ISMB 2014 Conference Schedule – As of July 14, 2014 (schedule subject to change) Thursday, July 10 3:00 p.m. - 6:00 p.m.
Registration and Information Desk Open - Hall C Pre-function space - Conference Location - Hynes Convention Center, Boston, United States
Friday, July 11 7:30 a.m. - 6:00 p.m.
8:30 a.m. - 10:15 a.m.
Registration and Information Desk Open - Hall C Pre-function space Room: 107
Room 210
Room 209
Room 201
Biology Teacher Tutorial (BT01): Starts at 9:00 am
3Dsig Satellite Meeting (2 days)
CAMDA Satellite Meeting (2 days)
Automated Bio-Ontologies Function Prediction (2 days) (AFP-SIG) (2 days)
10:15 a.m. - 10:45 a.m.
Coffee Break (various locations outside meeting rooms)
10:45 a.m. - 12:30 p.m.
Biology Teacher Tutorial (BT01):
12:30 p.m. - 1:30 p.m.
Lunch: Check lunch ticket for location
1:30 p.m. - 3:30 p.m.
Biology Teacher Tutorial (BT01): Ends at 3:00 pm
3:30 p.m. - 4:00 p.m.
Coffee Break (various locations outside meeting rooms)
4:00 p.m. - 6:00 p.m.
Room 204
Room 202
Room 203
BioVis SIG (2 days) BOSC (2 days)
Room 200
Room 206
Room 207
Room 208
HiTSeq: High Throughput Sequencing days)
Integrative RNA Biology (IRB-SIG) (1 day)
Network Biology (NetBio) SIG (1 day)
Student Council Symposium 10 (1 day) Program starts at 8:00 am
(2
Meetings Continue
SIGs continue
3Dsig Sessions Ends 5:30 / Dinner at 6:30 p.m. (ticketed event at Sheraton Hotel)
CAMDA ends at 5: 50 / Dinner at 6:30 p.m. (ticketed event at Summer Shack Boston)
Integrative RNA Biology (IRB-SIG) ends at 7:00 pm
6:00 p.m. - 6:30 p.m.
Orienteering Starts @ Meeting Point at Information Desk Open - Hall C Pre-function space
6:30 p.m. - 7:45 p.m. (aprox finish time)
Orienteering Event (delegates do not return to the convention center)
SCS 10 Ends 7:30 p.m. with Poster Reception
Saturday, July 12 7:30 a.m. - 6:00 p.m.
8:30 a.m. - 10:15 a.m.
Registration and Information Desk Open - Hall C Pre-function space Room 107
Room 210
Room 209
Room 201
Tutorial 1 (AMTUT): Computational Metagenomics Techniques and Challenges
3Dsig Satellite Meeting (2 days)
CAMDA Satellite Meeting
Automated Bio-Ontologies Function Prediction (2 days) (AFP-SIG) (2 days)
10:15 a.m. - 10:45 a.m.
Coffee Break (various locations outside meeting rooms)
10:45 a.m. - 12:30 p.m.
Tutorial (AMTUT): SIGs continue Continues to 12:30 p.m.
12:30 p.m. - 1:30 p.m.
Lunch: Check lunch ticket for location
1:30 p.m. - 3:30 p.m.
Tutorial 2 (PMTUT): Wikipedia: WikiProject Computational Biology
3:30 p.m. - 4:00 p.m.
Coffee Break (various locations outside meeting rooms)
4:00 p.m. - 6:00 p.m.
Tutorial (PMTUT): Continues to 5:30 p.m.
5:30 p.m. - 7:30 p.m.
Opening Reception with Exhibitors – Auditorium and Hall C (200 Level)
SIGs continue
SIGs continue
Sunday, July 13 7:30 a.m. - 6:30 p.m.
Registration and Information Desk Open
8:15 a.m. - 5:30 p.m.
Posters on Display - Exhibiton Area: Auditorium and Hall C
8:45 a.m. - 9:00 a.m.
Opening Welcome – Ballroom A/B
Room 204
Room 202
Room 203
BioVis SIG (2 days) BOSC (2 days)
Room 200 HiTSeq: High Throughput Sequencing days)
Room 206
Room 205
Challenges Single MS-SIG (1 day) Cell biology(1 day) (2
Room 208
Room 207
Regulatory Genomics (RegGenSIG) (1 day)
Vari SIG (1 day)
9:00 a.m. - 10:00 a.m.
Keynote: Good Things Come in Small Packages – Replicators and Innovators, Michal Linial, The Hebrew University of Jerusalem, Israel
10:00 a.m. - 10:30 a.m.
