Accepted Paper Number: 23
Title: Semiparametric Functional Mapping of Quantitative Trait Loci Governing Long-term HIV Dynamics
Author(s): Song Wu, Jie Yang and Rongling Wu

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Accepted Paper Number: 35
Title: Reconstruction of Highly Heterogeneous Gene-Content Evolution across the Three Domains of Life
Author(s): Wataru Iwasaki and Toshihisa Takagi

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Accepted Paper Number: 68
Title: Choosing where to look next in a mutation sequence space: Active Learning of informative p53 cancer rescue mutants
Author(s): Samuel A. Danziger, Jue Zeng, Ying Wang, Rainer Brachmann and Richard H. Lathrop

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Accepted Paper Number: 83
Title: A physical model for tiling array analysis
Author(s): Ho-Ryun Chung, Dennis Kostka and Martin Vingron

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Accepted Paper Number: 92
Title: Learning to Extract Relations For Protein Annotation
Author(s): Jee-Hyub Kim, Alex Mitchell, Teresa Attwood and Melanie Hilario

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Accepted Paper Number: 94
Title: Polyploids, Genome Halving and Phylogeny
Author(s): David Sankoff, Chunfang Zheng and Qian Zhu

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Accepted Paper Number: 117
Title: SPINE: A Framework for Signaling-Regulatory Pathway Inference from Cause-Effect Experiments
Author(s): Oved Ourfali, Tomer Shlomi, Trey Ideker, Eytan Ruppin and Roded Sharan

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Accepted Paper Number: 134
Title: Spectrum: Joint Bayesian Inference of Population Structure and Recombination Event
Author(s): Kyung-Ah Sohn and Eric P. Xing

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Accepted Paper Number: 141
Title: Genomic Characterization of Perturbation Sensitivity
Author(s): Jung Hun Ohn, Jihun Kim and Ju Han Kim

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Accepted Paper Number: 146
Title: Annotating Gene Function by Combining Expression Data with a Modular Gene Network
Author(s): Motoki Shiga, Ichigaku Takigawa and Hiroshi Mamitsuka

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Accepted Paper Number: 149
Title: Prediction of DNA binding residues from sequence
Author(s): Yanay Ofran, Venkatesh Mysore and Burkhard Rost

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Accepted Paper Number: 152
Title: Cotranslational protein folding – fact or fiction?
Author(s): Charlotte M. Deane, Mingqiang Dong, Fabien Huard, Braddon K. Lance and Graham R. Wood

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Accepted Paper Number: 160
Title: Towards realistic codon models: among site variability and de-pendency of synonymous and nonsynonymous rates
Author(s): Itay Mayrose, Adi Doron-Faigenboim, Eran Bacharach and Tal Pupko

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Accepted Paper Number: 164
Title: Translation initiation site prediction on a genomic scale: beauty in simplicity
Author(s): Yvan Saeys, Thomas Abeel, Sven Degroeve and Yves Van de Peer

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Accepted Paper Number: 171
Title: Nested Effects Models for High-Dimensional Phenotyping Screens
Author(s): Florian Markowetz, Dennis Kostka, Olga Troyanskaya and Rainer Spang

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Accepted Paper Number: 172
Title: Locomotif: From Graphical Motif Description to RNA Motif Search
Author(s): Janina Reeder, Jens Reeder and Robert Giegerich

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Accepted Paper Number: 173
Title: Different mechanistic requirements for prokaryotic and eukaryotic chaperonins: a lattice study
Author(s): Etai Jacob, Amnon Horovitz and Ron Unger

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Accepted Paper Number: 182
Title: Exploring the lipoprotein composition using Bayesian regression on serum lipidomic profiles
Author(s): Marko Tapani Sysi-Aho, Aki Vehtari, Vidya Velagapudi, Jukka Westerbacka, Laxman Yetukuri, Robert Bergholm, Marja-Riitta Taskinen, Hannele Yki-Järvinen and Matej Oresic

