PLoS Postcards

PLoS Postcards-ISCB is partnering with PLoS Computational Biology to have all presentations at ISMB 2010 potentially reported on by conference student and jr. scientist attendees and published in PLoS Computational Biology as part of an article summarizing the conference. This program is referred to as PLoS Postcards. Your permission is not a guarantee that the material will be published in PLoS Computational Biology.

The following presenters have agreed to make their research presentations available for the PLoS postcard at ISMB 2010


Posters

16953A02Comparison of RNA Sequencing (RNA-Seq) Methods for Counting and Testing Differential Expression Yongsheng Bai
17057A04Multi-task hierarchical Bayesian models for predicting outcomes of HIV combination therapies Jasmina Bogojeska
17058A05Molecular Modelling and Dynamics of Prolyl Oligopeptidase to Study Conformational Changes and Ligand Binding Swati Kaushik
17061A06Analysis of Complex human disorders from the systems biology perspective Sandhya Balasubramanian
17062A07Head ‘em off at the pass – Predicting Antigen Evolution ALBINA RAHIM
17083A08A Novel Approach to Predict Cancer Outcomes Based on the Relationship between Protein Structural Information and Protein Networks Kelvin Zhang
17094A09Development of a computer pipeline for next-generation RNA-Sequencing analysis SHAOJUN TANG
17101A10The Cancer Genome Atlas (TCGA) Data Coordinating Center and Data Portal John Greene
17121A11De novo assembly of Corynebacterium pseudotuberculosis genomes using short reads obtained from mate-paired libraries Louise Cerdeira
17119A12High Frequency of PfCRT 76T in Two Malian Villages and Its Prevalence in Severe Relative to Non-Severe Malaria Mamadou WELE
17142A13Consensus Measures for Genome-wide Association Studies – the PhenX Project Helen Pan
17147A14Bioinformatic and Comparative Analysis of Tumor Cardiolipin Remodeling Mechanisms Using Lipidomic Data Lu Zhang
17186A16Automatic detection of metastatic cancer cells in the blood Jesse Rodriguez
17190A17cell.line.plot - Visualizing gene expression profiles of cell model systems Vidal Fey
17143A19PATHWAY RESOURCES AT THE RAT GENOME DATABASE: A DYNAMIC PLATFORM FOR INTEGRATING GENE, PATHWAY AND DISEASE INFORMATION Weisong Liu
17236A20Characterization of genomic structural variations in a neuroblastoma cell line using mate-pair sequencing Valentina Boeva
17240A21Markov Chain Monte Carlo Computational Analysis of Chromosome Conformation Capture Carbon Copy data Mathieu Rousseau
17255A22Computational prediction of compound sensitivity with genomic signatures Kavitha Venkatesan
17257A23Adding structural information to the von Hippel-Lindau (VHL) tumor suppressor interaction network Emanuela Leonardi
17273A24Evaluation of computational miRNA target predictions in human Olivier Gevaert
17305A25Effector prediction in host-pathogen interaction based on a Markov model of a ubiquitous EPIYA motif Chao Zhang
17316A26An Integrated High Content Analysis Pipeline for Alzheimer’s Disease Drug Discovery Stephen Wong
17279A27Molecular Re-Classification of renal disease through approximate graph matching, clustering and pattern mining Ramakrishna Varadarajan
17332A28Transcriptional and post-transcriptional regulatory networks in biliary atresia Vivek Kaimal
17344A29Genome-Wide Primer and Probe Design Using PRIMEGENS Garima Kushwaha
17365A31A computational pipeline for diagnostic biomarker discovery in the human pathogen Trypanosoma cruzi Santiago Carmona
17295A32Systematic Evaluation of Disease Gene Identification in Molecular Interaction Networks Jiao Li
17408A33Genomic Analysis of Bacterial Pathogens to Identify Factors Contributing to Virulence Shannan Ho Sui
17423A34Phylogenetic methods for inferring tumor progression pathways from aCGH profiles of mixed cell populations Ayshwarya Subramanian
17431A35Next-Generation Sequencing workflow for Research and Clinical Applications Sivakumar Gowrisankar
17194A36An accurate prediction of bacterial effectors using a feature-based supervised learning approach Sneha Joshi
17103A38The implications of protein subcellular localization for disease profiling Solip Park
17307A39The Pearls of Swine Flu: The structural and sequence evolution of the H1N1 proteome Samantha Warren
19262A42The influence of sex on prognostic markers for non-small cell lung cancer Paul Boutros
16958A43Cancer-specific High-throughput Annotation of Somatic Mutations Hannah Carter
17129A44Gene variant databases need structured general disease information to facilitate automatic variant pathogenicity assessment Peter Taschner
19287A45Fixed-parameter haplotyping algorithms for general pedigrees with small number of sites Duong Doan
19335A47Phenotype-driven genetic analysis of Autism spectrum disorders Benjamin Georgi
19343A48IDENTIFICATION OF ALTERNATIVE POLYADENYLATION VARIANTS DIFFERENTIALLY EXPRESSED IN HUMAN ASTROCYTOMAS Suzana Ezquina
19374A49Transcriptional Profiling of Peripheral Neuropathy in Type 2 Diabetes using db/db mouse model Manjusha Pande
19383A51is-rSNP: A novel technique for in silico regulatory SNP detection Geoff Macintyre
19391A52Evolution model of host pathogen interaction applied to Mycobacterium Tuberculosis Ashwani Kumar
19402A53Comparing Two Computational Methods for Common Insertion Site Detection in Transposon Insertional Mutagenesis Data Jelle ten Hoeve
19439A54Robust Pharmacogenomic Predictors Identified from Breast Cancer Cell Lines by Meta-analysis Improve the Prediction Accuracy of Breast Cancer Patient Chemotherapy Responses Kui Shen
19427A56Stem Cell Discovery Engine Kimberly Begley
19495A57Identification of novel chromosomal rearrangements via massively parallel sequencing and primer-directed in silico assembly Joseph Fass
19496A58Integrative Biomarker Discovery from Gene Expression and Protein-protein Interaction Data Using Error-tolerant Pattern Mining Rohit Gupta
19529A59Brief Exposure Emmett Sprecher
19532A61Comparative pathway analysis of aging associated genes in humans and model organisms Ari Berman
19540A63Predictive Modeling of Macrophage Transcriptional Response to Nanoparticle Exposure Michelle Costa
19454A65Revealing the role of conserved disordered regions in the human proteome using comparative proteomics Taehyung Kim
19629A66Personalized Medicine: Optimizing HIV Treatment to Patient and Virus Betty Cheng
19566A67Novel statistics reveal cancer universal microRNA activity Roy Navon
17098B1Molecular Mechanics Analysis of Minimal Energy RNA Conformational Change Pathways Keith Van Nostrand
17122B2pKa's of Ionizable Groups and Energetics of Protein Conformational Transitions Zofia Pilat
17284B3Key Role of Flexibility of Aromatic Residues in Ligand Trafficking in the case of Acetylcholinesterases Pavan Ghatty
17335B4Protein kinase substrate prediction: Using protein kinase structural features to predict substrates Greg Ziegler
17343B5MONTE-CARLO SIMULATIONS OF PEPTIDE-MEMBRANE INTERACTIONS: WEB-SERVER Yana Gofman
19289B6Bridging the Gaps: Atomic Simulation of Macromolecular Environment Brings Together Protein Docking, Interaction Kinetics and Crowding Effects Xiaofan Li
17040C01Molwind – Exploring Molecule Spaces through Geospatial Browsing Oliver Karch
17080C02In silico screening for Phospholipase A2 of Apis Mellifera with HitFinder Library Daniel Jorge
17123C03In Silico Molecular Drug Design of Platelet Factor 4 Antagonists John Rux
17313C04Novel Fragment-based Quantitative Activity Prediction Method for Cannabinoid Drug Design Kyaw Zeyar Myint
17342C05Designing and implementing chemoinformatic approaches in TDR Targets Database: linking genes to chemical compounds in tropical disease causing pathogens María Magariños
17454C06Improved Visualization of Pathway Prediction Junfeng Gao
19273C07Chemical structure search in PubChem Jie Chen
19278C08Association of feature gene expression with structural fingerprints of chemical compounds Pei Hao
19295C09Novel Ligand Classification Algorithm and Application on Modeling Functionality for 5HT1A GPCR Ligands Chao Ma
19415C11A probabilistic method for identifying transient binding pockets on protein surfaces Paul Ashford
19426C12PrOCoil - Advances in predicting two- and three-stranded coiled coils Carsten Mahrenholz
19543C13HALO384: A Halo-Based Potency Prediction Algorithm for High-Throughput Detection of Antimicrobial Agents Marcos Woehrmann
19595C14Systematic drug target discovery via chemical and genetic interaction profiles Frederick Phillip Roth
17055D01Comparative genomics of cell envelope components in Mycobacteria Pankaj Vats
17074D03miRConSeq: A microRNA-Seq analysis portal with comparative studies Namshin Kim
17163D04Curating the Rat Genome: RGD’s Automated Data Integration Pipelines Maximize Coverage Marek Tutaj
17169D05Correlation between Gene-Gene Functional Association Patterns and Ecological Traits of Prokaryotes Yaming Lin
17302D06Biologically applied filter level interpretation of lung cancer data reveals markers for onset and progression Kevin Thompson
17300D07RECOG: Research Environment for Comparative Genomics Ikuo Uchiyama
17296D08The Rat Genome Database – Genome Browser Pushkala Jayaraman
17327D09Gene Order Comparison With Contigs And Scaffolds Adriana Munoz
17330D10Hybrid assembly of bacterial genomes using optical map, 454 and Illumina sequences William Hsiao
17381D11Evolution of Regulation in Primates Nathan Sheffield
17388D12Detecting rare copy number variations (CNVs) with sparse coding Andreas Mitterecker
17396D13Detection of gene orthology from gene co-expression and protein interaction networks Fadi Towfic
17400D14cn.FARMS - a probabilistic model to detect DNA copy numbers Djork-Arne Clevert
17417D15Bacterial whole-genome probabilistic alignment Colin Dewey
19284D19Microbial Variome Database: All Genetic Variations in a Species at One Glance. Sujay Chattopadhyay
19373D20Bacterial Phylogenomics Robert Stones
19428D21A global network of coexisting microbes from environmental and whole-genome sequence data Samuel Chaffron
19465D22GC-wave correction algorithm for microarray-based comparative genomic hybridization Angela Leo
19483D24Detecting Between-Pathway Model conservation across S. cerevisiae and S. pombe yeast species Daniel Malmer
19456D25POLYMORPHISM ANALYSIS OF WHEAT RUST FUNGI Sharadha Sakthikumar
19524D26Identification of gene transfers and duplications in closely related bacterial pathogens Joshua Earl
19338D28Comparative genomics of dormancy regulation in Mycobacteriaceae and Nocardiaceae Anna Gerasimova
16881E01The Roche Cancer Genome Database Jan Küntzer
19578E02An Advanced Web Query Interface for Biological Databases Peter Karp
16950E03Soybean Knowledge Base (SoyKB) : A Web Resource for Soybean Translational Genomics Trupti Joshi
17048E04BioPAX – A Community Standard for Pathway Data Sharing Nadia Anwar
17073E06DDBJ Read Annotation Pipeline: A web-based analytical tool for next-generation sequencing data Eli Kaminuma
17075E07Heterogeneous data integration in context of bioinformatics cloud computing Hoan Nguyen
17090E09ISA infrastructure: supporting standards-compliant experimental reporting and enabling curation at community level Philippe Rocca-Serra
17104E10G-language Bookmarklet: a gateway for Semantic Web, Linked Data, and Web Services Kazuharu Arakawa
