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Session A
Session B
- A06 A Computational Homology Analysis of CGH Data Finds Recurrent Genomic Instability in Older Breast Cancer Patients
Daniel DeWoskin, Catherine Park and Javier Arsuaga - A07 A Web Server for the Ancestral Genome Reconstruction
Abdoulaye Banire Diallo, Vladimir Makarenkov and Mathieu Blanchette - A08 Platform for Accurate Semi-Automatic Inference of Regulons by Comparative Genomics Approach
Pavel Novichkov, Elena Stavrovskaya, Mikhail Gelfand, Andrey Mironov, Inna Dubchak and Dmitry Rodionov - A09 Relations for Array CGH and Gene Expression datasets
Mira Oh - A10 Optimization of Segmentation for Large-scale array-CGH data
Mira Oh and Cheeyoun Roh - A11 A Web-Based Software System for Dynamic Gene Cluster Comparison across Multiple Genomes
Kashi Revanna, Vivek Krishnakumar and Qunfeng Dong - A12 An Application for Phylogeny and Alignment Reconstruction, from the Locus to the Genome Level
Andres Varon, Le Sy Vinh and Ward Wheeler - A13 Identification of Hot Spots and Cold Regions in Drosophila Genome and Reconstruction of the Ancestral Gene Order
Marcin von Grotthuss, Michael Ashburner and Jose M. Ranz - A14 Learning by Knowledge Transfer Between Organisms
Christian Widmer, Gabriele Schweikert, Bernhard Scholkopf and Gunnar Raetsch
- A15 Effects of Sampling Rate and Time Duration for Noisy Time Series with Application to Microarray Experiment
Lingling An, Fei Peng and James Lu - A16 Exploring Transcription Patterns in Arabidopsis thaliana
Vishal Bahirwani and Doina Caragea - A17 Comprehensive Solexa Based Annotation of Alternatively Spliced Transcripts in Drosophila melanogaster Male, Female, and tra Mutant Transcriptomes
Joseph Dunham, Frances Sung, Joyce Kao, Mazin Elhadary, Michelle Arbeitman and Sergey Nuzhdin - A18 Bayesian Infinite Mixture Models to Uncover Differential Co-Expression in Microarray Data
Johannes Freudenberg, Siva Sivaganesan and Mario Medvedovic - A19 Small-Module-Targeting (SMT) Coexpression: Prioritizing Gene and Module Specific Coexpressions by Accounting for Expression Heterogeneity
Nick Furlotte, Hyun Kang, Chun Ye and Eleazar Eskin - A20 Overlapping Splicing Regulatory Motifs: Two are Better than One
Amir Goren, Eddo Kim, Maayan Amit and Gil Ast - A21 Seeking the Common Ground: Regulation of Retrotransposed Genes in the Drosophila Genus
Lan Hu, Daniel Segre and Temple Smith - A22 Modeling Position Dependencies in Cis-regulatory Elements by Consensus Constraints
Hongshan Jiang, Wenguang Chen, Xuegong Zhang, Zhaocheng Fan and Weimin Zheng - A23 Computational Analysis System for Nuclear Hormone Receptors Based on Liver-Specific Expression Data
Ki-Bong Kim and Kyumyung Hwang - A24 Alignment and Classification of Time Series Gene Expression in Idiopathic Pulmonary Fibrosis
Tien-ho Lin, Jose D. Herazo, Kazuhisa Konishi, Naftali Kaminski and Ziv Bar-Joseph - A25 Significance Analysis of Gene Co-Expression Clusters
Marta Luksza, Michael Lassig and Johannes Berg - A26 Biothreat Detection by Pseudo-Random Oligomer-Based Microarray
Mojdeh Mohtashemi, Haley Smith, Felicia Sutton, David Walburger and James Diggans - A27 Prediction of Regulatory DNA Elements Involved in Human Embryonic Heart Development
Leelavati Narlikar, Noboru Sakabe, Alexander Blanski, Marcelo Nobrega and Ivan Ovcharenko - A28 A Novel Multiple Motif Scanning Algorithm Created to Identify Putative Methyltransferases
