Table of Contents

• Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction NetworksJacob Scott, Trey Ideker, Richard M. Karp, Roded Sharan. 1-13 [doi]
• Towards an Integrated Protein-Protein Interaction NetworkAriel Jaimovich, Gal Elidan, Hanah Margalit, Nir Friedman. 14-30 [doi]
• The Factor Graph Network Model for Biological SystemsIrit Gat-Viks, Amos Tanay, Daniela Raijman, Ron Shamir. 31-47 [doi]
• Pairwise Local Alignment of Protein Interaction Networks Guided by Models of EvolutionMehmet Koyutürk, Ananth Grama, Wojciech Szpankowski. 48-65 [doi]
• Finding Novel Transcripts in High-Resolution Genome-Wide Microarray Data Using the GenRate ModelBrendan J. Frey, Quaid Morris, Mark D. Robinson, Timothy R. Hughes. 66-82 [doi]
• Efficient Calculation of Interval Scores for DNA Copy Number Data AnalysisDoron Lipson, Yonatan Aumann, Amir Ben-Dor, Nathan Linial, Zohar Yakhini. 83-100 [doi]
• A Regulatory Network Controlling Drosophila DevelopmentDmitri A. Papatsenko, Mike Levine. 101-101 [doi]
• Yeast Cells as a Discovery Platform for Neurodegenerative DiseaseSusan Lindquist, Ernest Fraenkel, Tiago Outeiro, Aaron Gitler, Julie Su, Anil Cashikar, Smitha Jagadish. 102-102 [doi]
• RIBRA-An Error-Tolerant Algorithm for the NMR Backbone Assignment ProblemKuen-Pin Wu, Jia-Ming Chang, Jun-Bo Chen, Chi-Fon Chang, Wen-Jin Wu, Tai-Huang Huang, Ting-Yi Sung, Wen-Lian Hsu. 103-117 [doi]
• Avoiding Local Optima in Single Particle ReconstructionMarshall W. Bern, Jindong Chen, Hao Chi Wong. 118-132 [doi]
• A High-Throughput Approach for Associating microRNAs with Their Activity ConditionsChaya Ben-Zaken Zilberstein, Michal Ziv-Ukelson, Ron Y. Pinter, Zohar Yakhini. 133-151 [doi]
• RNA-RNA Interaction Prediction and Antisense RNA Target SearchCan Alkan, Emre Karakoç, Joseph H. Nadeau, Süleyman Cenk Sahinalp, Kaizhong Zhang. 152-171 [doi]
• Consensus Folding of Unaligned RNA Sequences RevisitedVineet Bafna, Haixu Tang, Shaojie Zhang. 172-187 [doi]
• Discovery and Annotation of Genetic ModulesCharles DeLisi. 188-188 [doi]
• Efficient q-Gram Filters for Finding All epsilon-Matches over a Given LengthKim R. Rasmussen, Jens Stoye, Eugene W. Myers. 189-203 [doi]
• A Polynomial Time Solvable Formulation of Multiple Sequence AlignmentSing-Hoi Sze, Yue Lu, Qingwu Yang. 204-216 [doi]
• A Fundamental Decomposition Theory for Phylogenetic Networks and Incompatible CharactersDan Gusfield, Vikas Bansal. 217-232 [doi]
• Reconstruction of Reticulate Networks from Gene TreesDaniel H. Huson, Tobias H. Klöpper, Pete J. Lockhart, Mike A. Steel. 233-249 [doi]
• A Hybrid Micro-Macroevolutionary Approach to Gene Tree ReconstructionDannie Durand, Bjarni V. Halldórsson, Benjamin Vernot. 250-264 [doi]
• Constructing a Smallest Refining Galled Phylogenetic NetworkTrinh N. D. Huynh, Jesper Jansson, Nguyen Bao Nguyen, Wing-Kin Sung. 265-280 [doi]
• Mapping Molecular Landscapes Inside CellsWolfgang Baumeister. 281-282 [doi]
• Information Theoretic Approaches to Whole Genome PhylogeniesDavid Burstein, Igor Ulitsky, Tamir Tuller, Benny Chor. 283-295 [doi]