17217E12SAHG: Structural Atlas of Human Genome Chie Motono
17266E14UniProt: The Universal Protein Resource Raja Mazumder
17288E15Generating a data platform for microarray gene expression experiments using MOLGENIS and MAGE-TAB Alexandros Kanterakis
17353E17The Reactome Reloaded Robin Haw
17405E18ZFNGenome: A gBrowse-based tool for identifying Zinc Finger Nuclease target sites in model organisms. Deepak Reyon
17410E19MOLGENIS: rapid generation of flexible software platforms for any genotype and phenotype experiment Morris Swertz
17452E20Web Tool OriginS Claudio Ferreira Junior
19271E22PhenoDB: A web-based database management system for storage, retrieval, visualization, and analysis of OmniLog phenotypic microarray data Wenling Chang
19290E24PRIDE, the PRoteomics IDEntifications database Florian Reisinger
19300E25Meeting the computational challenges of Metagenomics Naveen Kumar
19350E28Source of annotations in the UniProt Knowledgebase. Benoit BELY
19358E29ArrayExpress: Archive of Experiments and Gene Expression Atlas Anna Farne
19378E30Choosing a Genome Browser for a Model Organism Database: Surveying the Maize Community Taner Sen
19412E32COSMIC: Annotating whole-genome resequencing experiments in the Catalogue Of Somatic Mutations In Cancer. Simon Forbes
19425E33BioXSD: the canonical XML-Schema data model for bioinformatics Web services Matus Kalas
19475E36An Integrated Data Explorer for Genomic Studies on Mental Disorders Chun-Nan Hsu
19537E38TreeBASE2: Sharing Alignments, Trees, And the Analyses That Generated Them Hilmar Lapp
19544E39Gene annotation data in a “schema-free” paradise Chunlei Wu
19589E40Soybean Knowledge Base (SoyKB) : A Web Resource for Soybean Translational Genomics Trupti Joshi
19319E41BISSAP, Biological Sequence Submission Application for Patents Stephane Nauche
19621E42Adaptable Data Management for the Research Enterprise Sarah Killcoyne
17056F01Polar sidechains bridging to the backbone of proteins have conserved roles in their core Catherine Worth
17136F02Genome-wide influence of indel substitutions on evolution of bacteria of the PVC super-phylum, revealed using a novel computational framework Olga Kamneva
17271F05Phylogenomic inference of functional divergence brian caffrey
17297F06Understanding evolution at the SCOP family level via combined phylogenetics of sequence, structure and function. Ralph Pethica
17314F07Automatic dichotomy and polytomy classification and conversion Guan Ning Lin
17424F08Statistical phylogenetic tree analysis using differences of means David Haws
19265F10Evolutionary fingerprinting of genes Konrad Scheffler
19306F12Evolution of Structurally Disordered Regions Jessica Liberles
19332F13Inferring Genome Rearrangement Phylogeny based on Maximum Likelihood of Gene Adjacencies Jijun Tang
19361F14The Evolution and Structure Prediction of Coiled Coils Across All Genomes Julian Gough
19385F15Protein Interaction Evolution of the Yeast SH3 Domain Mark Sun
19433F16Filtering of Environmental Metagenomic Sequences (FEMS): a phylogenetic focus group-based framework for molecular evolution research Jeffrey Blanchard
19574F17Evolutionary dynamics of CRISPR systems in the Ocean metagenome Irena Artamonova
19514F19A New Methodology for Inferring Events in the History of a Multidomain Gene Family Maureen Stolzer
19526F20Investigating Homology Between Proteins Using Energetic Profiles James Wrabl
19624F21Analysis of functional profiles of eukaryotic genomes reveals strong trends related to morphological complexity Christian Zmasek
16945G01Detecting ssRNA loci with NiBLS Daniel MacLean
17068G02Gene Function Prediction via Morphological Phenotype Discovery in High-Content Screening Chen Lin
17110G03Selection and Evaluation of Gene-specific Biomarkers in Microarray Experiments Dan Lin
17134G04High Throughput Mutant Screening using Probabilistic Normalization and Identification Shannon Bell
17259G05FABIA: Factor Analysis for Bicluster Acquisition Martin Heusel
17270G06On Protein Biology Discoveries Using Domain-Based Methods Gloria Rendon
17294G08Integrated Interpretation of Genes Gang Feng
17311G09CRSH: Classes of Reiprocal Sequence Homologs Samuel Handelman
17323G10Predicting functional gene regulatory circuits using probability landscapes calculated from hundreds of transcriptome profiles Nicolas TCHITCHEK
17352G11Gene Set Interpreter: An open framework for analysis and management of gene sets and profiles Dmitri Bichko
17354G12Proteins, Pathways, and Macromolecular Complexes Judith Blake
19260G16Incorporating developmental information in functional networks for Arabidopsis thaliana Ana Pop
16786G18Studies of Sesame Phytoestrogenic Lignans Derivatives as Selective Endothelial Nitric Oxide Synthetase Modulators (SNOSM) in Male Sprague Rats Testis. lukeman joseph shittu
19268G20An effective statistical evaluation of ChIP-seq dataset similarity Maria Chikina
19275G21Beyond the Bounds of Orthology: Functional Inference from Metagenomic Context Gregory Vey
19303G22Identification and classification of ncRNAs in Trypanosoma cruzi through a multistep approach Priscila Grynberg
19360G24cis-Decoder: A web-based tool for searching a genome-wide conserved sequence cluster database to identify functionally related cis-regulatory elements Amarendra Yavatkar
19366G25Reconstruction of ancestral compositions of multi-domain proteins Roland Krause
19382G26Genome-scale methyltyping by statistical inference for determining methylation states in populations Meromit Singer
19397G27EBI R CLOUD - Cloud Computing for Functional Genomics at the EBI Andrew Tikhonov
19404G28The relative contribution of miRNAs in the regulation of di?erentiation Sylvia Tippmann
19423G30ChIP-seq versus ChIP-chip: a systematic comparison of two technologies Joshua Ho
19455G31The Ontological Discovery Environment: A Web-based Software System for Combinatorial Cross-Species Functional Genomic Data Integration Jeremy Jay
19464G32Joint ChIP-Seq event discovery using the Genome Positioning System (GPS) Yuchun Guo
19507G34A spectral clustering and information integration framework to mine gene sets using heterogeneous data sources Adam Richards
19525G35An integrative ChIP-sequencing analysis and motif discovery platform for genome-wide TFBS identification LAKSHMI KUTTIPPURATHU
19365G38Functional analysis of metagenome data using MEGAN4 Suparna Mitra
19580G39Illuminating Complete Functional Networks: Automation, Computation and the Single Cell Michael Fero
19560G40The Discern Active Site Predictor Sriram Sankararaman
19582G41The Genetic Landscape of a Cell Anastasia Baryshnikova
19613G42Quantitative functional annotation of H. sapiens genes Frederick Roth
17149H1Identification of Prokaryotic Small Proteins using a Comparative Genomic Approach Josue Samayoa
17407H2RGASP: Assessment of Gene-Finding Tools in the High-throughput Era Josep Abril
17105I03Scanning genomic data for structurally related RNAs Linda Stern
17157I04Ciport: A comparative and integrative transporter annotation tool and identification of lignin-related transporters Patrick Xuechun Zhao
17159I05Genome Annotation Test for Evaluation of CHiP-Seq Peaks Justin Bedo
17245I06Whole genome characterisation of Francisella orientalis from tilapia Sridhar Settu
17260I07Ensembl genome annotation for gorilla Amy Tang
17268I08Ensembl genome annotation for low- and high-coverage genomes Magali Ruffier
17359I09The comparative annotation and analysis platform at Canada's National Microbiology Laboratory Philip Mabon
17415I10ISGA - An Intuitive Web Server for Prokaryotic Genome Annotation and Other Analyses Christopher Hemmerich
17107I11A linear-time algorithm for reconstructing zero-recombinant haplotype con?guration on pedigree with a small number of loops Tao Jiang
19584I12Unique identifiers for alternative splicing isoforms Alberto Riva
19264I13The potential functional role of chimeric transcripts in higher eukaryotes Milana Frenkel-Morgenstern
19272I14MaxExon: A tool for selecting maximum number and length of exons for DNA sequencing enrichment strategies James Cavalcoli
19321I17Transcriptomics Platform Integration for Expression and Splice Variant Detection John Van Hemert
19342I18Finding Frameshifts in 1100+ Prokaryotic Genomes Ivan Antonov
19369I19The Oak Ridge National Lab Genome Annotation Pipeline Workflow Daniel Quest
19470I20CAFA: a Community Driven Effort to Assess Protein Function Predicitons Iddo Friedberg
19478I21Functional Gene Ontology Annotation across Species using PAINT Pascale Gaudet
19530I24DNA Annotation Induction: Intra- and Cross-Species in-silico Transcription Start Site Predictions Justin Bedo
19619I25Detecting Trans-Splicing Events and Non-co-Linear Transcripts in Transcriptome Assemblies Inanc Birol
19634I26Automated Gene-Model Curation using Global Discriminative Learning Axel Bernal
17071J03Comparison of methods finding the diversity of microbe communities based on 16S rRNA and metagenome shotgun sequencing Chaochun Wei
17112J05Visualizing the next generation of sequencing data Thomas Abeel
17152J06THE RAT GENOME DATABASE GENOME VIEWER Jeffrey De Pons
17171J07Comparative study of compositional symmetry in bacterial genomes using a novel method for replication terminus prediction Nobuaki Kono
17176J08BiNGS!SL-Seq: A Computational Analysis Workflow for Whole-Genome RNA Interference Screening Using the Next Generation Sequencing Technology Tzu Lip Phang
17182J09Transcriptome of embryonic and neonatal mouse cortex by RNA-seq Xinwei Han
17208J10De novo characterization of the transcriptome in mouse cortical neurons using RNA-Seq and ChIP-Seq Martin Hemberg
17241J11s it possible to detect phenotype determining genome differences using DNA reads from pooled individuals of species with huge haploid genomes? Rikard Erlandsson
17243J12Prioritization of pathogenic variants for monogenic diseases using targeted and exome resequencing data Christian Gilissen
17258J13Comparative Statistical Analysis on Identifying Differentially Expressed Reads in Next Generation Sequencing Data Dexiang Gao
17286J14Analysis of Genomic Data based on Information Theory Jang Yi
17291J15Statistical Analysis of Nondisjunction Assays in Drosophila Hua Li
17292J16The Bonobo de novo Genome Assembly Generated by CABOG Jason Miller
17397J17Gramene: A Database Platform For Comparative Genomics in Plants Joshua Stein
17350J19A normalization technique for next generation sequencing experiments Günter Klambauer
17324J20Identification of protein disorder in Corynebacterium pseudotuberculosis proteome using phage display data Sintia Almeida
17363J21Generalized Random Sets for Functional Enrichment Analysis Using Primary Genomics Datasets Johannes Freudenberg
17183J22Conserved G-quadruplexes May Regulate NF1 Gene Expression at Translational and Polyadenylation levels Rami Alrabaa
17351J23Alternative splicing of MECP2 gene involved in autism and related mental retardation syndromes may be regulated by G-quadruplex motifs Joetsaroop Bagga
17373J24GENOME-WIDE DISTRIBUTION OF G-QUADRUPLEXES SUGGESTS THEIR ROLE IN REGULATED SPLICING Paramjeet Bagga
17376J25Estimation of DNA Fragment Size Distribution and Reconstruction of DNA-binding Profiles from ChIP-seq Data Shouyong Peng
17411J26Using RNAi and RNA-Seq to Identify Alternative Exons Regulated by Individual RNA Binding Proteins and their Associated Regulatory Motifs Angela Brooks