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Accepted Paper Number: 184
Title: Biases induced by pooling samples in microarray experiments
Author(s): Tristan Mary-Huard, JeanJacques Daudin, Michela Baccini, Annibale Biggeri and Avner Bar-Hen

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Accepted Paper Number: 188
Title: Nucleotide variation of regulatory motifs may lead to distinct expression patterns
Author(s): Liat Segal, Michal Lapidot, Zach Solan, Eytan Ruppin, Yitzhak Pilpel and David Horn

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Accepted Paper Number: 195
Title: Negation of protein-protein interactions: analysis and extraction
Author(s): Olivia Sanchez-Graillet and Massimo Poesio

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Accepted Paper Number: 208
Title: Probabilistic whole-genome alignments reveal high indel rates in the human and mouse genomes
Author(s): Gerton Lunter

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Accepted Paper Number: 212
Title: Anisotropic Fluctuations of Amino Acids in Protein Structures: Insights from X-Ray Crystallography and Elastic Network Models
Author(s): Eran Eyal, Chakra Chennubhotla, Lee-Wey Yang and Ivet Bahar

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Accepted Paper Number: 220
Title: Kernel-based data fusion for gene prioritization
Author(s): Tijl De Bie, Leon-Charles Tranchevent, Liesbeth van Oeffelen and Yves Moreau

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Accepted Paper Number: 234
Title: Structural templates predict novel proteins interactions and targets from pancreas tumour gene expression data.
Author(s): Gihan Dawelbait, Christof Winter, Yanju Zhang, Christian Pilarsky, Robert Grützmann, Jörg-Christian Heinrich and Michael Schroeder

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Accepted Paper Number: 236

Title: A Chado Case Study: An Ontology-based Modular Schema for Representing Genome-Associated Biological Information
Author(s): Christopher J Mungall, David B Emmert, Suzanna Lewis and The FlyBase Consortium

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Accepted Paper Number: 245
Title: In search of lost introns
Author(s): Miklos Csuros, J. Andrew Holey and Igor Rogozin

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Accepted Paper Number: 247
Title: Adaptive Torsion-Angle Quasi-Statics: a General Simulation Method with Applications to Protein Structure Analysis and Design
Author(s): Romain Rossi, Mathieu Isorce, Sandy Morin, Julien Flocard, Karthik Arumugam, Serge Crouzy, Michel Vivaudou and Stephane Redon

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Accepted Paper Number: 253
Title: SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation
Author(s): Frank Panitz, Henrik Stengaard, Henrik Hornshøj, Jan Gorodkin, Jakob Hedegaard, Susanna Cirera, Bo Thomsen, Lone B. Madsen, Anette Høj, Rikke K. Vingborg, Bujie Zahn, Xuegang Wang, Xuefei Wang, Rasmus Wernersson, Claus B. Jørgensen, Karsten Scheibye-Knudsen, Troels Arvin, Steen Lumholdt, Milena Sawera, Trine Green, Bente J. Nielsen, Jakob H. Havgaard, Søren Brunak, Merete Fredholm and Christian Bendixen

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Accepted Paper Number: 255
Title: Automatic genome-wide reconstruction of phylogenetic gene trees
Author(s): Ilan Wapinski, Avi Pfeffer, Nir Friedman and Aviv Regev

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Accepted Paper Number: 262
Title: Identification of Functional Modules from Conserved Ancestral Protein-Protein Interactions
Author(s): Janusz Dutkowski and Jerzy Tiuryn

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Accepted Paper Number: 264
Title: Information Theory Applied to the Sparse Gene Ontology Annota-tion Network to Predict Novel Gene Function
Author(s): Ying Tao, Lee Sam, Jianrong Li, Carol Friedman and Yves A. Lussier

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Accepted Paper Number: 271
Title: Identification of New Drug Classification Terms in Textual Resources
Author(s): Corinna Kolarik, Martin Hofmann, Marc Zimmermann and Juliane Fluck

