Abstract is missing.
- Bacterial Community Reconstruction Using Compressed SensingAmnon Amir, Or Zuk. 1-15 [doi]
- Constrained De Novo Sequencing of Peptides with Application to ConotoxinsSwapnil Bhatia, Yong J. Kil, Beatrix Ueberheide, Brian Chait, Lemmuel L. Tayo, Lourdes J. Cruz, Bingwen Lu, John R. Yates III, Marshall W. Bern. 16-30 [doi]
- Metabolic Network Analysis DemystifiedLeonid Chindelevitch, Aviv Regev, Bonnie Berger. 31-33 [doi]
- Causal Reasoning on Biological Networks: Interpreting Transcriptional Changes - (Extended Abstract)Leonid Chindelevitch, Daniel Ziemek, Ahmed Enayetallah, Ranjit Randhawa, Ben Sidders, Christoph Brockel, Enoch Huang. 34-37 [doi]
- Hapsembler: An Assembler for Highly Polymorphic GenomesNilgun Donmez, Michael Brudno. 38-52 [doi]
- Discovery and Characterization of Chromatin States for Systematic Annotation of the Human GenomeJason Ernst, Manolis Kellis. 53 [doi]
- Disease Gene Prioritization Based on Topological Similarity in Protein-Protein Interaction NetworksSinan Erten, Gürkan Bebek, Mehmet Koyutürk. 54-68 [doi]
- Understanding Gene Sequence Variation in the Context of Transcription Regulation in YeastIrit Gat-Viks, Renana Meller, Martin Kupiec, Ron Shamir. 69 [doi]
- Identifying Branched Metabolic Pathways by Merging Linear Metabolic PathwaysAllison P. Heath, George N. Bennett, Lydia E. Kavraki. 70-84 [doi]
- A Probabilistic Model for Sequence Alignment with Context-Sensitive IndelsGlenn Hickey, Mathieu Blanchette. 85-103 [doi]
- Simultaneous Structural Variation Discovery in Multiple Paired-End Sequenced GenomesFereydoun Hormozdiari, Iman Hajirasouliha, Andrew McPherson, Evan E. Eichler, Süleyman Cenk Sahinalp. 104-105 [doi]
- Variable Selection through Correlation SiftingJim C. Huang, Nebojsa Jojic. 106-123 [doi]
- Weighted Genomic Distance Can Hardly Impose a Bound on the Proportion of TranspositionsShuai Jiang, Max A. Alekseyev. 124-133 [doi]
- PSAR: Measuring Multiple Sequence Alignment Reliability by Probabilistic Sampling - (Extended Abstract)Jaebum Kim, Jian Ma. 134-135 [doi]
- Pedigree Reconstruction Using Identity by DescentBonnie Kirkpatrick, Shuai Cheng Li, Richard M. Karp, Eran Halperin. 136-152 [doi]
- A Quantitative Model of Glucose Signaling in Yeast Reveals an Incoherent Feed Forward Loop Leading to a Specific, Transient Pulse of TranscriptionSooraj KuttyKrishnan, Jeffrey Sabina, Laura Langton, Mark Johnston, Michael R. Brent. 153 [doi]
- Inferring Mechanisms of Compensation from E-MAP and SGA Data Using Local Search Algorithms for Max CutMark D. M. Leiserson, Diana Tatar, Lenore J. Cowen, Benjamin J. Hescott. 154-167 [doi]
- IsoLasso: A LASSO Regression Approach to RNA-Seq Based Transcriptome Assembly - (Extended Abstract)Wei Li, Jianxing Feng, Tao Jiang. 168-188 [doi]
- Haplotype Reconstruction in Large Pedigrees with Many Untyped IndividualsXin Li, Jing Li. 189-203 [doi]
- Learning Cellular Sorting Pathways Using Protein Interactions and Sequence MotifsTien-ho Lin, Ziv Bar-Joseph, Robert F. Murphy. 204-221 [doi]
- A Geometric Arrangement Algorithm for Structure Determination of Symmetric Protein Homo-oligomers from NOEs and RDCsJeffrey W. Martin, Anthony K. Yan, Chris Bailey-Kellogg, Pei Zhou, Bruce Randall Donald. 222-237 [doi]
- Paired de Bruijn Graphs: A Novel Approach for Incorporating Mate Pair Information into Genome AssemblersPaul Medvedev, Son Pham, Mark Chaisson, Glenn Tesler, Pavel A. Pevzner. 238-251 [doi]
- An Optimization-Based Sampling Scheme for Phylogenetic TreesNavodit Misra, Guy E. Blelloch, R. Ravi, Russell Schwartz. 252-266 [doi]
- Multiplex De Novo Sequencing of Peptide AntibioticsHosein Mohimani, Wei-Ting Liu, Yu-Liang Yang, Susana P. Gaudêncio, William Fenical, Pieter C. Dorrestein, Pavel A. Pevzner. 267-281 [doi]