Coffee Break with Exhibitors - Exhibition Area: Auditorium & Hall C Room 306
Ballroom C
Room 312
Room 310
Room 309
Parallel Sessions
Room 311
Paper Paper Paper Presentation Oral Posters Presentations (PP) Presentations (PP) (PP) / LBR / Special Talks (ST)
Late Breaking Research (LBR)
Special Session (SS01): Human Microbiome Studies, Organizer: Mihai Pop, Niranjan Nagarajan
Special Session (SS02): COSI: Communities of Special Interest, Organizers: Christine Orengo, Lonnie Welch
Workshop Track (WK01): Junior Principal Investigators Meeting, Organizers: Jeroen de Ridder, Venkata Satagopam, Manuel Corpas, Yana Bromberg
Technology Track (TT)
10:30 a.m. - 10:55 a.m.
PP01: Simultaneous Identification of Multiple Driver Pathways in Cancer (HT), Mark Leiserson
PP02: Ragout - A reference-assisted assembly tool for bacterial genomes (PT), Mikhail Kolmogorov
LBR01: Transcriptome analysis reveals thousands of targets of nonsensemediated mRNA decay that offer clues to the mechanism in different species, Steven Brenner
OP01: Yi-Hung Huang; OP2: Raffaele Calogero; OP03: Caitlyn Mills
LBR02: Leveraging network structure to discover genetic interactions in genome-wide association studies, Wen Wang
SS01 – Part A: Human gut microbiome in health and disease, Stanislav Dusko Ehrlich
SS02 – Part A: WK01 – Part A: Brief overview of Introduction and the Communities of elevator pitches Special Interest and Plans for the Future, Christine Orengo, Rafael Najmanovich, Iddo Friedberg, David Kreil, Yana Bromberg
11:00 a.m. - 11:25 a.m.
PP03: Linking hypothetical patterns to disease molecular signatures in Alzheimer's disease (HT), Ashutosh Malhotra
PP04: AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references (PT), Ergude Bao
PP05: Cross-study validation for assessment of prediction models and algorithms (PT), Christoph Bernau
OP04: Amrita Roy Choudhury; OP05: Aik Choon Tan; OP06: Benedict Anchang
LBR03: Heterogeneous Network Link Prediction Prioritizes DiseaseAssociated Genes, Daniel Himmelstein
SS01 – Part B: Experimental exploration of the human gut microbiome, Peter Turnbaugh
SS02 – Overview Continued: Lonnie Welch, Alex Pico, Oliver Kohlbacher
WK01 – Part B: Elevator pitches by participants
11:30 a.m. - 11:55 p.m.
PP06: Constructing module maps for integrated analysis of heterogeneous biological networks (HT), David Amar
PP07: ExSPAnder: a Universal Repeat Resolver for DNA Fragment Assembly (PT), Andrey Prjibelski
ST01: Nobel Prize Celebration: Arieh Warshel’s Legacy Presented by Lynn Kamerlin
OP07: Kunal Kundu; OP08: Xiaojia Tang; OP09: Benjamin Good
TT28: Recent Developments in the Pathway Tools Software and BioCyc Databases, Peter Karp, SRI International
SS01 – Part C: Computational challenges in the analysis of microbiome data, Peer Bork
SS02 – Part C: Continued: Francisco De La Vega, Hilmar Lapp, Nigam Shah
WK01 – Part C: Keynote lecture: how to run a successful lab, Russ Altman
12:00 p.m. - 12:25 p.m.
PP08: Large scale analysis of signal reachability (PT), Andrei Todor
PP09: Complete Genome Assembly with Long Reads (HT), Adam Phillippy
ST02: Nobel Prize Celebration: Martin Karplus’s Legacy Presented by Roland Dunbrack
OP10: Andrew Quitadamo; OP11: Serdar Bozdag; OP12: Sergio Pulido Tamayo
SS01 – Part D: Evolution and dynamic nature of microbial systems, Eric Alm
SS02– Part D: Continued: Brent Richter, Fran Lewitter, Maneul Corpas
WK01 – Part D: Keynote (continued) and Round table
12:25 p.m. - 2:00 p.m.
Lunch (available for purchase: Exhibit hall or Food court) - Birds of a feather sessions (12:45 pm - 1:45 pm)
12:45 p.m - 1:45 p.m.
2:00 p.m. - 3:00 p.m.
