Agreement of PLoS Postcards Allowance

PLoS Postcards-ISCB is partnering with PLoS Computational Biology to have all presentations at ISMB/ECCB 2011 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 submitters have agreed


20098A02Bayesian Networks to Decision Making in Lymph Node Metastasis of Colorectal Cancer Md. Aminul Hoque
22172A04A large scale analysis in the human proteome detects correlation among disease associated mutations and perturbation of protein stability Rita Casadio
22173A05SNPs&GO: predicting the deleterious effect of human mutations using functional annotation. Emidio Capriotti
20308A07Uncovering Network Control Mechanisms in Induced Oncogenic Transformation of Human Mammary Epithelial Cells through Whole Transcriptome Analyses Sol Efroni
20322A09siRna – A Comprehensive Analysis Workflow Towards Better Understanding of High-throughput Screening Data. Vidal Fey
20323A10miRNA levels are associated with immune network activity and associate with disease outcome in Ovarian Cancer. A possible miRNA – network control mechanism. Sol Efroni
20339A11A Novel Bioinformatics Pipeline for Identification and Characterization of Fusion Transcripts in 31 Breast Cancer and Normal Cell Lines Yan Asmann
20353A12Feature extraction from Spinal cord images Sejong Oh
20375A14Cross-species candidate gene prioritization with MerKator Leon-Charles Tranchevent
20377A15A guide to web tools to prioritize candidate genes Leon-Charles Tranchevent
20379A16History-aware models for HIV therapy screening Jasmina Bogojeska
20301A17Network-based gene prioritization from expression data by diffusing through protein interaction networks Daniela Nitsch
20391A18Detecting cancer driving mutations by whole genome sequencing in the ICGC PedBrain project Barbara Hutter
20168A20Mapping the spread of HIV in Germany Glenn Lawyer
20406A21SNP4Disease: a knowledge database to detect disease associated SNPs David John
20447A25Transcriptomic profiles and gene networks of human Mesenchymal Stem Cells (MSCs) Beatriz Rosón
20481A27Association Rule Mining with Prior Knowledge for Alzheimer's Disease Peter Li
20486A29An Integrative Bioinformatic Predictor of Protein Sub-Cellular Localisation in Malaria Ben Woodcroft
20530A32Deconvoluting Cancer Genomes using an Optimal Scaffolder Niranjan Nagarajan
20555A34Chipster 2.0: User-friendly analysis software for next generation sequencing data with interactive genome viewer. Massimiliano Gentile
20567A37AllergenNet: a database applied to the study of allergenic proteins Helen Arcuri
20570A38Integrative analysis of expression and copy number profiles to find causal genes in cancer Celia Fontanillo
20595A39GUILDify: A web server for phenotypic characterization of genes by means of protein-protein interactions and graph algorithms Emre Guney
20623A41Bioinformatics for large scale characterization and tracking of gene-modified hematopoietic stem cells Manfred Schmidt
20627A42Detecting Intrahost Emergence of Recombinant Viruses within HIV-1 infections using Ultra-Deep Sequencing Felix Feyertag
20656A46Structural comparison of Erwinase and E. coli L-Asparaginase to facilitate rational engineering of a cancer drug Mainá Bitar
20659A47Inhaled Toxicant Interactions with Transcriptional Regulatory Networks in Frontline Lung Cells George Acquaah-Mensah
20671A48Multi-Harmony: detecting functional specificity in HIV differential replication rates K. Anton Feenstra
20670A49Data Based Identification of Estimation Models for Tumor Markers Using Evolutionary Computation Stephan Winkler
20698A50Models for reverse engineering of transcriptional networks in Yersinia enterocolitica infection Olivia Prazeres da Costa
20704A51A framework for whole-exome deep sequening data management and analysis Angelo Nuzzo
20706A52Genome-Wide Association Study of TB in the South African Colored Population: Comprehensive Gene and pathway-based Association Study Emile RUGAMIKA CHIMUSA
20468A54Hunting cancer predisposition genes by whole exome sequencing in relatives from affected family Tatiana Popova
20738A55deepBlockAlign: aligning profiles from short blocks of reads Jan Gorodkin
20742A56Integrating network co-expression analysis and gene expression in the analysis of coronary artery disease GWAS: application to CARDIoGRAM data Seraya Maouche
20711A57A Novel Algorithm for Identifying Non-canonical Splicing Regions Using RNA-Seq Data Yongsheng Bai
20789A59Personalized Medicine for Cancer Miguel García
20817A62Bioinformatics and Biodiversity: A holistic approach to enhancing drug discovery. Negusse Kitaba
20824A63Finding locally disrupted RNA structure from SNPs Jan Gorodkin
20827A64Heme Detoxification Protein: A promising antimalarial drug target. Dedan Githae
20829A65Network Analysis and validation of gene expression profiling of salivary gland from human and mice with primary Sjögren’s syndrome Hui Zhou
20850A67Candidate mutations for early-onset lung cancer by family genome sequencing Evangelos Simeonidis
22182A68Improving the detection of deleterious mutations integrating the predictions four well-tested methods Emidio Capriotti
20874A72Discovery of novel cancer pathway-activating genomic aberrations via a mutual information metric Olga Botvinnik
20929A74Prediction of miRNA gene targets – a combined computational and experimental approach Anastasis Oulas
22642A77Systematic Analysis of MicroRNAs Targeting the Androgen Receptor in Prostate Cancer Cells. Pekka Kohonen
22696A80Robust and accurate data enrichment statistics via distribution function of sum of weights Yi-Kuo Yu
22709A81Measuring the complexity of solving diseases Raul Rodriguez-Esteban
22677A82Nonparametric Estimation of an Unknown Probability Distribution Using Maximum Likelihood and Bayesian Approaches Alona Chubatiuk
22713A83Exploratory analysis of the structure and dynamics of healthy intestinal microbiota Leo Lahti
22720A85Identification of secondary targets for clinically used anti-tubercular drugs through binding site similarities Nagasuma Chandra
22727A86Re-visiting classification of HLA class-I molecules Nagasuma Chandra
22731A87A molecular based subtyping in juvenile idiopathic arthritis Margherita Squillario
20448B2Free energy and flexibility basis of SNP occurrence Luciana Oliveira
20465B3Pipeline for the training of NMR chemical shift prediction models Anna Katharina Dehof
20459B4Modeling of Actomyosin Interactions Cynthia Prudence
20798B5Fitting Comparative Models to X-ray Data with Kino-Geometric Sampling Henry van den Bedem
22690B6Insights to the Thrombospondin Signature Domain Thomas Haschka
22679B7Universal patterns of protein-ligand interactions: Gaussian Mixture Model analyses on three dimensional structure of proteins in Protein Data Bank. Kota Kasahara
22712B9Intrinsically disordered proteins/regions: an important factor in protein evolvability Akinori Sarai
20229C01Mining the FDA’s Adverse Event Reporting System (AERS) for Pathway Risk Mark Gosink
20354C02The use of virtual screening reveals a viral-like polymerase inhibitor, which complex with the M. perniciosa DNA polymerase Bruno Andrade
20382C03Consensus docking method Dariusz Plewczynski
20394C04Homology modeling and molecular docking studies of Mannosyl Transferase (pimB) in Mycobacterium tuberculosis Karthik Maddi
20743C06Homology Modeling and Molecular Dynamics Simulation of N-acetylglucosamine fosfomutase (AGM1) from Moniliphothora perniciosa Wagner Soares
20835C07EC-BLAST: A novel tool for searching similar enzymes based on chemical knowledge Syed Asad Rahman
