Table of Contents

• Integrated Protein Interaction Networks for 11 MicrobesBalaji S. Srinivasan, Antal F. Novak, Jason Flannick, Serafim Batzoglou, Harley H. McAdams. 1-14 [doi]
• Hypergraph Model of Multi-residue Interactions in Proteins: Sequentially-Constrained Partitioning Algorithms for Optimization of Site-Directed Protein RecombinationXiaoduan Ye, Alan M. Friedman, Chris Bailey-Kellogg. 15-29 [doi]
• Biological Networks: Comparison, Conservation, and Evolutionary TreesBenny Chor, Tamir Tuller. 30-44 [doi]
• Assessing Significance of Connectivity and Conservation in Protein Interaction NetworksMehmet Koyutürk, Ananth Grama, Wojciech Szpankowski. 45-59 [doi]
• Clustering Short Gene Expression ProfilesLing Wang, Marco Ramoni, Paola Sebastiani. 60-68 [doi]
• A Patient-Gene Model for Temporal Expression Profiles in Clinical StudiesNaftali Kaminski, Ziv Bar-Joseph. 69-82 [doi]
• Global Interaction Networks Probed by Mass SpectrometryAnne-Claude Gavin. 83-83 [doi]
• Statistical Evaluation of Genome RearrangementDavid Sankoff. 84-84 [doi]
• An Improved Statistic for Detecting Over-Represented Gene Ontology Annotations in Gene SetsSteffen Grossmann, Sebastian Bauer, Peter N. Robinson, Martin Vingron. 85-98 [doi]
• Protein Function Annotation Based on Ortholog Clusters Extracted from Incomplete Genomes Using Combinatorial OptimizationAkshay Vashist, Casimir A. Kulikowski, Ilya B. Muchnik. 99-113 [doi]
• Detecting MicroRNA Targets by Linking Sequence, MicroRNA and Gene Expression DataJim C. Huang, Quaid Morris, Brendan J. Frey. 114-129 [doi]
• RNA Secondary Structure Prediction Via Energy Density MinimizationCan Alkan, Emre Karakoç, Süleyman Cenk Sahinalp, Peter J. Unrau, H. Alexander Ebhardt, Kaizhong Zhang, Jeremy Buhler. 130-142 [doi]
• Structural Alignment of Pseudoknotted RNABanu Dost, Buhm Han, Shaojie Zhang, Vineet Bafna. 143-158 [doi]
• Stan Ulam and Computational BiologyMichael S. Waterman. 159-159 [doi]
• CONTRAlign: Discriminative Training for Protein Sequence AlignmentChuong B. Do, Samuel S. Gross, Serafim Batzoglou. 160-174 [doi]
• Clustering Near-Identical Sequences for Fast Homology SearchMichael Cameron, Yaniv Bernstein, Hugh E. Williams. 175-189 [doi]
• New Methods for Detecting Lineage-Specific SelectionAdam C. Siepel, Katherine S. Pollard, David Haussler. 190-205 [doi]
• A Probabilistic Model for Gene Content Evolution with Duplication, Loss, and Horizontal TransferMiklós Csürös, István Miklós. 206-220 [doi]
• A Sublinear-Time Randomized Approximation Scheme for the Robinson-Foulds MetricNicholas D. Pattengale, Bernard M. E. Moret. 221-230 [doi]
• Algorithms to Distinguish the Role of Gene-Conversion from Single-Crossover Recombination in the Derivation of SNP Sequences in PopulationsYun S. Song, Zhihong Ding, Dan Gusfield, Charles H. Langley, Yufeng Wu. 231-245 [doi]
• Inferring Common Origins from mtDNAAjay K. Royyuru, Gabriela Alexe, Daniel E. Platt, Ravi Vijaya Satya, Laxmi Parida, Saharon Rosset, Gyan Bhanot. 246-247 [doi]
• Efficient Enumeration of Phylogenetically Informative SubstringsStanislav Angelov, Boulos Harb, Sampath Kannan, Sanjeev Khanna, Junhyong Kim. 248-264 [doi]
• Phylogenetic Profiling of Insertions and Deletions in Vertebrate GenomesSagi Snir, Lior Pachter. 265-280 [doi]
• Maximal Accurate Forests from Distance MatricesConstantinos Daskalakis, Cameron Hill, Alexander Jaffe, Radu Mihaescu, Elchanan Mossel, Satish Rao. 281-295 [doi]
