| Bacterial Community Reconstruction Using Compressed Sensing / Amnon Amir ; Or Zuk |
| Constrained De Novo Sequencing of Peptides with Application to Conotoxins / Swapnil Bhatia ; Yong J. Kil ; Beatrix Ueberheide ; Brian Chait ; Lemmuel L. Tayo ; Lourdes J. Cruz ; Bingwen Lu ; John R. Yates III ; Marshall Bern |
| Metabolic Network Analysis Demystified / Leonid Chindelevitch ; Aviv Regev ; Bonnie Berger |
| Causal Reasoning on Biological Networks: Interpreting Transcriptional Changes (Extended Abstract) / Daniel Ziemek ; Ahmed Enayetallah ; Ranjit Randhawa ; Ben Sidders ; Christoph Brockel ; Enoch Huang |
| Hapsembler: An Assembler for Highly Polymorphic Genomes / Nilgun Donmez ; Michael Brudno |
| Discovery and Characterization of Chromatin States for Systematic Annotation of the Human Genome / Jason Ernst ; Manolis Kellis |
| Disease Gene Prioritization Based on Topological Similarity in Protein-Protein Interaction Networks / Sinan Erten ; Gurkan Bebek ; Mehmet Koyutürk |
| Understanding Gene Sequence Variation in the Context of Transcription Regulation in Yeast / Irit Gat- Viks ; Renana Meller ; Martin Kupiec ; Ron Shamir |
| Identifying Branched Metabolic Pathways by Merging Linear Metabolic Pathways / Allison P. Heath ; George N. Bennett ; Lydia E. Kavraki |
| A Probabilistic Model For Sequence Alignment with Context-Sensitive Indels / Glenn Hickey ; Mathieu Blanchette |
| Simultaneous Structural Variation Discovery in Multiple Paired-End Sequenced Genomes / Fereydoun Hormozdiari ; Iman Hajirasouliha ; Andrew McPherson ; Evan E. Eichler ; S. Cenk Sahinalp |
| Variable Selection through Correlation Sifting / Jim C. Huang ; Nebojsa Jojic |
| Weighted Genomic Distance Can Hardly Impose a Bound on the Proportion of Transpositions / Shuai Jiang ; Max A. Alekseyev |
| PSAR: Measuring Multiple Sequence Alignment Reliability by Probabilistic Sampling (Extended Abstract) / Jaebum Kim ; Jian Ma |
| Pedigree Reconstruction Using Identity by Descent / Bonnie Kirkpatrick ; Shuai Cheng Li ; Richard M. Karp ; Eran Halperin |
| A Quantitative Model of Glucose Signaling in Yeast Reveals an Incoherent Feed Forward Loop Leading to a Specific, Transient Pulse of Transcription / Sooraj KuttyKrishnan ; Jeffrey Sabina ; Laura Langton ; Mark Johnston ; Michael R. Brent |
| Inferring Mechanisms of Compensation from E-MAP and SGA Data Using Local Search Algorithms for Max Cut / Mark D.M. Leiserson ; Diana Tatar ; Lenore J. Cowen ; Benjamin J. Hescott |
| IsoLasso: A LASSO Regression Approach to RNA-Seq Based Transcriptome Assembly (Extended Abstract) / Wei Li ; Jianxing Feng ; Tao Jiang |
| Haplotype Reconstruction in Large Pedigrees with Many Untyped Individuals / Xin Li ; Jing Li |
| Learning Cellular Sorting Pathways Using Protein Interactions and Sequence Motifs / Tien-ho Lin ; Ziv Bar-Joseph ; Robert F. Murphy |
| A Geometric Arrangement Algorithm for Structure Determination of Symmetric Protein Homo-oligomers from NOEs and RDCs / Jeffrey W. Martin ; Anthony K. Yan ; Chris Bailey-Kellogg ; Pei Zhou ; Bruce R. Donald |
| Paired de Bruijn Graphs: A Novel Approach for Incorporating Mate Pair Information into Genome Assemblers / Paul Medvedev ; Son Pham ; Mark Chaisson ; Glenn Tesler ; Pavel Pevzner |
| An Optimization-Based Sampling Scheme for Phylogenetic Trees / Navodit Misra ; Guy Blelloch ; R. Ravi ; Russell Schwartz |
| Multiplex De Novo Sequencing of Peptide Antibiotics / Hosein Mohimani ; Wei-Ting Liu ; Yu-Liang Yang ; Susana P. Gaudêncio ; William Fenical ; Pieter C. Dorrestein ; Pavel A. Pevzner |
| Fractal and Transgenerational Genetic Effects on Phenotypic Variation and Disease Risk (Invited Talk) / Joe Nadeau |
| AREM: Aligning Short Reads from ChIP-Sequencing by Expectation Maximization / Daniel Newkirk ; Jacob Biesinger ; Alvin Chon ; Kyoko Yokomori ; Xiaohui Xie |