20864C09A systems approach to characterization of molecular targets of imaging agents Ting Liu
20893C10Stereological and hormonal evidences of epithelial hyperplasia with improved fertility capacity induced by aqueous sesame leaves Intake in adult male sprague dawley rats accessory organs LUKEMAN ADELAJA JOSEPH shittu
20267D01Characterization of a mannose-binding Insecticidal lectin gene from Allium sativum (Garlic) Nusrah Afolabi-Balogun
20389D04Tools for comparative metagenome analysis Kathrin Aßhauer
20485D05Identification of transcription factors and their correlation with the high diversity of Stramenopiles. Francisco Buitrago
20644D09A new Perl toolkit for the detection and analysis of polymorphic loci and their application for bacterial typing Ralf KOEBNIK
20705D11GECKO2: A software tool for de novo gene cluster detection Katharina Jahn
20739D12Automated Segmentation of DNA Sequences Brona Brejova
20772D13Antimicrobial Resistance and susceptility profiling of four pathogenic organisms using UV irradiation. Olugbenga Taiwo
20790D16Protein sequences of the human genome compared to those of several model organisms Edda Kloppmann
22649D19QuartetS: a fast and accurate program for large-scale orthology detection Jaques Reifman
22681D20Computational analysis of metagenomes and metatranscriptomes: challenges and opportunities. Larisa Kiseleva
22719D22Species-specific open chromatin has evidence of branch-specific selection. Nathan Sheffield
22718D23Comparative Genomics for expression QTL Steffen Möller
19914E01Seqcrawler – A cloud ready indexing platform Olivier Sallou
19916E02Creating a Concept Map Interface to Visualize and Interpret a Comparative Effectiveness Data Model David Fenstermacher
22615E03SolDB: A Database of Solanum lycopersicum and Solanum tuberosum Primers Hassan Tariq
22627E05miRGator v2.0 and the construction of miRNA-disease network Wankyu Kim
20209E08GWAS Central: an advanced database for the integration and comparative interrogation of genome-wide association study datasets Sirisha Gollapudi
20220E09ISA tools: standard-compliant reporting and curation at the community level Susanna-Assunta Sansone
20257E10DARNED (Database of RNA editing). Pavel Baranov
20264E11Graph-based queries of Semantic-Web integrated biological data Marco Moretto
20283E12TMPad: an integrated structural database for helix-packing folds in transmembrane proteins Cheng-Wei Cheng
20293E13EBI Search: a new way to explore biology Andrew Jenkinson
20355E17A web-based tool for functional investigation of microRNAs : miRGator v2.0 Wankyu Kim
20439E20Sierra: A simple LIMS system for small sequencing facilities Simon Andrews
20457E21Soybean Knowledge Base (SoyKB) : A Web Resource for Soybean Translational Genomics Trupti Joshi
20546E23easyDAS: Automatic creation of DAS servers Bernat Gel Moreno
20554E24Wheat international sequence repository integrated with genomic and genetic data in GnpIS Michael Alaux
20598E26Virtual Fly Brain 3D Interaction Tool Nestor Milyaev
20611E28GenomeRNAi: A Phenotype Database for Large-scale RNAi Screens Esther Schmidt
20638E29PROSITE: Enhancing the functional characterization of proteins Nicolas Hulo
20643E30PHI-base 4.0: A Second Generation Pathogen-Host Interaction database Jacek Grzebyta
20690E32Recent developments to the Ensembl website Stephen Trevanion
20701E33The Bioinformatics Links Directory: A Community Curated Collection of Bioinformatics Links, Tools and Databases Michelle Brazas
20722E34Structural Biology Knowledgebase: An Online Portal to Proteins, Functions, Methods, and More Margaret Gabanyi
20347E35Development of a Small Portable Application for Plant DNA Barcoding M Mehedi Hassan
20773E36MobiDB: a database of intrinsically disordered proteins Tomas Di Domenico
20788E39Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis - The CAMERA Resource Shulei Sun
22653E40Embryonic Stem Cell Database Elena Nikolaeva
22628E41RiceXPro and Rice TOGO Browser: Integrated Databases for Rice Functional and Applied Genomics Hajime Ohyanagi
22699E42SABIO-RK: Improvement of search capacities and user-friendliness Renate Kania
22764E45Correlation between annotation in the human gene database H-InvDB Katsuhiko Murakami
22766E46A Ruby API to query the Ensembl database for genomic features Jan Aerts
20331E47Identifying knowledge contributors – motivating online sharing of research data Gudmundur Thorisson
22620F01Multi-species integrative biclustering Richard Bonneau
20273F04The Operonic Location of Auto-Transcriptional Repressors is Highly Conserved in Bacteria Tal Pupko
20407F07Phylogenetic analysis of mapped sequence reads Jean-François Dufayard
20418F08Transcriptomic and metabolomic investigation of thermal stress response through metabolic modulations in seagrasses Jenny Gu
20421F09Positive Feedback and Tradeoff as Sources for Complexity in Social Interaction System Tomoyuki Yamamoto
20538F12Distribution patterns of genomic elements in bacteria using genome linguistic methods. Oliver Bezuidt
20668F13Gene expression evolution on the emergence of pathogenicity in Ascomycetes Aminael Sanchez-Rodriguez
20630F14Incorporating protein structure into coevolution analysis reveals functional side chain interactions in ABC-C exporters Attila Gulyas-Kovacs
22689F17A Phylogenetic Approach to Germline Methylome Reconstruction Lars Feuerbach
22668F18Probabilistic reconstruction of protein interaction histories using a simple measure of interaction affinity. Ryan Topping
22672F20TimeTree2: Species divergence times from molecular data Sudhir Kumar
20648F21Identifying Patterns of Balancing Selection by Comparing the Bonobo, Chimpanzee and Human Genomes Kay Prüfer
20691F22The Darwinian Tree Of Life In Light Of Horizontal Gene Transfer (Is Still Sound) Adam Sardar
22171G01Large-Scale Computational Identification of Regulatory SNPs Alberto Riva
20188G03Annotating New Genes: From In Silico Screening to Validations by Experiments Shizuka Uchida
20349G06Mining of Transcriptome of a climacteric fruit species Diospyros kaki Thunb for functional genomics Farzana Rahman
20451G10Human gene coexpression landscape and network: location of house-keeping and tissue-specific genes Alberto Risueño
20526G12Genomes and Evolutionary Analysese of Robust Oil Production in Microalgae Kang Ning
20577G14Analysis of protein functional sites encoding features Irina Medvedeva
20660G16An open source library for miRNA target prediction with a novel comparative genomics approach Charles Vejnar
20674G17From data to disease: Identification of genes with cell lineage specific expression in the human kidney Casey Greene
20759G22Estimating differential expression of transcripts with RNA-seq by using Bayesian Inference Peter Glaus
20785G23ARH-Seq: Alternative Splicing Robust Prediction by Entropy on RNA-Seq data Axel Rasche
22726G30The Limpopo MAGE-TAB Parser Tony Burdett
22728G31The Functional Genomics Software Suite Tomasz Adamusiak
20834G32Novel Method for Removal of Sequence Biases in ChIp-seq Data Joanna Raczynska
20472H2Improving the Accuracy of Automated Prokaryotic Gene Calling wih the Intergenic Region Scanner Heather Kent
20484H3Computing the probability of RNA hairpin and multiloop formation Peter Clote
20522H4A fast stochastic score based rank fusion method: application on miRNA target prediction Debarka Sengupta
20189I01Integrated prediction of protein functions in Arabidopsis thaliana by Bayesian Markov Random Fields Yiannis Kourmpetis
20346I06Nonparametric Approach to Analysis of Data-Rich Biological Problems Tatiana TATARINOVA