Tanya Petrossian and Steve Clarke - A29 Dissecting Transcriptional Deregulation between Different Cellular Conditions
Ewa Szczurek, Florian Markowetz, Irit Gat-Viks and Martin Vingron - A30 Binding Specificity of Zfx Transcription Factor: A Flexible Binding Signature, Not a Motif
Anahita Tafvizi, Jose Galan-Caridad, Boris Reizis and Leonid Mirny - A31 The CYRENE Project: A cis-Lexicon and a cis-Browser for Gene Regulatory Systems and Networks
Ryan Tarpine, Eric Davidson and Sorin Istrail - A32 An Ensemble Model of Competitive Multi-factor Binding of the Genome
Todd Wasson and Alexander Hartemink - A33 Non-Coding Transcripts Arise from Intrinsic Bidirectional Transcription
Ben Wilson, Debrah Thompson, Jason Slepicka, Roy Parker and Joanna Masel - A34 LSA: A Web Service for Local Similarity Analysis of Time Sequence Data
Li Xia
- A35 Fault Tolerance in Protein Interaction Networks: Stable Bipartite Subgraphs and Redundant Pathways
Arthur Brady, Kyle Maxwell, Noah Daniels and Lenore Cowen - A36 Incorporating Protein Flexibility in Predicting Free Energies of Association for Protein-protein Interactions
Hetunandan Kamisetty, Chris Bailey-Kellogg and Christopher Langmead - A37 An Interactive Environment for Visualizing, Interpreting, and Revising Biological Process Models
Pat Langley, Richard Chimera and David Stracuzzi - A38 Taking a Walk on the Loci: Simultaneous Gene Prioritization in Multiple Loci using Networks
Sonia Leach and Yves Moreau - A39 Probabilistic Approximations of Bio-pathway Dynamics
Bing Liu, David Hsu and P.S. Thiagarajan - A40 Generally Applicable Gene Set Enrichment (GAGE) and Pathway Analysis
Weijun Luo, Michael Friedman, Kerby Shedden, Kurt Hankenson and Peter Woolf - A41 Local Connectivity Patterns Improve Missing Link Prediction in Biological Networks
Victor Missirian and Vladimir Filkov - A42 Identifying Genetic Interactions with Sparse Hidden Factors
Leopold Parts, Oliver Stegle, John Winn and Richard Durbin
- A43 Algorithm to Improve Gene Consistency Across Bacterial Genomes
Judith D. Cohn, John Dunbar and Michael E. Wall - A44 Bioinformatics Workflows for Data and Tool Integration
Dominique Gorse, David Wood, Mhairi Marshall, Nick Rhodes and Jeremy Barker - A45 Optimal in silico Target Gene Deletion through Nonlinear Programming for Genetic Engineering
Chung-Chien Hong and Mingzhou (Joe) Song - A46 Using Side Knowledge to Design More Powerful Multiple Hypothesis Testing Procedures for Microarray Data
Peter Huggins - A47 Systematic Characterization of Gene Fusion Transcripts by using Information from the Express Sequence Tag Database
HoJoon Lee, Jose Cano-Buendia, Kristen Day, Patricia Carrigan, Phillip Stafford, Kathryn Sykes and Stephen Johnston - A48 Cluster and Compare Very Large Metagenomes
Weizhong Li - A49 Genomics Portals: Integrative Data Analysis Tool
Mukta Phatak, Kaustubh Shinde and Mario Medvedovic - A50 Comparative Analyses of Membrane Transporters from Global Ocean Sampling Metagenomic Samples
Qinghu Ren and Shibu Yooseph - A51 A Method for Detection of Functional Overlapping Genes
Niv Sabath and Dan Graur - A52 Design of Microarray Probes for the Identification of Groups of Related Pathogens
Ravi Vijaya Satya, Kamal Kumar, Nela Zavaljevski and Jaques Reifman - A53 mGene: Accurate Gene-finding with Discriminative Methods
Gabriele Schweikert and Gunnar Ratsch - A54 ConsensusCluster: A Software Tool for Unsupervised Cluster Discovery in Numerical Data
