| Computational Biology: Its Challenges Past, Present, and Future (Keynote) / Temple F. Smith |
| Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast / Caroline C. Friedel ; Jan Krumsiek ; Ralf Zimmer |
| CompostBin: A DNA Composition-Based Algorithm for Binning Environmental Shotgun Reads / Sourav Chatterji ; Ichitaro Yamazaki ; Zhaojun Bai ; Jonathan A. Eisen |
| Reconstructing the Evolutionary History of Complex Human Gene Clusters / Yu Zhang ; Giltae Song ; Tomas Vinar ; Eric D. Green ; Adam Siepel ; Webb Miller |
| Ab Initio Whole Genome Shotgun Assembly with Mated Short Reads / Paul Medevedev ; Michael Brudno |
| Orchestration of DNA Methylation (Keynote) / Howard Cedar |
| BayCis: A Bayesian Hierarchical HMM for Cis-Regulatory Module Decoding in Metazoan Genomes / Tien-ho Lin ; Pradipta Ray ; Geir K. Sandve ; Selen Uguroglu ; Eric P. Xing |
| A Combined Expression-Interaction Model for Inferring the Temporal Activity of Transcription Factors / Yanxin Shi ; Itamar Simon ; Tom Mitchell ; Ziv Bar-Joseph |
| A Fast, Alignment-Free, Conservation-Based Method for Transcription Factor Binding Site Discovery / Raluca Gordan ; Leelavati Narlikar ; Alexander J. Hartemink |
| The Statistical Power of Phylogenetic Motif Models / John Hawkins ; Timothy L. Bailey |
| Transcriptional Regulation and Cancer Genomics (Keynote) / Edison Liu |
| Automatic Recognition of Cells (ARC) for 3D Images of C. elegans / Fuhui Long ; Hanchuan Peng ; Xiao Liu ; Stuart Kim ; Gene Myers |
| Spectrum Fusion: Using Multiple Mass Spectra for De Novo Peptide Sequencing / Ritendra Datta ; Marshall Bern |
| A Fragmentation Event Model for Peptide Identification by Mass Spectrometry / Yu Lin ; Yantao Qiao ; Shiwei Sun ; Chungong Yu ; Gongjin Dong ; Dongbo Bu |
| A Bayesian Approach to Protein Inference Problem in Shotgun Proteomics / Yong Fuga Li ; Randy J. Arnold ; Yixue Li ; Predrag Radivojac ; Quanhu Sheng ; Haixu Tang |
| De Novo Sequencing of Nonribosomal Peptides / Nuno Bandeira ; Julio Ng ; Dario Meluzzi ; Roger G. Linington ; Pieter Dorrestein ; Pavel A. Pevzner |
| Systems Metabolic Engineering (Keynote) / Sang Yup Lee |
| Protein Function Prediction Based on Patterns in Biological Networks / Mustafa Kirac ; Gultekin Ozsoyoglu |
| Automatic Parameter Learning for Multiple Network Alignment / Jason Flannick ; Antal Novak ; Chuong B. Do ; Balaji S. Srinivason ; Serafim Batzoglou |
| An Integrative Network Approach to Map the Transcriptome to the Phenome / Michael R. Mehan ; Juan Nunez-Iglesias ; Mrinal Kalakrishnan ; Michael S. Waterman ; Xianghong Jasmine Zhou |
| Fast and Accurate Alignment of Multiple Protein Networks / Maxim Kalaev ; Vineet Bafna ; Roded Sharan |
| High-Resolution Modeling of Cellular Signaling Networks / Michael Baym ; Chris Bakal ; Norbert Perrimon ; Bonnie Berger |
| At the Origin of Life: How Did Folded Proteins Evolve? (Keynote) / Andrei Lupas |
| Locating Multiple Gene Duplications through Reconciled Trees / J. Gordon Burleigh ; Mukul S. Bansal ; Andre Wehe ; Oliver Eulenstein |
| Rapid and Accurate Protein Side Chain Prediction with Local Backbone Information / Jing Zhang ; Xin Gao ; Jinbo Xu ; Ming Li |
| Algorithms for Joint Optimization of Stability and Diversity in Planning Combinatorial Libraries of Chimeric Proteins / Wei Zheng ; Alan M. Friedman ; Chris Bailey-Kellogg |
| DLIGHT - Lateral Gene Transfer Detection Using Pairwise Evolutionary Distances in a Statistical Framework / Christophe Dessimoz ; Daniel Margadant ; Gaston H. Gonnet |
| Computation of Median Gene Clusters / Sebastian Bocker ; Katharina Jahn ; Julia Mixtacki ; Jens Stoye |
| BCL-2: From Translocation to Therapy (Keynote) / Suzanne Cory |
| Detecting Disease-Specific Dysregulated Pathways Via Analysis of Clinical Expression Profiles / Igor Ulitsky ; Richard M. Karp ; Ron Shamir |
| Constructing Treatment Portfolios Using Affinity Propagation / Delbert Dueck ; Brendan J. Frey ; Nebojsa Jojic ; Vladimir Jojic ; Guri Giaever ; Andrew Emili ; Gabe Musso ; Robert Hegele |
| Bubbles: Alternative Splicing Events of Arbitrary Dimension in Splicing Graphs / Michael Sammeth ; Gabriel Valiente ; Roderic Guigo |
| More Efficient Algorithms for Closest String and Substring Problems / Bin Ma ; Xiaoming Sun |
| Disruption of a Transcriptional Regulatory Pathway Contributes to Phenotypes in Carriers of Ataxia Telangiectasia (Keynote) / Denis Smirnov ; Vivian G. Cheung |
| Accounting for Non-genetic Factors Improves the Power of eQTL Studies / Oliver Stegle ; Anitha Kannan ; Richard Durbin ; John Winn |
| Effects of Genetic Divergence in Identifying Ancestral Origin Using HAPAA / Andreas Sundquist ; Eugene Fratkin |
| On the Inference of Ancestries in Admixed Populations / Sriram Sankararaman ; Gad Kimmel ; Eran Halperin ; Michael I. Jordan |
| Increasing Power in Association Studies by Using Linkage Disequilibrium Structure and Molecular Function as Prior Information / Eleazar Eskin |
| Panel Construction for Mapping in Admixed Populations Via Expected Mutual Information / Sivan Bercovici ; Dan Geiger ; Liran Shlush ; Karl Skorecki ; Alan Templeton |
| Constructing Level-2 Phylogenetic Networks from Triplets / Leo van Iersel ; Judith Keijsper ; Steven Kelk ; Leen Stougie ; Ferry Hagen ; Teun Boekhout |
| Accurate Computation of Likelihoods in the Coalescent with Recombination Via Parsimony / Rune B. Lyngso ; Yun S. Song ; Jotun Hein |
| Author Index |
| Computational Biology: Its Challenges Past, Present, and Future (Keynote) / Temple F. Smith |
| Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast / Caroline C. Friedel ; Jan Krumsiek ; Ralf Zimmer |
| CompostBin: A DNA Composition-Based Algorithm for Binning Environmental Shotgun Reads / Sourav Chatterji ; Ichitaro Yamazaki ; Zhaojun Bai ; Jonathan A. Eisen |
| Reconstructing the Evolutionary History of Complex Human Gene Clusters / Yu Zhang ; Giltae Song ; Tomas Vinar ; Eric D. Green ; Adam Siepel ; Webb Miller |
| Ab Initio Whole Genome Shotgun Assembly with Mated Short Reads / Paul Medevedev ; Michael Brudno |
| Orchestration of DNA Methylation (Keynote) / Howard Cedar |