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Accepted Paper Number: 273
Title: Dead-End Elimination with Backbone Flexibility
Author(s): Ivelin Georgiev and Bruce Randall Donald

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Accepted Paper Number: 275
Title: Using Dynamic Programming to Create Isotopic Distribution Maps from Mass Spectra
Author(s): Sean McIlwain, David Page, Edward Huttlin and Michael Sussman

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Accepted Paper Number: 276
Title: Kinetics Analysis Methods For Approximate Folding Landscapes
Author(s): Lydia Tapia, Xinyu Tang, Shawna Thomas and Nancy Amato

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Accepted Paper Number: 281
Title: Optimized Design and Assessment of Whole Genome Tiling Arrays
Author(s): Stefan Graf, Fiona G.G. Nielsen, Stefan Kurtz, Martijn A. Huynen, Ewan Birney, Henk Stunnenberg and Paul Flicek

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Accepted Paper Number: 282
Title: Comparative analysis of microarray normalization procedures: effects on reverse engineering gene networks
Author(s): Wei Keat Lim, Kai Wang, Celine Lefebvre and Andrea Califano

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Accepted Paper Number: 283
Title: Co-occurrence Analysis of Insertional Mutagenesis Data Reveals Cooperating Oncogenes
Author(s): Jeroen de Ridder, Jaap Kool, Anthony Uren, Jan Bot, Lodewyk Wessels and Marcel J.T. Reinders

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Accepted Paper Number: 284
Title: Functional Annotation of Regulatory Pathways
Author(s): Jayesh Pandey, Mehmet Koyuturk, Yohan Kim, Wojciech Szpankowski, Shankar Subramaniam and Ananth Grama

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Accepted Paper Number: 295
Title: Supervised reconstruction of biological networks with local models
Author(s): Kevin Bleakley, Gérard Biau and Jean-Phlippe Vert

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Accepted Paper Number: 296
Title: GPDTI: A Genetic Programming Decision Tree Induction method to find epistatic effects in common complex diseases
Author(s): Jesus K. Estrada-Gil, Juan C. Fernandez-Lopez, Enrique Hernadez-Lemus, Irma Silva-Zolezzi, Alfredo Hidalgo-Miranda, Gerardo Jimenez-Sanchez and Edgar E. Vallejo

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Accepted Paper Number: 297
Title: Automated Image Analysis of Protein Localization in Budding Yeast
Author(s): Shann-Ching Chen, Ting Zhao, Geoffrey Gordon and Robert Murphy

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Accepted Paper Number: 300
Title: From protein microarrays to diagnostic antigen discovery: A study of the pathogen Francisella tularensis
Author(s): Suman Sundaresh, Arlo Randall, Berkay Unal, Jeannine M. Petersen, John T. Belisle, M. Gill Hartley, Melanie Duffield, Richard W. Titball, D. Huw Davies, Philip L. Felgner and Pierre Baldi

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Accepted Paper Number: 301
Title: Computational Prediction of Host-Pathogen Protein-Protein Interactions
Author(s): Matthew D. Dyer, T. M. Murali and Bruno W. Sobral

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Accepted Paper Number: 306
Title: A Geometric Approach for the Alignment of Liquid Chromatography-Mass Spectrometry Data
Author(s): Eva Lange, Clemens Gröpl, Ole Schulz-Trieglaff and Knut Reinert

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Accepted Paper Number: 320
Title: Multiway Analysis of Epilepsy Tensors
Author(s): Evrim Acar Ataman, Canan Aykut-Bingol, Haluk Bingol, Bulent Yener and Rasmus Bro

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Accepted Paper Number: 335
Title: A Statistical Method for Alignment-free Comparison of Regulatory Sequences
Author(s): Miriam R. Kantorovitz, Gene E. Robinson and Saurabh Sinha