20435I08Genome Scale Annotation Using Rosetta De Novo Structure Predictions Kevin Drew
20548I09From next generation sequencing to knowledge: A case study of functional genomics annotation in prokaryotes Carlos Prieto
20562I10Human annotation in Ensembl Amonida Zadissa
20413I11Collaborative action between Spain and Austria to enhance the application of High Performance Computing to High throughput technologies Noura Chelbat
20634I12CHIPEAN – CHIP Seq Peak Annotation Agnes Hotz-Wagenblatt
20647I13Comprehensive Homeodomain Gene Annotation in Human and Mouse Veronika Boychenko
20661I14APPRIS - Canonical Isoforms for the Human Genome Michael Tress
20814I18Automated curation and assignment of massive DNA sequences Duong Vu
20832I19Characterization of Long Noncoding RNAs Andrea Tanzer
22691I21YGAP: the Yeast automatic Genome Annotation Pipeline Estelle Proux Wera
22758I22A genome-wide, functional analysis of transcription initiation and promoter architecture in the budding yeast Saccharomyces cerevisiae R. Taylor Raborn
22695I23Human transcriptome data in Ensembl Thibaut Hourlier
20191I24Extending Metagenomic Functional Annotation Through Functional Inference Gregory Vey
19928J01Microsoft Biology Initiative Beatriz Diaz Acosta
19931J02NUPTs and NUMTs from algae to land plants - a genomic analysis in 12 different species Noa Sela
20259J03Dissecting a massive parallel sequencing workflow for quantitative miRNA expression analysis Raffaele Calogero
20284J04Boosting the Principle Component Analysis for explorative analysis of genome-wide expressions reveals a common developmental pattern in human and mouse datasets Carlo Cannistraci
20400J09Rice-Map: a new-generation rice genome browser Ge Gao
20440J11The immense genomic variability of human olfactory receptor genes Tsviya Olender
20495J16Interactive Microbial Analysis and Visualization with GView and GView Server Aaron Petkau
20541J19SARUMAN - Using GPU programming for short read mapping Jochen Blom
20534J20Chipster genome browser: Smooth and interactive visualization of next generation sequencing data Aleksi Kallio
20593J22Associating Chromatin Features with Gene Expression Thomas Sakoparnig
20604J23Whole genome sequencing, assembly and annotation of the Saccharomyces cerevisiae strain CEN.PK 113-7D Dick de Ridder
20607J24Genometa - Accurate, flexible and fast taxonomic assignment for ultra-short metagenomic reads Colin Davenport
20619J25Comparing long maximal exact repeats in four human genome assemblies Sara Garcia
20632J26Revealing multiple nucleotide polymorphysms and indels in homopolymeric regions in human exome data Szilveszter Juhos
20650J27Double nucleotide polymorphisms in human pathogen Propionibacterium acnes strains Krisztina Rigo
20672J28Detecting homogenous methylation-domains within whole genome methylation maps Michael Hackenberg
20744J30Next generation sequencing and its application to study breast tumor subtypes Krishna Kalari
20761J31Bayesian Evaluation of de novo Genome Assembly Sergey Nikolenko
20783J32Extracting relationships from integrated functional genomics data with the Ontological Discovery Environment Jeremy Jay
20822J34Role of Conserved 3’-UTR Cis-elements in the Regulation of Human MECP2 and MAPT Genes Involved in Mental Disorders Joetsaroop Bagga
20833J35GARM - Genome Assembly, Reconciliation and Merging Fidel Sanchez-Flores
20809J38A-Bruijn graph approach to de novo genome assembly Mikhail Dvorkin
20878J39BLESS: mapping DNA double-strand breaks by next-generation sequencing Maga Rowicka
20884J41Identifying the Dynamic States of the 3D Genome Organization Andrzej Kudlicki
20811J42Instant-Seq - an integrated and fast Web-based program for analysis of (timecourse) ChIP-Seq data Abhishek Mitra
20924J43Statistical Tests for Detecting Differential RNA-Transcript Expression from Read Counts Philipp Drewe
22711J45Multi-Image Genome Viewer (MIG) Stephen Taylor
22683J47Resource-Efficient de novo Assembly of Eukaryotic Genomes Bryan Beresford-Smith
22667J48The SMALT Software for the Efficient and Accurate Alignment of DNA Sequencing Reads Hannes Ponstingl
22743J49SeqGI: Sequence Read Enrichment at Genomic Intervals Ines de Santiago
22752J50Genome3D: A viewer-model framework for integrating and visualizing multi-scale epigenomic information within a three-dimensional genome Wenjin Zheng
19899K1Partial Purification of Cellulase obtained from Tomato (Lycopersicon lycopersicum Karst) Fruits deteriorated by Aspergillus flavus Linn Adesola Ajayi
20291K2The EMBL-EBI User Survey Jennifer Cham
20325K3Identification of NMR Resonances Using EM Algorithms Martin Krone
20046K4In-silico analysis and prevention of Coksackie virus induced Insulin Dependent Diabetes Mellitus in human Ambuj Kumar
20602K5The Hellenic Society for Computational Biology and Bioinformatics Christos Ouzounis
20703K6A Need for Specific, Advanced Topic Bioinformatics Training: The Canadian Bioinformatics Workshop Series Michelle Brazas
22656K7Spanish National Bioinformatics Institute (INB) Allan Orozco
20049L01GENS2: a simulator for multiloci/whole-genome case-control studies with gene-environment interactions Roberto Amato
22636L02Universal epitope prediction for class II MHC Andrew Bordner
20336L06Characterization of compound gene regulation mechanisms Reiko Tanaka
20380L09Unraveling protein-protein interactions by a semi-automated high-throughput platform Dominik Mertens
20399L10Discovery of a 3D Motif Essential to LDLR-Protein Complexes: Application to docking prediction evaluation Reyhaneh Esmaielbeiki
20420L11Coevolution and Predicted Solvent Accessibility David Ochoa
20499L13On sequential conservation space of RNA-recognizing residues in protein sequences Li Xue
20753L14Functional assessment of topological characterization using graphlet degrees in PPI networks Marco Mina
20560L15SNP-SNP synergy discovery with SNPsyn Tomaz Curk
20854L16RISEARCH: Fast RNA Interaction Search Jan Gorodkin
22631L17Predicting conserved interactions and structures of two multiple alignments of RNA sequences. Stefan Seemann
22682L20A novel ultra-fast comparison method for known and potential ligand-binding sites of proteins Kentaro Tomii
22572L21New methods for finding common insertion sites and co-occurring common insertion sites in transposon- and virus-based genetic screens Tracy Bergemann
22744L23An alternative approach to protein docking: Complexes via homology modeling Ozlem Tastan Bishop
22619M01Fast and Efficient Dynamic Nested Effects Models Holger Fröhlich
20035M02Prediction of bioluminescent proteins based on Discrete Wavelet Transform and Support Vector Machine Krishna Kumar kandaswamy
22609M03A new approach for discovering knowledge from a large mass of data and optimisation of the numbers of variables before learning Bayesian Networks structure: Application in genetic studies of complex g Heni Bouhamed
20265M04R-value: A new measure for dataset evaluation Sejong Oh
20321M05Transcription Regulation: models for combinatorial regulation and functional specificity David Thomas
20343M06Contrasting the Molecular Basis of Human and Mouse Embryonic Stem Cell Self-Renewal Using Bayesian Network Machine Learning Methods Karen Dowell
20350M07A new feature selection method based on classes overlap Sejong Oh
20395M08Protein subnuclear localization using a spectrum kernel minimum distance probability method Esteban Vegas
20409M09SVM-based prediction of granzyme B cleavage sites Lawrence Wee
20425M10Genome-wide enhancer discovery from chromatin methylation marks using Genetic Algorithm-optimized Support Vector Machines Michael Fernandez