17432J27Graphical Analyser of Contig for all Sequencers generation - G4ALL Rommel Ramos
17117J28Preliminary comparative analysis of four novel Mycoplasma genomes Iddo Friedberg
17135J29Indel detection using guided reassembly of unaligned paired-end reads Ole Schulz-Trieglaff
19256J30De novo Coral Genome Assembly by Short-Read Sequencing Arthur Hsu
19308J32Comparative Epigenomic Analysis of Repetitive DNA Elements Fabian Mueller
19293J33AltAnalyze: Assessing Functional Implications of Alternative Splicing on a Genome-Wide Scale Nathan Salomonis
19362J34Graphical quasi-species analyses of a deep sequencing sample of avian influenza A (H5N1) virus Lars Steinbrück
19395J36Short read assembly of subtelomeric regions and multi-gene families in Plasmodium falciparum Sammy Assefa
19400J37Large scale detection and analysis of RNA editing in grape mtDNA by RNA deep-sequencing Graziano Pesole
19291J38Wobble Patterns in Plants and Animals Tatiana Tatarinova
19418J39Using GPU programming for short read mapping Tobias Jakobi
19434J40A computational study of cross-hybridizing stable loop structures in oligonucleotide sequences. D. Andrew Carr
19446J42Dynamics and evolution of genome – nuclear lamina interactions Wouter Meuleman
19449J43Quality guided correction and filtration of errors in short reads David Kelley
19481J44De Novo Transcriptome Assembly Using 454 Sequencing Daniel Fasulo
19510J45Discovery and characterization of chromatin states for systematic annotation of the human genome. Jason Ernst
19516J46Knowing when to stop: A framework for threshold selection in gene family classification Jacob Joseph
19519J47Multiple Sequence Realignment-Enhanced Detection of Short Germline and Somatic Indels Andrey Sivachenko
19339J48Sequence variability is reflected in nucleosome occupancy profiles in the human genome Michael Tolstorukov
19547J49Integrative analysis of gene expression and epigenomic data in stem cells, progentiors and cancer stem cells Amit Sinha
19548J50Online Quantitative Transcriptome Analysis Regina Bohnert
19551J51Statistical Tests for Detecting Differential RNA-Transcript Expression from Read Counts Philipp Drewe
19269J52gee_fu: a RESTful web-services database for next-generation sequencing data Dan MacLean
19593J56ExpressionPlot: A web-based framework for the comparative analysis of gene expression and RNA processing data from exon array and RNA-Seq platforms Brad Friedman
19576J57Histone modification levels are predictive for gene expression Martin Vingron
19570J60WebGBrowse - A Web Server for GBrowse Ram Podicheti
17148K1Cognitive based requirements for systems biology and networks Felix Eichinger
19267K2Detecting internally symmetric protein structures Byungkook (BK) Lee
17052L02Structural and Energetic insights into TEM-1 and SHV-1 beta-lactamase ligand binding Pinar KANLIKILICER
17054L03Atomic motion knock-on effect and large scale anharmonic motion: Correlation of calmodulin-peptide binding entropy with intramolecular dynamics Jeremy Harris
17072L04Comparative analysis of binding site residues and recognition mechanisms of protein-protein and protein-RNA complexes using energy based approach Gromiha Michael
17216L06Computational redesign of Itk self-association: a tool to probe kinase regulation Scott Boyken
17250L07Pattern of Physical-Chemical and Structural Properties in Protein-Protein Interfaces Fabio de Moraes
17086L08i-Patch: inter-protein contact prediction using local network information Rebecca Hamer
17262L09Investigating the Specificity of the Histidine Kinase-Response Regulator Complexes using Mutual Information Mireille Gomes
17416L12Modeling Interactions of Lentiviral Rev Proteins with Viral RNA and Cellular Proteins Usha Muppirala
17377L13Efficient Retrieval of Protein Interfaces with a Machine Learning-based Similarity Measure Bin Pang
17331L14Similarity in protein-protein interactions: Disappearing and reappearing act by key interface residues Nan Zhao
19569L15A Novel Scoring Approach for Protein Co-Purification Data Reveals High Interaction Specificity Jaques Reifman
17130L17Properties and evolution of specificity-determining residues in yeast protein-protein interactions David Talavera
17084L18Prediction of Domain-Peptide Binding Affinity from Primary Sequence Xiaojian Shao
19286L19Machine learning approaches for prediction of SH2-peptide interactions Kousik Kundu
19302L20PIPs - Human Protein-Protein Interaction Prediction Mark McDowall
19462L23Protein interface residues amenable to small molecule modulation predicted using structure Fred Davis
19511L24SVM methods for prediction of Calmodulin binders and binding sites Asa Ben-Hur
19499L25A GO-Based Search Engine for Protein-Protein Interactions Kyungsook Han
19628L26Similarity in protein-protein interactions: Disappearing and reappearing act by key interface residues Dmitry Korkin
19600L27Towards the prediction of protein interaction partners using physical docking Mark Wass
16897M02Plasma metabolites in the mammalian hibernation cycle Anis Karimpour-Fard
17076M03Discovering knowledge hidden in mutation data using Inductive Logic Programming TIEN-DAO LUU
17165M04CONFIDENT PREDICTABILITY: A STATISTICAL TOOL FOR IDENTIFYING PATIENTS FOR WHICH A MACHINE LEARNING ALGORITHM PROVIDES A RELIABLE DIAGNOSIS Lee Jones
17201M05ProQM : The first membrane MQAP Arjun Ray
17214M06Machine Learning Studies on Subcellular Localization of Human Cytosolic Sulfotransferase SULT1C1 George Acquaah-Mensah
17234M07SVM-based prediction of linear B-cell epitopes using Bayes Feature Extraction Lawrence Wee
17261M08VT-shift: a novel density-based clustering algorithm and its applications multivariate biological datasets Nikolay Samusik
17348M09Evolutionary distances between divergent sequences - A rational kernel approach Roland Schwarz
17661M11Sparse Dynamic Models for Detecting Responsive Pathways Prasad Siddavatam
17283M12Identification of biological features distinguishing meiotic recombination hot and cold spots in yeast. Loren Hansen
19258M13Multitask Learning: Combining Various Genomic Features To Better Explain Phenotypic Variation Brian Bennett
19297M14Nonlinear dimension reduction and clustering by Minimum Curvilinearity unfold neuropathic pain and tissue embryological classes Carlo Vittorio Cannistraci
19326M15A method for predicting compound-protein interactions using canonical correlational analysis Takuya Hashimoto
19356M19ClanTox: A predictor tool for toxin-like proteins reveals 500 such proteins within viral genomes Michal Linial
19416M21The e-LICO project Simon Jupp
19471M22Cancer Outcome Prediction by Feature Selection with Top Scoring Pairs Ping Shi
19493M23L1-L2 regularization framework for Alzheimer's molecular characterization Annalisa Barla
19494M25A Mixture of Experts model for predicting expression from sequence Sushmita Roy
19549M26A mixture model approach to high-throughput cell cycle analysis in budding yeast David Warde-Farley
19489M27Experimental design for genome-wide association studies Christoph Lippert
19591M29Optimizing Genome Context Methods and their Combination Luciana Ferrer
19609M30High resolution models of transcription factor-DNA affinities improve in vitro and in vivo binding predictions Phaedra Agius
13085N01INSECTICIDE RESISTANCE MECHANISMS AND GENE EXPRESSION PROFILE IN MALARIA VECTOR - Anopheles gambiae s.s ISAAC OYEWOLE
17047N02miRNA data integration Pekka Kohonen
17051N03Correcting Array Position Artifacts using GPU Computing Dirar Homouz
17070N04Estimating the Proportion of Microarray Probes Expressed in an RNA sample Wei Shi
17077N05gcExplorer: Interactive Exploration of Gene Clusters Theresa Scharl
17099N06An Expression Profiling Data Repository for Lung Disease Gene Discovery Soumyaroop Bhattacharya
17118N07The Exon Array Analyzer: a web interface for analyzing exon arrays Pascal Gellert
17145N08Novel thermodynamics-based algorithm for probe-speci?c position-dependent hybridization free energy Hosna Jabbari
17189N09Geometric representation of transcriptomic phase space provide by Molecular Dynamics MDS combine to SVD algorithms using references datasets. Christophe Becavin
17197N11Detecting mosaic structural variation in genomic microarray data Jayne Hehir-Kwa
17212N12The LO-BaFL pipeline for microarray expression analysis Cristina Baciu
17224N14Identification of non reliable probes on customized Affymetrix Mouse430_2 platform Noura Chelbat
17225N15Accurate estimates of microarray target concentration from a simple sequence-independent Langmuir model Cynthia Gibas
17227N16Detection of oncogenic fusion transcripts by custom-made oligo microarrays Gard Thomassen
17228N17Comparative analysis of transcriptome and proteome E. coli cultivation data Karoline Marisch
17230N18COLOMBOS: access port for bacterial cross-platform microarray compendia Kristof Engelen
17246N20A Pathway Based Correlation Method for Identifying Perturbation in Follicular Lymphoma from Microarray Gene Expression Data Allison Tegge
17308N21ArrayInitiative: a generic tool for creating custom Affymetrix CDFs Christopher Overall
17322N22A Transcript-level Gene Model Validation Tool Timothy Tickle
17281N23Comparative analysis of gene expression profiles in human breast cancer from microarray data using breast tissues and peripheral blood samples Xing Li
17362N24ExonSVD: a new model for exon and splice junction microarrays Peter Munson
17337N25Annotare – a tool for annotating microarray investigations and data Ravi Shankar
17401N26Timing the Expression of Ribosomal Proteins Gang Chen
17402N27Unsupervised clustering of high-dimensional datasets without prior knowledge using AutoSOME Aaron Newman
17421N28Modeling proteome dynamics using microarray data Maga Rowicka
17434N29SLAM: Gaussian Dynamic Linear Analysis of Methylated-chip Data William Johnson
17435N30A Systems Biology Strategy to Accelerate the Development of Predictive Biomarkers for Novel Anti-cancer Agents Heather Selby
19567N31Comparative analyses of time-course expression profiles of yeast ageing Huanying Ge
17370N33An open-source pipeline of analyzing Illumina Methylation data Pan Du
17175N34Parkinson Disease Microarray Analysis in Frontal Cortex Alexandra Dumitriu
17043N35ROAST: rotation gene set tests for complex microarray experiments Di Wu
19277N36Identification of classifier genes from earthworm microarray data using an integrated statistical and machine learning approach Nan Wang
19281N37Identification of common disease mechanisms and novel drug targets from multiple disease signatures using a causal network Ben Sidders
19298N38Global transcriptome analysis of the Escherichia coli O157 response to Houttuynia Cordata Thunb Hyeung-Jin Jang
19346N39Computational workflows for miRNA-mRNA co-expression analysis Ketan Patel
19372N40The Transcriptional Network Governed by Interferon Regulatory Factor (IRF8) in Germinal Center B cells Dong-Mi Shin
19388N41Widespread alternate splicing in the TLR signalling cascade contributes to functional diversification of the innate immune system Alistair Chalk
19399N42Chipster: Biologist-friendly analysis software for high-throughput data Aleksi Kallio
19405N43Evaluating the Goodness of Pairwise Probability Models in Reconstructing Gene Regulatory Networks Jarkko Salojärvi