Room 304
ISCB Student Council - Career Central
Room 302
Room 313
BoF: Open Source Communities with Impact, Leader: Manuel Corpas (Room 302)
TT01: Monitoring, analyzing, and exploring Ion Torrent™ NGS data with Torrent Suite™ Software and Torrent Variant Caller, Daryl Leon, Thermofisher
TT02: Computational biology careers at Pfizer R&D, Enoch S Huang, Pfizer
Lunch and Learn (12:45 - 2:00 pm): The Appistry Pipeline Challenge: Rewarding Researchers for Translating NGS Data into Clinical Action, Brett McCann, Appistry, Inc.
ISCB Senior Scientist Accomplishment Award Keynote: DNA Assembly: Past, Present, and Future, Eugene (Gene) Myers, Max Planck Institute Dresden, Germany, Ballroom A/B Room 311
Room 304
Room 302
Room 313
Room 306
Room 312
Ballroom C
Room 310
Room 309
Parallel Sessions
Paper Paper Paper Oral Posters Presentations (PP) Presentations (PP) Presentations (PP)
Late Breaking Research (LBR)
Special Session (SS03): Celebrating 20 Years: Journal of Computational Biology, Organizer: Michael Waterman, Sorin Istrail
Special Session (SS04): Celebrating Michael Levitt and his Nobel Prize in Chemistry, Organizers: Steven Brenner, Mark Gerstein, Yu Xia, Andrea Scalewicz
Workshop Track (WK02): Bioinformatics Core Facilities, Organizers: Brent Richter, David Sexton, Simon Andrews, Matthew Eldridge, HansRudolf Hotz
Technology Track (TT)
3:05 p.m. - 3:30 p.m.
PP10: GRASP: Analysis of genotypephenotype results from 1,390 genome-wide association studies and corresponding open access database (PT), Andrew Johnson
PP11: Capturing short tandem repeat variation from paired-end sequencing data (HT), Mikael Boden
PP12: How antibodies chase antigens, how Antigens try to escape and how we can use this to predict antibody specificity (HT), Inbal Sela
OP13: Perry Haaland; OP14: Emma Schwager; OP15: Shany Ofaim
LBR04: Genome annotation of multiple cell types and chromatin architecture using graph-based regularization, Maxwell Libbrecht
SS03 – Part A: Algorithms for Large-Scale Identity-By-Descent Detection, Serafim Batzoglou
SS04 – Part A: Human Genome Analysis, Mark Gerstein
WK02 – Part A: “Core on a Budget” vs “EnterpriseLevel Bioinformatics”, Alistair Kerr, Michael Poidinger
TT03: Interactive Visual Analysis with Galaxy Charts, Aysam Guerler, Johns Hopkins University
3:35 p.m. - 4:00 p.m.
PP13: A comparative metaanalysis of prognostic gene signatures for latestage ovarian cancer (HT), Levi Waldron
PP14: BlockClust: efficient clustering and classification of non-coding RNAs from short read profiles (PT), Fabrizio Costa
PP15: Tertiary structure-based prediction for conformational Bcell epitopes through B factors (PT), Jing Ren
OP16: Tomislav Ilicic; OP17: Naisha Shah; OP18: Hong Yu
LBR05: Deconvolution of massively-parallel reporter assays tiling 15,000 human regulatory regions reveal activating and repressive regulatory sites at nucleotide-level resolution, Jason Ernst
SS03 – Part B: Compressive Genomics, Bonnie Berger
SS04 – Part B: Interactomics: Computational Analysis of Novel Drug Opportunities / Natural Modeling in Structural Biology, Ram Samudrala, Peter Minary
WK02 – Part B: Open Forum Discussion, David Sexton, Matthew Eldridge
TT04: KeyPathwayMiner Extracting relevant pathways by combining OMICS data and biological networks, Alexander Junge, University of Copenhagen Denmark
4:05 p.m. - 4:30 p.m.
PP16: Dissecting Cancer Heterogeneity with network based approach (HT), Teresa Przytycka
PP17: WISECONDOR detects small fetal chromosomal aberrations in lowcoverage NGS data of maternal plasma (HT), Roy Straver
PP18: An Efficient Parallel Algorithm for Accelerating Computational Protein Design (PT), Yichao Zhou
OP19: Alistair Martin; OP20: Reazur Rahman; OP21: Christopher Schlosberg
LBR06: Linking SS03 – Part C: tumor mutations to TBD drug responses via a quantitative chemical-genetic interaction map, Sourav Bandyopadhyay
SS04 – Part C: The Language of the Protein Universe / A bird's eye view of protein space: peeking at the relationships between sequence, structure, and function , Andrea Scaiewicz, Rachel Kolodny
WK02 – Part C: Breaking topics in core facilities, Simon Andrews, Hans-Rudolf Hotz
TT05: Synapse: Software infrastructure for collaborative reproducible research, Abhishek Pratap, SAGE Bionetworks
4:35 p.m. - 5:00 p.m.