20449M11Machine Learning Approaches to Identify and Characterize Effector Proteins in Pathogenic Bacteria David Burstein
20576M13Assessment of protein interaction prediction from sequence data using n-gram analysis Guray Kuzu
20575M14Model selection for predictive and prognostic gene signatures Miika Ahdesmaki
20662M16Dealing with Uncertainty in Support Vector Machines Prediction Sorin Draghici
20665M17Identification of SH2-peptide interactions using support vector machine Kousik Kundu
20688M18A Support Vector Machine approach for rapid genome-wide epistasis detection Barbara Rakitsch
20717M19Time series classifier model for miR-mRNA interaction Jovan Rebolledo-Mendez
20719M20mTiM: margin-based transcript mapping from RNA-seq Nico Görnitz
20855M21A Computational Paradigm for More Specific TFBS Detection Heike Sichtig
20896M22Combined Approach to Anaphora Resolution for Disease-Determinants Ontology Learning from Web Sources Jae-Hong Eom
20156N01Power and minimal sample size for multivariate analysis of microarrays Maarten Iterson
20344N05caArray: make microarray data easily accessible and exchangeable Xiaopeng Bian
20351N06A combination technique for microarray dataset to improve classification accuracy Sejong Oh
20462N09ASPIRE: An improved tool for the analysis of alternative splicing using AltSplice microarrays Melis Kayikci
20498N10Meta-analysis of gene expression microarrays with missing replicates Fan Shi
20505N12Feature selection for specifying experimental conditions that activate gene transcriptions Sho Ohsuga
20387N13A Method for Inference of Gene Regulatory Network based on Bayesian Network with Uniting of Partial Problems Yukito Watanabe
20550N15Prediction of specific versus non-specific RBP-RNA interaction Eleonora Kulberkyte
20561N16cn.FARMS: a latent variable model to detect copy number variations in microarray data with a low false discovery rate Djork-Arné Clevert
20608N18COLOMBOS: Access Port for Cross-Platform Bacterial Expression Compendia Kristof Engelen
20666N24Simulation strategies to evaluate the performance of pathway-based gene expression analysis methods Shailesh Tripathi
20747N25Signaling Pathway Coupling Phenomena Michele Donato
20699N27Alternative Splicing in Malignant Lymphoma Karin Zimmermann
20823N29Flanking sequence effects on oligonucleotide hybridization D. Andrew Carr
20872N30Elimination of spatial autocorrelation in microarray data Sébastien Lemieux
22647N31A Computational Study of Carotenoid Gene Expression using Micro-array Data Firdous Khan
22662N32A survey of batch effects in public gene expression data Paul Pavlidis
22735N36Using R through a Tiki web interface to implement bioinformatics pipelines Xavier Pedro Puente
22750N37Combining omics data and biological knowledge using multiple factor analysis Jose Luis Mosquera
20287O1An integrated approach to the alignment and classification of 3D neuronal morphology in the Drosophila brain chao-chun chuang
20569O2Effect of Leaky Channels in Calcium Homeostasis Suhas Vasaikar
22618P01Benchmarking Ontologies: Bigger or Better? Lixia Yao
20032P03A Modular Annotation Framework for Mathematical Models Michael Cooling
20327P04An ontology of bioinformatics tool functions, data types and formats Jon Ison
20328P05Multiple Ontology Based System for Integrating and Display Rat Phenotype Data Mary Shimoyama
20473P06ontoCAT R package for ontologies traversal and search Natalja Kurbatova
20527P07What does semantic similarity mean in terms of protein function comparison? The analysis of relation between functional and structural similarity. Bogumil Konopka
20566P08A Semantic Web Infrastructure for Bioinformatics of Staphylococcus aureus Cândida Delgado
20581P09A standard for cooperative interactions Kim Van Roey
20801P11BioPAX – A Community Standard for Pathway Data Sharing Nadia Anwar
20299Q01Signatures of positive selection on genes of the N-Glycosylation pathway concentrate on genes with regulatory positions Giovanni Marco Dall'Olio
20417Q03cn.MOPS: Mixture of Poissons for Discovering Copy Number Variations in Next Generation Sequencing Data Günter Klambauer
20490Q04Deep-sequencing reveals phage-driven diversification of Pseudomonas aerugionsa biofilms Kerensa McElroy
20810Q07INRICH: improved enrichment testing method that integrates an unbiased GWAS strategy with prior biological knowledge: application to Type 2 diabetes Phil Lee
20363R01Statistical approach to absolute protein quantification Sarah Gerster
20633R03Chimeras knocking at the door Milana Frenkel-Morgenstern
20676R04Bioinformatics for Proteomics: developing new tools for the analysis of experimental data Angelo Facchiano
20707R05Predict subcellular localization for proteins in all kingdoms Tatyana Goldberg
20637R06Quantitative mass spectrometry data based pathway analysis Philipp Gormanns
20752R08PRIDE, the PRoteomics IDEntifications database Johannes Griss
20756R09Lost Data – The Consequences of Changing Protein Accession Johannes Griss
20768R10Proteomics based genome annotation using conceptually translated ESTs Paul Blakeley
20825R11Data mining on a leukemia phosphoproteome dataset: insights on chemoresistant cell signaling Renato Milani
22659R12Identification of protein expression dynamics during germination in Streptomyces Eva Strakova
22748R13Tracing Evolutionary Events Over Ancestral Proteomes Matt Oates
22767R14Viral proteins acquired from a host converge to simplified domain architectures Nadav Rappoport
20174S01Gene Array Analyzer (GAA): Alternative usage of gene arrays to study alternative splicing events Pascal Gellert
20271S02Cell specific gene expression from histome modifications and transcription factor binding Thaís Rêgo
20311S05Induction of Effectors in Diuraphis noxia after Feeding on Preference and Non-preference Wheat Hosts Nicolaas Burger
20370S06ConTra v2: a tool to identify transcription factor binding sites across species, update 2011 Stefan Broos
20535S08Unveiling combinatorial regulation through the combination of ChIP information and in silico cis-regulatory module detection Kathleen Marchal
20542S09Transcriptional cross-regulation as survival mechanism in bacteria Pieter Monsieurs
20558S10A probabilistic model for prediction of Transcription Start Regions in both intra- and inter-genic miRNAs Annalisa Marsico
20587S11Analysis of the structure and evolutionary conservation of regulatory networks in prokaryotes. Richard Münch
20657S12PRODORIC - a platform for the elucidation of gene regulatory networks in prokaryotes - from data to models Richard Münch
20876S14Identifying CNVs of regulatory elements which impact overall survival in serous cystadenocarcinoma Geoff Macintyre
20889S16Improved in silico regulatory SNP detection facilitates large scale SNP scanning Geoff Macintyre
22737S18Identification of shortened 3’untranslated regions by Affymetrix genechip arrays Loredana Martignetti
22757S19Integrative approach at building and analyzing gene regulatory networks Julia Ponomarenko
20493T1A Framework for the Evaluation of Bioinformatics Methods José M. Fernández
20612T2eBiomics: an e-Learning Environment on Bioinformatics for Life Scientists Patrick Koks
20873T3Practical NGS Analysis: A Bioinformatician’s Perspective Abhishek Pratap
20891T4A Review of Software for Visualization and Interpretation of Genome Wide Association Studies Results Armita Zarnegar
22626U03Accurate quantification of transcriptome from RNA-Seq data by effective length normalization Sanghyuk Lee
