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

Posters

20098	A02	Bayesian Networks to Decision Making in Lymph Node Metastasis of Colorectal Cancer	Md. Aminul Hoque
22172	A04	A large scale analysis in the human proteome detects correlation among disease associated mutations and perturbation of protein stability	Rita Casadio
22173	A05	SNPs&GO: predicting the deleterious effect of human mutations using functional annotation.	Emidio Capriotti
20308	A07	Uncovering Network Control Mechanisms in Induced Oncogenic Transformation of Human Mammary Epithelial Cells through Whole Transcriptome Analyses	Sol Efroni
20322	A09	siRna – A Comprehensive Analysis Workflow Towards Better Understanding of High-throughput Screening Data.	Vidal Fey
20323	A10	miRNA levels are associated with immune network activity and associate with disease outcome in Ovarian Cancer. A possible miRNA – network control mechanism.	Sol Efroni
20339	A11	A Novel Bioinformatics Pipeline for Identification and Characterization of Fusion Transcripts in 31 Breast Cancer and Normal Cell Lines	Yan Asmann
20353	A12	Feature extraction from Spinal cord images	Sejong Oh
20375	A14	Cross-species candidate gene prioritization with MerKator	Leon-Charles Tranchevent
20377	A15	A guide to web tools to prioritize candidate genes	Leon-Charles Tranchevent
20379	A16	History-aware models for HIV therapy screening	Jasmina Bogojeska
20301	A17	Network-based gene prioritization from expression data by diffusing through protein interaction networks	Daniela Nitsch
20391	A18	Detecting cancer driving mutations by whole genome sequencing in the ICGC PedBrain project	Barbara Hutter
20168	A20	Mapping the spread of HIV in Germany	Glenn Lawyer
20406	A21	SNP4Disease: a knowledge database to detect disease associated SNPs	David John
20447	A25	Transcriptomic profiles and gene networks of human Mesenchymal Stem Cells (MSCs)	Beatriz Rosón
20481	A27	Association Rule Mining with Prior Knowledge for Alzheimer's Disease	Peter Li
20486	A29	An Integrative Bioinformatic Predictor of Protein Sub-Cellular Localisation in Malaria	Ben Woodcroft
20530	A32	Deconvoluting Cancer Genomes using an Optimal Scaffolder	Niranjan Nagarajan
20555	A34	Chipster 2.0: User-friendly analysis software for next generation sequencing data with interactive genome viewer.	Massimiliano Gentile
20567	A37	AllergenNet: a database applied to the study of allergenic proteins	Helen Arcuri
20570	A38	Integrative analysis of expression and copy number profiles to find causal genes in cancer	Celia Fontanillo
20595	A39	GUILDify: A web server for phenotypic characterization of genes by means of protein-protein interactions and graph algorithms	Emre Guney
20623	A41	Bioinformatics for large scale characterization and tracking of gene-modified hematopoietic stem cells	Manfred Schmidt
20627	A42	Detecting Intrahost Emergence of Recombinant Viruses within HIV-1 infections using Ultra-Deep Sequencing	Felix Feyertag
20656	A46	Structural comparison of Erwinase and E. coli L-Asparaginase to facilitate rational engineering of a cancer drug	Mainá Bitar
20659	A47	Inhaled Toxicant Interactions with Transcriptional Regulatory Networks in Frontline Lung Cells	George Acquaah-Mensah
20671	A48	Multi-Harmony: detecting functional specificity in HIV differential replication rates	K. Anton Feenstra
20670	A49	Data Based Identification of Estimation Models for Tumor Markers Using Evolutionary Computation	Stephan Winkler
20698	A50	Models for reverse engineering of transcriptional networks in Yersinia enterocolitica infection	Olivia Prazeres da Costa
20704	A51	A framework for whole-exome deep sequening data management and analysis	Angelo Nuzzo
20706	A52	Genome-Wide Association Study of TB in the South African Colored Population: Comprehensive Gene and pathway-based Association Study	Emile RUGAMIKA CHIMUSA
20468	A54	Hunting cancer predisposition genes by whole exome sequencing in relatives from affected family	Tatiana Popova
20738	A55	deepBlockAlign: aligning profiles from short blocks of reads	Jan Gorodkin
20742	A56	Integrating network co-expression analysis and gene expression in the analysis of coronary artery disease GWAS: application to CARDIoGRAM data	Seraya Maouche
20711	A57	A Novel Algorithm for Identifying Non-canonical Splicing Regions Using RNA-Seq Data	Yongsheng Bai
20789	A59	Personalized Medicine for Cancer	Miguel García
20817	A62	Bioinformatics and Biodiversity: A holistic approach to enhancing drug discovery.	Negusse Kitaba
20824	A63	Finding locally disrupted RNA structure from SNPs	Jan Gorodkin
20827	A64	Heme Detoxification Protein: A promising antimalarial drug target.	Dedan Githae
20829	A65	Network Analysis and validation of gene expression profiling of salivary gland from human and mice with primary Sjögren’s syndrome	Hui Zhou
20850	A67	Candidate mutations for early-onset lung cancer by family genome sequencing	Evangelos Simeonidis
22182	A68	Improving the detection of deleterious mutations integrating the predictions four well-tested methods	Emidio Capriotti
20874	A72	Discovery of novel cancer pathway-activating genomic aberrations via a mutual information metric	Olga Botvinnik
20929	A74	Prediction of miRNA gene targets – a combined computational and experimental approach	Anastasis Oulas
22642	A77	Systematic Analysis of MicroRNAs Targeting the Androgen Receptor in Prostate Cancer Cells.	Pekka Kohonen
22696	A80	Robust and accurate data enrichment statistics via distribution function of sum of weights	Yi-Kuo Yu
22709	A81	Measuring the complexity of solving diseases	Raul Rodriguez-Esteban
22677	A82	Nonparametric Estimation of an Unknown Probability Distribution Using Maximum Likelihood and Bayesian Approaches	Alona Chubatiuk
22713	A83	Exploratory analysis of the structure and dynamics of healthy intestinal microbiota	Leo Lahti
22720	A85	Identification of secondary targets for clinically used anti-tubercular drugs through binding site similarities	Nagasuma Chandra
22727	A86	Re-visiting classification of HLA class-I molecules	Nagasuma Chandra
22731	A87	A molecular based subtyping in juvenile idiopathic arthritis	Margherita Squillario
20448	B2	Free energy and flexibility basis of SNP occurrence	Luciana Oliveira
20465	B3	Pipeline for the training of NMR chemical shift prediction models	Anna Katharina Dehof
20459	B4	Modeling of Actomyosin Interactions	Cynthia Prudence
20798	B5	Fitting Comparative Models to X-ray Data with Kino-Geometric Sampling	Henry van den Bedem
22690	B6	Insights to the Thrombospondin Signature Domain	Thomas Haschka
22679	B7	Universal patterns of protein-ligand interactions: Gaussian Mixture Model analyses on three dimensional structure of proteins in Protein Data Bank.	Kota Kasahara
22712	B9	Intrinsically disordered proteins/regions: an important factor in protein evolvability	Akinori Sarai
20229	C01	Mining the FDA’s Adverse Event Reporting System (AERS) for Pathway Risk	Mark Gosink
20354	C02	The use of virtual screening reveals a viral-like polymerase inhibitor, which complex with the M. perniciosa DNA polymerase	Bruno Andrade
20382	C03	Consensus docking method	Dariusz Plewczynski
20394	C04	Homology modeling and molecular docking studies of Mannosyl Transferase (pimB) in Mycobacterium tuberculosis	Karthik Maddi
20743	C06	Homology Modeling and Molecular Dynamics Simulation of N-acetylglucosamine fosfomutase (AGM1) from Moniliphothora perniciosa	Wagner Soares
20835	C07	EC-BLAST: A novel tool for searching similar enzymes based on chemical knowledge	Syed Asad Rahman