19474N44Mining Large Gene Expression Corpora with Market-Basket Analysis to Find Condition-Dependent Correlations Steve Rowley
19482N45Multiplex Meta-Analysis for Microarrays Alexander Morgan
19488N46Large-scale expression profiling using a reduced representation of the transcriptome. Rajiv Narayan
19430N47GAGE: Generally Applicable Gene Set Enrichment Weijun Luo
19550N48Computationally Efficient Analysis and Visualization of Exon Array Data Ping Chen
19413N49Ontology-guided Visual Exploration of the ArrayExpress Archive Nils Gehlenborg
19598N50Genome-scale percentage DNA methylation estimates from microarray data Martin Aryee
17356O1Analysis of Alternative RNA Splicing in Early Stages of SCA1 Smita Agrawal
17093P2Ontology Based Phenotype Database and Mining Tool Mary Shimoyama
17205P4An Application Ontology for Gene Expression Sample Variables James Malone
17095P6GeneRIFcompendiate: Quantitative gene annotation using collective GeneRIF associations and ontology terms Pan Du
19498P7Biomedical ontologies for Parasite research Vinh Nguyen
17251Q03Multi-SNP models for complex phenotypes Alberto Riva
17289Q04Haplotyping Population Samples of Short Fragment Data Shawn O'Neil
17321Q05Identification of Structural Variation in Next-Generation Sequence Data by Multiple-Signal Integration Suzanne Sindi
17418Q07Interactions in Genetic Association Ronald Schuyler
17425Q08Genome wide association study of non synonymous Single Nucleotide Polymorphisms with seven common diseaes Praveen Surendran
19466Q12MAVEN 2.0: a tool for integration analysis of association results and automatic variant annotation Jing Li
17059R01Evaluation of computational platforms for LC-MS based label-free quantitative proteomics Runxuan Zhang
16814R02A Machine Learning approach to Protein Secondary Structure Prediction, using Position Specific Residue Preferences saraswathi sundararajan
17108R03QuantProReloaded: Software for the statistical analysis of Microspot Immunoassays Anika Joecker
17267R05Detection of Alternative Splice Variants at the Protein Level in the Human Genome Iakes Ezkurdia
17278R06Subgraphs of the Protein-Protein Interaction Network with High Connectivity Suzanne Gallagher
17320R07A modular method to prediction of protein-protein interaction patches Rafael Jordan
17374R08The bait compatibility index: a computational approach towards bait selection for interaction proteomics experiments Sudipto Saha
17382R09Global in silico identification of General and Kinase-Specific Phosphorylation Sites Jianjiong Gao
17422R10Replicate feature matching improves the identification of proteins via tandem mass spectrometry Karin Noy
17328R11A statistical model for quantitative proteomics Yuping Zhang
17156R12OpenFreezer LARISA: A web-based laboratory information and workflow management system Marina Olhovsky
19577R14Discriminative Motif Finding for Predicting Protein Subcellular Localization Tien-Ho Lin
19294R15The Human Protein Atlas Lisa Berglund
19469R19The Complete Peptide Dictionary – A Meta-Proteomics Resource Manor Askenazi
19521R20MSProcess – Mass Spectrometry Identification and Annotation Pipeline Jill Wegrzyn
19476R21PIE - A protein inference engine: integrating proteomics data for comprehensive posttranslational modi?cation prediction Stuart Jefferys
19546R22Bioinformatics Solutions to Enable the Generation of Complete Quantitative Proteomics Datasets Required for Modeling & Systems Biology Christian Ahrens
16939S01A Concordance Approach for ChIP-Seq Binding Site Detection Facilitates Localization of Beta-catenin in Colorectal Cancer Cells. Daniel Bottomly
16970S02The computational discovery and evolutionary implications of regulatory motif patterns responsible for transcriptional activation of ribosome biogenesis Robert Gross
17067S03Evaluating methods for Expression Quantitative Trait Loci (eQTL) detection in complex mouse crosses Priscila Darakjian
17079S04Improved prediction of in vivo transcription factor binding sites by using DNA structure Bart Hooghe
17106S05Gene Regulatory Network Reconstruction based on Gene Expression and Transcription Factor Activities Yao Fu
17146S06ModuleDigger: an itemset mining framework for the detection of cis-regulatory modules. Kathleen Marchal
17153S07Roles of Signal Transducer and Activator of Transcription in Tuning Epigenetic Modification and Transcription during Helper T Cell Differentiation Golnaz Vahedi
17345S10Decoding the cis-regulatory logic of stress-regulated genes in Arabidopsis thaliana Shin-Han Shiu
17398S11Systematic Discovery of cis-regulatory Elements in the Mouse Genome Feng Yue
17448S12Genome-wide computational prediction of core promoter elements in Arabidopsis. Sunita Kumari
19285S13CBS: a database of Conserved regulatory Binding Sites in the genome of multiple Drosophilas Enrique Blanco
19323S14RNAcontext: a new method for learning the sequence and structure binding preferences of RNA-binding proteins Hilal Kazan
19394S15Improved Prediction of Transcription Binding Sites from Chromatin Modification Dat Paul Horton
19409S16Predict gene expression with genetic and epigenetic features Xiaowo Wang
19457S18Toward a Unified Framework for Motif Discovery Methods Lonnie Welch
19460S19Mapping of cell-type specific transcription factor binding from chromatin accessibility assays and genome annotation Roger Pique-Regi
19485S20Towards Decoding The Regulatory Code of The Human Forebrain Hani Girgis
19491S21Identification of Novel Transcriptional Interactions for Mesoderm Inducer in Xenopus Like1(MIXL1) Aaron Raymond
19424S22PolyA site strength is important for gene expression and tissue-specific alternative polyadenylation Wencheng Li
19627S23Down-regulation by microRNAs depends on target mRNA abundance Aaron Arvey
19605S24Positional Variations among Heterogeneous Nucleosome Maps Give Dynamic Information on Chromatin Yoshiaki Tanaka
19573S25A systems approach shows competition and saturation drives microRNA and siRNA target gene regulation – its more than target site efficacy Debora Marks
17133T1Bioinformatics Visualization: A review on the novel technique used in Interactorium. Arijit Nandi
17429T2BioPerl at 15 : New Features, New Directions Mark Jensen
19266T3Comparative Analysis of next-generation Sequence Alignment Algorithms Gabriela Persinoti
19623T4Visualizing biological data Seán O'Donoghue
16780U01Anvaya: A Workflow environment for High Throughput Comparative Genomics Ruma Banerjee
17087U02Prediction of KOPS motifs involved in segregating of bacterial chromosomes in Lactocoques / Streptocoques Fabrice Touzain
17096U03RNA Secondary Structure Prediction of Multiple Sequences Zhenjiang Xu
17125U04A systematic approach to predicting organism-specific subcellular localization suggests species-specific sorting patterns Patrick Xuechun Zhao
17161U06An SNN-GA Approach for the Prediction of Transcription Factor Binding Sites Heike Sichtig
17168U07Computational Analysis of Genome-wide Synthetic Lethal Screen with a tyrosine kinase inhibitor in Leukemia cell using BiNGS!SL-seq Jihye Kim
17172U09Probeset design for target-capture sequencing FANG FANG
17211U11Quantitative Deep Sequencing and Detecting HIV-1 Drug Resistance John Archer
17247U12Inferring de novo genomic homology with sets of minimal absent words Sara Garcia
17253U13Threading Alignments Based on Sampling and Sequence Dependent Scoring Function Zhiquan He
17269U14SMALT - a new mapper for DNA sequencing reads Hannes Ponstingl
17303U15Alternative Isoforms Identification and Quantification from RNA-Seq Data Xiaobo Zhou
17312U16Choosing the right coverage depth and read length for an RNA-seq experiment Madelaine Gogol
17333U17Novel Epitopes of the Ebola Virus for Rational Vaccine Design: Therapeutic Development and Protein Conservation. Sophia Banton
17346U18Structural Variation Analysis with Strobe Reads Anna Ritz
17379U19An exact approach to mapping next-generation sequencing reads containing structural variation Anne-Katrin Emde
17384U20Exploring Enviornmental Niches Via Short Read Metagenomic Sequencing Vinicio Reynoso
17386U21A method for detecting small scale human tandem repeat length polymorphism using Illumina paired-end sequencing data Weldon Whitener
17412U22Identification of Putative Novel Protein Coding Genes from Metagenomic Samples David Messina
17414U23Analyses of reagents developed for Oligomerized Pool ENgineering (OPEN) reveal insights into interactions between zinc finger proteins and DNA Fengli Fu
17427U24he GNUMAP project: probabilistic mapping of next generation sequencing reads with applications William Johnson
17445U25Modeling the sequencing background in ChIP-Seq experiments Abhishek Mitra
17438U27An Accuracy Evaluation of Read Alignment Algorithms André Kahles
19575U29Protein interactions and ligand binding: from protein subfamilies to functional specificity Antonio Rausell
19255U30Algorithm for Phylogenetic Tree Building and Taxonomic Classification using Curated Phylogenetic Tree David Knox
19572U31Detecting Breakpoints of Large Deletions and Medium Sized Insertions from Pair-end Short Reads in 1000 Genomes Project and Cancer genome project Kai Ye
19279U33A fast mapping tool for DNA sequence reads from the SOLiD™ System: part of Bioscope™ Zheng Zhang
19299U34Jalview: Now and Next. James Procter
19304U35Sequence read information improves accuracy of SNP detection Allison Regier
19310U36Neighbourhood effect and amino acid preference in extremophiles Chinmay Dwibedi
19312U37FastQC – A Quality Control tool for High Throughput Sequencing Data Simon Andrews
19318U38Bismark, a New Tool for Mapping and Methylation Analysis of Bisulfite-Seq Data Felix Krueger
19320U39A congruent objective function for key steps in the phylogenomic method Marcin Cieslik
19322U40Analysis of AB SOLiD™ System Targeted Resequencing Reads Jonathan Manning
19325U41A method for detecting structural variants from massive paired end genome sequences by mapping signatures Daisuke Ueta
19331U42Structural filters for RNA homology search Diana Kolbe
19352U45A novel profile Hidden Markov Model to predict microRNAs and their targets simultaneously Shu Yang
19353U46MISO: an open-source LIMS for small-to-large scale sequencing centres Robert Davey
19363U47A Robust High-Throughput Second Generation Sequencing Analysis Pipeline Sanjeev Bhaskar
19364U48Threshold Average Precision (TAP-k): A Retrieval E?cacy Measure for Bioinformatics Hyrum Carroll
19367U49EMBOSS: European Molecular Biology Open Software Suite Peter Rice
19368U50Ultra-deep sequencing of HIV quasi-species to detect minority variants Oliver Hofmann
19370U51Identification of disease associated variants using the Carpe Novus tool elizabeth worthey
19371U52Increasing the Genome Analyzer’s output using IBIS Martin Kircher
19376U53Detection of Fusion Genes in mRNA-Seq Data Sven Bilke
19379U54A novel probabilistic approach based framework for sequence assembly Limin Fu
19406U57High-throughput DNA sequencing – concepts and limitations Janet Kelso
19421U58Mining for cancer causing mutations in whole genome sequence data Andrew Menzies
19422U59Makeflow for Bioinformatics Andrew Thrasher
19431U60Galaxy NGS functionality from sample tracking to SNP calling: An interactive poster Ramkrishna Chakrabarty