20183U04Application of whole genome resequencing to detect sequence polymorphisms underlying boar taint Rahul Agarwal
20186U05High-throughput protein analysis in the cloud Guy Yachdav
20197U06Evolutionary Conservation and Genetic Variability of Hepatitis C Virus Core Protein (HCVc) Muhammad Ilyas
20256U07A method to separate function and fold specific residues in a protein. Andrew Lynn
20298U10EMBOSS: EuropeanMolecular Biology Open Software Suite Peter Rice
20383U11SKM: A String Kernel Motifs Classifier for Nucleic Acid and Protein Sequences Hugh Shanahan
20392U12P-value based motif identification using positional weight matrices Holger Hartmann
20450U14Toolbox for the analysis of Roche 454 Sequencing data Christian Ruckert
20460U15Comrad: Detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data Andrew McPherson
20470U16The Interlaboratory Robustness of Next-Generation Sequencing (IRON) Study Hans-Ulrich Klein
20502U20Improved performance of sequence search algorithms in remote homology detection Ramanathan Sowdhamini
20513U21New method of detecting pathogenic viruses using high-throughput sequencing data Shumpei Ishikawa
20520U22Perfect Hamming Code as Hash key for Fast Genome Mapping Yoichi Takenaka
20524U24fastapl -- a utility for versatile and easy processing of multifasta format data Paul Horton
20539U25Behind the significance in NGS reads assembly Antonio Muñoz
20559U26Computational Analysis of DNA Replicases in Double-Stranded DNA Viruses: Relationship with the Genome Size Darius Kazlauskas
20565U27A novel miRNA prediction method based on next generation sequencing technology Kui Qian
20580U28Sequence alignment of coiled coil proteins: adapting to restricted sequence variation Michael Kuhn
20592U29Computational prediction of transposon insertion sites in bacterial genomes Michael Steinert
20606U30Improving SNV calling sensitivity by probabilistically combining SNVs reported by different calling tools Alejandro Balbin
20547U31Integrating Protein Domain Prediction in Multiple Sequence Alignment Layal Al-Ait
20663U32A new algorithm for sequencing by hybridization based on non-classical approach Marcin Radom
20682U34Computational challenges in the production and analysis of Illumina Genome Analyzer data Martin Kircher
20685U35Simulating Quality and Depth of Sequence for Genotype Accuracy Iain Bancarz
20730U37Using next-generation sequencing “dark matter” to identify a new transposable element location in the mouse genome. James Cavalcoli
20750U39A Conditional Random Fields Model for RNA Conformation Sampling Jinbo Xu
20763U40A new approach to suboptimal pairwise sequence alignment Feng Lou
20758U41Support Vector Machines for finding deletions and short insertions using paired-end short reads Dominik Grimm
20770U42A combination of amino acid composition and matching for conotoxin superfamily classification Nazar Zaki
20781U43Ranking and filtering translocations in paired-end sequencing data using BLAT realignment Christoph Bartenhagen
20808U45Distributed Web Services for Bioinformatics: Multiple Sequence Alignment Peter Troshin
20806U46Pythoscape: A Software Framework for Generation of Large Protein Similarity Networks Alan Barber
20596U47LaTcOm: A web server for visualizing rare codon clusters Athina Theodosiou
20830U48SRS 3D - Integrating structures, sequences and annotations Andrea Schafferhans
20680U49Multiobjective sequence alignment: Formulation and Algorithms Maryam Abbasi
20838U50An improved RIP-Seq Toolkit to Reveal Genome-wide Exon Junction Complex Landscape Alper Kucukural
20870U54Visualizing the next generation of sequencing data with GenomeView Thomas Abeel
22643U55SlideSort: Fast and exact algorithm for Next Generation Sequencing data analysis Kana Shimizu
22706U56Who & How: Investigating miRNA Regulation in Ranked Gene Lists using miRnaPursuit. Teresa Colombo
22736U60Performing Functional Site Prediction on Protein Sequences Generated by De Novo Transcriptome Assembly Chien-Yu Chen
22671U61MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods Sudhir Kumar
22739U62Twenty-Five Fold Diversity Overestimation Revealed by Analyzing a MOCK Sample using 454 Amplicon Pyrosequencing Sebastian Jünemann
22654U64ADDAPTS: A Data-Driven Automated Pipeline and Tracking System Risha Narayan
20048V1P.R.E.S.S.--- An R-package for Exploring Residual-Level Protein Structural Statistics Yuanyuan huang
22630V2DIBER: protein, dna or both? Grzegorz Chojnowski
20736V6The Biochemical Algorithms Library (BALL) - Rapid Application Development in Structural Bioinformatics Andreas Hildebrandt
20745V7SymD server: a platform for detecting internally symmetric protein structures Chin-Hsien (Emily) Tai
19881W01A Time-Dependent Framework for Solving the Degeneracy Problem in RNA Secondary Structure Deleterious Mutation Prediction Danny Barash
22613W02Correcting protein alignment errors using a novel multiple-template threading method Jinbo Xu
22602W03All-atom knowledge-based potential for RNA structure prediction and assessment Emidio Capriotti
22601W04A structural and dynamical model of human telomerase Samuel Flores
20359W05Optimization of residual electrostatic environment to enhance protein thermal stability Chi-Wen Lee
22616W06Complex networks govern coiled coil oligomerization - predicting and profiling by means of a machine learning approach Ulrich Bodenhofer
22634W08The imprint of codons on protein structure Charlotte Deane
20154W09PyRy3D: a software tool for modelling of large macromolecular complexes Joanna Kasprzak
20177W10Planar shape representation based Protein function prediction Heng Yang
20212W12MODORAMA - a web application for comparative protein structure modeling Jan Kosinski
20275W13Mean Scaled RMSD: A Size Independent Measure For Superimposition of Protein Structures Seyed Shahriar Arab
20286W14Probabilistic model for secondary structure prediction from protein chemical shifts Martin Mechelke
20294W15Multi-LZerD: Multiple protein docking for asymmetric complexes Juan Esquivel-Rodríguez
20297W16Modelling Protein Domain Binding to Kinase Structures altered by Phosphorylation Christoph Gernert
20345W17Full atom comparative three-dimensional modeling of protein-DNA complexes Francisco Melo
20352W18Identification of cavities on protein surface using multiple compu-tational approaches for drug binding site prediction Bingding Huang
20364W19Physical contacts-based score for evaluation of protein three-dimensional models Kliment Olechnovic
20373W21The influence of the local sequence environment on RNA loop structures Dirk Walther
20402W23Peptides modulating conformational changes: From in silico design to preclinical proof of concept Itamar Borukhov
20412W24Spritz: Intrinsic protein disorder prediction for genomes and insights into protein function. Ian Walsh
20433W26Slip symmetry – a new type of symmetry in protein structures Dukka KC
20474W27A multiple-template approach to protein threading Jinbo Xu
20483W28A novel type of methyltransferase encoded by a conserved domain of GRAS Magdalena Dymecka
20461W29Implementation of the Protein Fluorescence And Structural Toolkit (PFAST) Cynthia Prudence
20504W30Maximal Use of Information Found in All Protein Structure Data Armando Solis
20557W33Protein function prediction using clustering method of Protein-Protein Interaction network Sejong Oh
20588W34Comprehensive study of HOX transcription factors DNA binding specificity Katarzyna Kokoszynska
20597W36The MULTICOM Toolbox for Protein Structure Prediction Jianlin Cheng