• Maximum Likelihood of Evolutionary Trees Is HardBenny Chor, Tamir Tuller. 296-310 [doi]
• Graph Theoretical Insights into Evolution of Multidomain ProteinsTeresa M. Przytycka, George Davis, Nan Song, Dannie Durand. 311-325 [doi]
• Peptide Sequence Tags for Fast Database Search in Mass-SpectrometryAri Frank, Stephen Tanner, Pavel A. Pevzner. 326-341 [doi]
• A Hidden Markov Model Based Scoring Function for Mass Spectrometry Database SearchYunhu Wan, Ting Chen. 342-356 [doi]
• EigenMS: De Novo Analysis of Peptide Tandem Mass Spectra by Spectral Graph PartitioningMarshall W. Bern, David Goldberg. 357-372 [doi]
• Biology as InformationEric S. Lander. 373-373 [doi]
• Using Multiple Alignments to Improve Gene PredictionSamuel S. Gross, Michael R. Brent. 374-388 [doi]
• Learning Interpretable SVMs for Biological Sequence ClassificationSören Sonnenburg, Gunnar Rätsch, Christin Schäfer. 389-407 [doi]
• Segmentation Conditional Random Fields (SCRFs): A New Approach for Protein Fold RecognitionYan Liu, Jaime G. Carbonell, Peter Weigele, Vanathi Gopalakrishnan. 408-422 [doi]
• Rapid Protein Side-Chain Packing via Tree DecompositionJinbo Xu. 423-439 [doi]
• Recognition of Binding Patterns Common to a Set of Protein StructuresMaxim Shatsky, Alexandra Shulman-Peleg, Ruth Nussinov, Haim J. Wolfson. 440-455 [doi]
• Predicting Protein-Peptide Binding Affinity by Learning Peptide-Peptide Distance FunctionsChen Yanover, Tomer Hertz. 456-471 [doi]
• Amino Acid Sequence Control of the Folding of the Parallel beta-Helix, the Simplest beta-Sheet FoldJonathan King, Cammie Haase-Pettingell, Ryan Simkovsky, Peter Weigele. 472-473 [doi]
• A Practical Approach to Significance Assessment in Alignment with GapsNicholas Chia, Ralf Bundschuh. 474-488 [doi]
• Alignment of Optical MapsAnton Valouev, Lei Li, Yu-Chi Liu, David C. Schwartz, Yi Yang, Yu Zhang, Michael S. Waterman. 489-504 [doi]
• Engineering Gene Regulatory Networks: A Reductionist Approach to Systems BiologyJames J. Collins. 505-505 [doi]
• Modeling the Combinatorial Functions of Multiple Transcription FactorsChen-Hsiang Yeang, Tommi Jaakkola. 506-521 [doi]
• Predicting Transcription Factor Binding Sites Using Structural KnowledgeTommy Kaplan, Nir Friedman, Hanah Margalit. 522-537 [doi]
• Motif Discovery Through Predictive Modeling of Gene RegulationManuel Middendorf, Anshul Kundaje, Mihir Shah, Yoav Freund, Chris Wiggins, Christina S. Leslie. 538-552 [doi]
• HAPLOFREQ - Estimating Haplotype Frequencies E.cientlyEran Halperin, Elad Hazan. 553-568 [doi]
• Improved Recombination Lower Bounds for Haplotype DataVineet Bafna, Vikas Bansal. 569-584 [doi]
• A Linear-Time Algorithm for the Perfect Phylogeny Haplotyping (PPH) ProblemZhihong Ding, Vladimir Filkov, Dan Gusfield. 585-600 [doi]
• Human Genome Sequence Variation and the Inherited Basis of Common DiseaseDavid Altshuler. 601-602 [doi]
• Stability of Rearrangement Measures in the Comparison of Genome SequencesDavid Sankoff, Matthew Mazowita. 603-614 [doi]
• On Sorting by TranslocationsAnne Bergeron, Julia Mixtacki, Jens Stoye. 615-629 [doi]