19437U61Identify unknown population structure based on DNA sequence and geography Melanie Lou
19444U62Finding sequence-specific DNA methylation sites using base resolution methylome data WENYU CHUNG
19450U63Hidden Chromosome Symmetry, Gigantic Palindromes and Nonlinear Dynamics Model Sergei Larionov
19463U64CloVR: Automated Sequence Analysis using Virtual Machines and Cloud Computing Malcolm Matalka
19477U66HMM to HMM Alignment in the UCSC SAM System Richard Hughey
19497U67Mapping Reads with Insertion and Deletion Error using BLASR Mark Chaisson
19501U68Evolutionary classification and understanding the catalytic diversity of the Tautomerase Superfamily Abhiman Saraswathi
19505U70nhmmer : DNA-to-DNA database search with HMMER3 Travis Wheeler
19527U71Visualizing protein family nanoanatomy using ProfileGrids Alberto Roca
19518U72Centroid series: fundamental programs of sequence analysis for non-coding RNAs Michiaki Hamada
19377U73Comparison of SNP calling methods in 454 Sequencing data Wayne Clarke
19607U75Characterization of genomic structural variations in a neuroblastoma cell line using mate-pair sequencing Valentina Boeva
19608U76Drastic Speed Gain for RNA Folding Achieved with Modified Dynamic Programming Algorithm Philipp Bucher
19522U78MG-RAST to the Clouds Jared Wilkening
19563V01Finding co-occurrence of copy number changes in tumors. Christiaan Klijn
16965V02Protein-ligand interaction network predicts novel targets for known drugs Olga Kalinina
17037V03Protein domain assignment from the recurrence of locally similar structures Chin-Hsien Tai
17263V04A Computational Pipeline to Determine the Alternative Secondary Structures for Purine Riboswitches Yang Ding
17277V05Insight into the active site of a Structural Genomics protein – a Phenolic Acid Decarboxylase Ramya Parasuram
19583V06Protein crystallization analysis on the World Community Grid Christian Cumbaa
17114V07One size doesn’t fit all: The classification of CNV associated genes K. Cara Woodwark
19307V08Structural Refinement Using Distribution and Correlation of Structural Elements in Proteins Yuanyuan Huang
19340V09Extending Three-Dimensional Structural View of Thermotoga maritima Ying Zhang
19588V10The three-dimensional folding of the alpha-globin gene domain reveals formation of chromatin globules Davide Baù
16880W02DescFold:A web server for protein fold recognition Yan Xiang
16957W03Ab initio Prediction of E5 Protein Structure from Cervical Human Papillomavirus (HPV) Nilson Nicolau Junior
16977W04Advanced TOPS+ Comparison Method for Enhanced TOPS models Mallika Veeramalai
17030W05Sequence-to-structure prediction errors can reveal conformational flexibility in helical membrane proteins Shandar Ahmad
17046W06Developing an integrated, knowledge-based, protein-protein docking scoring function Jawon Song
17060W07Accurate Antibody Complementarity Determining Region Loop Structure Prediction Using Contact Profeils Yoonjoo Choi
17078W09Functional dynamics of NhaA predict motion implicated in alternating access and pH-induced activation Maya Schushan
17085W10ConQuass: using evolutionary conservation for quality assessment of protein model structures Matan Kalman
17092W11Prediction of dinucleotide-specific RNA-binding sites in proteins using sequence and evolutionary information Michael Fernandez
17100W12Automated All-Atom RNA Tertiary Structure Prediction Matthew Seetin
17102W13Multiple protein docking prediction based on genetic algorithms and physics-based scoring Juan Esquivel-Rodriguez
17113W14MEDELLER: Homology-Based Coordinate Generation for Membrane Proteins Sebastian Kelm
17124W15Evolution of apparently inactive active sites in the HexxH metalloproteases Teresa Szczepinska
17181W16A machine learning application for the high-performance prediction of functional sites in proteins of unknown function Srinivas Somarowthu
17231W17CompaRNA: a server for continuous benchmarking of automated methods for RNA structure prediction. Tomasz Puton
17233W18Functional Annotation of a Structural Genomics Protein from the ClpP/crotonase Superfamily using Local Structure Analysis Pengcheng Yin
17248W19Parametric maximum expected accurate RNA structure Feng LOU
17252W20Modeling protein-peptide interactions using protein fragments: fitting the pieces? Peter Vanhee
17256W21PETcofold: Prediction of structurally conserved RNA-RNA interactions Andreas Richter
17274W22Predicting ligand binding residues across the Human Genome Gonzalo Lopez
17319W25Rapid Estimation of RNA Kinetics Andy Lorenz
17325W26MUFOLD: A new solution for protein 3D structure prediction Jingfen Zhang
17329W27RNA Structural-BLAST: Unleashing the Power of RNA Structure by Using RNA Fingerprint KEJIE LI
17361W28Evaluation of the capabilities of the Consensus of Prediction (CoP) Approach for the Prediction of Catalytic Residues Implemented in the ENDURANCE Natalia Petrova
17364W29Finding Conserved Topology in RNA Structure Reazur Rahman
17378W30Gapped GDT_TS – A score for detecting variations in structural similarity Sheenal Srivastava
19257W31GeneMANIA: Intelligent gene function prediction and interactive network visualization Gary Bader
17385W32A network based study of GPCRs AJ Venkatakrishnan
17393W33RNA structural segmentation Peter Clote
19590W34New sequence-based and structure-based methods for predicting class II MHC epitopes Andrew Bordner
17406W35Structural classification of the catalytic domain of DNA polymerases using a standard measure to assess structural alignments from different methods. Alex Slater
17440W36Determining RNA folding pathways with minimum energy barrier Chris Thachuk
17446W37Identify the metal-binding sites in proteins by the protein contact number model Jau-Ji Lin
19581W38Clustering large domain sequence families for function transfer and structural genomics Robert Rentzsch
19282W39Distribution and Extension of Conformational Diversity on proteins domains Ezequiel Juritz
19301W40SCORER 2.0: Improving the prediction of coiled-coil oligomeric state Thomas Vincent
19359W42Insights into the DNA Damage Response: a tale of dry and wet science. Ana Rojas
19408W43Automatic Recognition of Antifreeze Protein Based On n-peptide Composition Chin-Sheng Yu
19411W44Comparison of the efficiency of different protein structure refinement techniques. Arne Elofsson
19414W45Consensus-based protein structure prediction by means of distance restraints Marcin Skwark
19435W46Low-homology protein modeling Jian Peng
19445W47Integrative Workflow Pipeline for Functional and Structural Analysis of C-type Lectins in Immunoinformatics - Elucidating the Ligand Binding Residues of CLEC5A and Its Potential Interaction with Glyca Dong-Yup Lee
19448W48Efficient Fragment-free Approach to Protein Folding Feng Zhao
19440W49Domain Integrity Verification of Alternative Splicing Hedi Hegyi
19490W50A new probabilistic model of RNA conformational space Jinbo Xu
19504W51Predicting the protein-binding sites in RNA using the interaction propensity of nucleotide triplets Yanga Byun
19513W52Structure Refinement of Integral Membrane Proteins Using Energy Minimization Christopher Summa
19517W53POLYVIEW: Web-based Platform for Protein Structure Analysis and Visualization Alexey Porollo
19528W54A RESOURCE FOR EVALUATION OF MISANNOTATION IN ENZYMES Alexandra Schnoes
19536W55Protein Annotation Enrichment using Gene Ontology Hierarchical Structure and Protein-Protein Interactions Seshan Ananthasubramanian
19552W56Structure prediction of a protein channel based on probabilistic formal grammars Witold Dyrka
19596W57Structure based design of novel small molecule inhibitors to apical membrane antigen-1 of Plasmodium falciparum Sandhya Kortagere
19603W58ProBiS: A web server for detection of structurally similar protein binding sites Janez Konc
19586W60Structure-based redesign of selective G-protein inactivation by RGS proteins Mickey Kosloff
19611W61A Genetic Algorithm Based Model for Predicting Functional Classification of Proteins Yasin Bakış
16959X003An algorithm for smart oligo pooling to construct synthetic gene library Shanrong Zhao
17008X004Uncertainty Quantification and Minimization in Gene Expression Data Lee Falin
16963X005The Function of Communities in Protein Interaction Networks at multiple scales Anna Lewis
17132X007Non-linear predictive modeling of toxicological metabonomics data using simulated annealing optimized kernel-OPLS Judith Fonville
17139X008Modelling of protein-protein interactions network in parasite genomes Antonio Rezende
17137X009A Systems Approach to Understanding Embryonic Stem Cell Self Renewal Mechanisms Karen Dowell
17160X010Towards More Fine and Robust Stochastic Gene Expression Modeling with Hill Functions of Protein Degradation Haseong Kim
17167X011TRANSCRIPTIONAL REGULATORY SUBNETWORKS IN THE MOUSE BRAIN AS DERIVED FROM DATA SETS IN THE ALLEN MOUSE BRAIN ATLAS Ronald Taylor
17178X012Integrative analysis of time course microarray data and DNA sequence data via log-linear models for identifying dynamic transcriptional regulatory networks Hyung-Seok Choi
17206X015Prediction of Functional Gene Associations Using Domain Co-occurrence Approach Jung Eun Shim
17210X016Efficient query-driven biclustering of gene expression data using Probabilistic Relational Models Lore Cloots
17235X020Correction for ascertainment bias in literature-curated interaction networks Jonathan Dickerson
17238X021Edge Clipper: an algorithm for Bayesian consensus network refinement and its application in microarray-based pathway analysis Andrew Hodges
17166X022Clusters of innovation in the mammalian metabolic network Michaël Bekaert
16991X023Exploring the Monochromatic Landscape in Yeast using Genetic Interactions and Known Processes Reveals the Importance of Protein Complexes Magali Michaut
17249X024The human E3 ubiquitin ligase enzyme protein interaction network Gozde Kar
17229X025Dual Role of miRNAs in NF-kB signaling pathway Candida Vaz
17285X026Structural models predict changes of SH3 domain mediated protein interactions in yeast species erik verschueren
17293X027Mathematical modeling of preserved red blood cells towards improvement of blood storage Taiko Nishino
17301X028Identification of essential genes associated with aging using correlation networks Kathryn Dempsey
17317X030simplyGO: a Cytoscape plug-in for quick and easy graph visualization and functional analyses Alberto Paccanaro
17326X031Comparison of different null hypotheses to identify differentially expressed pathways Shailesh Tripathi
17339X032Network biomarkers of C. elegans aging Kristen Fortney
17340X033Model SEED: a resource for high-throughput generation, optimization, and analysis of genome-scale metabolic models Matt DeJongh
17349X034Functional implications of tissue-specific gene expression using RNA-sequencing data Dorothea Emig
17355X035Mathematical modeling of the gene regulatory network controlling the cold shock response in Saccharomyces cerevisiae Kam Dahlquist
17357X036Systematic modeling study on mechanism of p38 MAPK activation in MDS Xiaobo Zhou
17369X038Inferring physical protein contacts in protein complex purifications Sven-Eric Schelhorn
17383X039MP Editor : visualization, integration and functional analysis of signaling pathways using molecule pages Ashok Reddy Dinasarapu