20601W37Comprehensive structure-to-function analysis of transcription factor IID (TFIID) complex Maja Małkowska
20616W38Structure-based classification of the plant non-specific lipid transfer protein superfamily towards its functional characterization Cécile Fleury
20635W39A comparative study on filtering protein secondary structure prediction Chris Christodoulou
20645W40firestar in 2011 Michael Tress
20675W42BOCTOPUS: Topology prediction of Transmembrane beta barrel proteins Sikander Hayat
20679W43Analysis of Functional Islands using Structural Clustering Anne-Christin Hauschild
20712W45Predicting the 3d DNA structure of the human genome Sven Bilke
20734W46Binding Ligand Prediction by Comparing Local Surface Patches of Potential Pocket Regions Daisuke Kihara
20764W48ProBiS: A web server for detection of structurally similar protein binding sites Janez Konc
20478W49Protein conformational movements modeling based on the average action principle Alexander Krass
20767W50Evaluation of transmembrane helix (TMH) packing prediction methods on successive in sequence TMHs Vasilis Promponas
20792W52Are Protein Disordered Regions Equal to Loops? Esmeralda Vicedo
20695W53Environment Specific Substitution Tables Improve Membrane Protein Alignment Jamie Hill
20819W54Quality or Quantity of Structural Dynamics Information: That is the Question! (when improving performance of structure-based function prediction methods) Dariya Glazer
20837W55Nearest-Neighbor Approaches to Predict Protein Function by Sequence Homology Alone Tobias Hamp
20578W58Is the biological hydrophobicity scale correct? Christoph Peters
20892W60A comprehensive review of protein fold space and the correlation of structure with function Spencer Bliven
20897W61Protein interaction partners revealed by their dynamical properties Jau-Ji Lin
22693W65Is It Biologically Relevant? An Evolutionary Method for Distinguishing Biological Interfaces from Crystal Contacts Guido Capitani
22670W66SAHG, a comprehensive database of annotated structure models for human proteins Chie Motono
22721W67Training bidirectional recurrent neural networks with Conjugate gradient-type algorithms for protein secondary structure prediction Chris Christodoulou
22759W68Protein Sequence Design Using Ensemble-Based Energetic Information James Wrabl
22761W69Predicting Functions of the Universal Stress Proteins in Metabolically Versatile Rhodopseudomonas palustris Shaneka Simmons
22663W70The Impact of Multifunctional Genes on "Guilt by Association" Analysis Jesse Gillis
22717W71Understanding protein-protein interactions: Efficient classification of physiological and non-physiological protein complexes and unexpected conservation in interaction interfaces Dmitry Korkin
20622W72Protein Structural Domain Assignment Using Delaunay Tessellation Todd Taylor
19952X01A regulatory network model of CD4+ lymphocytes Luis Mendoza
20054X03ALISSA-An Automated Live Cell Imaging System for Signal Transduction Analyses Heinrich Huber
22605X04Interactive, multiscale navigation of large and complicated biological networks Thanet Praneenararat
22637X05Finding out what happened -- Highlighting the essence of a biological experiment Georg Fuellen
22639X06Topological network alignment uncovers biological function and phylogeny Natasa Przulj
20159X07Inferring the role of alternative splicing on biological pathways: Studies using cancer transcriprome data Murlidharan Nair
20258X08Genetic Design Through Branch and Bound Dennis Egen
20276X09Bridging clinical knowledge to molecular events through integration of imaging biomarkers and protein interactions in Alzheimer’s disease Erfan Younesi
20281X10Network-based approach towards candidate gene prioritisation using TargetMine Lokesh Tripathi
20285X11Integrated cell cycle and DNA repair signalling network modelling for identification of key molecular regulators in basal-like breast cancer Inna Kuperstein
20292X12An interface analysis of human E2-E3 complexes: structural insights into specificity Gozde Kar
20296X13How little do we actually know? – Towards the size of gene regulatory networks. Richard Röttger
20367X16A Directed Graphical Gaussian Model for Inferring Gene Regulatory Networks Tomoshige Ohno
20368X18Fast and Efficient Dynamic Nested Effects Models Holger Fröhlich
20378X20bioCompendium: high-throughput experimental data analysis platform Venkata Satagopam
20424X22Detection of nonlinear effects in gene expression pathways Andreas Mayr
20434X23Network topology complements sequence as a source of biological information Tijana Milenkovic
20436X24Understanding temporal patterns in cell cycle regulation through visualization Maria Secrier
20444X25From WIPA (Web Interface Protein Atlas) to Systems Biology Analysis of Protein Atlas Tissue Microarrays (TMAs) Hans-Juergen Thiesen
20341X27Mapping Genetic Interactions in Various Contexts Provides Complementary Information Magali Michaut
20496X30Construction of a drug-target-disease network and its application to drug repositioning and mode of action analysis Charny Park
20511X31Finding sets of shortest elementary flux modes that decompose genome-scale metabolic flux distributions Siu Hung Joshua Chan
20521X34Different regulatory networks of SOX2 in embryonic and neural stem cells Sanghyuk Lee
20528X35Interspecies translation of disease networks increases robustness and predictive accuracy Yahya Anvar
20553X38An Integrated Approach To Identify Human MicroRNA-Targets. Kim Wan Kyu
20582X42Cholesterol-Responsive Gene Network Reconstruction from Hypercholesterolemic Mice Transcriptome Data Gustavo Hime
20477X47Integrated Inference and Analysis of Regulatory Networks Using Multi-level Measurements Christopher Poultney
20651X49Topological features predict misannotations in metabolic network Rodrigo Liberal
20654X51Candidate gene prediction using integrative and network-based approaches - Mining Pig QTL Keywan Hassani-Pak
20673X52Organizational structure of the peripheral gene regulatory network in B-cell lymphoma Ricardo de Matos Simoes
20713X56A Novel Reverse Engineering Method for Gene/Protein Network Reconstruction - Divergence Weighted Independence Graphs Yang Xiang
20714X57Joint Dynamic Networks of miRNA and Transcripton Factor Regulation Marcel Schulz
20740X58KeyPathwayMiner - Detecting case-specific biological pathways by using expression data Hande Kucuk
20749X59Finding Consistent Explanations for Observations from Genome-Wide Mutant Assays Deborah Chasman
20786X61Delineating signaling network from cancer related pathways Chandrajit Lahiri
20796X63A network topology-based machine learning approach to extract relevant cancer-related signaling subnetworks Marcio Acencio
20802X65HotRegion: A web server of cooperative hot spots Engin Cukuroglu
20803X66GraphCrunch 2 Network Analysis Tool and MI-GRAAL Network Aligner Natasa Przulj
20804X67Minimum Curvilinearity to address high-throughput protein-protein interaction experiments Gregorio Alanis-Lobato
20828X69Aligning multiple time-series experiments to learn regulatory models: An application to modeling the core network in stem cell differentiation Irene Ong
20841X70Structural Analysis of Correlation Networks in Bioinformatics: Graph Theoretic Substructures and the Corresponding Cellular Functions Kathryn Dempsey
20863X71Systematic, comparative network analysis related to human disease Serene Wong
20871X72Systematically mapping the druggable pathways of Saccharomyces cerevisiae Kristen Fortney
20868X73Global gene network alignment among species by using graph summarization Aika Terada