20864	C09	A systems approach to characterization of molecular targets of imaging agents	Ting Liu
20893	C10	Stereological 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
20267	D01	Characterization of a mannose-binding Insecticidal lectin gene from Allium sativum (Garlic)	Nusrah Afolabi-Balogun
20389	D04	Tools for comparative metagenome analysis	Kathrin Aßhauer
20485	D05	Identification of transcription factors and their correlation with the high diversity of Stramenopiles.	Francisco Buitrago
20644	D09	A new Perl toolkit for the detection and analysis of polymorphic loci and their application for bacterial typing	Ralf KOEBNIK
20705	D11	GECKO2: A software tool for de novo gene cluster detection	Katharina Jahn
20739	D12	Automated Segmentation of DNA Sequences	Brona Brejova
20772	D13	Antimicrobial Resistance and susceptility profiling of four pathogenic organisms using UV irradiation.	Olugbenga Taiwo
20790	D16	Protein sequences of the human genome compared to those of several model organisms	Edda Kloppmann
22649	D19	QuartetS: a fast and accurate program for large-scale orthology detection	Jaques Reifman
22681	D20	Computational analysis of metagenomes and metatranscriptomes: challenges and opportunities.	Larisa Kiseleva
22719	D22	Species-specific open chromatin has evidence of branch-specific selection.	Nathan Sheffield
22718	D23	Comparative Genomics for expression QTL	Steffen Möller
19914	E01	Seqcrawler – A cloud ready indexing platform	Olivier Sallou
19916	E02	Creating a Concept Map Interface to Visualize and Interpret a Comparative Effectiveness Data Model	David Fenstermacher
22615	E03	SolDB: A Database of Solanum lycopersicum and Solanum tuberosum Primers	Hassan Tariq
22627	E05	miRGator v2.0 and the construction of miRNA-disease network	Wankyu Kim
20209	E08	GWAS Central: an advanced database for the integration and comparative interrogation of genome-wide association study datasets	Sirisha Gollapudi
20220	E09	ISA tools: standard-compliant reporting and curation at the community level	Susanna-Assunta Sansone
20257	E10	DARNED (Database of RNA editing).	Pavel Baranov
20264	E11	Graph-based queries of Semantic-Web integrated biological data	Marco Moretto
20283	E12	TMPad: an integrated structural database for helix-packing folds in transmembrane proteins	Cheng-Wei Cheng
20293	E13	EBI Search: a new way to explore biology	Andrew Jenkinson
20355	E17	A web-based tool for functional investigation of microRNAs : miRGator v2.0	Wankyu Kim
20439	E20	Sierra: A simple LIMS system for small sequencing facilities	Simon Andrews
20457	E21	Soybean Knowledge Base (SoyKB) : A Web Resource for Soybean Translational Genomics	Trupti Joshi
20546	E23	easyDAS: Automatic creation of DAS servers	Bernat Gel Moreno
20554	E24	Wheat international sequence repository integrated with genomic and genetic data in GnpIS	Michael Alaux
20598	E26	Virtual Fly Brain 3D Interaction Tool	Nestor Milyaev
20611	E28	GenomeRNAi: A Phenotype Database for Large-scale RNAi Screens	Esther Schmidt
20638	E29	PROSITE: Enhancing the functional characterization of proteins	Nicolas Hulo
20643	E30	PHI-base 4.0: A Second Generation Pathogen-Host Interaction database	Jacek Grzebyta
20690	E32	Recent developments to the Ensembl website	Stephen Trevanion
20701	E33	The Bioinformatics Links Directory: A Community Curated Collection of Bioinformatics Links, Tools and Databases	Michelle Brazas
20722	E34	Structural Biology Knowledgebase: An Online Portal to Proteins, Functions, Methods, and More	Margaret Gabanyi
20347	E35	Development of a Small Portable Application for Plant DNA Barcoding	M Mehedi Hassan
20773	E36	MobiDB: a database of intrinsically disordered proteins	Tomas Di Domenico
20788	E39	Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis - The CAMERA Resource	Shulei Sun
22653	E40	Embryonic Stem Cell Database	Elena Nikolaeva
22628	E41	RiceXPro and Rice TOGO Browser: Integrated Databases for Rice Functional and Applied Genomics	Hajime Ohyanagi
22699	E42	SABIO-RK: Improvement of search capacities and user-friendliness	Renate Kania
22764	E45	Correlation between annotation in the human gene database H-InvDB	Katsuhiko Murakami
22766	E46	A Ruby API to query the Ensembl database for genomic features	Jan Aerts
20331	E47	Identifying knowledge contributors – motivating online sharing of research data	Gudmundur Thorisson
22620	F01	Multi-species integrative biclustering	Richard Bonneau
20273	F04	The Operonic Location of Auto-Transcriptional Repressors is Highly Conserved in Bacteria	Tal Pupko
20407	F07	Phylogenetic analysis of mapped sequence reads	Jean-François Dufayard
20418	F08	Transcriptomic and metabolomic investigation of thermal stress response through metabolic modulations in seagrasses	Jenny Gu
20421	F09	Positive Feedback and Tradeoff as Sources for Complexity in Social Interaction System	Tomoyuki Yamamoto
20538	F12	Distribution patterns of genomic elements in bacteria using genome linguistic methods.	Oliver Bezuidt
20668	F13	Gene expression evolution on the emergence of pathogenicity in Ascomycetes	Aminael Sanchez-Rodriguez
20630	F14	Incorporating protein structure into coevolution analysis reveals functional side chain interactions in ABC-C exporters	Attila Gulyas-Kovacs
22689	F17	A Phylogenetic Approach to Germline Methylome Reconstruction	Lars Feuerbach
22668	F18	Probabilistic reconstruction of protein interaction histories using a simple measure of interaction affinity.	Ryan Topping
22672	F20	TimeTree2: Species divergence times from molecular data	Sudhir Kumar
20648	F21	Identifying Patterns of Balancing Selection by Comparing the Bonobo, Chimpanzee and Human Genomes	Kay Prüfer
20691	F22	The Darwinian Tree Of Life In Light Of Horizontal Gene Transfer (Is Still Sound)	Adam Sardar
22171	G01	Large-Scale Computational Identification of Regulatory SNPs	Alberto Riva
20188	G03	Annotating New Genes: From In Silico Screening to Validations by Experiments	Shizuka Uchida
20349	G06	Mining of Transcriptome of a climacteric fruit species Diospyros kaki Thunb for functional genomics	Farzana Rahman
20451	G10	Human gene coexpression landscape and network: location of house-keeping and tissue-specific genes	Alberto Risueño
20526	G12	Genomes and Evolutionary Analysese of Robust Oil Production in Microalgae	Kang Ning
20577	G14	Analysis of protein functional sites encoding features	Irina Medvedeva
20660	G16	An open source library for miRNA target prediction with a novel comparative genomics approach	Charles Vejnar
20674	G17	From data to disease: Identification of genes with cell lineage specific expression in the human kidney	Casey Greene
20759	G22	Estimating differential expression of transcripts with RNA-seq by using Bayesian Inference	Peter Glaus
20785	G23	ARH-Seq: Alternative Splicing Robust Prediction by Entropy on RNA-Seq data	Axel Rasche
22726	G30	The Limpopo MAGE-TAB Parser	Tony Burdett
22728	G31	The Functional Genomics Software Suite	Tomasz Adamusiak
20834	G32	Novel Method for Removal of Sequence Biases in ChIp-seq Data	Joanna Raczynska
20472	H2	Improving the Accuracy of Automated Prokaryotic Gene Calling wih the Intergenic Region Scanner	Heather Kent
20484	H3	Computing the probability of RNA hairpin and multiloop formation	Peter Clote
20522	H4	A fast stochastic score based rank fusion method: application on miRNA target prediction	Debarka Sengupta
20189	I01	Integrated prediction of protein functions in Arabidopsis thaliana by Bayesian Markov Random Fields	Yiannis Kourmpetis