Michael Seiler, Gabriela Alexe, Chris Huang, Shridar Ganesan, Sandor Szalma and Gyan Bhanot - A55 Biclustering of High-Throughput Data with Frequent Itemset Approach
Akdes Serin and Martin Vingron - A56 Error-Correction Coding Theory of DNA Repair
Bane Vasic, David Galbraith, Shashi Kiran Chilappagari and Michael Marcellin - A57 Predicting Potentiators of Antibiotic Sensitivity Among Potential Gene Targets: A Classification Approach
Michael Molla
- B01 De-novo Assembly using Illumina Genome Analyzer Data
Markus Bauer, Ole Schulz-Trieglaff, Michael Eberle, Nan Leng, David Williamson, Anthony Cox and Dirk Evers - B02 Parametric Complexity of Sequence Assembly: Theory and Applications to Next Generation Sequencing
Niranjan Nagarajan and Mihai Pop - B03 De novo Assembly of Large Genomes from Illumina Whole-Genome Shotgun Data
Dariusz Przybylski, Sante Gnerre, Jain A. MacCallum, Joshua Burton, Genome Sequencing Platform, Chad Nusbaum, David B. Jaffe - B04 Error Detection Models in High Throughput Di-Nucleotide Sequencing
Onur Sakarya, Fiona Hyland, Charles Scafe, Heinz Breu, Thomas Wessel, Francisco De La Vega and Hadar Isaac
- B05 Linkage Disequilibrium Based Single Individual Genotyping from Low-Coverage Short Sequencing Reads
Sanjiv Dinakar, Jorge Duitama, Yozen Hernandez, Justin Kennedy, Ion Mandoiu and Yufeng Wu - B06 MoDIL: Detecting INDEL Variation with Mixtures of Distributions
Seunghak Lee, Fereydoun Hormozdiari, Can Alkan and Michael Brudno - B07 CNV Discovery Using High Coverage Reads
Paul Medvedev, Marc Fiume, Tim Smith, Adrian Dalca, Seunghak Lee and Michael Brudno - B08 A General Graphical Framework for Detecting Copy Number Variation
Xiaolin Yin and Jing Li
- B09 High Resolution Detection of Crossover Breakpoints with High Density SNP Markers in Three Generation Tri-Trio Pedigrees
Allen Chen, Janet Luo, Rainer Sachs, Jack Chen, Lior Pachter, Cao-An Wang, Hua Chen, Norris Hung, Johnson Poh and Lynn Hlatky - B10 Beyond Standard Network Centrality Measures for Gene-Disease Association Predictions: A Case Study with Prostate Cancer Genes
Graciela Gonzalez and Juan Uribe - B11 Optimal Algorithm for Haplotype Assembly from Whole-Genome Sequence Data
Dan He and Eleazar Eskin - B12 Identification of SNP-SNP Interactions in Association
Carlos M. Herrera Jr., Samuel D. Palmer, Yang Zhang, Jiannong Xu and Mingzhou (Joe) Song - B13 Maximum Likelihood Haplotyping through Parallelized Search on a Grid of Computers
Lars Otten, Rina Dechter, Mark Silberstein and Dan Geiger - B14 Reconstructing Parents from Genotyping Data in Wild Populations
Saad Sheikh, Tanya Berger-Wolf, Bhaskar DasGupta, Ashfaq Khokhar, Mary Ashley, Wanpracha Chaovalitwongse and Isabel C. Caballero - B15 Comparison of Haplotype Block Partitions
Natarajan Sivamani, Lawrence Shimmin and James Hixson - B16 An Consensus Tree Approach for the Detection of Population Substructure
Ming-Chi Tsai, Guy Blelloch, R. Ravi and Russell Schwartz
- B32 A Dynamic Bayesian Network Approach for Protein Secondary Structure Prediction
Zafer Aydin, Sheila Reynolds, Jeffrey Bilmes and William Noble - B33 Identification of Sets of Structurally Neighboring Amino Acids in Base-Excision Repair Enzymes that Cooperate for Activity
Ramiro Barrantes-Reynolds, Ian Odell, Susan Wallace and Jeffrey Bond - B34 MultiLoc2 and SherLoc2: Improved Prediction of Subcellular Protein Localization
Torsten Blum, Sebastian Briesemeister, Scott Brady, Yin Lam, Oliver Kohlbacher and Hagit Shatkay - B35 Prediction of Protein Binding Sites in Membrane Proteins