PP19: Inductive Matrix Completion for Predicting Gene-Disease Associations (PT), Nagarajan Natarajan
TT06: BioJS: an open source standard for biological visualization, Guy Yachdav, TU Munich
SS04 – Part D: WK02 – Part D: Panel: Enoch Session continues Huang, Marie Brutt, Chris Lee, Gaurav Chopra, Jerry Tsai
TT07: PAGIT: Post Assembly Genome Improvement Toolkit, Thomas Otto, Sanger Centre
5:00 p.m. - 7:00 p.m.
PP20: Probabilistic PP21: BioC: a Method for minimalist Detecting Copy approach to Number Variation interoperability for in a Fetal Genome biomedical text using Maternal processing (HT), Plasma Rezarta Islamaj Sequencing (PT), Dogan Ladislav Rampášek Poster Reception with authors - Odd Numbered Posters
SS03 – Part D: TBD
Monday, July 14 7:30 a.m. - 7:30 p.m.
Registration and Information Desk Open -
8:15 a.m. - 5:30 p.m.
Posters on Display - Exhibiton Area: Auditorium and Hall C
8:45 a.m. - 9:00 a.m.
Morning Welcome – Ballroom A/B
9:00 a.m. - 10:00 a.m.
Keynote Presentation: Biomedical Quants of the World Unite! We only have our disease burden to lose, Isaac (Zak) Kohane, Harvard Medical School and Children's Hospital Boston, United States
10:00 a.m. - 10:30 a.m.
Coffee Break with Exhibitors - Exhibition Area: Auditorium & Hall C Room 311
Room 304
Room 302
Room 312
Ballroom C
Room 310
Room 306
Room 309
Parallel Sessions
Paper Paper Paper Paper Special Session Presentations (PP) Presentations (PP) Presentations (PP) Presentations (PP) (SS05): Postgenomic medical decision making in cancer, Organizers: Melissa Cline, Rachel Karchin
Workshop Track Technology Track (WK03): Workshop (TT) on Education in Bioinformatics (WEB 2014), Organizers: Michelle Brazas, Fran Lewitter, Patricia Palagi, Vicky Schneider
Technology Track (TT)
10:30 a.m. - 10:55 a.m.
PP22: Countryspecific antibiotic use practices impact the human gut resistome (HT), Kristoffer Forslund
PP23: RNA-Skim: a rapid method for RNA-Seq quantification at transcript level (PT), Zhaojun Zhang
PP24: Metabolite Identification through Multiple Kernel Learning on Fragmentation Trees (PT), Huibin Shen
PP25: Methods for time series analysis of RNAseq data with application to human Th17 cell differentiation (PT), Tarmo Äljö
SS05 – Part A: Benefits of Genomic Medicine: What to Tell the Patient, Christine Chung
WK03 – Part A: Details on running a MOOC in Bioinformatics and Biostatistics, Michael Love
TT09: Using D2P2 the Database of Disordered Protein Predictions, Matt Oates, University of Bristol
11:00 a.m. - 11:25 a.m.
PP26: Relating the metatranscriptome and metagenome of the human gut (HT), Eric Franzosa
PP27: Power and Limitations of RNASeq: findings from the SEQC (MAQCIII) consortium (HT), David Kreil
PP28: Computational Biology in Medicine: Novel Targets and Drug Repositioning Use Cases (HT), Pankaj Agarwal
PP29: Cellselective labeling using amino acid precursors for proteomic studies of multicellular environments (HT), Nicholas Gauthier
SS05– Part B: Evaluating Tumor Exome Sequencing in the Oncology Clinic: Lessons from the BASIC3 Study, William Parsons
WK03 – Part B: Games that teach, games that learn: an introduction to serious games for bioinformatics, Benjamin Good
11:30 a.m. - 11:55 p.m.