20346	I06	Nonparametric Approach to Analysis of Data-Rich Biological Problems	Tatiana TATARINOVA
20435	I08	Genome Scale Annotation Using Rosetta De Novo Structure Predictions	Kevin Drew
20548	I09	From next generation sequencing to knowledge: A case study of functional genomics annotation in prokaryotes	Carlos Prieto
20562	I10	Human annotation in Ensembl	Amonida Zadissa
20413	I11	Collaborative action between Spain and Austria to enhance the application of High Performance Computing to High throughput technologies	Noura Chelbat
20634	I12	CHIPEAN – CHIP Seq Peak Annotation	Agnes Hotz-Wagenblatt
20647	I13	Comprehensive Homeodomain Gene Annotation in Human and Mouse	Veronika Boychenko
20661	I14	APPRIS - Canonical Isoforms for the Human Genome	Michael Tress
20814	I18	Automated curation and assignment of massive DNA sequences	Duong Vu
20832	I19	Characterization of Long Noncoding RNAs	Andrea Tanzer
22691	I21	YGAP: the Yeast automatic Genome Annotation Pipeline	Estelle Proux Wera
22758	I22	A genome-wide, functional analysis of transcription initiation and promoter architecture in the budding yeast Saccharomyces cerevisiae	R. Taylor Raborn
22695	I23	Human transcriptome data in Ensembl	Thibaut Hourlier
20191	I24	Extending Metagenomic Functional Annotation Through Functional Inference	Gregory Vey
19928	J01	Microsoft Biology Initiative	Beatriz Diaz Acosta
19931	J02	NUPTs and NUMTs from algae to land plants - a genomic analysis in 12 different species	Noa Sela
20259	J03	Dissecting a massive parallel sequencing workflow for quantitative miRNA expression analysis	Raffaele Calogero
20284	J04	Boosting the Principle Component Analysis for explorative analysis of genome-wide expressions reveals a common developmental pattern in human and mouse datasets	Carlo Cannistraci
20400	J09	Rice-Map: a new-generation rice genome browser	Ge Gao
20440	J11	The immense genomic variability of human olfactory receptor genes	Tsviya Olender
20495	J16	Interactive Microbial Analysis and Visualization with GView and GView Server	Aaron Petkau
20541	J19	SARUMAN - Using GPU programming for short read mapping	Jochen Blom
20534	J20	Chipster genome browser: Smooth and interactive visualization of next generation sequencing data	Aleksi Kallio
20593	J22	Associating Chromatin Features with Gene Expression	Thomas Sakoparnig
20604	J23	Whole genome sequencing, assembly and annotation of the Saccharomyces cerevisiae strain CEN.PK 113-7D	Dick de Ridder
20607	J24	Genometa - Accurate, flexible and fast taxonomic assignment for ultra-short metagenomic reads	Colin Davenport
20619	J25	Comparing long maximal exact repeats in four human genome assemblies	Sara Garcia
20632	J26	Revealing multiple nucleotide polymorphysms and indels in homopolymeric regions in human exome data	Szilveszter Juhos
20650	J27	Double nucleotide polymorphisms in human pathogen Propionibacterium acnes strains	Krisztina Rigo
20672	J28	Detecting homogenous methylation-domains within whole genome methylation maps	Michael Hackenberg
20744	J30	Next generation sequencing and its application to study breast tumor subtypes	Krishna Kalari
20761	J31	Bayesian Evaluation of de novo Genome Assembly	Sergey Nikolenko
20783	J32	Extracting relationships from integrated functional genomics data with the Ontological Discovery Environment	Jeremy Jay
20822	J34	Role of Conserved 3’-UTR Cis-elements in the Regulation of Human MECP2 and MAPT Genes Involved in Mental Disorders	Joetsaroop Bagga
20833	J35	GARM - Genome Assembly, Reconciliation and Merging	Fidel Sanchez-Flores
20809	J38	A-Bruijn graph approach to de novo genome assembly	Mikhail Dvorkin
20878	J39	BLESS: mapping DNA double-strand breaks by next-generation sequencing	Maga Rowicka
20884	J41	Identifying the Dynamic States of the 3D Genome Organization	Andrzej Kudlicki
20811	J42	Instant-Seq - an integrated and fast Web-based program for analysis of (timecourse) ChIP-Seq data	Abhishek Mitra
20924	J43	Statistical Tests for Detecting Differential RNA-Transcript Expression from Read Counts	Philipp Drewe
22711	J45	Multi-Image Genome Viewer (MIG)	Stephen Taylor
22683	J47	Resource-Efficient de novo Assembly of Eukaryotic Genomes	Bryan Beresford-Smith
22667	J48	The SMALT Software for the Efficient and Accurate Alignment of DNA Sequencing Reads	Hannes Ponstingl
22743	J49	SeqGI: Sequence Read Enrichment at Genomic Intervals	Ines de Santiago
22752	J50	Genome3D: A viewer-model framework for integrating and visualizing multi-scale epigenomic information within a three-dimensional genome	Wenjin Zheng
19899	K1	Partial Purification of Cellulase obtained from Tomato (Lycopersicon lycopersicum Karst) Fruits deteriorated by Aspergillus flavus Linn	Adesola Ajayi
20291	K2	The EMBL-EBI User Survey	Jennifer Cham
20325	K3	Identification of NMR Resonances Using EM Algorithms	Martin Krone
20046	K4	In-silico analysis and prevention of Coksackie virus induced Insulin Dependent Diabetes Mellitus in human	Ambuj Kumar
20602	K5	The Hellenic Society for Computational Biology and Bioinformatics	Christos Ouzounis
20703	K6	A Need for Specific, Advanced Topic Bioinformatics Training: The Canadian Bioinformatics Workshop Series	Michelle Brazas
22656	K7	Spanish National Bioinformatics Institute (INB)	Allan Orozco
20049	L01	GENS2: a simulator for multiloci/whole-genome case-control studies with gene-environment interactions	Roberto Amato
22636	L02	Universal epitope prediction for class II MHC	Andrew Bordner
20336	L06	Characterization of compound gene regulation mechanisms	Reiko Tanaka
20380	L09	Unraveling protein-protein interactions by a semi-automated high-throughput platform	Dominik Mertens
20399	L10	Discovery of a 3D Motif Essential to LDLR-Protein Complexes: Application to docking prediction evaluation	Reyhaneh Esmaielbeiki
20420	L11	Coevolution and Predicted Solvent Accessibility	David Ochoa
20499	L13	On sequential conservation space of RNA-recognizing residues in protein sequences	Li Xue
20753	L14	Functional assessment of topological characterization using graphlet degrees in PPI networks	Marco Mina
20560	L15	SNP-SNP synergy discovery with SNPsyn	Tomaz Curk
20854	L16	RISEARCH: Fast RNA Interaction Search	Jan Gorodkin
22631	L17	Predicting conserved interactions and structures of two multiple alignments of RNA sequences.	Stefan Seemann
22682	L20	A novel ultra-fast comparison method for known and potential ligand-binding sites of proteins	Kentaro Tomii
22572	L21	New methods for finding common insertion sites and co-occurring common insertion sites in transposon- and virus-based genetic screens	Tracy Bergemann
22744	L23	An alternative approach to protein docking: Complexes via homology modeling	Ozlem Tastan Bishop
22619	M01	Fast and Efficient Dynamic Nested Effects Models	Holger Fröhlich
20035	M02	Prediction of bioluminescent proteins based on Discrete Wavelet Transform and Support Vector Machine	Krishna Kumar kandaswamy
22609	M03	A 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
20265	M04	R-value: A new measure for dataset evaluation	Sejong Oh
20321	M05	Transcription Regulation: models for combinatorial regulation and functional specificity	David Thomas
20343	M06	Contrasting the Molecular Basis of Human and Mouse Embryonic Stem Cell Self-Renewal Using Bayesian Network Machine Learning Methods	Karen Dowell
20350	M07	A new feature selection method based on classes overlap	Sejong Oh
20395	M08	Protein subnuclear localization using a spectrum kernel minimum distance probability method	Esteban Vegas
