ISMB 2016 TALKS

The full listing of talks can be found below.

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

Type Title Presenter Keywords
002 - The Hague ECCB 2016 Presentation ,
003 - PhRMA PhRMA Award Presentations ,
AKES/AKES02_ISMB2016_Crus Common Workflow Language Michael Crusoe ,
AKES/AKES02_ISMB2016_Gaur Enabling National-Scale Genomics on the Cloud Gaurav Kaushik ,
AKES/AKES02_ISMB2016_OCon Dockstore Tutorial Brian O'Connor ,
AKES/AKES04_ISMB2016-Fre Utilizing genomic data in clinical systems Robert R. Freimuth ,
AKES/AKES04_ISMB2016-Frey Collection of data for research Lewis Frey ,
AKES/AKES04_ISMB2016-Mad Practical Precision Medicine: Integration of clinical and genomic data to support cancer care Subha Madhavan ,
AKES/AKES04_ISMB2016-Over Increasing the reach of clinical genomics research and genomics-informed care Casey Overby ,
AKES/AKES04_ISMB2016-Tene Ethical, legal, and social implications of genomic testing Jessie Tenenbaum ,
AKES/AKES04_ISMB2016-Volc Overview of bioinformatics techniques and uses in clinical practice and research Samuel Volchenboum ,
Awards ISCB Distinguished Fellows 2016 ,
ClosingAwards Awards & Closing ,
COSI 2 STRING: Protein networks from data and text mining Lars Jensen ,
COSI 4 Patient-Specific Network Data Fusion for Stratification, Biomarker Discovery and Personalizing Treatment Natasa Przulj ,
COSI 5 Whole-cell models: combining genomics and dynamical modeling Jonathan Karr ,
Keynote Using Single-Cell Transcriptome Sequencing to Infer Olfactory Stem Cell Fate Trajectories Sandrine Dudoit ,
Keynote Understanding Cellular Heterogeneity Sarah Teichmann ,
Keynote Personalized Genomics and Computation Serafim Batzoglou ,
OP01 Assessing the Differential Significance of Transcription Factors Leslie D. Seitz Systems Biology and Networks,
OP02 Anti-aging and aging molecular networks database Byeongchul Kang Systems Biology and Networks,
OP03 Fair Evaluation of Global Network Aligners Joseph Crawford Systems Biology and Networks,
OP04 Estimation of ribosome profiling performance and reproducibility at various levels of resolution Alon Diament Systems Biology and Networks,
OP05 Urothelial cancer cell line models of tumor biology and drug response Nicolle Witte Bioinformatics of Disease and Treatment,
OP06 The Landscape of Circular RNA in Cancer Nguyen Vo Sequence Analysis, Functional Genomics
OP07 Defining the genetic overlap of patient tumors and patient derived xenograft models in colorectal cancer Deepthi Rajagopalan Bioinformatics of Disease and Treatment, Genetic Variation Analysis
OP08 Visualization of TCGA RNA-Seq information with an user-friendly mobile application Wen-Chang Lin Sequence Analysis, Sequence Analysis
OP09 A bioinformatics tool to improve the efficacy of exon skipping therapy for Duchenne muscular dystrophy Hosna Jabbari Bioinformatics of Disease and Treatment,
OP10 Epigenetic age predicted from H3K9ac ChIP-seq data is associated with Alzheimer's disease pathologies in the human prefrontal cortex Hans-Ulrich Klein Bioinformatics of Disease and Treatment, Epigenetics
OP11 ZIKV-CDB: A collaborative database to help understanding symptoms induced by ZIKA virus infection mediated by small noncoding RNAs Francislon Silva de Oliveira Bioinformatics of Disease and Treatment, Pathogen informatics
OP12 Metabolome wide association of DDT exposure in humans and in mice Loukia Lili Systems Biology and Networks, Systems Biology and Networks
OP13 Multiscale, multifactorial response network of immunization in humans Sophia Banton Systems Biology and Networks, Systems Biology and Networks
OP14 Widespread misannotation of samples in genomics studies Lilah Toker Bioinformatics of Disease and Treatment,
OP15 Sample alignment: A critical QC step for integrative analysis using multi-omics data Seungyeul Yoo Bioinformatics of Disease and Treatment, Epigenetics
OP16 Knowledge-guided fuzzy logic network modeling to infer cancer signaling pathways from time-series data Jie Zheng Systems Biology and Networks, Systems Biology and Networks
