Abstract is missing.
- Reconciliation Revisited: Handling Multiple Optima When Reconciling with Duplication, Transfer, and LossMukul S. Bansal, Eric J. Alm, Manolis Kellis. 1-13 [doi]
- SEME: A Fast Mapper of Illumina Sequencing Reads with Statistical EvaluationShijian Chen, Anqi Wang, Lei M. Li. 14-29 [doi]
- Dissecting Cancer Heterogeneity with a Probabilistic Genotype-Phenotype ModelDong-Yeon Cho, Teresa M. Przytycka. 30-31 [doi]
- eALPS: Estimating Abundance Levels in Pooled Sequencing Using Available Genotyping DataItamar Eskin, Farhad Hormozdiari, Lucía Conde, Jacques Riby, Chris Skibola, Eleazar Eskin, Eran Halperin. 32-44 [doi]
- Analysis of Metabolic Evolution in Bacteria Using Whole-Genome Metabolic ModelsAli A. Faruqi, William A. Bryant, John W. Pinney. 45-57 [doi]
- Detecting Protein Conformational Changes in Interactions via Scaling Known StructuresFei Guo, Shuai Cheng Li, Wenji Ma, Lusheng Wang. 58-74 [doi]
- IPED: Inheritance Path Based Pedigree Reconstruction Algorithm Using Genotype DataDan He, Zhanyong Wang, Buhm Han, Laxmi Parida, Eleazar Eskin. 75-87 [doi]
- An Optimal Algorithm for Building the Majority Rule Consensus TreeJesper Jansson, Chuanqi Shen, Wing-Kin Sung. 88-99 [doi]
- UniNovo: A Universal Tool for de Novo Peptide SequencingKyowon Jeong, Sangtae Kim, Pavel A. Pevzner. 100-117 [doi]
- Efficiently Identifying Significant Associations in Genome-Wide Association StudiesEmrah Kostem, Eleazar Eskin. 118-131 [doi]
- Identification of Ultramodified Proteins Using Top-Down SpectraXiaowen Liu, Shawna Hengel, Si Wu, Nikola Tolic, Ljiljana Pasa-Tolic, Pavel A. Pevzner. 132-144 [doi]
- Distinguishing between Genomic Regions Bound by Paralogous Transcription FactorsAlina Munteanu, Raluca Gordân. 145-157 [doi]
- Assembling Genomes and Mini-metagenomes from Highly Chimeric ReadsSergey Nurk, Anton Bankevich, Dmitry Antipov, Alexey A. Gurevich, Anton Korobeynikov, Alla Lapidus, Andrey Prjibelsky, Alex Pyshkin, Alexander Sirotkin, Yakov Sirotkin, Ramunas Stepanauskas, Jeffrey S. McLean, Roger Lasken, Scott R. Clingenpeel, Tanja Woyke, Glenn Tesler, Max A. Alekseyev, Pavel A. Pevzner. 158-170 [doi]
- Inferring Intra-tumor Heterogeneity from High-Throughput DNA Sequencing DataLayla Oesper, Ahmad Mahmoody, Benjamin J. Raphael. 171-172 [doi]
- NP-MuScL: Unsupervised Global Prediction of Interaction Networks from Multiple Data SourcesKriti Puniyani, Eric P. Xing. 173-185 [doi]
- High Resolution Modeling of Chromatin InteractionsChristopher Reeder, David Gifford. 186-198 [doi]
- A Linear Inside-Outside Algorithm for Correcting Sequencing Errors in Structured RNAsVladimir Reinharz, Yann Ponty, Jérôme Waldispühl. 199-211 [doi]
- An Accurate Method for Inferring Relatedness in Large Datasets of Unphased Genotypes via an Embedded Likelihood-Ratio TestJesse M. Rodriguez, Serafim Batzoglou, Sivan Bercovici. 212-229 [doi]
- Learning Natural Selection from the Site Frequency SpectrumRoy Ronen, Nitin Udpa, Eran Halperin, Vineet Bafna. 230-233 [doi]
- Considering Unknown Unknowns - Reconstruction of Non-confoundable Causal Relations in Biological NetworksMohammad Javad Sadeh, Giusi Moffa, Rainer Spang. 234-248 [doi]
- Inference of Tumor Phylogenies with Improved Somatic Mutation DiscoveryRaheleh Salari, Syed Shayon Saleh, Dorna Kashef Haghighi, David Khavari, Daniel E. Newburger, Robert B. West, Arend Sidow, Serafim Batzoglou. 249-263 [doi]
- Abstract: Using the Fast Fourier Transform to Accelerate the Computational Search for RNA Conformational SwitchesEvan Senter, Saad Sheikh, Iván Dotú, Yann Ponty, Peter Clote. 264-265 [doi]
- MethylCRF, an Algorithm for Estimating Absolute Methylation Levels at Single CpG Resolution from Methylation Enrichment and Restriction Enzyme Sequencing MethodsMichael Stevens, Jeffrey B. Cheng, Mingchao Xie, Joseph F. Costello, Ting Wang. 266-268 [doi]
- Counting Motifs in the Entire Biological Network from Noisy and Incomplete Data - (Extended Abstract)Ngoc Hieu Tran, Kwok Pui Choi, Louxin Zhang. 269-270 [doi]
- Extracting Structural Information from Residual Chemical Shift Anisotropy: Analytic Solutions for Peptide Plane Orientations and Applications to Determine Protein StructureChittaranjan Tripathy, Anthony K. Yan, Pei Zhou, Bruce Randall Donald. 271-284 [doi]
- Genome-Wide Survival Analysis of Somatic Mutations in CancerFabio Vandin, Alexandra Papoutsaki, Benjamin J. Raphael, Eli Upfal. 285-286 [doi]
- Spectral Library Generating Function for Assessing Spectrum-Spectrum Match SignificanceMingxun Wang, Nuno Bandeira. 287-288 [doi]
- SPARSE: Quadratic Time Simultaneous Alignment and Folding of RNAs without Sequence-Based HeuristicsSebastian Will, Christina Schmiedl, Milad Miladi, Mathias Möhl, Rolf Backofen. 289-290 [doi]
- An Algorithm for Constructing Parsimonious Hybridization Networks with Multiple Phylogenetic TreesYufeng Wu. 291-303 [doi]
- Fast and Accurate Calculation of Protein Depth by Euclidean Distance TransformDong Xu, Hua Li, Yang Zhang. 304-316 [doi]
- Inference of Spatial Organizations of Chromosomes Using Semi-definite Embedding Approach and Hi-C DataZhiZhuo Zhang, Guoliang Li, Kim-Chuan Toh, Wing-Kin Sung. 317-332 [doi]
- Boosting Prediction Performance of Protein-Protein Interaction Hot Spots by Using Structural Neighborhood Properties - (Extended Abstract)Lei Deng, Jihong Guan, Xiaoming Wei, Yuan Yi, Shuigeng Zhou. 333-344 [doi]