20409	M09	SVM-based prediction of granzyme B cleavage sites	Lawrence Wee
20425	M10	Genome-wide enhancer discovery from chromatin methylation marks using Genetic Algorithm-optimized Support Vector Machines	Michael Fernandez
20449	M11	Machine Learning Approaches to Identify and Characterize Effector Proteins in Pathogenic Bacteria	David Burstein
20576	M13	Assessment of protein interaction prediction from sequence data using n-gram analysis	Guray Kuzu
20575	M14	Model selection for predictive and prognostic gene signatures	Miika Ahdesmaki
20662	M16	Dealing with Uncertainty in Support Vector Machines Prediction	Sorin Draghici
20665	M17	Identification of SH2-peptide interactions using support vector machine	Kousik Kundu
20688	M18	A Support Vector Machine approach for rapid genome-wide epistasis detection	Barbara Rakitsch
20717	M19	Time series classifier model for miR-mRNA interaction	Jovan Rebolledo-Mendez
20719	M20	mTiM: margin-based transcript mapping from RNA-seq	Nico Görnitz
20855	M21	A Computational Paradigm for More Specific TFBS Detection	Heike Sichtig
20896	M22	Combined Approach to Anaphora Resolution for Disease-Determinants Ontology Learning from Web Sources	Jae-Hong Eom
20156	N01	Power and minimal sample size for multivariate analysis of microarrays	Maarten Iterson
20344	N05	caArray: make microarray data easily accessible and exchangeable	Xiaopeng Bian
20351	N06	A combination technique for microarray dataset to improve classification accuracy	Sejong Oh
20462	N09	ASPIRE: An improved tool for the analysis of alternative splicing using AltSplice microarrays	Melis Kayikci
20498	N10	Meta-analysis of gene expression microarrays with missing replicates	Fan Shi
20505	N12	Feature selection for specifying experimental conditions that activate gene transcriptions	Sho Ohsuga
20387	N13	A Method for Inference of Gene Regulatory Network based on Bayesian Network with Uniting of Partial Problems	Yukito Watanabe
20550	N15	Prediction of specific versus non-specific RBP-RNA interaction	Eleonora Kulberkyte
20561	N16	cn.FARMS: a latent variable model to detect copy number variations in microarray data with a low false discovery rate	Djork-Arné Clevert
20608	N18	COLOMBOS: Access Port for Cross-Platform Bacterial Expression Compendia	Kristof Engelen
20666	N24	Simulation strategies to evaluate the performance of pathway-based gene expression analysis methods	Shailesh Tripathi
20747	N25	Signaling Pathway Coupling Phenomena	Michele Donato
20699	N27	Alternative Splicing in Malignant Lymphoma	Karin Zimmermann
20823	N29	Flanking sequence effects on oligonucleotide hybridization	D. Andrew Carr
20872	N30	Elimination of spatial autocorrelation in microarray data	Sébastien Lemieux
22647	N31	A Computational Study of Carotenoid Gene Expression using Micro-array Data	Firdous Khan
22662	N32	A survey of batch effects in public gene expression data	Paul Pavlidis
22735	N36	Using R through a Tiki web interface to implement bioinformatics pipelines	Xavier Pedro Puente
22750	N37	Combining omics data and biological knowledge using multiple factor analysis	Jose Luis Mosquera
20287	O1	An integrated approach to the alignment and classification of 3D neuronal morphology in the Drosophila brain	chao-chun chuang
20569	O2	Effect of Leaky Channels in Calcium Homeostasis	Suhas Vasaikar
22618	P01	Benchmarking Ontologies: Bigger or Better?	Lixia Yao
20032	P03	A Modular Annotation Framework for Mathematical Models	Michael Cooling
20327	P04	An ontology of bioinformatics tool functions, data types and formats	Jon Ison
20328	P05	Multiple Ontology Based System for Integrating and Display Rat Phenotype Data	Mary Shimoyama
20473	P06	ontoCAT R package for ontologies traversal and search	Natalja Kurbatova
20527	P07	What does semantic similarity mean in terms of protein function comparison? The analysis of relation between functional and structural similarity.	Bogumil Konopka
20566	P08	A Semantic Web Infrastructure for Bioinformatics of Staphylococcus aureus	Cândida Delgado
20581	P09	A standard for cooperative interactions	Kim Van Roey
20801	P11	BioPAX – A Community Standard for Pathway Data Sharing	Nadia Anwar
20299	Q01	Signatures of positive selection on genes of the N-Glycosylation pathway concentrate on genes with regulatory positions	Giovanni Marco Dall'Olio
20417	Q03	cn.MOPS: Mixture of Poissons for Discovering Copy Number Variations in Next Generation Sequencing Data	Günter Klambauer
20490	Q04	Deep-sequencing reveals phage-driven diversification of Pseudomonas aerugionsa biofilms	Kerensa McElroy
20810	Q07	INRICH: improved enrichment testing method that integrates an unbiased GWAS strategy with prior biological knowledge: application to Type 2 diabetes	Phil Lee
20363	R01	Statistical approach to absolute protein quantification	Sarah Gerster
20633	R03	Chimeras knocking at the door	Milana Frenkel-Morgenstern
20676	R04	Bioinformatics for Proteomics: developing new tools for the analysis of experimental data	Angelo Facchiano
20707	R05	Predict subcellular localization for proteins in all kingdoms	Tatyana Goldberg
20637	R06	Quantitative mass spectrometry data based pathway analysis	Philipp Gormanns
20752	R08	PRIDE, the PRoteomics IDEntifications database	Johannes Griss
20756	R09	Lost Data – The Consequences of Changing Protein Accession	Johannes Griss
20768	R10	Proteomics based genome annotation using conceptually translated ESTs	Paul Blakeley
20825	R11	Data mining on a leukemia phosphoproteome dataset: insights on chemoresistant cell signaling	Renato Milani
22659	R12	Identification of protein expression dynamics during germination in Streptomyces	Eva Strakova
22748	R13	Tracing Evolutionary Events Over Ancestral Proteomes	Matt Oates
22767	R14	Viral proteins acquired from a host converge to simplified domain architectures	Nadav Rappoport
20174	S01	Gene Array Analyzer (GAA): Alternative usage of gene arrays to study alternative splicing events	Pascal Gellert
20271	S02	Cell specific gene expression from histome modifications and transcription factor binding	Thaís Rêgo
20311	S05	Induction of Effectors in Diuraphis noxia after Feeding on Preference and Non-preference Wheat Hosts	Nicolaas Burger
20370	S06	ConTra v2: a tool to identify transcription factor binding sites across species, update 2011	Stefan Broos
20535	S08	Unveiling combinatorial regulation through the combination of ChIP information and in silico cis-regulatory module detection	Kathleen Marchal
20542	S09	Transcriptional cross-regulation as survival mechanism in bacteria	Pieter Monsieurs
20558	S10	A probabilistic model for prediction of Transcription Start Regions in both intra- and inter-genic miRNAs	Annalisa Marsico
20587	S11	Analysis of the structure and evolutionary conservation of regulatory networks in prokaryotes.	Richard Münch
20657	S12	PRODORIC - a platform for the elucidation of gene regulatory networks in prokaryotes - from data to models	Richard Münch
20876	S14	Identifying CNVs of regulatory elements which impact overall survival in serous cystadenocarcinoma	Geoff Macintyre
20889	S16	Improved in silico regulatory SNP detection facilitates large scale SNP scanning	Geoff Macintyre
22737	S18	Identification of shortened 3’untranslated regions by Affymetrix genechip arrays	Loredana Martignetti
22757	S19	Integrative approach at building and analyzing gene regulatory networks	Julia Ponomarenko
20493	T1	A Framework for the Evaluation of Bioinformatics Methods	José M. Fernández