OP17 DECONVOLUTION OF CELL AND ENVIRONMENT SPECIFIC SIGNALS AND THEIR INTERACTIONS FROM COMPLEX MIXTURES IN BIOLOGICAL SAMPLES Urszula Czerwinska Systems Biology and Networks, Systems Biology and Networks
OP18 Comprehensive profiling of somatic mosaicism in the human brain Alexej Abyzov Genome Organization and Annotation, Functional Genomics
OP19 BayesTyping: a Tool for HLA typing with PacBio CCS Reads Chia-Jung Chang Sequence Analysis, Sequence Analysis
OP20 AODP: An improved method for signature oligonucleotide design Christine Lowe Comparative Genomics, Metagenomics
OP21 Tech Startups of the Genome: De novo genes arise frequently, try to be useful, and occasionally succeed and survive Amir Karger Protein Structure and Function Prediction and Anal, Protein Structure and Function Prediction and Anal
OP22 Substitution rate variability causes memory effects on protein sequence evolution and is triggered by sequence coevolution Francesca Rizzato Sequence Analysis, Sequence Analysis
OP23 The evolutionary origin of orphan genes Zebulun Arendsee Comparative Genomics, Genome Organization and Annotation
OP24 Tertiary Structural Propensities Reveal Basic Sequence-Structure Relationships in Proteins Fan Zheng Protein Structure and Function Prediction and Anal,
OP25 Natural language processing in text mining for protein docking Varsha D. Badal Protein Structure and Function Prediction and Anal,
OP26 Protein Classification using Specific Domain Architectures Zhouxi Wang Protein Structure and Function Prediction and Anal, Sequence Analysis
OP27 TRACE: Reconstructing trajectories of cell cycle evolution using single-cell mass cytometry data Maria Anna Rapsomaniki Systems Biology and Networks, Systems Biology and Networks
OP28 Protein-level regulation drives coordinated gene functions Jing Wang Systems Biology and Networks, Systems Biology and Networks
OP29 TEtranscripts: A package for including transposable elements in differential expression analysis of RNA-seq datasets Ying Jin Sequence Analysis,
OP30 Supervised learning enables detection of duplicates in biological databases Karin Verspoor Sequence Analysis,
OP31 BioStudies – a database of biological studies Catherine Snow Open Science and Citizen Science,
OP32 Next generation genomic computing Marco Masseroli Sequence Analysis, Sequence Analysis
OP33 Disturbances of transcriptional networks in congenital heart disease Marcel Grunert Epigenetics, Systems Biology and Networks
OP34 Hidden RNA Codes Revealed from in vivo RNA Structurome Yin Tang Sequence Analysis, Sequence Analysis
OP35 To identify and functional validate of novel long intergenic noncoding RNAs in myogenesis using integrated genomic approach Hao Sun Sequence Analysis, Sequence Analysis
OP36 Comparison of normalization methods for single cell RNA-seq Bo Ding Sequence Analysis, Sequence Analysis
OP37 Through a glass darkly: Single-cell co-expression as seen through the Gene Ontology Megan Crow Functional Genomics, Systems Biology and Networks
OP38 The SNPs associated with protein-drug binding sites Amrita Roy Choudhury Genetic Variation Analysis,
OP39 Detection and genotyping of short indels using sequence data from multiple samples Alastair M. Kilpatrick Genetic Variation Analysis,
Rost Award ISCB Outstanding Contributions Award - Recipient: Burkhard Rost ,
SST02- Part B Trends and Methods in Genomic Data Compression. Idoia Ochoa ,
SST02- Part C Meaningful Data Compression and Reduction of High-Throughput Sequencing Data. Alexander Schliep ,
SST02- Part D Compressive Structural Bioinformatics: High Efficiency 3D Structure Compression. Peter Rose ,
SST02- Part E Theoretical Foundations and Software Infrastructure for Biological Network Databases. Mehmet Koyutürk ,
SST02- Part F Task-Specific Compression for Biomedical Big Data. Ali Bilgin ,
SST03 A Genomic big data management and the GenoMetric Query Language Stefano Ceri ,
