of glioblastoma patients Nikolaus Fortelny ,
TransMed Using Multi-Scale Genetic, Protein, Neuroimaging and Clinical Data for Predicting Alzheimer's Disease and Reconstruction of Relevant Biological Mechanisms Holger Fröhlich ,
TransMed Integrating personalized gene expression profiles into predictive disease-associated gene pools Emre Guney ,
TransMed Integrating genomics and transcriptomics to dissect the pathogenic mechanism of X-Linked Dystonia-Parkinsonism Rachita Yadav ,
TransMed Classification of Paediatric Inflammatory Bowel Disease using Machine Learning Enrico Mossotto ,
TransMed Understanding human knockouts Suganthi Balasubramanian ,
TransMed Prediction of HIV-1 sensitivity to broadly neutralizing antibodies shows a trend towards resistance over time Anna Hake ,
VarI Increasing the power of meta-analysis of genome-wide association studies to detect heterogeneous effects. Cue Hyunkyu Lee ,
VarI Evaluating Variant Calling Tools for Non-Matched Next Generation Sequencing Data. Sarah Sandmann ,
WK02 Developing Reliable QC at the Swedish National Genomics Infrastructure Philip Ewels ,
WK02 Reproducible and fully documented data analyses at the Functional Genomics Center Zurich Lennart Opitz ,