20612	T2	eBiomics: an e-Learning Environment on Bioinformatics for Life Scientists	Patrick Koks
20873	T3	Practical NGS Analysis: A Bioinformatician’s Perspective	Abhishek Pratap
20891	T4	A Review of Software for Visualization and Interpretation of Genome Wide Association Studies Results	Armita Zarnegar
22626	U03	Accurate quantification of transcriptome from RNA-Seq data by effective length normalization	Sanghyuk Lee
20183	U04	Application of whole genome resequencing to detect sequence polymorphisms underlying boar taint	Rahul Agarwal
20186	U05	High-throughput protein analysis in the cloud	Guy Yachdav
20197	U06	Evolutionary Conservation and Genetic Variability of Hepatitis C Virus Core Protein (HCVc)	Muhammad Ilyas
20256	U07	A method to separate function and fold specific residues in a protein.	Andrew Lynn
20298	U10	EMBOSS: EuropeanMolecular Biology Open Software Suite	Peter Rice
20383	U11	SKM: A String Kernel Motifs Classifier for Nucleic Acid and Protein Sequences	Hugh Shanahan
20392	U12	P-value based motif identification using positional weight matrices	Holger Hartmann
20450	U14	Toolbox for the analysis of Roche 454 Sequencing data	Christian Ruckert
20460	U15	Comrad: Detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data	Andrew McPherson
20470	U16	The Interlaboratory Robustness of Next-Generation Sequencing (IRON) Study	Hans-Ulrich Klein
20502	U20	Improved performance of sequence search algorithms in remote homology detection	Ramanathan Sowdhamini
20513	U21	New method of detecting pathogenic viruses using high-throughput sequencing data	Shumpei Ishikawa
20520	U22	Perfect Hamming Code as Hash key for Fast Genome Mapping	Yoichi Takenaka
20524	U24	fastapl -- a utility for versatile and easy processing of multifasta format data	Paul Horton
20539	U25	Behind the significance in NGS reads assembly	Antonio Muñoz
20559	U26	Computational Analysis of DNA Replicases in Double-Stranded DNA Viruses: Relationship with the Genome Size	Darius Kazlauskas
20565	U27	A novel miRNA prediction method based on next generation sequencing technology	Kui Qian
20580	U28	Sequence alignment of coiled coil proteins: adapting to restricted sequence variation	Michael Kuhn
20592	U29	Computational prediction of transposon insertion sites in bacterial genomes	Michael Steinert
20606	U30	Improving SNV calling sensitivity by probabilistically combining SNVs reported by different calling tools	Alejandro Balbin
20547	U31	Integrating Protein Domain Prediction in Multiple Sequence Alignment	Layal Al-Ait
20663	U32	A new algorithm for sequencing by hybridization based on non-classical approach	Marcin Radom
20682	U34	Computational challenges in the production and analysis of Illumina Genome Analyzer data	Martin Kircher
20685	U35	Simulating Quality and Depth of Sequence for Genotype Accuracy	Iain Bancarz
20730	U37	Using next-generation sequencing “dark matter” to identify a new transposable element location in the mouse genome.	James Cavalcoli
20750	U39	A Conditional Random Fields Model for RNA Conformation Sampling	Jinbo Xu
20763	U40	A new approach to suboptimal pairwise sequence alignment	Feng Lou
20758	U41	Support Vector Machines for finding deletions and short insertions using paired-end short reads	Dominik Grimm
20770	U42	A combination of amino acid composition and matching for conotoxin superfamily classification	Nazar Zaki
20781	U43	Ranking and filtering translocations in paired-end sequencing data using BLAT realignment	Christoph Bartenhagen
20808	U45	Distributed Web Services for Bioinformatics: Multiple Sequence Alignment	Peter Troshin
20806	U46	Pythoscape: A Software Framework for Generation of Large Protein Similarity Networks	Alan Barber
20596	U47	LaTcOm: A web server for visualizing rare codon clusters	Athina Theodosiou
20830	U48	SRS 3D - Integrating structures, sequences and annotations	Andrea Schafferhans
20680	U49	Multiobjective sequence alignment: Formulation and Algorithms	Maryam Abbasi
20838	U50	An improved RIP-Seq Toolkit to Reveal Genome-wide Exon Junction Complex Landscape	Alper Kucukural
20870	U54	Visualizing the next generation of sequencing data with GenomeView	Thomas Abeel
22643	U55	SlideSort: Fast and exact algorithm for Next Generation Sequencing data analysis	Kana Shimizu
22706	U56	Who & How: Investigating miRNA Regulation in Ranked Gene Lists using miRnaPursuit.	Teresa Colombo
22736	U60	Performing Functional Site Prediction on Protein Sequences Generated by De Novo Transcriptome Assembly	Chien-Yu Chen
22671	U61	MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods	Sudhir Kumar
22739	U62	Twenty-Five Fold Diversity Overestimation Revealed by Analyzing a MOCK Sample using 454 Amplicon Pyrosequencing	Sebastian Jünemann
22654	U64	ADDAPTS: A Data-Driven Automated Pipeline and Tracking System	Risha Narayan
20048	V1	P.R.E.S.S.--- An R-package for Exploring Residual-Level Protein Structural Statistics	Yuanyuan huang
22630	V2	DIBER: protein, dna or both?	Grzegorz Chojnowski
20736	V6	The Biochemical Algorithms Library (BALL) - Rapid Application Development in Structural Bioinformatics	Andreas Hildebrandt
20745	V7	SymD server: a platform for detecting internally symmetric protein structures	Chin-Hsien (Emily) Tai
19881	W01	A Time-Dependent Framework for Solving the Degeneracy Problem in RNA Secondary Structure Deleterious Mutation Prediction	Danny Barash
22613	W02	Correcting protein alignment errors using a novel multiple-template threading method	Jinbo Xu
22602	W03	All-atom knowledge-based potential for RNA structure prediction and assessment	Emidio Capriotti
22601	W04	A structural and dynamical model of human telomerase	Samuel Flores
20359	W05	Optimization of residual electrostatic environment to enhance protein thermal stability	Chi-Wen Lee
22616	W06	Complex networks govern coiled coil oligomerization - predicting and profiling by means of a machine learning approach	Ulrich Bodenhofer
22634	W08	The imprint of codons on protein structure	Charlotte Deane
20154	W09	PyRy3D: a software tool for modelling of large macromolecular complexes	Joanna Kasprzak
20177	W10	Planar shape representation based Protein function prediction	Heng Yang
20212	W12	MODORAMA - a web application for comparative protein structure modeling	Jan Kosinski
20275	W13	Mean Scaled RMSD: A Size Independent Measure For Superimposition of Protein Structures	Seyed Shahriar Arab
20286	W14	Probabilistic model for secondary structure prediction from protein chemical shifts	Martin Mechelke
20294	W15	Multi-LZerD: Multiple protein docking for asymmetric complexes	Juan Esquivel-Rodríguez
20297	W16	Modelling Protein Domain Binding to Kinase Structures altered by Phosphorylation	Christoph Gernert
20345	W17	Full atom comparative three-dimensional modeling of protein-DNA complexes	Francisco Melo
20352	W18	Identification of cavities on protein surface using multiple compu-tational approaches for drug binding site prediction	Bingding Huang
20364	W19	Physical contacts-based score for evaluation of protein three-dimensional models	Kliment Olechnovic
20373	W21	The influence of the local sequence environment on RNA loop structures	Dirk Walther
20402	W23	Peptides modulating conformational changes: From in silico design to preclinical proof of concept	Itamar Borukhov
20412	W24	Spritz: Intrinsic protein disorder prediction for genomes and insights into protein function.	Ian Walsh
20433	W26	Slip symmetry – a new type of symmetry in protein structures	Dukka KC