- AREM: Aligning Short Reads from ChIP-Sequencing by Expectation MaximizationDaniel Newkirk, Jacob Biesinger, Alvin Chon, Kyoko Yokomori, Xiaohui Xie. 283-297 [doi]
- Blocked Pattern Matching Problem and Its Applications in ProteomicsJulio Ng, Amihood Amir, Pavel A. Pevzner. 298-319 [doi]
- A Three-Dimensional Model of the Yeast GenomeWilliam Noble, Zhi-jun Duan, Mirela Andronescu, Kevin Schutz, Sean McIlwain, Yoo-Jung Kim, Choli Lee, Jay Shendure, Stanley Fields, C. Anthony Blau. 320 [doi]
- Optimization of Combinatorial MutagenesisAndrew S. Parker, Karl E. Griswold, Chris Bailey-Kellogg. 321-335 [doi]
- Seeing More Is Knowing More: V3D Enables Real-Time 3D Visualization and Quantitative Analysis of Large-Scale Biological Image Data SetsHanchuan Peng, Fuhui Long. 336 [doi]
- T-IDBA: A de novo Iterative de Bruijn Graph Assembler for Transcriptome - (Extended Abstract)Yu Peng, Henry C. M. Leung, Siu-Ming Yiu, Francis Y. L. Chin. 337-338 [doi]
- Experiment Specific Expression PatternsTobias Petri, Robert Küffner, Ralf Zimmer. 339-354 [doi]
- Geometric Interpretation of Gene Expression by Sparse Reconstruction of Transcript ProfilesYosef Prat, Menachem Fromer, Michal Linial, Nathan Linial. 355-357 [doi]
- A Ribosome Flow Model for Analyzing Translation Elongation - (Extended Abstract)Shlomi Reuveni, Isaac Meilijson, Martin Kupiec, Eytan Ruppin, Tamir Tuller. 358-360 [doi]
- Design of Protein-Protein Interactions with a Novel Ensemble-Based Scoring AlgorithmKyle E. Roberts, Patrick R. Cushing, Prisca Boisguerin, Dean R. Madden, Bruce Randall Donald. 361-376 [doi]
- Computing Fragmentation Trees from Metabolite Multiple Mass Spectrometry DataKerstin Scheubert, Franziska Hufsky, Florian Rasche, Sebastian Böcker. 377-391 [doi]
- Metric Labeling and Semi-metric Embedding for Protein Annotation PredictionEmre Sefer, Carl Kingsford. 392-407 [doi]
- Efficient Traversal of Beta-Sheet Protein Folding Pathways Using Ensemble ModelsSolomon Shenker, Charles W. O Donnell, Srinivas Devadas, Bonnie Berger, Jérôme Waldispühl. 408-423 [doi]
- Optimally Orienting Physical NetworksDana Silverbush, Michael Elberfeld, Roded Sharan. 424-436 [doi]
- Opera: Reconstructing Optimal Genomic Scaffolds with High-Throughput Paired-End SequencesSong Gao, Niranjan Nagarajan, Wing-Kin Sung. 437-451 [doi]
- Increasing Power of Groupwise Association Test with Likelihood Ratio TestJae Hoon Sul, Buhm Han, Eleazar Eskin. 452-467 [doi]
- Conservative Extensions of Linkage Disequilibrium Measures from Pairwise to Multi-loci and Algorithms for Optimal Tagging SNP SelectionRyan Tarpine, Fumei Lam, Sorin Istrail. 468-482 [doi]
- Protein Loop Closure Using Orientational Restraints from NMR DataChittaranjan Tripathy, Jianyang Zeng, Pei Zhou, Bruce Randall Donald. 483-498 [doi]
- ::::De Novo:::: Discovery of Mutated Driver Pathways in CancerFabio Vandin, Eli Upfal, Benjamin J. Raphael. 499-500 [doi]
- An Unbiased Adaptive Sampling Algorithm for the Exploration of RNA Mutational Landscapes under Evolutionary PressureJérôme Waldispühl, Yann Ponty. 501-515 [doi]
- Nonparametric Combinatorial Sequence ModelsFabian L. Wauthier, Michael I. Jordan, Nebojsa Jojic. 516-530 [doi]
- Algorithms for MDC-Based Multi-locus Phylogeny InferenceYun Yu, Tandy Warnow, Luay Nakhleh. 531-545 [doi]
- Rich Parameterization Improves RNA Structure PredictionShay Zakov, Yoav Goldberg, Michael Elhadad, Michal Ziv-Ukelson. 546-562 [doi]
- A Bayesian Approach for Determining Protein Side-Chain Rotamer Conformations Using Unassigned NOE DataJianyang Zeng, Kyle E. Roberts, Pei Zhou, Bruce Randall Donald. 563-578 [doi]