Abstract is missing.
- Protein Structure by Semidefinite Facial ReductionBabak Alipanahi, Nathan Krislock, Ali Ghodsi, Henry Wolkowicz, Logan Donaldson, Ming Li. 1-11 [doi]
- Ancestry Inference in Complex Admixtures via Variable-Length Markov Chain Linkage ModelsSivan Bercovici, Jesse M. Rodriguez, Megan Elmore, Serafim Batzoglou. 12-28 [doi]
- Charge Group Partitioning in Biomolecular SimulationStefan Canzar, Mohammed El-Kebir, René Pool, Khaled M. Elbassioni, Alpeshkumar K. Malde, Alan E. Mark, Daan P. Geerke, Leen Stougie, Gunnar W. Klau. 29-43 [doi]
- Increased Methylation Variation in Epigenetic Domains across Cancer TypesHéctor Corrada Bravo. 44 [doi]
- Estimating the Accuracy of Multiple Alignments and its Use in Parameter AdvisingDan F. DeBlasio, Travis J. Wheeler, John D. Kececioglu. 45-59 [doi]
- Quantifying the Dynamics of Coupled Networks of Switches and OscillatorsMatthew R. Francis, Elana J. Fertig. 60-61 [doi]
- lobSTR: A Short Tandem Repeat Profiler for Personal GenomesMelissa Gymrek, David Golan, Saharon Rosset, Yaniv Erlich. 62-63 [doi]
- Hap-seq: An Optimal Algorithm for Haplotype Phasing with Imputation Using Sequencing DataDan He, Buhm Han, Eleazar Eskin. 64-78 [doi]
- Ballast: A Ball-Based Algorithm for Structural MotifsLu He, Fabio Vandin, Gopal Pandurangan, Chris Bailey-Kellogg. 79-93 [doi]
- Evolution of Genome Organization by Duplication and Loss: An Alignment ApproachPatrick Holloway, Krister M. Swenson, David H. Ardell, Nadia El-Mabrouk. 94-112 [doi]
- LoopWeaver - Loop Modeling by the Weighted Scaling of Verified ProteinsDaniel Holtby, Shuai Cheng Li, Ming Li. 113-126 [doi]
- A Robust Method for Transcript Quantification with RNA-seq DataYan Huang, Yin Hu, Corbin D. Jones, James N. MacLeod, Derek Y. Chiang, Yufeng Liu, Jan F. Prins, Jinze Liu. 127-147 [doi]
- Modeling the Breakage-Fusion-Bridge Mechanism: Combinatorics and Cancer GenomicsMarcus Kinsella, Vineet Bafna. 148-162 [doi]
- TrueSight: Self-training Algorithm for Splice Junction Detection Using RNA-seqYang Li, Hong-Mei Li, Paul Burns, Mark Borodovsky, Gene E. Robinson, Jian Ma. 163-164 [doi]
- Synthetic Sequence Design for Signal Location SearchYaw-Ling Lin, Charles B. Ward, Steven Skiena. 165-179 [doi]
- The Three-Dimensional Architecture of a Bacterial Genome and Its Alteration by Genetic PerturbationMarc A. Martí-Renom. 180 [doi]
- Discovery of Complex Genomic Rearrangements in Cancer Using High-Throughput SequencingAndrew McPherson, Chunxiao Wu, Alexander Wyatt, Sohrab P. Shah, Colin Collins, Süleyman Cenk Sahinalp. 181-182 [doi]
- Network-Based Prediction and Analysis of HIV Dependency FactorsT. M. Murali, Matthew D. Dyer, David Badger, Brett M. Tyler, Michael G. Katze. 183 [doi]
- Structure-Guided Deimmunization of Therapeutic ProteinsAndrew S. Parker, Karl E. Griswold, Chris Bailey-Kellogg. 184-198 [doi]