20474	W27	A multiple-template approach to protein threading	Jinbo Xu
20483	W28	A novel type of methyltransferase encoded by a conserved domain of GRAS	Magdalena Dymecka
20461	W29	Implementation of the Protein Fluorescence And Structural Toolkit (PFAST)	Cynthia Prudence
20504	W30	Maximal Use of Information Found in All Protein Structure Data	Armando Solis
20557	W33	Protein function prediction using clustering method of Protein-Protein Interaction network	Sejong Oh
20588	W34	Comprehensive study of HOX transcription factors DNA binding specificity	Katarzyna Kokoszynska
20597	W36	The MULTICOM Toolbox for Protein Structure Prediction	Jianlin Cheng
20601	W37	Comprehensive structure-to-function analysis of transcription factor IID (TFIID) complex	Maja Małkowska
20616	W38	Structure-based classification of the plant non-specific lipid transfer protein superfamily towards its functional characterization	Cécile Fleury
20635	W39	A comparative study on filtering protein secondary structure prediction	Chris Christodoulou
20645	W40	firestar in 2011	Michael Tress
20675	W42	BOCTOPUS: Topology prediction of Transmembrane beta barrel proteins	Sikander Hayat
20679	W43	Analysis of Functional Islands using Structural Clustering	Anne-Christin Hauschild
20712	W45	Predicting the 3d DNA structure of the human genome	Sven Bilke
20734	W46	Binding Ligand Prediction by Comparing Local Surface Patches of Potential Pocket Regions	Daisuke Kihara
20764	W48	ProBiS: A web server for detection of structurally similar protein binding sites	Janez Konc
20478	W49	Protein conformational movements modeling based on the average action principle	Alexander Krass
20767	W50	Evaluation of transmembrane helix (TMH) packing prediction methods on successive in sequence TMHs	Vasilis Promponas
20792	W52	Are Protein Disordered Regions Equal to Loops?	Esmeralda Vicedo
20695	W53	Environment Specific Substitution Tables Improve Membrane Protein Alignment	Jamie Hill
20819	W54	Quality or Quantity of Structural Dynamics Information: That is the Question! (when improving performance of structure-based function prediction methods)	Dariya Glazer
20837	W55	Nearest-Neighbor Approaches to Predict Protein Function by Sequence Homology Alone	Tobias Hamp
20578	W58	Is the biological hydrophobicity scale correct?	Christoph Peters
20892	W60	A comprehensive review of protein fold space and the correlation of structure with function	Spencer Bliven
20897	W61	Protein interaction partners revealed by their dynamical properties	Jau-Ji Lin
22693	W65	Is It Biologically Relevant? An Evolutionary Method for Distinguishing Biological Interfaces from Crystal Contacts	Guido Capitani
22670	W66	SAHG, a comprehensive database of annotated structure models for human proteins	Chie Motono
22721	W67	Training bidirectional recurrent neural networks with Conjugate gradient-type algorithms for protein secondary structure prediction	Chris Christodoulou
22759	W68	Protein Sequence Design Using Ensemble-Based Energetic Information	James Wrabl
22761	W69	Predicting Functions of the Universal Stress Proteins in Metabolically Versatile Rhodopseudomonas palustris	Shaneka Simmons
22663	W70	The Impact of Multifunctional Genes on "Guilt by Association" Analysis	Jesse Gillis
22717	W71	Understanding protein-protein interactions: Efficient classification of physiological and non-physiological protein complexes and unexpected conservation in interaction interfaces	Dmitry Korkin
20622	W72	Protein Structural Domain Assignment Using Delaunay Tessellation	Todd Taylor
19952	X01	A regulatory network model of CD4+ lymphocytes	Luis Mendoza
20054	X03	ALISSA-An Automated Live Cell Imaging System for Signal Transduction Analyses	Heinrich Huber
22605	X04	Interactive, multiscale navigation of large and complicated biological networks	Thanet Praneenararat
22637	X05	Finding out what happened -- Highlighting the essence of a biological experiment	Georg Fuellen
22639	X06	Topological network alignment uncovers biological function and phylogeny	Natasa Przulj
20159	X07	Inferring the role of alternative splicing on biological pathways: Studies using cancer transcriprome data	Murlidharan Nair
20258	X08	Genetic Design Through Branch and Bound	Dennis Egen
20276	X09	Bridging clinical knowledge to molecular events through integration of imaging biomarkers and protein interactions in Alzheimer’s disease	Erfan Younesi
20281	X10	Network-based approach towards candidate gene prioritisation using TargetMine	Lokesh Tripathi
20285	X11	Integrated cell cycle and DNA repair signalling network modelling for identification of key molecular regulators in basal-like breast cancer	Inna Kuperstein
20292	X12	An interface analysis of human E2-E3 complexes: structural insights into specificity	Gozde Kar
20296	X13	How little do we actually know? – Towards the size of gene regulatory networks.	Richard Röttger
20367	X16	A Directed Graphical Gaussian Model for Inferring Gene Regulatory Networks	Tomoshige Ohno
20368	X18	Fast and Efficient Dynamic Nested Effects Models	Holger Fröhlich
20378	X20	bioCompendium: high-throughput experimental data analysis platform	Venkata Satagopam
20424	X22	Detection of nonlinear effects in gene expression pathways	Andreas Mayr
20434	X23	Network topology complements sequence as a source of biological information	Tijana Milenkovic
20436	X24	Understanding temporal patterns in cell cycle regulation through visualization	Maria Secrier
20444	X25	From WIPA (Web Interface Protein Atlas) to Systems Biology Analysis of Protein Atlas Tissue Microarrays (TMAs)	Hans-Juergen Thiesen
20341	X27	Mapping Genetic Interactions in Various Contexts Provides Complementary Information	Magali Michaut
20496	X30	Construction of a drug-target-disease network and its application to drug repositioning and mode of action analysis	Charny Park
20511	X31	Finding sets of shortest elementary flux modes that decompose genome-scale metabolic flux distributions	Siu Hung Joshua Chan
20521	X34	Different regulatory networks of SOX2 in embryonic and neural stem cells	Sanghyuk Lee
20528	X35	Interspecies translation of disease networks increases robustness and predictive accuracy	Yahya Anvar
20553	X38	An Integrated Approach To Identify Human MicroRNA-Targets.	Kim Wan Kyu
20582	X42	Cholesterol-Responsive Gene Network Reconstruction from Hypercholesterolemic Mice Transcriptome Data	Gustavo Hime
20477	X47	Integrated Inference and Analysis of Regulatory Networks Using Multi-level Measurements	Christopher Poultney
20651	X49	Topological features predict misannotations in metabolic network	Rodrigo Liberal
20654	X51	Candidate gene prediction using integrative and network-based approaches - Mining Pig QTL	Keywan Hassani-Pak
20673	X52	Organizational structure of the peripheral gene regulatory network in B-cell lymphoma	Ricardo de Matos Simoes
20713	X56	A Novel Reverse Engineering Method for Gene/Protein Network Reconstruction - Divergence Weighted Independence Graphs	Yang Xiang
20714	X57	Joint Dynamic Networks of miRNA and Transcripton Factor Regulation	Marcel Schulz
20740	X58	KeyPathwayMiner - Detecting case-specific biological pathways by using expression data	Hande Kucuk
20749	X59	Finding Consistent Explanations for Observations from Genome-Wide Mutant Assays	Deborah Chasman
20786	X61	Delineating signaling network from cancer related pathways	Chandrajit Lahiri
20796	X63	A network topology-based machine learning approach to extract relevant cancer-related signaling subnetworks	Marcio Acencio