Andrew Bordner - B36 Graph Theoretic Properties of Known Protein Complexes
Suzanne Gallagher and Debra Goldberg - B37 Predicting Phosphorylation Sites in Plants
Jianjiong Gao, Ganesh Agrawal, Jay Thelen, Zoran Obradovic, Keith Dunker and Dong Xu - B38 An Energy-Based Approach Boosted by Evolutionary Analysis to Predict Binding Sites in Protein Structures
Dario Ghersi and Roberto Sanchez - B39 Sub-HMMs for Detecting Evolutionary and Functional Relationships Among Proteins
Kevin Horan, Christian Shelton and Thomas Girke - B40 Molecular Dynamics Study of a Bifunctional Transglycosylase PBP1b from Escherichia Coli
Yen-Ting Lai and Che Ma - B41 TransportTP: A Two-phase Classification Approach for Transporter Prediction and Functional Categorization
Haiquan Li, Vagner A. Benedito, Xinbin Dai, Michael K. Udvardi and Patrick Xuechun Zhao - B42 Discriminative Motif Finding for Predicting Protein Subcellular Localization
Tien-ho Lin, Robert F. Murphy and Ziv Bar-Joseph - B43 Assessing Conformational Diversity in Proteins using Evolutionary Information
Nicolas Palopoli, Ezequiel Juritz, Sebastian Fernandez Alberti and Gustavo Parisi - B44 Protein Threading with a Nonlinear Scoring Function
Jian Peng and Jinbo Xu - B45 Peptide Detectability Revised: Peptide Kernels for Improved Prediction of Peptide Detectability
Ermir Qeli, Erich Brunner, Konrad Basler and Christian Ahrens - B46 Integrative Data Analysis Provides Realistic Priors for Protein Detection via Mass Spectrometry
Smriti Ramakrishnan, Christine Vogel, Edward Marcotte and Daniel Miranker - B47 Identifying Allosteric Mechanisms in Proteins via Belief Propagation
Arvind Ramanathan, Hetunandan Kamisetty and Christopher Langmead - B48 Features Predictive of Cell Penetrating Peptide Potential Validated by Machine Learning Classifiers
Wiliam Sanders, Kenneth Willeford and Susan Bridges - B49 Catalytic Residue Prediction using 3D Structure and Phylogenetic Conservation
Sriram Sankararaman, Fei Sha, Mike Jordan and Kimmen Sjolander - B50 Determining Critical Sites in Protein Structures using SIMBAL (Sites Inferred by Metabolic Background Assertion Labelling)
Jeremy Selengut, Douglas Rusch and Daniel Haft - B51 Rapid Identification of Key Residues in Viral Proteins using Combinatorial Filtering and Active Learning
Chuang Wu, Andrew Walsh and Roni Rosenfeld - B52 Statistical Lower Bounds on Protein Copy Number from Fluorescence Expression Images
Lee Zamparo and Theodore Perkins - B53 A Probabilistic Graphical Model for Ab Initio Folding
Feng Zhao, Jian Peng and Jinbo Xu
- B54 Serodiagnostic Potential of Mammalian Cell Entry (MCE) Proteins Encoded by mce3 Operon of Mycobacterium Tuberculosis
Sherief El-Shazly, A.S. Mustafa, Suhail Ahmad and Raja Al-Attiyah - B55 Unexpected Introns in Blood Stem Cells
Madeleine Lemieux, Ziming Cheng, Qing Zhou, John Cornell, Andrew Kung and Vivienne Rebel - B56 Efficiency and Optimal Pool Size for Pooled Drug Screening with Synergy and Antagonism
Kyle Li, Doina Precup and Theodore Perkins - B57 k-NN Metric Learning for Human Cancer Classification using the Gene Expression Profiles
Manuel Martin-Merino and Javier De Las Rivas - B58 Identification of Potential Virulence Factors by Genome-Scale Comparison of Large Double-stranded DNA Viruses
Stefan Ponko, Steven Wiley and Ajamete Kaykas - B59 Prediction of Patient Outcomes from Longitudinal Microarray Data
Yuping Zhang, Robert Tibshirani, Wenzhong Xiao and Ronald Davis
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