| Blocked Pattern Matching Problem and Its Applications in Proteomics / Julio Ng ; Amihood Amir |
| A Three-Dimensional Model of the Yeast Genome / William Noble ; Zhi-jun Duan ; Mirela Andronescu ; Kevin Schutz ; Sean McIlwain ; Yoo Jung Kim ; Choli Lee ; Jay Shendure ; Stanley Fields ; C. Anthony Blau |
| Optimization of Combinatorial Mutagenesis / Andrew S. Parker ; Karl E. Griswold |
| Seeing More Is Knowing More: V3D Enables Real-Time 3D Visualization and Quantitative Analysis of Large-Scale Biological Image Data Sets / Hanchuan Peng ; Fuhui Long |
| T-IDBA: A de novo Iterative de Bruijn Graph Assembler for Transcriptome (Extended Abstract) / Yu Peng ; Henry C.M. Leung ; S.M. Yiu ; Francis Y.L. Chin |
| Experiment Specific Expression Patterns / Tobias Petri ; Robert Küffner ; Ralf Zimmer |
| Geometric Interpretation of Gene Expression by Sparse Reconstruction of Transcript Profiles / Yosef Prat ; Menachem Fromer ; Michal Linial ; Nathan Linial |
| A Ribosome Flow Model for Analyzing Translation Elongation (Extended Abstract) / Shlomi Reuveni ; Isaac Meilijson ; Eytan Ruppin ; Tamir Tuller |
| Design of Protein-Protein Interactions with a Novel Ensemble-Based Scoring Algorithm / Kyle E. Roberts ; Patrick R. Cushing ; Prisca Boisguerin ; Dean R. Madden |
| Computing Fragmentation Trees from Metabolite Multiple Mass Spectrometry Data / Kerstin Scheubert ; Franziska Hufsky ; Florian Rasche ; Sebastian Böcker |
| Metric Labeling and Semi-metric Embedding for Protein Annotation Prediction / Emre Sefer ; Carl Kingsford |
| Efficient Traversal of Beta-Sheet Protein Folding Pathways Using Ensemble Models / Solomon Shenker ; Charles W. O'Donnell ; Srinivas Devadas ; Jérôme Waldispühl |
| Optimally Orienting Physical Networks / Dana Silverbush ; Michael Elberfeld ; Roded Sharan |
| Opera: Reconstructing Optimal Genomic Scaffolds with High-Throughput Paired-End Sequences / Song Gao ; Niranjan Nagarajan ; Wing-Kin Sung |
| Increasing Power of Groupwise Association Test with Likelihood Ratio Test / Jae Hoon Sul ; Buhm Han ; Eleazar Eskin |
| Conservative Extensions of Linkage Disequilibrium Measures from Pairwise to Multi-loci and Algorithms for Optimal Tagging SNP Selection / Ryan Tarpine ; Fumei Lam ; Sorin Istrail |
| Protein Loop Closure Using Orientational Restraints from NMR Data / Chittaranjan Tripathy ; Jianyang Zeng ; Bruce Randall Donald |
| De Novo Discovery of Mutated Driver Pathways in Cancer / Fabio Vandin ; Eli Upfal ; Benjamin J. Raphael |
| An Unbiased Adaptive Sampling Algorithm for the Exploration of RNA Mutational Landscapes under Evolutionary Pressure / Yann Ponty |
| Nonparametric Combinatorial Sequence Models / Fabian L. Wauthier ; Michael I. Jordan |
| Algorithms for MDC-Based Multi-locus Phylogeny Inference / Yun Yu ; Tandy Warnow ; Luay Nakhleh |
| Rich Parameterization Improves RNA Structure Prediction / Shay Zakov ; Yoav Goldberg ; Michael Elhadad ; Michal Ziv- Ukelson |
| A Bayesian Approach for Determining Protein Side-Chain Rotamer Conformations Using Unassigned NOE Data |
| Author Index |
| Bacterial Community Reconstruction Using Compressed Sensing / Amnon Amir ; Or Zuk |
| Constrained De Novo Sequencing of Peptides with Application to Conotoxins / Swapnil Bhatia ; Yong J. Kil ; Beatrix Ueberheide ; Brian Chait ; Lemmuel L. Tayo ; Lourdes J. Cruz ; Bingwen Lu ; John R. Yates III ; Marshall Bern |
| Metabolic Network Analysis Demystified / Leonid Chindelevitch ; Aviv Regev ; Bonnie Berger |
| Causal Reasoning on Biological Networks: Interpreting Transcriptional Changes (Extended Abstract) / Daniel Ziemek ; Ahmed Enayetallah ; Ranjit Randhawa ; Ben Sidders ; Christoph Brockel ; Enoch Huang |
| Hapsembler: An Assembler for Highly Polymorphic Genomes / Nilgun Donmez ; Michael Brudno |
| Discovery and Characterization of Chromatin States for Systematic Annotation of the Human Genome / Jason Ernst ; Manolis Kellis |