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Accepted Paper Number: 337
Title: An Ensemble Framework for Clustering Protein-Protein Interaction Networks
Author(s): Sitaram Asur, Srinivasan Parthasarathy and Duygu Ucar

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Accepted Paper Number: 342
Title: Using genome context data to identify specific types of functional associations in pathway/genome databases
Author(s): Michelle Green and Peter Karp

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Accepted Paper Number: 343
Title: Computational Modeling of C. elegans Vulval Induction
Author(s): Xiaoyun Sun and Pengyu Hong

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Accepted Paper Number: 353
Title: Inferring protein-DNA dependencies using motif alignments and mutual information
Author(s): Shaun Mahony, Philip Auron and Panayiotis Benos

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Accepted Paper Number: 359
Title: Gene Selection via the BAHSIC Family of Algorithms
Author(s): Le Song, Justin Bedo, Karsten Borgwardt, Arthur Gretton and Alex Smola

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Accepted Paper Number: 363
Title: Bayesian association of haplotypes and non-genetic factors to regulatory and phenotypic variation in human populations
Author(s): Jim Huang, Anitha Kannan and John Winn

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Accepted Paper Number: 387
Title: Continuous Hidden Process Model for Time Series Expression Experiments
Author(s): Yanxin Shi, Michael Klutstein, Itamar Simon, Tom Mitchell and Ziv Bar-Joseph

Accepted Paper Number: 388
Title: Reconstructing Sibling Relationships in Wild Populations
Author(s): Tanya Berger-Wolf, Saad Sheikh, Bhaskar DasGupta, Mary Ashley, Isabel C. Caballero and Satya Lahari Putrevu

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Accepted Paper Number: 389
Title: Inferring Missing Genotypes in Large SNP Panels Using Fast Nearest-Neighbor Searches Over Sliding Windows
Author(s): Adam Roberts, Leonard McMillan, Wei Wang, Joel Parker, Ivan Rusyn and David Threadgill

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Accepted Paper Number: 392
Title: Modeling recurrent DNA copy number alterations in array CGH data
Author(s): Sohrab P. Shah, Wan L. Lam, Raymond T. Ng and Kevin P. Murphy

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Accepted Paper Number: 395
Title: Systematic Discovery of Functional Modules and Context-Specific Functional Annotation of Human Genome
Author(s): Yu Huang, Haifeng Li, Haiyan Hu, Xifeng Yan, Michael Waterman, Haiyan Huang and Jasmine Zhou

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Accepted Paper Number: 406
Title: Efficient parameter estimation for RNA secondary structure prediction
Author(s): Mirela Andronescu, Anne Condon, Holger Hoos, David H. Mathews and Kevin P. Murphy

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Accepted Paper Number: 410
Title: RankMotif++: a motif-search algorithm that accounts for relative ranks of K-mers in binding transcription factors
Author(s): Xiaoyu Chen, Timothy Hughes and Quaid Morris

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Accepted Paper Number: 413
Title: Homology Search for Genes Using Biased HMMs
Author(s): Xuefeng Cui, Tomas Vinar, Brona Brejova, Dennis Shasha and Ming Li

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Accepted Paper Number: 427
Title: Computing multiple sequence alignments by aligning alignments
Author(s): Travis Wheeler and John Kececioglu

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Accepted Paper Number: 428
Title: A graph-based approach to systematically reconstruct human transcriptional regulatory modules
Author(s): Xifeng Yan, Michael Mehan, Yu Huang, Michael Waterman, Philip Yu and Jasmine Zhou

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Accepted Paper Number: 432
Title: Connecting Quantitative Regulatory-Network Models to genome
Author(s): Yue Pan, Timothy Durfee, Joseph Bockhorst and Mark Craven

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Accepted Paper Number: 436
Title: Manual curation is not sufficient for annotation of genomic databases
Author(s): William Baumgartner, Lynne Fox, George Acquaah-Mensah, K. Bretonnel Cohen and Lawrence Hunter