20851X74A systems approach to learning the regulatory network of T helper-17 differentiation Aviv Madar
20880X76Modeling the Spatiotemporal Pattern of Gene Expression During Somitogenesis with Maximum Entropy Deconvolution. Andrzej Kudlicki
20848X77Characterization of transcription factor and microRNA regulatory networks involved in myelination Li-Wei Chang
20931X78Extending the Yeast Metabolic Network Using Integrated System Biology Approach Paul Fisher
22658X79An Epistatic Profile of the Cell Envelope Biogenesis in Escherichia coli Evidences Extensive Genetic and Functional Crosstalk Between Processes Juan Diaz-Mejia
22686X84Correction for ascertainment bias in S. cerevisiae interactions: an insight Jonathan Dickerson
22688X85Using community structure for complex network layout Oliver Duerr
22722X86Quantifying the Response of a Biological System using Network Perturbation Amplitudes Sam Ansari
22741X88Causal Reasoning on Biological Networks: Interpreting transcriptional changes Daniel Ziemek
22760X91A multi-level Bayesian model for identifying predictive combinations of signaling network modules, proteins, and phosphopeptides for cancer treatments Ann Chen
22646X94Generative Probabilistic Models for Protein-Protein Interaction Networks – The Biclique Perspective Regev Schweiger
22607Y01Biomedical Natural Language figure Processing for Intelligent Figure Search Hong Yu
20365Y04ANDCell-ANDVisio system: knowledge extraction using text-mining in the systems biology Pavel Demenkov
20366Y05Self-Training Improves Robustness of Protein-Protein Interaction Extraction from Text Philippe Thomas
20385Y06Extraction of protein cellular localization using the Locminer text mining system Martin Krallinger
20438Y07Reflect: a browser plugin for life scientist Janos Binder
20573Y08Biomedical text mining from multiple views: information fusion and vertical xinhai Liu
20677Y09Keyword Clustering in Biomedical Information Retrieval Using Evolutionary Algorithms Viktoria Dorfer
20715Y10Automating host-pathogen interaction discovery: an HIV case study Daniel Jamieson
20754Y11Relation-mining workflows to extract animal host-microorganism interactions in free text BalaKrishna Kolluru
22747Y12Overview of the second CALBC Challenge Senay Kafkas
22751Y13An exercise in kidney factomics: From article titles to RDF Knowledgebase James Eales
22622Z01BOOST: A Boolean Representation-based Method for Detecting SNP-SNP Interactions in Genome-wide Association Studies Xiang Wan
22573Z02Linguistic analysis of genomic islands reveals a recent acquisition of genetic materials by Mycobacterium tuberculosis from alpha-Proteobacteria Oleg Reva
22562Z07Structural Biology Meets Systems Biology: A Structural Systems Biology Approach for Gauging the Systemic Effect of Single Nucleotide Polymorphisms Tammy Cheng
22560Z08In silico prediction of the calpain degradome Lawrence Wee
22559Z09A scalable signaling map identifies cross-talk between gene modules inferred from multi-parametric RNAi phenotypes Xin Wang
22557Z11PINALOG: a novel approach to align protein interaction networks – implications for function prediction and complex detection Hang Phan
22553Z14Comparing nucleotide-based and codon-based alignment of human next-gen sequencing exome data Szilveszter Juhos
22575Z15RIBER and DIBER: a software suite for crystal content analysis in the studies of protein-nucleic acid complexes. Grzegorz Chojnowski
22576Z16SpliceGrapher: Predicting Splice Graphs from Diverse Evidence Asa Ben-Hur
22578Z17Topological features predict misannotations in metabolic networks Rodrigo Liberal
22579Z18A Theoretical Approach to Identify Indispensable Proteins of the Type III Secretion Systems of Salmonella enterica Serovar Typhimurium Strain LT2 Chandrajit Lahiri
22583Z19Analysis of bacterial genes with disrupted ORFs reveals frequent utilization of Programmed Ribosomal Frameshifting (PRF) and Programmed Transcriptional Realignment (PTR). Pavel Baranov
22584Z20An Event-driven Approach to Study Operon Evolution Iddo Friedberg
22586Z21RTA and MultiRTA: Simple yet Accurate Methods for Predicting Class II MHC Epitopes Andrew Bordner
22587Z22Metagenomic Biomarker Discovery and Explanation Curtis Huttenhower
22585Z25RDyNet: bridging functional analyses and network visualization Mauro Alves Castro
22593Z26Modulators of microRNA Activity Regulate Glioblastoma Pathogenesis Xuerui Yang
22599Z27Scalable metabolic reconstruction for metagenomic data and the human microbiome Curtis Huttenhower
22600Z28Systems-level insights from modular decomposition of the yeast genetic interaction network Jeremy Bellay
22592Z29Large scale merging of microarrays. From curation to meta-curation Colin Molter
20312Z30INBIOMEDvision: Promoting and Monitoring Biomedical Informatics in Europe Victoria López Alonso
20525Z31Conveyor - A strong type workflow library Burkhard Linke
20591Z32New types of services in Mobyle 1.0 Herve Menager
20620Z33An integrated core facility to go from biology to data and answers Laurent Gautier
20888Z34Toward Genomic Data Sharing Directly at the Lab Site in the New Agent-Based Infrastructure OpenKnowledge Dietlind Gerloff
22608Z35New tools for RNA 3D structure modeling: inspirations from the protein world Janusz Bujnicki
22604Z36REPAIRtoire - a database of DNA repair pathways. Kaja Milanowska
22603Z37FABIA: Factor Analysis for Bicluster Acquisition Djork-Arné Clevert
22621Z38Malaria Endemicity among Pregnant Women in Urban and Semi-Urban Area in Southwest, Nigeria Tony Ojiezeh
22641Z39Strengths and limitations of the federal guidance on synthetic DNA Jean Peccoud
22701Z41Extraction protocol optimization for the LC-MS based global metabolite profiling of grapes Matthias Scholz
22666Z43Jalview 2.7 James Procter
22753Z52The reference species tree of (sequenced) life Julian Gough


LBR01Milana Frenkel-MorgensternPotential function of proteins encoded by chimeric transcriptsSunday, July 17 10:45 a.m. - 11:10 a.m.
LBR04David GfellerThe multiple Specificity Landscape of Peptide Recognition DomainsSunday, July 17 4:00 p.m. - 4:25 p.m.
LBR06Yinyin YuanQuantitative analysis of cellular composition in primary breast tumours deconvolutes molecular signatures and elucidates impact of tumour microenvironmentSunday, July 17 3:00 p.m. - 3:25 p.m.
LBR08Wei-Jen ChungPost-transcriptional regulators of microRNA biogenesis regulate pathogenesis of cancerSunday, July 17 4:00 p.m. - 4:25 p.m.
LBR10Tamir TullerA Comprehensive Computational Model for Analyzing Gene TranslationMonday, July 18 11:15 a.m. - 11:40 a.m.
LBR11Ana ConesaDifferential expression with RNA-seq: a matter of DepthMonday, July 18 11:45 a.m. - 12:10 p.m.
LBR12Van Anh Huynh-ThuInferring Gene Regulatory Networks from Expression Data using Tree-based MethodsMonday, July 18 12:15 p.m. - 12:40 p.m.
LBR14Pavel BaranovAnalysis of bacterial genes with disrupted ORFs reveals frequent utilization of Programmed Ribosomal Frameshifting (PRF) and Programmed Transcriptional Realignment (PTR).Monday, July 18 3:00 p.m. - 3:25 p.m.
LBR15Nicola SegataMetagenomic Biomarker Discovery and ExplanationMonday, July 18 3:30 p.m. - 3:55 p.m.
LBR17Egor DolzhenkoSTAGR: Software To Annotate Genome RearrangementTuesday, July 19 10:45 a.m. - 11:10 a.m.
LBR21Roman BriskineCo-expression network analysis reveals rewiring of maize transcriptome by domesticationTuesday, July 19 2:30 p.m. - 2:55 p.m.

Tech Track

TT01Michael Schuster Ensembl Genome Browser: Harnessing the Next Generation Sequencing Wave Sunday, July 17 10:45 a.m. - 11:10 a.m.