PP30: Pipasic: Similarity and Expression Correction for Strain-Level Identification and Quantification in Metaproteomics (PT), Bernhard Y. Renard
PP31: Deep learning of the tissue-regulated splicing code (PT), Michael Leung
PP32: DrugComboRanker : Drug Combination Discovery Based on Target Network Analysis (PT), Lei Huang
PP33: Automated detection and tracking of many cells by using 4D live-cell imaging data (PT), Terumasa Tokunaga
SS05– Part C: Guiding clinical decision-making with omics data, Josh Stuart
WK03 – Part C: The MOOC Universe from the Learners' Perspective, David B. Searls
TT11: Application of HGMD database within a typical variant analysis pipeline, and the unique challenges of annotating pharmacogenomic variants, Jennifer Hogan, BIOBASE
TT12: The DOE Systems Biology Knowledgebase (KBase): Progress towards a system for collaborative and reproducible inference and modeling of biological function, Robert Cottingham (DOE ORNL)
12:00 p.m. - 12:25 p.m.
PP34: Primate Transcript and Protein Expression Levels Evolve under Compensatory Selection Pressures (HT), Zia Khan
PP35: Systematically Differentiating Functions for Alternatively Spliced Isoforms through Integrating RNA-seq Data (HT), Yuangfan Guan
PP36: Drug synergy screen and network modeling in dedifferentiated liposarcoma identifies CDK4 and IGF1R as synergistic drug targets (HT), Martin Miller
PP37: NaviCell: a SS05 – Part D: web-based Session Continues environment for navigation, curation, maintenance and data analysis in the context of large molecular interaction maps (HT), Emmanuel Barillot
WK03 – Part D: Panel Discussion: The Merits and Pitfalls of Online Learning for Bioinformatics, Benjamin Good, Michael Love, Nicholas Provart, David Searls
TT13: When silent mutations scream: revisiting annotation of regulatory elements, Alexander Kaplun, BIOBASE
TT14: Sequencing and Genomic Analysis Onsite and in the Cloud, Raymond Tecotzky, Illumina
12:25 p.m. - 2:10 p.m.
ISCB and ISCB Student Council Open Business Meeting - 12:35 p.m. - 2:00 p.m. - Room 313 (Lunch available for purchase: Exhibit hall or Food court) Room 311
Parallel Sessions
Room 304
Room 302
Room 312
Room 306
Paper Paper Paper Paper Late Breaking Presentations (PP) Presentations (PP) Presentations (PP) Presentations (PP) Research (LBR)
Ballroom C
TT08: Ceci n’est pas une pipe. An open standard for reproducible genomics pipelines, Nebojsa Tijanic, Seven Bridges Genomics
TT10: Pathview: an R/Bioconductor package for pathway-based data integration and visualization, Weijun Luo, UNC Charlotte
Room 310
Workshop Track Technology Track (WK04): (TT) Harnessing Genetic Diversity to Enable Personalized Medicine, Organizers: Frank EmmertStreib, Sol Efroni, Christos Hatzis
Room 309 Technology Track (TT)
2:10 p.m. - 2:35 p.m.
PP38: Efficient Modeling and Active Learning Discovery of Biological Responses (HT), Armaghan Naik
PP39: Analyzing DNase I biases reveals a novel DNA methylation readout mechanism (HT), Harmen Bussemaker
PP40: Statistical challenges in whole-exome sequencing of 7000 individuals with schizophrenia and controls (HT), Menachem Fromer
PP41: ParetoOptimal Phylogenetic Tree Reconciliation (PT), Yi-Chieh Wu
LBR07: Linking Signaling Pathways to Transcriptional Programs in Breast Cancer, Hatice Ulku Osmanbeyoglu
WK04 – Part A: John Quackenbush, Doug Lauffenburger
TT15: Some Research Topics at the AIST Computational Biology Research Center in Japan, Paul Horton, AIST
TT16: Elastic-R: Connecting the dots of scientific computing, from the pi to the clouds, Karim Chine, Cloud Era Ltd.
2:40 p.m. - 3:05 p.m.
PP42: Stochastic EM-based TFBS motif discovery with MITSU (PT), Alastair Kilpatrick
PP43: Constructing PP44: Genome Hepitypes:Phasing leaks (HT), Steven Local Genotyping Brenner and DNA Methylation (HT), Weng-Yu Chung
PP45: Human disease locus discovery and mapping to molecular pathways through phylogenetic profiling (HT), Yuval Tabach
LBR08: Beyond Argonaute: understanding microRNA dysregulation in cancer and its effect on protein interaction and transcriptional regulatory networks, Sara Gosline
WK04 – Part B: Joel Dudley, Gad Getz
TT17: Privacy Preserving Search in Bioinformatics, Kana Shimizu, AIST
TT18: Protein and RNA alignment and analysis with Jalview 2.8.2 and JABA 2.1, James Procter, University of Dundee
3:10 p.m. - 3:35 p.m.