20802	X65	HotRegion: A web server of cooperative hot spots	Engin Cukuroglu
20803	X66	GraphCrunch 2 Network Analysis Tool and MI-GRAAL Network Aligner	Natasa Przulj
20804	X67	Minimum Curvilinearity to address high-throughput protein-protein interaction experiments	Gregorio Alanis-Lobato
20828	X69	Aligning multiple time-series experiments to learn regulatory models: An application to modeling the core network in stem cell differentiation	Irene Ong
20841	X70	Structural Analysis of Correlation Networks in Bioinformatics: Graph Theoretic Substructures and the Corresponding Cellular Functions	Kathryn Dempsey
20863	X71	Systematic, comparative network analysis related to human disease	Serene Wong
20871	X72	Systematically mapping the druggable pathways of Saccharomyces cerevisiae	Kristen Fortney
20868	X73	Global gene network alignment among species by using graph summarization	Aika Terada
20851	X74	A systems approach to learning the regulatory network of T helper-17 differentiation	Aviv Madar
20880	X76	Modeling the Spatiotemporal Pattern of Gene Expression During Somitogenesis with Maximum Entropy Deconvolution.	Andrzej Kudlicki
20848	X77	Characterization of transcription factor and microRNA regulatory networks involved in myelination	Li-Wei Chang
20931	X78	Extending the Yeast Metabolic Network Using Integrated System Biology Approach	Paul Fisher
22658	X79	An Epistatic Profile of the Cell Envelope Biogenesis in Escherichia coli Evidences Extensive Genetic and Functional Crosstalk Between Processes	Juan Diaz-Mejia
22686	X84	Correction for ascertainment bias in S. cerevisiae interactions: an insight	Jonathan Dickerson
22688	X85	Using community structure for complex network layout	Oliver Duerr
22722	X86	Quantifying the Response of a Biological System using Network Perturbation Amplitudes	Sam Ansari
22741	X88	Causal Reasoning on Biological Networks: Interpreting transcriptional changes	Daniel Ziemek
22760	X91	A multi-level Bayesian model for identifying predictive combinations of signaling network modules, proteins, and phosphopeptides for cancer treatments	Ann Chen
22646	X94	Generative Probabilistic Models for Protein-Protein Interaction Networks – The Biclique Perspective	Regev Schweiger
22607	Y01	Biomedical Natural Language figure Processing for Intelligent Figure Search	Hong Yu
20365	Y04	ANDCell-ANDVisio system: knowledge extraction using text-mining in the systems biology	Pavel Demenkov
20366	Y05	Self-Training Improves Robustness of Protein-Protein Interaction Extraction from Text	Philippe Thomas
20385	Y06	Extraction of protein cellular localization using the Locminer text mining system	Martin Krallinger
20438	Y07	Reflect: a browser plugin for life scientist	Janos Binder
20573	Y08	Biomedical text mining from multiple views: information fusion and vertical	xinhai Liu
20677	Y09	Keyword Clustering in Biomedical Information Retrieval Using Evolutionary Algorithms	Viktoria Dorfer
20715	Y10	Automating host-pathogen interaction discovery: an HIV case study	Daniel Jamieson
20754	Y11	Relation-mining workflows to extract animal host-microorganism interactions in free text	BalaKrishna Kolluru
22747	Y12	Overview of the second CALBC Challenge	Senay Kafkas
22751	Y13	An exercise in kidney factomics: From article titles to RDF Knowledgebase	James Eales
22622	Z01	BOOST: A Boolean Representation-based Method for Detecting SNP-SNP Interactions in Genome-wide Association Studies	Xiang Wan
22573	Z02	Linguistic analysis of genomic islands reveals a recent acquisition of genetic materials by Mycobacterium tuberculosis from alpha-Proteobacteria	Oleg Reva
22562	Z07	Structural Biology Meets Systems Biology: A Structural Systems Biology Approach for Gauging the Systemic Effect of Single Nucleotide Polymorphisms	Tammy Cheng
22560	Z08	In silico prediction of the calpain degradome	Lawrence Wee
22559	Z09	A scalable signaling map identifies cross-talk between gene modules inferred from multi-parametric RNAi phenotypes	Xin Wang
22557	Z11	PINALOG: a novel approach to align protein interaction networks – implications for function prediction and complex detection	Hang Phan
22553	Z14	Comparing nucleotide-based and codon-based alignment of human next-gen sequencing exome data	Szilveszter Juhos
22575	Z15	RIBER and DIBER: a software suite for crystal content analysis in the studies of protein-nucleic acid complexes.	Grzegorz Chojnowski
22576	Z16	SpliceGrapher: Predicting Splice Graphs from Diverse Evidence	Asa Ben-Hur
22578	Z17	Topological features predict misannotations in metabolic networks	Rodrigo Liberal
22579	Z18	A Theoretical Approach to Identify Indispensable Proteins of the Type III Secretion Systems of Salmonella enterica Serovar Typhimurium Strain LT2	Chandrajit Lahiri
22583	Z19	Analysis of bacterial genes with disrupted ORFs reveals frequent utilization of Programmed Ribosomal Frameshifting (PRF) and Programmed Transcriptional Realignment (PTR).	Pavel Baranov
22584	Z20	An Event-driven Approach to Study Operon Evolution	Iddo Friedberg
22586	Z21	RTA and MultiRTA: Simple yet Accurate Methods for Predicting Class II MHC Epitopes	Andrew Bordner
22587	Z22	Metagenomic Biomarker Discovery and Explanation	Curtis Huttenhower
22585	Z25	RDyNet: bridging functional analyses and network visualization	Mauro Alves Castro
22593	Z26	Modulators of microRNA Activity Regulate Glioblastoma Pathogenesis	Xuerui Yang
22599	Z27	Scalable metabolic reconstruction for metagenomic data and the human microbiome	Curtis Huttenhower
22600	Z28	Systems-level insights from modular decomposition of the yeast genetic interaction network	Jeremy Bellay
22592	Z29	Large scale merging of microarrays. From curation to meta-curation	Colin Molter
20312	Z30	INBIOMEDvision: Promoting and Monitoring Biomedical Informatics in Europe	Victoria López Alonso
20525	Z31	Conveyor - A strong type workflow library	Burkhard Linke
20591	Z32	New types of services in Mobyle 1.0	Herve Menager
20620	Z33	An integrated core facility to go from biology to data and answers	Laurent Gautier
20888	Z34	Toward Genomic Data Sharing Directly at the Lab Site in the New Agent-Based Infrastructure OpenKnowledge	Dietlind Gerloff
22608	Z35	New tools for RNA 3D structure modeling: inspirations from the protein world	Janusz Bujnicki
22604	Z36	REPAIRtoire - a database of DNA repair pathways.	Kaja Milanowska
22603	Z37	FABIA: Factor Analysis for Bicluster Acquisition	Djork-Arné Clevert
22621	Z38	Malaria Endemicity among Pregnant Women in Urban and Semi-Urban Area in Southwest, Nigeria	Tony Ojiezeh
22641	Z39	Strengths and limitations of the federal guidance on synthetic DNA	Jean Peccoud
22701	Z41	Extraction protocol optimization for the LC-MS based global metabolite profiling of grapes	Matthias Scholz
22666	Z43	Jalview 2.7	James Procter
22753	Z52	The reference species tree of (sequenced) life	Julian Gough

LBR

LBR01	Milana Frenkel-Morgenstern	Potential function of proteins encoded by chimeric transcripts	Sunday, July 17 10:45 a.m. - 11:10 a.m.
LBR04	David Gfeller	The multiple Specificity Landscape of Peptide Recognition Domains	Sunday, July 17 4:00 p.m. - 4:25 p.m.
LBR06	Yinyin Yuan	Quantitative analysis of cellular composition in primary breast tumours deconvolutes molecular signatures and elucidates impact of tumour microenvironment	Sunday, July 17 3:00 p.m. - 3:25 p.m.
LBR08	Wei-Jen Chung	Post-transcriptional regulators of microRNA biogenesis regulate pathogenesis of cancer	Sunday, July 17 4:00 p.m. - 4:25 p.m.