SST03 B TCGA2BED and CAMUR for cancer NGS data processing Emanuel Weitschek ,
SST03 C Searching patterns in genomic feature regions Ilaria Bartolini ,
SST03 E Semi-automated human genome annotation using chromatin data Michael Hoffman ,
SST04 A Biological Basis for Modeling Bacterial Communities Luisa Hiller ,
SST04 B Molecular Tweeting: Bacteria Network Formation, Dynamics, and Control with Healthcare Applications Radu Marculescu ,
SST04 C Data-Driven Modeling and In Silico Simulation of Cell Signaling Pathways Diana Marculescu ,
SST04 D On Scaling Graph Algorithms for Microbiome Applications Ananth Kalyanaraman ,
TP001 Robust Detection of Alternative Splicing in a Population of Single Cells Joshua Welch GENES, Gene Regulation
TP002 DFLpred: High throughput prediction of disordered flexible linker regions in protein sequences Fanchi Meng PROTEINS, Protein Structure & Function
TP003 FUNCTIONALLY PROFILING METAGENOMES AND METATRANSCRIPTOMES AT SPECIES-LEVEL RESOLUTION Eric Franzosa SYSTEMS / GENES, Gene / Protein Sequence Analysis
TP005 Unexpected Features of the Dark Proteome Sean O'Donoghue PROTEINS, Protein Structure & Function
TP006 Integrating very large multi'omics data by hierarchical all-against-all association testing Gholamali Rahnavard SYSTEMS, Applied Bioinformatics
TP007 Lightweight transcriptomics Surojit Biswas GENES, Applied Bioinformatics
TP009 Single molecule-level characterization of bacterial epigenomes, heterogeneity and gene regulation Gang Fang GENES, Gene Regulation
TP010 Analysis of aggregated cell-cell statistical distances within pathways unveils therapeutic-resistance mechanisms in circulating tumor cells Alfred Schissler DISEASE / SYSTEMS, Disease Models & Epidemiology
TP012 Genetic Architectures of Quantitative Variation in RNA Editing Pathways Tongjun Gu GENES, Population Genomics
TP013 DEVELOPMENT OF A BAYESIAN TENSOR FACTORIZATION MODEL TO PREDICT DRUG RESPONSE CURVES IN CANCER CELL LINES Nathan Lazar DISEASE / DATA, Applied Bioinformatics
TP015 A novel algorithm for calling mRNA m6A peaks by modeling biological variances in MeRIP-seq data Yufei Huang GENES, RNA Bioinformatics
TP016 DrugE-Rank: Improving Drug-Target Interaction Prediction of New Candidate Drugs or Targets by Ensemble Learning to Rank Shanfeng Zhu DISEASE / DATA, Applied Bioinformatics
TP017 Good news: we are getting better at predicting protein function Iddo Friedberg PROTEINS / DATA, Protein Structure & Function r
TP018 RNAiFold2T: Constraint Programming design of thermo-IRES switches Juan Antonio Garcia-Martin GENES, RNA Bioinformatics
TP021 Boosting alignment accuracy through adaptive local realignment Dan Deblasio PROTEINS, Gene / Protein Sequence Analysis
TP025 Efficient Data-Driven Model Learning for Dynamical Systems Ermao Cai SYSTEMS / DATA, Protein Interactions & Molecular Networks
TP027 Covariation Is a Poor Measure of Molecular Coevolution David Talavera PROTEINS, Evolution & Comparative Genomics/Proteomics
TP028 Quantitative analysis of microRNA mediated regulation on competing endogenous RNAs Xiaowo Wang SYSTEMS / GENES, Gene Regulation
TP029 A Weighted Exact Test for Significance of Mutually Exclusive Mutations in Cancer Mark Leiserson DISEASE / GENES, Disease Models & Epidemiology
TP030 CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure prediction Xin Gao PROTEINS, Protein Structure & Function
TP031 Reconstructing the temporal progression of HIV-1 immune response pathways Siddhartha Jain SYSTEMS / DISEASE, Protein Interactions & Molecular Networks
TP032 Clonal evolution inference and visualization in metastatic colorectal cancer Ha X. Dang DISEASE / GENES, Disease Models & Epidemiology
TP033 Ensemble-Based Evaluation for Protein Structure Models Daisuke Kihara PROTEINS, Protein Structure & Function
TP034 Identification of essential molecular and cellular processes controlling the response time and intensity of inflammation Alexander Mitrophanov SYSTEMS / DISEASE, Protein Interactions & Molecular Networks