17390X040Refining the protein interaction network generated by NASCENT using sequence alignment Gabor Ivan
17392X041Detection of nonlinear effects in gene expression pathways Andreas Mayr
17403X043Comparison of de novo Network Reverse Engineering Methods with Applications to Ecotoxicology Lyle Burgoon
17371X044Using remote structural similarities in protein complex modeling Qiangfeng Zhang
17409X045Interpreting expression data based on large-scale, high-quality literature networks: the Causal Reasoning Engine Daniel Ziemek
17442X046A new framework for evaluating theoretical models of protein interaction network evolution Todd Gibson
19558X048A systems biology approach to study drug-induced growth inhibition of Mycobacterium tuberculosis Anders Wallqvist
19616X049Detection of Mutated Pathways in Cancer Fabio Vandin
17282X050Uncovering general principles of regulation in protein interaction networks Guilhem Chalancon
17180X051Construction of perturbation network among diseases, drugs and miRNAs Minjeong Ko
17394X052Exploring building principles of metabolic networks with respect to information spread Frank Emmert-Streib
17088X053Network analysis defines the impact of gene-physical activity interactions Laurence Parnell
19283X054Fold change detection and scalar symmetry of sensory input fields Oren Shoval
19292X055Inferring the sRNA-mediated post-transcriptional regulatory network in Mycobacterium tuberculosis Diogo Veiga
19311X058bioCompendium: high-throughput experimental data analysis platform Venkata Satagopam
19317X059“ePlant: integrative systems biology in 3D on the world wide web” Geoffrey Fucile
19327X060An Estimation Method of S-system Model of Gene Regulatory Networks Using Immune Algorithm Tomoyoshi Nakayama
19341X062Active Pathways: Visualization and analysis of pathways and expression data. Joseph Whitney
19351X063ANALYSIS OF THE FUNCTIONAL PROPERTIES OF THE CREATINE KINASE SYSTEM USING A MULTISCALE “SLOPPY” MODELING APPROACH Hannes Hettling
19354X064Metabolic network destruction: relating topology to robustness Wynand Winterbach
19337X065Measuring the Temperature of the Yeast Genome: A Parametric Approach to Genomewide Analysis Sandy Shaw
19384X066Pathway Guided Modules – a method to identify key proteins Jieun Jeong
19386X067A comparative modeling framework to estimate conserved and differential gene-gene interactions Zhengyu Ouyang
19396X068Analyzing protein interaction networks using structural information. Anne Campagna
19438X070Systematic Identification of YY1/miRNAs Mediated Regulatory Networks in Skeletal Myogenesis Hao Sun
19441X071Inferring regulatory network structures for canonical pathways from gene expression data Diogo Camacho
19316X073Protein Evolution in Yeast Transcription Factor Subnetworks Eric Franzosa
19458X075Predicting Functionally Important Co-evolving Secondary Structures from Mutation Events using Mutual Information and Network Theory Scooter Willis
19461X076twzPEA: A topology and working-zone based pathway enrichment analysis framework Yang Zhang
19472X077A Boolean Network Model of Nuclear Receptor Mediated Cell Cycle Progression John Jack
19486X078Finding optimal subgraph measures for protein complexes Debra Goldberg
19492X079Comparative Interactions between Wild Type and Transgenic Alfalfa Travis Cotton
19523X080A platform for computation of microbial ecosystems in time and space: COMETS William Riehl
19429X081Predicting Gene Function from Interaction Networks Sara Mostafavi
19534X082Unsupervised detection of lung cancer biomarkers using biological networks Anna Goldenberg
19535X083Association Analysis Approach For Finding Coherent Value Bicliques In Genetic Interaction Data Gowtham Atluri
19557X087Genome-Wide Association Data Reveal a Global Map of Genetic Interactions among Protein Complexes Rohith Srivas
19618X088Exploring Disease Interactions Using Combined Gene and Phenotype Networks Nitesh Chawla
19565X089Modeling information flow from metabolomics to transcriptomics Xinghua Lu
19571X091Cell-specific information processing in segregating populations of Eph receptor ephrin-expressing cells. Claus Jørgensen
19561X092Cooperativity within proximal phosphorylation sites is revealed from large-scale proteomics data Regev Schweiger
19599X093Automaton Based Analysis Of Affected Cells in a 3-Dim Coordinated SYstem jitesh dundas
19587X094Macroscopic Kinetic Effect of Cell-to-Cell Variation in Biochemical Reactions Nathan Price
19579X095Topological network alignment uncovers biological function, phylogeny, and disease Natasa Przulj
19620X096OpenFreezer LARISA: A web-based laboratory information and workflow management system Marina Olhovsky
19562X097Comparative Network Analysis of Complex Diseases Rune Linding
19601X098Characterization of Primary Breast Tumors based on miRNA-mRNA Integrated Analysis Israel Steinfeld
19555X099Deriving Kinase-Substrate Network Models from Co-Modulated Phosphorylation Events. Erwin Schoof
19509X100Cloud based scientific workflow for NMR data analysis Ashwin Manjunatha
17138Y01Gaining biological insights from text-mined facts through automated reasoning Luis Tari
17219Y02Towards efficient search tools for biomedical databases: Characterizing user search habits and recognizing their information needs Rezarta Islamaj Dogan
17334Y04Text Mining for Protein Function Prediction: Detection of Active Residues in Full-text publications Karin Verspoor
17341Y05Bio-Jigsaw: A Biological Application of the Jigsaw System. Hannah Tipney
17420Y06Improving Biomedical Text Mining by using Existing Background Knowledge Kevin Livingston
17336Y07Mining host-pathogen interactions from biomedical literature Thanh Thieu
19585Y08Reflect: improving how biological research is communicated Seán O'Donoghue
17272Y09A test suite for ontology concept recognition systems: The Gene Ontology K. Bretonnel Cohen
19324Y11Machine Learning for Identifying Abbreviation Definitions Lana Yeganova
19442Y12Building the Scientific Knowledge Mine (SciKnowMine ): a community-driven framework for text mining tools in direct service to biocuration Cartic Ramakrishnan
19453Y13Scaling Text Mining to One Million Documents Christophe Roeder
19468Y14CALBC Challenge I: first results Dietrich Rebholz-Schuhmann
19480Y15Considering alternative views when modeling cancer metastasis. Anna Divoli
19622Y16MspecLINE: Bridging knowledge of human disease with the proteome Sarah Killcoyne
17151Z01Advancing Research with Bioinformatics Training: The Canadian Bioinformatics Workshop Series Michelle Brazas
17158Z02Towards automated high-throughput screening of C. elegans on agar Mayank Kabra
19615Z03Occupancy Classification of Position Weight Matrix-inferred Transcription Factor Binding Sites Hollis Wright
19508Z04Motion-compensated in vivo microscopy of heart morphogenesis and function in developing embryos Jungho Ohn
19597Z05Design of Inorganic Binding Peptides Kemal Sonmez
19604Z06Effector prediction in host-pathogen interaction based on a Markov model of a ubiquitous EPIYA motif Chao Zhang
17215Z07Mobyle Platform: Bioinformatics applications from command-line to web-based workflows and services Herve Menager
17213Z09BioCatalogue: The curated registry of Life Science Web Services Franck Tanoh
17428Z10Improved models for in vitro selection of aptamers Alexandra Teslya
19436Z11Methodological analysis of QR markers to identify and classify functional parts Allan Orozco
17280Z12A User Study of Attribute Presentation Tools and Their Role in Understanding Biological Networks Hande Küçük
17199Z13MobyleNet: user-centered large spectrum service integration over distributed sites. Herve Menager
19614Z14Decipher the protein cofactors for small RNA function by comprehensive phylogenetic analysis, protein interactions, expression data, high throughput screens and other data sets. Yuval Tabach


LBR

LBR01Aaron ArveyDown-regulation by microRNAs depends on target mRNA abundanceSunday, July 11 10:45 a.m. - 11:10 a.m.
LBR02Yuval TabachDecipher the protein cofactors for small RNA function by comprehensive phylogenetic analysis, protein interactions, expression data, high throughput screens and other data setsSunday, July 11 11:15 a.m. - 11:40 a.m.
LBR04S. Joshua SwamidassMarginal Cost of Discovery: An Economic Alternative to False Discovery RateSunday, July 11 12:15 p.m. - 12:40 p.m.
LBR05Anders JacobsenSystematic discovery of novel motifs which modulate microRNA regulationSunday, July 11 2:30 p.m. - 2:55 p.m.
LBR07Doron BetelComprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sitesSunday, July 11 3:30 p.m. - 3:55 p.m.
LBR08Inanc BirolDetecting Trans-Splicing Events and Non-co-Linear Transcripts in Transcriptome AssembliesSunday, July 11 4:00 p.m. - 4:25 p.m.
LBR10Karine Le RochGenome-wide nucleosome positioning and DNA methylation in the malaria parasite: Insights into differentiation and virulenceMonday, July 12 11:15 a.m. - 11:40 a.m.
LBR11Mark WassTowards the prediction of protein interaction partners using physical dockingMonday, July 12 11:45 a.m. - 12:10 p.m.
LBR13Felix KokocinskiRGASP: The RNASeq Genome Annotation Assessment ProjectMonday, July 12 2:30 p.m. - 2:55 p.m.
LBR15David RossellQuantification of Alternative Splicing from Paired-End ReadsMonday, July 12 3:30 p.m. - 3:55 p.m.
LBR17Dina SchneidmanIntegrative Structure Determination of Protein-Protein Complexes Using SAXS, EM and NMRTuesday, July 13 10:45 a.m. - 11:10 a.m.
LBR19Murat TasanQuantitative functional annotation of H. sapiens genesTuesday, July 13 11:45 a.m. - 12:10 p.m.
LBR20Phaedra AgiusHigh resolution models of transcription factor-DNA affinities improve in vitro and in vivo binding predictionsTuesday, July 13 12:15 p.m. - 12:40 p.m.
LBR21Christian ZmasekAnalysis of functional profiles of eukaryotic genomes reveals strong trends related to morphological complexityTuesday, July 13 2:15 p.m. - 2:40 p.m.
LBR22Nitesh ChawlaExploring Disease Interactions Using Combined Gene and Phenotype NetworksTuesday, July 13 2:45 p.m. - 3:10 p.m.
LBR24Chad MyersGenetic interactions reveal the evolutionary trajectories of duplicate genesTuesday, July 13 3:45 p.m. - 4:10 p.m.


Tech Track

TT01Thomas Wilhelm DASS-GUI – a new data mining tool Sunday, July 11 10:45 a.m. - 11:10 a.m.
TT02Jan Baumbach Detection of functionally related proteins with Transitivity Clustering Sunday, July 11 10:45 a.m. - 11:10 a.m.
TT03Ross Curtis GenAMap: An integrated analytic and visualization software platform for structured GWA and eQTL analysis Sunday, July 11 11:15 a.m. - 11:40 a.m.
TT04Jesse Paquette Divining Systems Biology Knowledge from High-throughput Experiments Using EGAN Sunday, July 11 11:15 a.m. - 11:40 a.m.
TT06Samuel Patient The Universal Protein Resource (UniProt) Sunday, July 11 11:45 a.m. - 12:10 p.m.
TT07Chao Ma Novel Ligand Classification Algorithm and Application on Modeling Functionality for 5HT1A GPCR Ligands Sunday, July 11 12:15 p.m. - 12:40 p.m.
TT09Weizhong Li Sequence clustering program CD-HIT and its applications in next-generation sequences Sunday, July 11 2:30 p.m. - 2:55 p.m.
TT10Peter Karp Demonstration of The Pathway Tools Software and BioCyc Databases Sunday, July 11 3:00 p.m. - 3:25 p.m.
TT11Raymond DiDonato BIOBASE Knowledge Libraryª and ExPlainª Analysis System: A data analysis platform for life science researchers. Sunday, July 11 3:30 p.m. - 4:25 p.m.