PP46: Gene network inference by probabilistic scoring of relationships from a factorized model of interactions (PT), Marinka Zitnik
PP47: Cancelled: A-to-I RNA editing occurs at over a hundred million genomic sites, located in a majority of human genes (HT), Erez Levanon
PP48: Privacy Preserving Protocol for Detecting Genetic Relatives Using Rare Variants (PT), Farhad Hormozdiari
PP49: Arboretum: reconstruction and analysis of the evolutionary history of conditionspecific transcriptional modules (HT), Sushmita Roy
LBR09: Extensive WK04 – Part C: trans and cis-QTLs Atul Butte, Manolis revealed by large Kellis scale cancer genome analysis, Kjong-Van Lehmann
TT19: The khmer project: cloudbased raw sequencing analysis on a budget. Michael Crusoe, Michigan State University
3:40 p.m. - 4:05 p.m.
PP50: Functional Association Networks as Priors for Gene Regulatory Network Inference (PT), Erik Sonnhammer
PP51: Ubiquitously transcribed genes use alternative polyadenylation to achieve tissuespecific expression (HT), Steve Lianoglou
PP52: Detecting chromatin modifications in cancer samples: challenges and solutions (HT), Valentina Boeva
PP53: Proteomic Universal Correlate of Evolution (HT), David Horn
LBR10: Utilizing a WK04 – Part D: Phylogeographic Session continues Generalized Linear Model for Identifying Predictors Driving H5N1 Diffusion within Egypt, Matthew Scotch
TT21: Garuda: Fly to the future of biology, Hiroaki Kitano, RIKEN Center for Integrative Medical Sciences
TT20: Hyperplexed biomarker imaging using the MultiOmyx platform enables novel systems biology insights for the diagnosis and treatment of disease, Brion Sarachan, GE Global Research
4:05 p.m. - 4:35 p.m.
Coffee Break with Exhibitors - Exhibition Area: Auditorium & Hall C
4:45 p.m. - 5:45 p.m.
ISCB Overton Prize Lecture: A multidimensional single cell approach to understand cellular behavior, Dana Pe'er, Columbia University, United States, Ballroom A/B
5:45 p.m. - 7:30 p.m.
Poster Reception with authors - Even Numbered Posters
7:00 p.m. - 10:00 p.m.
Conference Reception at MIT Museum (ticketed event) - 265 Massachusetts Avenue, Cambridge
Tuesday, July 15 7:30 a.m. - 6:00 p.m.
Registration and Information Desk Open
8:15 a.m. - 3:00 p.m.
Posters on Display - Exhibiton Area: Auditorium and Hall C
8:45 a.m. - 9:00 a.m.
Morning Welcome – Ballroom A/B
9:00 a.m. - 10:00 a.m.
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, Massachussetts Institute of Technology, United States
10:00 a.m. - 10:30 a.m.
Coffee Break with Exhibitors - Exhibition Area: Auditorium & Hall C Room 311
Parallel Sessions
Room 304
Room 302
Room 312
Room 306
Paper Paper Paper Paper Late Breaking Presentations (PP) Presentations (PP) Presentations (PP) Presentations (PP) Research (LBR)
Ballroom C
Room 310
Room 313
Room 309
Special Session (SS06): Dissecting Complex Disease Architecture, Organizers: Manolis Kellis, Joel Hirschhorn, Alkes Price, Shamil Sunyaev
Workshop Track (WK05): Trends in genomic data analysis with R/Bioconductor: Organizer: Levi Waldron
Technology Track (TT)
Technology Track (TT)
10:30 a.m. - 10:55 a.m.
PP54: Novel Burkholderia mallei Virulence Factors Linked to Specific Host-Pathogen Protein Interactions (HT), Jacques Reifman
PP55: Mapping Functional Transcription Factor Networks from Gene Expression Data (HT), Michael Brent
PP56: Protein Expansion Is Primarily due to Indels in Intrinsically Disordered Regions (HT), Arne Elofsson
PP57: Graph Regularized Dual Lasso for Robust eQTL Mapping (PT), Wei Cheng
LBR11: Clonality Inference in Multiple Tumor Samples Using Phylogeny, Nilgun Donmez
SS06 – Part A: From GWAS to biology using large diverse data sets and large number of loci, Joel Hirschorn
WK05 – Part A: An overview of genomic data analysis in Bioconductor, Levi Waldron
TT22: BaseSpace® Onsite Bioinformatics Platform, Raymond Tecotzky, Illumina
11:00 a.m. - 11:25 a.m.