TP036 Investigating molecular determinants of ebolavirus pathogenicity Mark Wass DISEASE / PROTEINS, Gene / Protein Sequence Analysis
TP037 LINEs between species: Evolutionary dynamics of LINE-1 retrotransposons across the eukaryotic tree of life David Adelson GENES, Evolution & Comparative Genomics/Proteomics
TP039 What Time is It? Deep Learning Approaches for Circadian Rhythms Forest Agostinelli SYSTEMS / GENES, Applied Bioinformatics
TP040 phRAIDER: Pattern-Hunter Based Rapid Ab Initio Detection of Elementary Repeats John Karro GENES, Gene / Protein Sequence Analysis
TP041 RCK: accurate and efficient inference of sequenceand structure-based protein-RNA binding models from RNAcompete data Yaron Orenstein DATA / GENES, RNA Bioinformatics
TP043 DNA editing of LTR retrotransposons reveals the impact of APOBECs on vertebrate genomes Binyamin Knisbacher GENES, Evolution & Comparative Genomics/Proteomics
TP044 Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning Hannes Bretschneider DATA / PROTEINS, Disease Models & Epidemiology
TP045 A Framework for Integrating Co-expression Networks with GWAS to Prioritize Candidate Genes in Maize Chad Myers SYSTEMS / GENES, Population Genomics
TP046 Read-Based Phasing of Related Individuals Shilpa Garg GENES / SYSTEMS, Population Genomics
TP047 Revisiting the computational analysis of DNase sequencing Ivan G. Costa GENES, Gene Regulation
TP049 An Algorithm for Computing the Gene Tree Probability under the Multispecies Coalescent and its Application in the Inference of Population Tree Yufeng Wu GENES / SYSTEMS, Population Genomics
TP050 The Role of Genome Accessibility in Transcription Factor Binding in Bacteria Antonio Gomes GENES / PROTEINS, Gene Regulation
TP051 A Network-driven Approach for Genome-wide Association Mapping Seunghak Lee GENES / DISEASE, Gene Regulation
TP054 Integrative genomics analyses unveil downstream biological effectors of disease-specific polymorphisms buried in intergenic regions Haiquan Li GENES / DISEASE, Disease Models & Epidemiology
TP055 DeepMeSH: Deep Semantic Representation for Improving Large-scale MeSH Indexing Shanfeng Zhu DATA, Databases, Ontologies & Text Mining
TP057 A Cross-Species Bi-Clustering Approach to Identifying Conserved Co-regulated Genes Jiangwen Sun GENES / SYSTEMS, Gene Regulation
TP058 Candidate gene prioritization with Endeavour Amin Ardeshirdavani DISEASE / DATA, Disease Models & Epidemiology
TP059 Translation of Genotype to Phenotype by a Hierarchy of Cell Subsystems Michael Ku Yu DATA / SYSTEMS, Protein Interactions & Molecular Networks
TP061 Structure-Based Prediction of Transcription Factor Binding Specificity using an Integrative Energy Function Alvin Farrel PROTEINS, Protein Structure & Function
TP063 Jumping across biomedical contexts using compressive data fusion Marinka Zitnik DATA / DISEASE, Disease Models & Epidemiology
TP064 Multi-Genome Scaffold Co-Assembly Based on the Analysis of Gene Orders and Genomic Repeats Sergey Aganezov GENES, Evolution & Comparative Genomics/Proteomics
TP068 deBWT: parallel construction of Burrows-Wheeler Transform for large collection of ge-nomes with de Bruijn-branch encoding Bo Liu GENES / DATA, Gene / Protein Sequence Analysis
TP069 Finding correct protein-protein docking models using ProQDock Sankar Basu PROTEINS, Protein Interactions & Molecular Networks
TP071 Solving the influence maximization problem on biological networks; a case study involving the cell cycle regulatory network in Saccharomyces Cerevisiae David Gibbs DATA / SYSTEMS, Protein Interactions & Molecular Networks
TP072 Compacting de Bruijn graphs from sequencing data quickly and in low memory Rayan Chikhi GENES / DATA, Gene / Protein Sequence Analysis
TP074 Influence maximization in time bounded network identifies transcription factors regulating perturbed pathways Kyuri Jo GENES, Gene Regulation