TT02Fan Meng and Barbara Mirel PubAnatomy: A Rich Internet Application for Integrated Literature and Data Exploration Sunday, July 17 10:45 a.m. - 11:10 a.m.
TT03Rachel Harte UCSC Genome Browser: Visualization tools for high-throughput sequencing Sunday, July 17 11:15 a.m. - 11:40 a.m.
TT04Michael Reich GenomeSpace Sunday, July 17 11:15 a.m. - 11:40 a.m.
TT06Hienke Sminia Bioinformatics@school Sunday, July 17 11:45 a.m. - 12:10 p.m.
TT07Zhong Li Supporting Inter-connected Biomedical Open-source Software Sunday, July 17 12:15 p.m. - 12:40 p.m.
TT08Sanghyuk Lee MONGKIE: Modular Network Generation and Visualization Platform with Knowledge Integration Environment Sunday, July 17 2:30 p.m. - 3:25 p.m.
TT09Attila Berces Cloud Computing for Computational Biology Sunday, July 17 2:30 p.m. - 2:55 p.m.
TT11George Vacek Efficient Graph Based Assembly of Short-Read Sequences on a Hybrid Core Architecture Sunday, July 17 3:30 p.m. - 4:25 p.m.
TT13Scott Markel, Ruth Dunn Analyzing Next Gen Sequencing Data with Pipeline Pilot Monday, July 18 10:45 a.m. - 11:40 a.m.
TT14Janez Konc ProBiS: a web server for detection of protein binding sites Monday, July 18 10:45 a.m. - 11:10 a.m.
TT15Katy Wolstencroft RightField: The Semantic Annotation of Experimental Data using Spreadsheets Monday, July 18 10:45 a.m. - 11:10 a.m.
TT16Jo McEntyre UK PubMed Central: a database of life science research articles. Monday, July 18 11:15 a.m. - 11:40 a.m.
TT17Paul Fisher Software for the data-driven researcher: Annotation of Next Generation Sequencing SNP Data using scientific workflows Monday, July 18 11:15 a.m. - 11:40 a.m.
TT18Irina Dalah GeneCards: The Human Gene ReSearcher Monday, July 18 11:45 a.m. - 12:10 p.m.
TT19Elissa Chesler Integrating Heterogeneous Data using the Ontological Discovery Environment Monday, July 18 11:45 a.m. - 12:10 p.m.
TT22Julian Gough SUPERFAMILY Monday, July 18 12:15 p.m. - 12:40 p.m.
TT23Kostas Karasavvas Enacting Taverna Workflows through Galaxy Monday, July 18 12:15 p.m. - 12:40 p.m.
TT24Peter Rice EMBOSS: New developments and extended data access Monday, July 18 2:30 p.m. - 2:55 p.m.
TT25Guy Yachdav PredictProtein sequence analysis in the cloud Monday, July 18 2:30 p.m. - 2:55 p.m.
TT26Peter Rose Become an Expert User of the RCSB Protein Data Bank Website and Web Services Monday, July 18 2:30 p.m. - 2:55 p.m.
TT27Allan Orozco The Spanish National Bioinformatics Institute (INB) Monday, July 18 3:00 p.m. - 3:25 p.m.
TT28Michael Remmert HHblits: Lightning-fast iterative sequence searching by HMM-HMM comparison Monday, July 18 3:00 p.m. - 3:25 p.m.
TT30Mickael Goujon Using the EMBL-EBI services through the JDispatcher framework Monday, July 18 3:30 p.m. - 3:55 p.m.
TT31Eija Korpelainen Chipster 2.0: User-friendly NGS data analysis software with interactive genome browser Monday, July 18 3:30 p.m. - 3:55 p.m.
TT32Esther Schmidt GenomeRNAi: A Phenotype Database for Large-scale RNAi Screens Monday, July 18 3:30 p.m. - 3:55 p.m.
TT33Mickael Goujon EBI Search: a new way to explore biology Monday, July 18 4:00 p.m. - 4:25 p.m.
TT34Ray Fergerson Introduction to National Center for Biomedical Ontology (NCBO) Technology Monday, July 18 4:00 p.m. - 4:25 p.m.
TT35Jean Peccoud GenoCAD: A Web-Based Open Source Application to Design Synthetic DNA Molecules Tuesday, July 19 3:00 p.m. - 3:25 p.m.
TT36Benoit Bely Overview of The Universal Protein Resource (UniProt) Tuesday, July 19 10:45 a.m. - 11:10 a.m.
TT37Daniel Blankenberg NGS Best Practices through Galaxy: Cloud-based variant discovery with visual analytics Tuesday, July 19 10:45 a.m. - 11:10 a.m.
TT39Jinbo Xu RaptorX: an integrated web server for protein sequence-structure alignment and protein structure prediction Tuesday, July 19 11:15 a.m. - 11:40 a.m.
TT40Matthew Bellgard YABI: A sophisticated Internet-based cross–omics analytic environment Tuesday, July 19 11:15 a.m. - 11:40 a.m.
TT41Desmond Higgins Clustal Omega for Protein Multiple Sequence Alignment Tuesday, July 19 11:15 a.m. - 11:40 a.m.
TT42Craig McAnulla Introducing InterProScan 5 Tuesday, July 19 11:45 a.m. - 12:10 p.m.
TT43Matus Kalas EDAM ontology and BioXSD: The unifying semantics and syntax for bioinformatics tools Tuesday, July 19 11:45 a.m. - 12:10 p.m.
TT44Seán O'Donoghue Killer App Award Tuesday, July 19 11:45 a.m. - 12:40 p.m.
TT45Shulei Sun CAMERA: Metagenomic Resources and Tools Tuesday, July 19 12:15 p.m. - 12:40 p.m.
TT46Keywan Hassani-Pak Knowledge-driven QTL analysis and network-based candidate gene discovery with Ondex Tuesday, July 19 12:15 p.m. - 12:40 p.m.
TT47Fady Mohareb SORF, a web application for heterogeneous data management and visualisation Tuesday, July 19 2:30 p.m. - 2:55 p.m.
TT49Patricia Whetzel NCBO Web Services and Development of Semantic Applications Tuesday, July 19 2:30 p.m. - 2:55 p.m.
TT50Arek Kasprzyk OncoPortal, a data management and analysis framework for cancer research Tuesday, July 19 2:30 p.m. - 2:55 p.m.
TT51Peter Karp Recent Developments in the Pathway Tools Software and BioCyc Databases Tuesday, July 19 3:00 p.m. - 3:25 p.m.
TT52Pål Puntervoll eSysbio - an online system for interdisciplinary life science research Tuesday, July 19 3:00 p.m. - 3:25 p.m.
TT54Junjun Zhang BioMart: A data federation framework for large collaborative projects Tuesday, July 19 3:00 p.m. - 3:25 p.m.
TT55Rajarajan Swaminathan Database on Potential “Antibiotics” From Flowering Plants Tuesday, July 19 3:30 p.m. - 3:55 p.m.
TT56Geoffrey Barton Jalview 2.7 Tuesday, July 19 3:30 p.m. - 3:55 p.m.
TT57Claire O'Donovan The International Society for Biocuration and the efforts of its members Tuesday, July 19 3:30 p.m. - 3:55 p.m.
TT58Nicolas Alcaraz KeyPathwayMiner - Detecting case-specific biological pathways by using expression data Tuesday, July 19 4:00 p.m. - 4:25 p.m.
TT59Jeremy Goecks The Galaxy Track Browser: Transforming the Genome Browser from Visualization Tool to Analysis Tool Tuesday, July 19 4:00 p.m. - 4:25 p.m.