PP58: Mathematical Modeling of VirusHost Interactions (HT), Lars Kaderali
PP59: Chromatin landscapes and long-range interactions of retroviral and transposon integrations (HT), Jeroen de Ridder
PP60: Characterizing changes in the rate of protein-protein dissociation upon interface mutation using hotspot energy and organization (HT), Rudi Agius
PP61: EPIQ Efficient detection of SNP-SNP epistatic interactions for quantitative traits (PT), Yaara Arkin
LBR12: Expansion of biological pathways based on evolutionary inference, Sarah Calvo
SS06 – Part B: Partitioning heritability across functional categories, Alkes Price
WK05 – Part B: Genomic data and annotation through AnnotationHub, Martin Morgan
TT24: From the Ground to the Cloud in 25 minutes: Building a Customized Galaxy Analysis Server Using Only a Web Browser, Daniel Blankenberg, Galaxy Team/Penn State
11:30 a.m. - 11:55 p.m.
PP62: Accurate viral population assembly from ultra-deep sequencing data (PT), Serghei Mangul
PP63: Large-scale reconstruction of 3D structures of human chromosomes from chromosomal contact data (HT), Jianlin Cheng
PP64: Why NTerminal domains tend to be shorter than C-Terminal domains? (HT), Ron Unger
PP65: A combinatorial approach for analyzing intratumor heterogeneity from high-throughput sequencing data (PT), Iman Hajirasouliha
LBR13: Accurate prediction of mitochondrial presequences and their cleavage sites with MitoFates identifies hundreds of novel human mitochondrial protein candidates, Yoshinori Fukasawa
SS06 – Part C: Genetics and evolution of complex traits in light of DNA sequencing data, Shamil Sunyaev
WK05 – Part C: Scalable integrative bioinformatics with Bioconductor, Vincent Carey
12:00 p.m. - 12:25 p.m.
PP66: Deciphering human disease mutations through the atomicresolution protein interactome network (HT), Haiyuan Yu
PP67: A statistical approach for inferring the 3D structure of the genome (PT), Nelle Varoquaux
PP68: New Directions for Diffusion-Based Network Prediction of Protein Function: Incorporating Pathways with Confidence (PT), Mengfei Cao
PP69: Reconstructing tumor evolution using simple somatic mutation frequencies (HT), Quaid Morris
LBR14: Stable identifiability of the human microbiome based on metagenomic hitting sets, Eric Franzosa
SS06 – Part D: Insights on complex disease aarchitecture from regulatory genomics and epigenomics, Manolis Kellis
WK05 – Part D: RNA-Seq workflows in Bioconductor, Michael Love
12:25 p.m. - 2:00 p.m.
Lunch (available for purchase: Exhibit hall or Food court) - Birds of a feather sessions (12:45 pm - 1:45 pm)
12:45 p.m - 1:45 p.m.
BoF: Business Meeting of the Computational Mass Spectrometry CoSI, Leader: Oliver Kohlbacher (Room 311)
BoF: Career Development for Women in Science, Leader: Lucia Peixoto (Room 304)
BoF: Bioinformatics Curriculum Guidelines, Leader: Lonnie Welch (Room 302)
Room 311
Room 304
Room 302
Parallel Sessions
TT23: The EMBLEBI Job Dispatcher framework for bioinformatic applications, Weizhong Li, EMBL-EBI
TT25: A reputationbased web application (sbv IMPROVER Network Verification Challenge) that facilitates collaboration on biological network models, Julia Hoeng, PMI & TT26: Persephone. Anselmo Di Fabio, A Very Fast Multi- ADS Genome Browser, Maxim Troukhan, Ceres Inc.
TT27: Bioinformatics and Computer Biology Systems design applied to Medical Molecular Nanobiotechnology , Allan Orozco, University of Costa Rica
BoF: Critical Assessment of Function Annotation followup, Leader: Iddo Friedberg (Room 306) Room 312
Room 306
Paper Paper Paper Paper Late Breaking Presentations (PP) Presentations (PP) Presentations (PP) Presentations (PP) Research (LBR)
Ballroom C
Room 313
Workshop Track Technology Track (WK06): What (TT) Bioinformaticians need to know about digital publishing beyond the PDF2I, Organizers: Scott Edmunds, Marco Roos , Carole Goble, Jun Zhao, Amye Kenall, Barend Mons
Room 310
Room 309
Technology Track (TT)
Technology Track (TT)
2:00 p.m. - 2:25 p.m.