TP075 Scalable Tools for Quantitative Analysis of Chemical-Genetic Interactions from Sequencing-Based Chemical-Genetic Interaction Screens Scott Simpkins DATA / SYSTEMS, Applied Bioinformatics
TP077 An Integer Programming Framework for Inferring Disease Complexes from Network Data Konrad Klockmeier PROTEINS / DISEASE, Protein Interactions & Molecular Networks
TP081 Classifying Cancer Samples by microRNA Profiles: Read the Fine Print! Roni Rasnic DISEASE / GENES, Disease Models & Epidemiology
TP082 RapMap: A Rapid, Sensitive and Accurate Tool for Mapping RNA-seq Reads to Transcriptomes Avi Srivastava GENES, Gene / Protein Sequence Analysis
TP083 A convex optimization approach for identification of human tissue-specific interactomes Shahin Mohammadi SYSTEMS / DISEASE, Protein Interactions & Molecular Networks
TP084 RNA sequencing-based cell proliferation analysis across 19 cancers identifies a subset of proliferation-informative cancers with a common survival signature Brittany Lasseigne DISEASE, Disease Models & Epidemiology
TP085 ADAGE-Based Extraction of Biological Context from Public Gene Expression Data Jie Tan GENES / DATA, Applied Bioinformatics
TP088 SHARAKU: An algorithm for aligning and clustering read mapping profiles of deep sequencing in non-coding RNA processing Yasubumi Sakakibara GENES, RNA Bioinformatics
TP089 NUCLEOTIDE SEQUENCE COMPOSITION ADJACENT TO INTRONIC 5’ END IMPROVES TRANSLATION COSTS IN FUNGI Zohar Zafrir SYSTEMS / GENES, Gene Regulation
TP091 Analysis of differential splicing suggests different modes of short-term splicing regulation Hande Topa GENES, Gene Regulation
TP092 Prediction of Ribosome Footprint Profile Shapes from Transcript Sequences Tzu-Yu Liu SYSTEMS / GENES, Gene / Protein Sequence Analysis
TP093 Leveraging electronic medical records for systematic drug repositioning Hyojung Paik DISEASE / DATA, Applied Bioinformatics
TP094 Fast and accurate computation of differential splicing across multiple conditions Eduardo Eyras GENES, Gene Regulation
TP096 Comparative Analyses of Population-scale Phenomic Data in Electronic Medical Records Reveal Race-specific Disease Networks Benjamin S. Glicksberg DISEASE / SYSTEMS, Disease Models & Epidemiology
TP097 Using genomic annotations increases statistical power to detect eGenes Dat Duong GENES, Gene Regulation
TP098 Simultaneous prediction of enzyme orthologs from chemical transformation patterns for de novo metabolic pathway reconstruction Masaaki Kotera SYSTEMS / PROTEINS, Protein Interactions & Molecular Networks
TP099 Classifying and Segmenting Microscopy Images with Deep Multiple Instance Learning Oren Kraus DATA, Bioimaging
TP100 GeneiASE: Detection of conditiondependent and static allele-specific expression from RNA-seq data without haplotype information Daniel Edsgärd GENES, Gene / Protein Sequence Analysis
TP101 Fast metabolite identification with Input Output Kernel Regression Céline Brouard SYSTEMS / DATA, Applied Bioinformatics
TP103 Data-driven mechanistic analysis method to reveal dynamically evolving regulatory networks Jukka Intosalmi GENES / SYSTEMS, Protein Interactions & Molecular Networks
TP104 Faster and More Accurate Graphical Model Identification of Tandem Mass Spectra using Trellises Shengjie Wang PROTEINS, Protein Structure & Function
TP105 CD30 cell graphs of Hodgkin lymphoma are not scale-free—an image analysis approach Tim Schäfer DATA / DISEASE, Bioimaging
TP106 A novel method for discovering local spatial clusters of genomic regions with functional relationships from DNA contact maps Kevin Yip GENES, Gene Regulation
TP107 BioASF: A Framework for Automatically Generating Executable Pathway Models Specified in BioPAX Reza Haydarlou SYSTEMS / DATA, Databases, Ontologies & Text Mining
TP110 A Low-Latency, Big Database System and Browser for Storage, Querying and Visualization of 3D Genomic Data Alexander Butyaev GENES / DATA, Databases, Ontologies & Text Mining
WK02 Part B How to Scale Science and People Using the Cloud. Nirav Merchant ,