TT12Jiten Bhagat BioCatalogue: The curated catalogue of Life Science Web Services Sunday, July 11 3:30 p.m. - 3:55 p.m.
TT13Scooter Morris Cytoscape 2.7 Sunday, July 11 4:00 p.m. - 4:25 p.m.
TT14Michael Gromiha Challenging algorithms and comprehensive databases in protein structure and function Monday, July 12 10:45 a.m. - 11:10 a.m.
TT15James Procter Jalview: Past, Present and Future. Monday, July 12 10:45 a.m. - 11:10 a.m.
TT16Paul Horton Software for RNA and Next-gen Sequencer Analysis Monday, July 12 11:15 a.m. - 11:40 a.m.
TT17Jianjiong Gao Musite: Global Prediction of General and Kinase-Specific Phosphorylation Sites Monday, July 12 11:15 a.m. - 11:40 a.m.
TT18Herve Menager Mobyle: An integrated bioinformatics platform for performing web-based analyses Monday, July 12 11:45 a.m. - 12:10 p.m.
TT20Suparna Mitra Taxonomical and functional analysis of metagenome data using MEGAN4 Monday, July 12 12:15 p.m. - 12:40 p.m.
TT21Gary Bader Web-based gene function prediction and interactive network visualization with GeneMANIA Monday, July 12 12:15 p.m. - 12:40 p.m.
TT22Katy Wolstencroft SysMO-DB: Sharing and Exchanging Data and Models in Systems Biology Monday, July 12 2:30 p.m. - 2:55 p.m.
TT23Florian Reisinger Tools of PRIDE Monday, July 12 2:30 p.m. - 2:55 p.m.
TT24Shulei Sun CAMERA: Metagenomic Resources and Tools Monday, July 12 3:00 p.m. - 3:25 p.m.
TT25James Cavalcoli Using the NCIBI Suite of Integrated Tools and Data Monday, July 12 3:00 p.m. - 3:25 p.m.
TT27Jeffrey Grethe The Neuroscience Information Framework (NIF): A Unified Semantic Framework for Discovery and Integration of Biomedical Data and Resources on the Web Monday, July 12 3:30 p.m. - 3:55 p.m.
TT29Aaron McKenna The Genome Analysis Toolkit (GATK) Monday, July 12 4:00 p.m. - 4:25 p.m.
TT30Matt DeJongh The Model SEED pipeline for Genome Scale Metabolic Modeling Tuesday, July 13 10:45 a.m. - 11:10 a.m.
TT35Matus Kalas EMBRACE, BioXSD, EDAM: How to provide smoothly interoperable bioinformatics tools on the World Wide Web of Services Tuesday, July 13 11:45 a.m. - 12:10 p.m.
TT36Morris Swertz MOLGENIS: rapid prototyping of biosoftware at the push of a button Tuesday, July 13 12:15 p.m. - 12:40 p.m.
TT37Zhenjun Hu VisANT: multi-scale network visualization, analysis and inference based on the Gene Ontology Tuesday, July 13 2:15 p.m. - 2:40 p.m.
TT38John Beaver Tools for Functional Genomics: Synergizer, FuncAssociate and FuncBase Tuesday, July 13 2:45 p.m. - 3:10 p.m.



Track Date Time Room ID Name Title
Highlights Track Sunday, July 11 10:45 a.m. - 11:10 a.m. Ballroom A/B HL01 Sriram Sankararaman Genomic privacy and limits of individual detection in a pool
Highlights Track Sunday, July 11 10:45 a.m. - 11:10 a.m. Ballroom C HL02 Luay Nakhleh Species Tree Inference by Minimizing Deep Coalescences
Highlights Track Sunday, July 11 11:15 a.m. - 11:40 a.m. Ballroom A/B HL03 Pankaj Agarwal Can literature analysis identify innovation drivers in drug discovery?
Highlights Track Sunday, July 11 11:45 a.m. - 12:10 p.m. Ballroom A/B HL05 Christiaan Klijn Finding co-occurrence of copy number changes in tumors
Highlights Track Sunday, July 11 11:45 a.m. - 12:10 p.m. Ballroom C HL06 Erez Levanon Genome-wide Identification of Human RNA Editing Sites by Massively Parallel DNA Capturing and Sequencing
Highlights Track Sunday, July 11 12:15 p.m. - 12:40 p.m. Ballroom C HL08 Noam Kaplan The effect of histone sequence preferences on nucleosome organization and gene regulation
Highlights Track Sunday, July 11 2:30 p.m. - 2:55 p.m. Ballroom C HL10 Ivan Ovcharenko Cracking the genetic code of heart regulatory elements
Highlights Track Sunday, July 11 3:00 p.m. - 3:25 p.m. Ballroom A/B HL11 Joel Dudley The robustness of disease signatures across tissues and experiments
Highlights Track Sunday, July 11 3:00 p.m. - 3:25 p.m. Ballroom C HL12 Han Xu Interrogating high-level DNA structure from ChIA-PET Data
Highlights Track Sunday, July 11 3:30 p.m. - 3:55 p.m. Ballroom A/B HL13 Richard Lathrop Predicting Positive p53 Cancer Rescue Regions Using Most Informative Positive (MIP) Active Learning
Highlights Track Sunday, July 11 3:30 p.m. - 3:55 p.m. Ballroom C HL14 Florian Markowetz Systems-level dynamic analyses of fate change in murine embryonic stem cells
Highlights Track Sunday, July 11 4:00 p.m. - 4:25 p.m. Ballroom A/B HL15 Rune Linding Comparative Network Analysis of Complex Diseases
Highlights Track Monday, July 12 10:45 a.m. - 11:10 a.m. Ballroom A/B HL17 Yanjun Qi Systematic prediction of human membrane receptor interactions
Highlights Track Monday, July 12 10:45 a.m. - 11:10 a.m. Ballroom C HL18 Robert Murphy Determining the distribution of probes between different subcellular locations through automated unmixing of subcellular patterns
Highlights Track Monday, July 12 11:15 a.m. - 11:40 a.m. Ballroom C HL20 Smita Agrawal Computational Models of the Notch Network Elucidate Mechanisms of Context-dependent Signaling
Highlights Track Monday, July 12 11:45 a.m. - 12:10 p.m. Ballroom C HL22 Anastasia Baryshnikova The Genetic Landscape of a Cell
Highlights Track Monday, July 12 3:00 p.m. - 3:25 p.m. Ballroom A/B HL26 Antonio Rausell Protein interactions and ligand binding: from protein subfamilies to functional specificity
Highlights Track Monday, July 12 3:30 p.m. - 3:55 p.m. Ballroom A/B HL27 Ying Zhang Three-Dimensional Structural View of the Central Metabolic Network of Thermotoga maritima
Highlights Track Monday, July 12 4:00 p.m. - 4:25 p.m. Ballroom A/B HL28 Rod Nibbe An Integrative Proteomics Approach to Identify Functional Sub-networks In Cancer
Highlights Track Tuesday, July 13 10:45 a.m. - 11:10 a.m. Ballroom C HL30 Rohith Srivas Genome-Wide Association Data Reveal a Global Map of Genetic Interactions among Protein Complexes
Highlights Track Tuesday, July 13 11:15 a.m. - 11:40 a.m. Ballroom A/B HL31 Sujay Chattopadhyay Selection for hotspot mutations in core genes of Escherichia coli
Highlights Track Tuesday, July 13 11:15 a.m. - 11:40 a.m. Ballroom C HL32 Ernest Fraenkel Network models for understanding what Ôomic data really mean
Highlights Track Tuesday, July 13 11:45 a.m. - 12:10 p.m. Ballroom A/B HL33 Todd Gibson Neofunctionalization in interaction network evolution
Highlights Track Tuesday, July 13 12:15 p.m. - 12:40 p.m. Ballroom A/B HL35 Liran Carmel A universal relationship between gene compactness and expression level in multicellular eukaryotes
Highlights Track Tuesday, July 13 12:15 p.m. - 12:40 p.m. Ballroom C HL36 Zhidong Tu Pathway and network based approaches to prioritize reliable hits from high throughput RNAi screening experiments
Highlights Track Tuesday, July 13 2:15 p.m. - 2:40 p.m. Ballroom A/B HL37 Lawrence Hunter Scaling to PubMedCentral: Bringing Ontology-based Biomedical Language Processing into the Full Text Era
Highlights Track Tuesday, July 13 2:45 p.m. - 3:10 p.m. Ballroom A/B HL39 Benedict Anchang Modeling the temporal interplay of molecular signalling and gene expression by using dynamic nested effects models
Highlights Track Tuesday, July 13 3:15 p.m. - 3:40 p.m. Ballroom A/B HL41 Michael Fero Illuminating Complete Functional Networks: Automation, Computation and the Single Cell
Highlights Track Tuesday, July 13 3:15 p.m. - 3:40 p.m. Ballroom C HL42 Xinghua Lu Modeling information flow from metabolomics to transcriptomics
Keynotes Sunday, July 11 4:30 p.m. – 5:30 p.m. Ballroom A/B K02 Susan Lindquist Protein Folding and Environmental Stress REDRAW the Relationship between Genotype and Phenotype
Keynotes Monday, July 12 9:00 a.m. – 10:00 a.m. Ballroom A/B K03 Svante Paabo Analyses of Pleistocene Genomes
Keynotes Tuesday, July 13 9:00 a.m. – 10:00 a.m. Ballroom A/B K05 David Altshuler Genomic Variation and the Inherited Basis of Common Disease
Keynotes Tuesday, July 13 4:15 p.m. - 5:15 p.m. Ballroom A/B K06 Robert A. Weinberg
Keynotes Tuesday, July 13 5:15 p.m. – 6:15 p.m. Ballroom A/B K07 George Church Reading and Writing Genomes
Proceedings Track Sunday, July 11 10:45 a.m. - 11:10 a.m. Room: 302 PT01 Jian Peng Low-homology protein threading
Proceedings Track Sunday, July 11 10:45 a.m. - 11:10 a.m. Room: 304 PT02 Xiang Zhang TEAM: Efficient Two-Locus Epistasis Tests in Human Genome-Wide Association Study
Proceedings Track Sunday, July 11 11:15 a.m. - 11:40 a.m. Room: 302 PT03 Feng Zhao Fragment-free Approach to Protein Folding Using Conditional Neural Fields
Proceedings Track Sunday, July 11 11:15 a.m. - 11:40 a.m. Room: 304 PT04 David Allen Tolliver Robust Unmixing of Tumor States in Array Comparative Genomic Hybridization Data
Proceedings Track Sunday, July 11 11:45 a.m. - 12:10 p.m. Room: 302 PT05 Mitul Saha MOTIF-EM: an Automated Computational Tool for Identifying Conserved Regions in CryoEM Structures
Proceedings Track Sunday, July 11 11:45 a.m. - 12:10 p.m. Room: 304 PT06 Kai Zhang Sparse Multitask Regression for Identifying Common Mechanism of Response to Therapeutic Targets
Proceedings Track Sunday, July 11 12:15 p.m. - 12:40 p.m. Room: 302 PT07 Peter G Clote Thermodynamics of RNA structures by Wang-Landau sampling
Proceedings Track Sunday, July 11 12:15 p.m. - 12:40 p.m. Room: 304 PT08 Charles J. Vaske Inference of patient-speciÞc pathway activities from multi-dimensional cancer genomics data usingÊPARADIGM