LBR10	Tamir Tuller	A Comprehensive Computational Model for Analyzing Gene Translation	Monday, July 18 11:15 a.m. - 11:40 a.m.
LBR11	Ana Conesa	Differential expression with RNA-seq: a matter of Depth	Monday, July 18 11:45 a.m. - 12:10 p.m.
LBR12	Van Anh Huynh-Thu	Inferring Gene Regulatory Networks from Expression Data using Tree-based Methods	Monday, July 18 12:15 p.m. - 12:40 p.m.
LBR14	Pavel Baranov	Analysis 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.
LBR15	Nicola Segata	Metagenomic Biomarker Discovery and Explanation	Monday, July 18 3:30 p.m. - 3:55 p.m.
LBR17	Egor Dolzhenko	STAGR: Software To Annotate Genome Rearrangement	Tuesday, July 19 10:45 a.m. - 11:10 a.m.
LBR21	Roman Briskine	Co-expression network analysis reveals rewiring of maize transcriptome by domestication	Tuesday, July 19 2:30 p.m. - 2:55 p.m.

Tech Track

TT01	Michael Schuster	Ensembl Genome Browser: Harnessing the Next Generation Sequencing Wave	Sunday, July 17 10:45 a.m. - 11:10 a.m.
TT02	Fan 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.
TT03	Rachel Harte	UCSC Genome Browser: Visualization tools for high-throughput sequencing	Sunday, July 17 11:15 a.m. - 11:40 a.m.
TT04	Michael Reich	GenomeSpace	Sunday, July 17 11:15 a.m. - 11:40 a.m.
TT06	Hienke Sminia	Bioinformatics@school	Sunday, July 17 11:45 a.m. - 12:10 p.m.
TT07	Zhong Li	Supporting Inter-connected Biomedical Open-source Software	Sunday, July 17 12:15 p.m. - 12:40 p.m.
TT08	Sanghyuk Lee	MONGKIE: Modular Network Generation and Visualization Platform with Knowledge Integration Environment	Sunday, July 17 2:30 p.m. - 3:25 p.m.
TT09	Attila Berces	Cloud Computing for Computational Biology	Sunday, July 17 2:30 p.m. - 2:55 p.m.
TT11	George 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.
TT13	Scott Markel, Ruth Dunn	Analyzing Next Gen Sequencing Data with Pipeline Pilot	Monday, July 18 10:45 a.m. - 11:40 a.m.
TT14	Janez Konc	ProBiS: a web server for detection of protein binding sites	Monday, July 18 10:45 a.m. - 11:10 a.m.
TT15	Katy Wolstencroft	RightField: The Semantic Annotation of Experimental Data using Spreadsheets	Monday, July 18 10:45 a.m. - 11:10 a.m.
TT16	Jo McEntyre	UK PubMed Central: a database of life science research articles.	Monday, July 18 11:15 a.m. - 11:40 a.m.
TT17	Paul 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.
TT18	Irina Dalah	GeneCards: The Human Gene ReSearcher	Monday, July 18 11:45 a.m. - 12:10 p.m.
TT19	Elissa Chesler	Integrating Heterogeneous Data using the Ontological Discovery Environment	Monday, July 18 11:45 a.m. - 12:10 p.m.
TT22	Julian Gough	SUPERFAMILY	Monday, July 18 12:15 p.m. - 12:40 p.m.
TT23	Kostas Karasavvas	Enacting Taverna Workflows through Galaxy	Monday, July 18 12:15 p.m. - 12:40 p.m.
TT24	Peter Rice	EMBOSS: New developments and extended data access	Monday, July 18 2:30 p.m. - 2:55 p.m.
TT25	Guy Yachdav	PredictProtein sequence analysis in the cloud	Monday, July 18 2:30 p.m. - 2:55 p.m.
TT26	Peter 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.
TT27	Allan Orozco	The Spanish National Bioinformatics Institute (INB)	Monday, July 18 3:00 p.m. - 3:25 p.m.
TT28	Michael Remmert	HHblits: Lightning-fast iterative sequence searching by HMM-HMM comparison	Monday, July 18 3:00 p.m. - 3:25 p.m.
TT30	Mickael Goujon	Using the EMBL-EBI services through the JDispatcher framework	Monday, July 18 3:30 p.m. - 3:55 p.m.
TT31	Eija 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.
TT32	Esther Schmidt	GenomeRNAi: A Phenotype Database for Large-scale RNAi Screens	Monday, July 18 3:30 p.m. - 3:55 p.m.
TT33	Mickael Goujon	EBI Search: a new way to explore biology	Monday, July 18 4:00 p.m. - 4:25 p.m.
TT34	Ray Fergerson	Introduction to National Center for Biomedical Ontology (NCBO) Technology	Monday, July 18 4:00 p.m. - 4:25 p.m.
TT35	Jean Peccoud	GenoCAD: A Web-Based Open Source Application to Design Synthetic DNA Molecules	Tuesday, July 19 3:00 p.m. - 3:25 p.m.
TT36	Benoit Bely	Overview of The Universal Protein Resource (UniProt)	Tuesday, July 19 10:45 a.m. - 11:10 a.m.
TT37	Daniel Blankenberg	NGS Best Practices through Galaxy: Cloud-based variant discovery with visual analytics	Tuesday, July 19 10:45 a.m. - 11:10 a.m.
TT39	Jinbo 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.
TT40	Matthew Bellgard	YABI: A sophisticated Internet-based cross–omics analytic environment	Tuesday, July 19 11:15 a.m. - 11:40 a.m.
TT41	Desmond Higgins	Clustal Omega for Protein Multiple Sequence Alignment	Tuesday, July 19 11:15 a.m. - 11:40 a.m.
TT42	Craig McAnulla	Introducing InterProScan 5	Tuesday, July 19 11:45 a.m. - 12:10 p.m.
TT43	Matus Kalas	EDAM ontology and BioXSD: The unifying semantics and syntax for bioinformatics tools	Tuesday, July 19 11:45 a.m. - 12:10 p.m.
TT44	Seán O'Donoghue	Killer App Award	Tuesday, July 19 11:45 a.m. - 12:40 p.m.
TT45	Shulei Sun	CAMERA: Metagenomic Resources and Tools	Tuesday, July 19 12:15 p.m. - 12:40 p.m.
TT46	Keywan 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.
TT47	Fady Mohareb	SORF, a web application for heterogeneous data management and visualisation	Tuesday, July 19 2:30 p.m. - 2:55 p.m.
TT49	Patricia Whetzel	NCBO Web Services and Development of Semantic Applications	Tuesday, July 19 2:30 p.m. - 2:55 p.m.
TT50	Arek Kasprzyk	OncoPortal, a data management and analysis framework for cancer research	Tuesday, July 19 2:30 p.m. - 2:55 p.m.
TT51	Peter Karp	Recent Developments in the Pathway Tools Software and BioCyc Databases	Tuesday, July 19 3:00 p.m. - 3:25 p.m.
TT52	Pål Puntervoll	eSysbio - an online system for interdisciplinary life science research	Tuesday, July 19 3:00 p.m. - 3:25 p.m.
TT54	Junjun Zhang	BioMart: A data federation framework for large collaborative projects	Tuesday, July 19 3:00 p.m. - 3:25 p.m.
TT55	Rajarajan Swaminathan	Database on Potential “Antibiotics” From Flowering Plants	Tuesday, July 19 3:30 p.m. - 3:55 p.m.
TT56	Geoffrey Barton	Jalview 2.7	Tuesday, July 19 3:30 p.m. - 3:55 p.m.
TT57	Claire O'Donovan	The International Society for Biocuration and the efforts of its members	Tuesday, July 19 3:30 p.m. - 3:55 p.m.
TT58	Nicolas Alcaraz	KeyPathwayMiner - Detecting case-specific biological pathways by using expression data	Tuesday, July 19 4:00 p.m. - 4:25 p.m.
TT59	Jeremy 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.