• Leveraging Information Across HLA Alleles/Supertypes Improves Epitope PredictionDavid Heckerman, Carl Myers Kadie, Jennifer Listgarten. 296-308 [doi]
• Improving Prediction of Zinc Binding Sites by Modeling the Linkage Between Residues Close in SequenceSauro Menchetti, Andrea Passerini, Paolo Frasconi, Claudia Andreini, Antonio Rosato. 309-320 [doi]
• An Important Connection Between Network Motifs and Parsimony ModelsTeresa M. Przytycka. 321-335 [doi]
• Ultraconserved Elements, Living Fossil Transposons, and Rapid Bursts of Change: Reconstructing the Uneven Evolutionary History of the Human GenomeDavid Haussler. 336-337 [doi]
• Permutation Filtering: A Novel Concept for Significance Analysis of Large-Scale Genomic DataStefanie Scheid, Rainer Spang. 338-347 [doi]
• Genome-Wide Discovery of Modulators of Transcriptional Interactions in Human B LymphocytesKai Wang, Ilya Nemenman, Nilanjana Banerjee, Adam A. Margolin, Andrea Califano. 348-362 [doi]
• A New Approach to Protein IdentificationNuno Bandeira, Dekel Tsur, Ari Frank, Pavel A. Pevzner. 363-378 [doi]
• Markov Methods for Hierarchical Coarse-Graining of Large Protein DynamicsChakra Chennubhotla, Ivet Bahar. 379-393 [doi]
• Simulating Protein Motions with Rigidity AnalysisShawna L. Thomas, Xinyu Tang, Lydia Tapia, Nancy M. Amato. 394-409 [doi]
• Predicting Experimental Quantities in Protein Folding Kinetics Using Stochastic Roadmap SimulationTsung-Han Chiang, Mehmet Serkan Apaydin, Douglas L. Brutlag, David Hsu, Jean-Claude Latombe. 410-424 [doi]
• An Outsider s View of the GenomeCarl Zimmer. 425 [doi]
• Alignment Statistics for Long-Range Correlated Genomic SequencesPhilipp W. Messer, Ralf Bundschuh, Martin Vingron, Peter F. Arndt. 426-440 [doi]
• Simple and Fast Inverse AlignmentJohn D. Kececioglu, Eagu Kim. 441-455 [doi]
• Revealing the Proteome Complexity by Mass SpectrometryRoman A. Zubarev. 456-457 [doi]
• Motif Yggdrasil: Sampling from a Tree Mixture ModelSamuel A. Andersson, Jens Lagergren. 458-472 [doi]
• A Study of Accessible Motifs and RNA Folding ComplexityYdo Wexler, Chaya Ben-Zaken Zilberstein, Michal Ziv-Ukelson. 473-487 [doi]
• A Parameterized Algorithm for Protein Structure AlignmentJinbo Xu, Feng Jiao, Bonnie Berger. 488-499 [doi]
• Geometric Sieving: Automated Distributed Optimization of 3D Motifs for Protein Function PredictionBrian Y. Chen, Viacheslav Fofanov, Drew H. Bryant, Bradley D. Dodson, David M. Kristensen, Andreas Martin Lisewski, Marek Kimmel, Olivier Lichtarge, Lydia E. Kavraki. 500-515 [doi]
• A Branch-and-Reduce Algorithm for the Contact Map Overlap ProblemWei Xie, Nikolaos V. Sahinidis. 516-529 [doi]
• A Novel Minimized Dead-End Elimination Criterion and Its Application to Protein Redesign in a Hybrid Scoring and Search Algorithm for Computing Partition Functions over Molecular EnsemblesIvelin Georgiev, Ryan H. Lilien, Bruce Randall Donald. 530-545 [doi]
• 10 Years of the International Conference on Research in Computational Molecular Biology (RECOMB)Sarah J. Aerni, Eleazar Eskin. 546-562 [doi]
• Sorting by Weighted Reversals, Transpositions, and Inverted TranspositionsMartin Bader, Enno Ohlebusch. 563-577 [doi]
• A Parsimony Approach to Genome-Wide Ortholog AssignmentZheng Fu, Xin Chen, Vladimir Vacic, Peng Nan, Yang Zhong, Tao Jiang. 578-594 [doi]
• Detecting the Dependent Evolution of BiosequencesJeremy Darot, Chen-Hsiang Yeang, David Haussler. 595-609 [doi]