Proceedings Track Sunday, July 11 2:30 p.m. - 2:55 p.m. Room: 302 PT09 Anoop Kumar Recognition of Beta-Structural Motifs Using Hidden Markov Models Trained with Simulated Evolution
Proceedings Track Sunday, July 11 2:30 p.m. - 2:55 p.m. Room: 304 PT10 Xin Li Efficient identification of identical-by-descent status in pedigrees with many untyped individuals
Proceedings Track Sunday, July 11 3:00 p.m. - 3:25 p.m. Room: 302 PT11 Tsung-Han Chiang Markov Dynamic Models for Long-Timescale Protein Motion
Proceedings Track Sunday, July 11 3:00 p.m. - 3:25 p.m. Room: 304 PT12 Eric Yi Liu Efficient Genome Ancestry Inference in Complex Pedigrees with Inbreeding
Proceedings Track Sunday, July 11 3:30 p.m. - 3:55 p.m. Room: 302 PT13 Shihua Zhang A fast mathematical programming procedure for simultaneous fitting of assembly components into cryo-EM density maps
Proceedings Track Sunday, July 11 3:30 p.m. - 3:55 p.m. Room: 304 PT14 Kriti Puniyani Multi-Population GWA Mapping via Multi-Task Regularized Regression
Proceedings Track Sunday, July 11 4:00 p.m. - 4:25 p.m. Room: 302 PT15 Ding Ye Open MS/MS Spectral Library Search to Identify Unanticipated Post-Translational Modifications and Increase Spectral Identification Rate
Proceedings Track Monday, July 12 10:45 a.m. - 11:10 a.m. Room: 302 PT17 Marco Pellegrini TRStalker: an Efficient Heuristic for Finding Fuzzy Tandem Repeats
Proceedings Track Monday, July 12 10:45 a.m. - 11:10 a.m. Room: 304 PT18 Rendong Yang Analyzing circadian expression data by harmonic regression based on autoregressive spectral estimation
Proceedings Track Monday, July 12 11:15 a.m. - 11:40 a.m. Room: 302 PT19 Yoseph Barash Model-Based Detection of Alternative Splicing Signals
Proceedings Track Monday, July 12 11:15 a.m. - 11:40 a.m. Room: 304 PT20 Ilkka Huopaniemi Multivariate multi-way analysis of multi-source data
Proceedings Track Monday, July 12 11:45 a.m. - 12:10 p.m. Room: 302 PT21 Xiaoyu Chen A dynamic Bayesian network for identifying protein binding footprints from single molecule based sequencing data
Proceedings Track Monday, July 12 11:45 a.m. - 12:10 p.m. Room: 304 PT22 Richard Savage Discovering Transcriptional Modules by Bayesian Data Integration
Proceedings Track Monday, July 12 12:15 p.m. - 12:40 p.m. Room: 302 PT23 Vikas Bansal A statistical method for the detection of variants from next-generation resequencing of DNA pools
Proceedings Track Monday, July 12 12:15 p.m. - 12:40 p.m. Room: 304 PT24 Jeroen de Ridder Inferring Combinatorial Association Logic Networks in Multimodal Genome-Wide Screens
Proceedings Track Monday, July 12 2:30 p.m. - 2:55 p.m. Room: 302 PT25 Dan He Optimal Algorithms for Haplotype Assembly From Whole-Genome  Sequence Data
Proceedings Track Monday, July 12 2:30 p.m. - 2:55 p.m. Room: 304 PT26 Ruty Rinott Modularity and Directionality in Genetic Interaction Maps
Proceedings Track Monday, July 12 3:00 p.m. - 3:25 p.m. Room: 302 PT27 Fereydoun Hormozdiari Next Generation VariationHunter : Combinatorial Algorithms for Transposon Insertion Discovery
Proceedings Track Monday, July 12 3:30 p.m. - 3:55 p.m. Room: 302 PT29 Jared Simpson Efficient construction of an assembly string graph using the FM-index
Proceedings Track Monday, July 12 3:30 p.m. - 3:55 p.m. Room: 304 PT30 Keren Yizhak Integrating Quantitative Proteomics and Metabolomics with a Genome-scale Metabolic Network Model
Proceedings Track Monday, July 12 4:00 p.m. - 4:25 p.m. Room: 302 PT31 Adrian V. Dalca VARiD: A Variation Detection Framework for Colorspace and Letterspace platforms
Proceedings Track Monday, July 12 4:00 p.m. - 4:25 p.m. Room: 304 PT32 Sophia Ananiadou PathText: A Text Mining Integrator for Biological Pathway Visualizations
Proceedings Track Tuesday, July 13 10:45 a.m. - 11:10 a.m. Room: 302 PT33 Adam Richards Assessing the functional coherence of gene sets with metrics based on the Gene Ontology graph
Proceedings Track Tuesday, July 13 10:45 a.m. - 11:10 a.m. Room: 304 PT34 Chun-Nan Hsu A Spectral Graph Theoretic Approach to Quantification and Calibration of Collective Morphological Differences in Cell Images
Proceedings Track Tuesday, July 13 11:15 a.m. - 11:40 a.m. Room: 302 PT35 Thomas WŠchter Semi-automated ontology generation within OBO-Edit
Proceedings Track Tuesday, July 13 11:15 a.m. - 11:40 a.m. Room: 304 PT36 Stephan Saalfeld As-rigid-as-possible mosaicking and serial section registration of large ssTEM datasets
Proceedings Track Tuesday, July 13 11:45 a.m. - 12:10 p.m. Room: 302 PT37 Matt Holford Using Semantic Web Rules To Reason On An Ontology Of Pseudogenes
Proceedings Track Tuesday, July 13 11:45 a.m. - 12:10 p.m. Room: 304 PT38 Sinan Kochara A Soft Kinetic Data Structure for Lesion Border Detection
Proceedings Track Tuesday, July 13 12:15 p.m. - 12:40 p.m. Room: 302 PT39 Jari Bjorne Complex Event Extraction at PubMed Scale
Proceedings Track Tuesday, July 13 12:15 p.m. - 12:40 p.m. Room: 304 PT40 Ranga Srinivasan Reconstruction of the Neuromuscular Junction Connectome
Proceedings Track Tuesday, July 13 2:15 p.m. - 2:40 p.m. Room: 302 PT41 Steven Kelk Phylogenetic Networks Do not Need to Be Complex: Using Fewer Reticulations to Represent Conflicting Clusters
Proceedings Track Tuesday, July 13 2:15 p.m. - 2:40 p.m. Room: 304 PT42 Steffen Jaensch Automated tracking and analysis of centrosomes in early Caenorhabditis elegans embryos
Proceedings Track Tuesday, July 13 2:45 p.m. - 3:10 p.m. Room: 302 PT43 Emmanuel Douzery SUPERTRIPLETS: A triplet-based supertree approach to phylogenomics
Proceedings Track Tuesday, July 13 2:45 p.m. - 3:10 p.m. Room: 304 PT44 Kriti Puniyani SPEX^2 : Automated Concise Extraction of Spatial Gene Expression Patterns from Fly Embryo ISH Images
Proceedings Track Tuesday, July 13 3:15 p.m. - 3:40 p.m. Room: 302 PT45 Nikolaos Alachiotis Time and memory efficient likelihood-based tree searches on gappy phylogenomic alignments
Proceedings Track Tuesday, July 13 3:15 p.m. - 3:40 p.m. Room: 304 PT46 Hanchuan Peng Automatic Reconstruction of 3D Neuron Structures Using a Graph-Augmented Deformable Model
Proceedings Track Tuesday, July 13 3:45 p.m. - 4:10 p.m. Room: 302 PT47 Yufeng Wu Close Lower and Upper Bounds for the Minimum Reticulate Network of Multiple Phylogenetic Trees
Proceedings Track Tuesday, July 13 3:45 p.m. - 4:10 p.m. Room: 304 PT48 Tao Peng Quantifying the distribution of probes between subcellular locations using unsupervised pattern unmixing
Special Session Monday, July 12 2:30 p.m. - 4:25 p.m. Room: 312 SS04 Theodora Bloom The Future of Scientific Publishing 
Special Session Monday, July 12 2:30 p.m. - 4:25 p.m. Room: 312 SS04 Jennifer Boyd The Future of Scientific Publishing 
Special Session Sunday, July 11 10:45 a.m. - 11:10 a.m. Room: 312 SS1 Jonathan Widom Nucleosome positioning from archaebacteria to man
Special Session Monday, July 12 10:45 a.m. - 11:10 a.m. Room: 312 SS3 Nadav Ahituv Identification and Pharmacogenomic Characterization of Liver Membrane Transporter Enhancers
Special Session Monday, July 12 11:45 a.m. - 12:10 p.m. Room: 312 SS3 Itsik PeÕer Genetic factors affecting severe adverse effects for common drugs
Special Session Tuesday, July 13 10:45 a.m. - 12:40 p.m. Room: 312 SS5 Igor Jurisica  Visualization of biological networks
Special Session Tuesday, July 13 10:45 a.m. - 11:10 a.m. Room: 312 SS5 Igor Jurisica  Introduction Ð Tools and their features for biological network analysis and visualization
Special Session Tuesday, July 13 10:45 a.m. - 11:10 a.m. Room: 312 SS5 Frank van Ham Visualization of large networks
Special Session Tuesday, July 13 10:45 a.m. - 11:10 a.m. Room: 312 SS5 Gary Bader Visual interpretation of biological data using networks
Special Session Tuesday, July 13 2:30 p.m. - 4:25 p.m. Room: 312 SS6 Xiaohua Douglas Zhang Data Analysis in Genome-scale RNAi Research
Special Session Tuesday, July 13 3:30 p.m. - 3:55 p.m. Room: 312 SS6 Amanda Birmingham Computational Assessment of Screening Statistics for RNAi
Special Session Tuesday, July 13 3:30 p.m. - 3:55 p.m. Room: 312 SS6 Xiaohua Douglas Zhang Development of analytic methods in genome-scale RNAi researches
Workshops Sunday, July 11 3:00 p.m. - 3:25 p.m. Room: 311 WK02 Vared Caspi Impact of Study Designs on the Relative Efficiency and Error Rates of Next Generation Sequencing Studies
Workshops Sunday, July 11 3:30 p.m. - 3:55 p.m. Room: 311 WK02 Hemant Kelkar Technical - Managing large data sets in core facilities
Workshops Monday, July 12 10:45 a.m. - 12:40 p.m. Room: 311 WK03 Matthew Meyerson Integrative Genomic Analysis of TCGA Data
Workshops Monday, July 12 10:45 a.m. - 12:40 p.m. Room: 311 WK03 Doug Levine Integrative Genomic Analysis of TCGA Data
Workshops Monday, July 12 2:30 p.m. - 4:25 p.m. Room: 311 WK04 Judith Blake Evidence Codes: Assay Tracking, ECO and OBI
Workshops Monday, July 12 2:30 p.m. - 4:25 p.m. Room: 311 WK04  Michelle Giglio Evidence Codes: Assay Tracking, ECO and OBI
Workshops Tuesday, July 13 10:45 a.m. - 12:40 p.m. Room: 311 WK05 Andrej Sali  Where and How to Get Published
Workshops Tuesday, July 13 10:45 a.m. - 12:40 p.m. Room: 311 WK05 Mark Gerstein Where and How to Get Published
Workshops Tuesday, July 13 10:45 a.m. - 12:40 p.m. Room: 311 WK05 Phil Bourne Where and How to Get Published
Workshops Tuesday, July 13 10:45 a.m. - 12:40 p.m. Room: 311 WK05 Alfonso Valencia Where and How to Get Published