PP70: Cancelled Genomic underpinnings for network patterns and evolution (HT), Luay Nakhleh
PP71: Inferring Gene Ontologies from Pairwise Similarity Data (PT), Michael Kramer
PP72: Evaluating Synteny for Improved Comparative Studies (PT), Cristina Ghiurcuta
PP73: Networkbased stratification of tumor mutations (HT), Matan Hofree
LBR15: Novel Computational Approach for Integration of Omics-platforms with Application to Hypertension in Recombinant Rat Strains, Stefka Tyanova
WK06 – Part A: Alternative models of Peer Review, Ciaran O'Neill
TT28: MOVED TO SUNDAY 11: 30AM. Room 306 Recent Developments in the Pathway Tools Software and BioCyc Databases, Peter Karp, SRI International
TT29: Scaling Galaxy: Preparing for Those Next Few Orders of Magnitude, John Chilton, Galaxy Project
TT30: UniProt: New website and latest developments, Sangya Pundir, EMBL-EBI
2:30 p.m. - 2:55 p.m.
PP74: Scale-space measures for graph topology link protein network architecture to function (PT), Marc Hulsman
PP75: Cancelled: Using association rule mining to determine promising secondary phenotyping hypotheses (PT), Anika Oellrich
PP76: Robust Clinical Outcome Prediction based on Bayesian Analysis of Transcriptional Profiles and Prior Causal Networks (PT), Kourosh Zarringhalam
PP77: Detecting independent and recurrent copy number aberrations using interval graphs (PT), HsinTa Wu
LBR16: Systematic Evaluation of the Prognostic Impact and Intratumour Heterogeneity of clear cell Renal Cell Carcinoma biomarkers, Sakshi Gulati
WK06 – Part B: Recent insights from experiments in reproducibility: What's the plan again?, Philippe Rocca-Serra, Alejandra Gonzalez-Beltran
TT31: Using HPC techniques to accelerate NGS workflows, Pierre Carrier, Cray, Inc.
TT32: GenomeSpace: An Environment for Frictionless Bioinformatics, Ted Liefeld, Broad Institute
TT33: Alignments with Annotations, William Pearson, University of Virginia
3:00 p.m. - 3:25 p.m.
PP78: GraphProt: How to make sense out of CLIPseq data (HT), Rolf Backofen
PP79: Improved exome prioritization of disease genes through crossspecies phenotype comparison (HT), Peter Robinson
PP80: MIRA: Mutual InformationBased Reporter Algorithm for Metabolic Networks (PT), A. Ercument Cicek
PP81: Emerging landscape of oncogenic signatures across human cancers (HT), Giovanni Ciriello
LBR17: Utilizing Docking Score Distributions to Identify Novel Protein-Drug Interactions, Ariel Feiglin
WK06 – Part C: Trends in data publishing, Barend Mons
TT34: GTFAR: Genome and Transcriptome Free Analysis of RNA, Tade Souaiaia, University of Southern California
TT35: geWorkbenchWeb: An integrated web interface to a multitude of bioinformatics tools, Aris Floratos, Columbia University
TT36: Lynx: A REST based platform for annotations and systems analysis of multi-gene disorders, Dinanath Sulakhe, University of Chicago
3:30 p.m. - 3:55 p.m.
PP82: From 1D to 3D and back: Genome scaffolding from DNA interaction frequency (HT), Noam Kaplan
PP83: A community effort to assess drug sensitivity prediction algorithms identifies approaches for improved performance (HT), James Costello
PP84: Metabolome-scale prediction of intermediate compounds in multi-step metabolic pathways with a recursive supervised approach (PT), Masaaki Kotera
PP85: MicroRNAgene association as a prognostic biomarker in cancer exposes disease mechanisms (HT), Rotem Ben-Hamo
LBR18: Interactomics: Computational Analysis of Novel Drug Opportunities, Gaurav Chopra
WK06 – Part D: Software Review Panel: Q&A and audience participation, Kaitlin Thaney, Carole Goble, Phil Bourne
TT37: Construct, analyze and interpret the network using biomedical knowledge in VisANT, Zhenjun Hu, Boston University
TT38: Cellular Phenotype Database with Ontology assisted data browsing, Catherine Kirsanova, EMBLEBI
3:55 p.m. - 4:30 p.m.
Coffee Break with Exhibitors - Exhibition Area: Auditorium & Hall C
4:40 p.m. - 5:40 p.m.
ISCB Fellows Keynote: Informatics for understanding drug response at all scales. Russ Altman, Stanford University, United States, Ballroom A/B
5:40 p.m. - 6:00 p.m.
ISCB Awards and Closing – Ballroom A/B