- Evidence for Widespread Association of Mammalian Splicing and Conserved Long-Range RNA StructuresDmitri D. Pervouchine, Ekaterina Khrameeva, Marina Pichugina, Olexii Nikolaienko, Mikhail S. Gelfand, Petr Rubtsov, Andrey A. Mironov. 199 [doi]
- Pathset Graphs: A Novel Approach for Comprehensive Utilization of Paired Reads in Genome AssemblySon K. Pham, Dmitry Antipov, Alexander Sirotkin, Glenn Tesler, Pavel A. Pevzner, Max A. Alekseyev. 200-212 [doi]
- Finding Maximum Colorful Subtrees in PracticeImran Rauf, Florian Rasche, François Nicolas, Sebastian Böcker. 213-223 [doi]
- Recovering the Tree-Like Trend of Evolution Despite Extensive Lateral Genetic Transfer: A Probabilistic AnalysisSebastien Roch, Sagi Snir. 224-238 [doi]
- RESQUE: Network Reduction Using Semi-Markov Random Walk Scores for Efficient Querying of Biological Networks (Extended Abstract)Sayed Mohammad Ebrahim Sahraeian, Byung-Jun Yoon. 239-240 [doi]
- Detecting SNP-Induced Structural Changes in RNA: Application to Disease StudiesRaheleh Salari, Chava Kimchi-Sarfaty, Michael M. Gottesman, Teresa M. Przytycka. 241-243 [doi]
- A Model for Biased Fractionation after Whole Genome DuplicationDavid Sankoff, Chunfang Zheng, Baoyong Wang. 244 [doi]
- Exact Pattern Matching for RNA Structure EnsemblesChristina Schmiedl, Mathias Möhl, Steffen Heyne, Mika Amit, Gad M. Landau, Sebastian Will, Rolf Backofen. 245-260 [doi]
- Reconstructing Boolean Models of SignalingRoded Sharan, Richard M. Karp. 261-271 [doi]
- Alignment-Free Sequence Comparison Based on Next Generation Sequencing Reads: Extended AbstractKai Song, Jie Ren, Zhiyuan Zhai, Xuemei Liu, Minghua Deng, Fengzhu Sun. 272-285 [doi]
- Differential Oestrogen Receptor Binding is Associated with Clinical Outcome in Breast CancerRory Stark. 286 [doi]
- Simultaneous Reconstruction of Multiple Signaling Pathways via the Prize-Collecting Steiner Forest ProblemNurcan Tuncbag, Alfredo Braunstein, Andrea Pagnani, Shao-Shan Carol Huang, Jennifer T. Chayes, Christian Borgs, Riccardo Zecchina, Ernest Fraenkel. 287-301 [doi]
- Function-Function Correlated Multi-Label Protein Function Prediction over Interaction NetworksHua Wang, Heng Huang, Chris H. Q. Ding. 302-313 [doi]
- Predicting Protein-Protein Interactions from Multimodal Biological Data Sources via Nonnegative Matrix Tri-FactorizationHua Wang, Heng Huang, Chris H. Q. Ding, Feiping Nie. 314-325 [doi]
- CNVeM: Copy Number Variation Detection Using Uncertainty of Read MappingZhanyong Wang, Farhad Hormozdiari, Wen-Yun Yang, Eran Halperin, Eleazar Eskin. 326-340 [doi]
- Structure-Based Whole Genome Realignment Reveals Many Novel Non-coding RNAsSebastian Will, Michael Yu, Bonnie Berger. 341 [doi]
- Probabilistic Inference of Viral Quasispecies Subject to RecombinationOsvaldo Zagordi, Armin Töpfer, Sandhya Prabhakaran, Volker Roth, Eran Halperin, Niko Beerenwinkel. 342-354 [doi]
- Simultaneously Learning DNA Motif along with Its Position and Sequence Rank Preferences through EM AlgorithmZhiZhuo Zhang, Cheng-Wei Chang, Hugo Willy, Edwin Cheung, Wing-Kin Sung. 355-370 [doi]