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ORCIDJournal of Computational Biology, Volume 20
Volume 20, Number 1, January 2013
- Viet-An Nguyen, Jordan L. Boyd-Graber
, Stephen F. Altschul:
Dirichlet Mixtures, the Dirichlet Process, and the Structure of Protein Space. 1-18 - Lianping Yang, Xiangde Zhang, Tianming Wang, Hegui Zhu:
Large Local Analysis of the Unaligned Genome and Its Application. 19-29 - Guilherme P. Telles, Nalvo F. Almeida, Rosane Minghim, Maria Emília M. T. Walter:
Live Phylogeny. 30-37 - Zhi-Zhong Chen, Lusheng Wang:
An Ultrafast Tool for Minimum Reticulate Networks. 38-41 - Hong Huang, Yongji Li:
MASTtreedist: Visualization of Tree Space Based on Maximum Agreement Subtree. 42-49 - Elizabeth S. Allman, James H. Degnan, John A. Rhodes:
Species Tree Inference by the STAR Method and Its Generalizations. 50-61
Volume 20, Number 2, February 2013
- Benny Chor:
Preface: RECOMB 2012. 63
- Kai Song, Jie Ren, Zhiyuan Zhai, Xuemei Liu, Minghua Deng, Fengzhu Sun:
Alignment-Free Sequence Comparison Based on Next-Generation Sequencing Reads. 64-79 - Dan He, Buhm Han, Eleazar Eskin:
Hap-seq: An Optimal Algorithm for Haplotype Phasing with Imputation Using Sequencing Data. 80-92 - Sebastien Roch, Sagi Snir:
Recovering the Treelike Trend of Evolution Despite Extensive Lateral Genetic Transfer: A Probabilistic Analysis. 93-112 - Armin Töpfer, Osvaldo Zagordi, Sandhya Prabhakaran, Volker Roth, Eran Halperin, Niko Beerenwinkel:
Probabilistic Inference of Viral Quasispecies Subject to Recombination. 113-123 - Nurcan Tuncbag, Alfredo Braunstein, Andrea Pagnani, Shao-Shan Carol Huang, Jennifer T. Chayes, Christian Borgs, Riccardo Zecchina, Ernest Fraenkel:
Simultaneous Reconstruction of Multiple Signaling Pathways via the Prize-Collecting Steiner Forest Problem. 124-136 - Lu He, Fabio Vandin, Gopal Pandurangan, Chris Bailey-Kellogg:
Ballast: A Ball-based Algorithm for Structural Motifs. 137-151 - Andrew S. Parker, Yoonjoo Choi, Karl E. Griswold, Chris Bailey-Kellogg:
Structure-Guided Deimmunization of Therapeutic Proteins. 152-165
Volume 20, Number 3, March 2013
- Yan Huang, Yin Hu, Corbin D. Jones, James N. MacLeod, Derek Y. Chiang, Yufeng Liu, Jan F. Prins, Jinze Liu:
A Robust Method for Transcript Quantification with RNA-Seq Data. 167-187 - Stefan Canzar, Mohammed El-Kebir, René Pool, Khaled M. Elbassioni, Alan E. Mark, Daan P. Geerke, Leen Stougie, Gunnar W. Klau:
Charge Group Partitioning in Biomolecular Simulation. 188-198 - Jesse M. Rodriguez, Sivan Bercovici, Megan Elmore, Serafim Batzoglou:
Ancestry Inference in Complex Admixtures via Variable-length Markov Chain Linkage Models. 199-211 - Daniel Holtby, Shuai Cheng Li, Ming Li:
LoopWeaver: Loop Modeling by the Weighted Scaling of Verified Proteins. 212-223 - Zhanyong Wang, Farhad Hormozdiari, Wen-Yun Yang, Eran Halperin, Eleazar Eskin:
CNVeM: Copy Number Variation Detection Using Uncertainty of Read Mapping. 224-236 - ZhiZhuo Zhang, Cheng Wei Chang, Hugo Willy, Edwin Cheung, Wing-Kin Sung:
Simultaneously Learning DNA Motif Along with Its Position and Sequence Rank Preferences Through Expectation Maximization Algorithm. 237-248 - Roded Sharan, Richard M. Karp:
Reconstructing Boolean Models of Signaling. 249-257
Volume 20, Number 4, April 2013
- John D. Kececioglu, Dan F. DeBlasio:
Accuracy Estimation and Parameter Advising for Protein Multiple Sequence Alignment. 259-279 - Patrick Holloway, Krister M. Swenson, David H. Ardell, Nadia El-Mabrouk:
Ancestral Genome Organization: An Alignment Approach. 280-295 - Babak Alipanahi, Nathan Krislock, Ali Ghodsi, Henry Wolkowicz, Logan Donaldson, Ming Li:
Determining Protein Structures from NOESY Distance Constraints by Semidefinite Programming. 296-310 - Imran Rauf, Florian Rasche, François Nicolas, Sebastian Böcker:
Finding Maximum Colorful Subtrees in Practice. 311-321 - Hua Wang, Heng Huang, Chris H. Q. Ding:
Function-Function Correlated Multi-label Protein Function Prediction over Interaction Networks. 322-343 - Hua Wang, Heng Huang, Chris H. Q. Ding, Feiping Nie:
Predicting Protein-Protein Interactions from Multimodal Biological Data Sources via Nonnegative Matrix Tri-Factorization. 344-358 - Son K. Pham, Dmitry Antipov, Alexander Sirotkin, Glenn Tesler, Pavel A. Pevzner, Max A. Alekseyev:
Pathset Graphs: A Novel Approach for Comprehensive Utilization of Paired Reads in Genome Assembly. 359-371
Volume 20, Number 5, May 2013
- Andrea Califano, Manolis Kellis, Gustavo Stolovitzky:
Preface: RECOMB Systems Biology, Regulatory Genomics, and DREAM 2012 Special Issue. 373-374
- Yaron Orenstein, Eran Mick, Ron Shamir:
RAP: Accurate and Fast Motif Finding Based on Protein-Binding Microarray Data. 375-382 - Roberto Pagliarini, Diego di Bernardo:
A Genome-Scale Modeling Approach to Study Inborn Errors of Liver Metabolism: Toward an In Silico Patient. 383-397 - Andreas Tjärnberg, Torbjörn E. M. Nordling, Matthew Studham, Erik L. L. Sonnhammer:
Optimal Sparsity Criteria for Network Inference. 398-408 - Christopher L. Poirel, Richard R. Rodrigues, Katherine C. Chen, John J. Tyson, T. M. Murali:
Top-Down Network Analysis to Drive Bottom-Up Modeling of Physiological Processes. 409-418
Volume 20, Number 6, June 2013
- Emmanuel Faure, Isabelle S. Peter, Eric H. Davidson:
A New Software Package for Predictive Gene Regulatory Network Modeling and Redesign. 419-423 - Franco P. Preparata:
On Contigs and Coverage. 424-432 - Michael Antosh, David Fox, Leon N. Cooper, Nicola Neretti:
CORaL: Comparison of Ranked Lists for Analysis of Gene Expression Data. 433-443 - Cong-Jun Wang, Rong-Hua Xu, Qiong-Ying Yuan, Yong-Kun Wang, Dong-Wei Shen, Xu-Jing Wang, Wei Gao, Hui Zhang, Hua Jiang:
Bioinformatics Method to Analyze the Mechanism of Pancreatic Cancer Disorder. 444-452 - Shruthi Prabhakara, Raunaq Malhotra, Raj Acharya, Mary Poss:
Mutant-Bin: Unsupervised Haplotype Estimation of Viral Population Diversity Without Reference Genome. 453-463 - Huilan Chang, Hung-Lin Fu, Chih-Huai Shih:
Threshold Group Testing on Inhibitor Model. 464-470
Volume 20, Number 7, July 2013
- Ehsan Behnam, Michael S. Waterman, Andrew D. Smith:
A Geometric Interpretation for Local Alignment-Free Sequence Comparison. 471-485 - Hamidreza Chitsaz, Elmirasadat Forouzmand, Gholamreza Haffari:
An Efficient Algorithm for Upper Bound on the Partition Function of Nucleic Acids. 486-494 - Jing Qin, Christian M. Reidys:
On Topological RNA Interaction Structures. 495-513 - Yalu Wen, Ming Li, Wenjiang J. Fu:
Catching the Genomic Wave in Oligonucleotide Single-Nucleotide Polymorphism Arrays by Modeling Sequence Binding. 514-523 - Jaejik Kim, Jiaxu Li, Srirangapatnam G. Venkatesh, Douglas S. Darling, Grzegorz A. Rempala:
Model Discrimination in Dynamic Molecular Systems: Application to Parotid De-differentiation Network. 524-539 - Henry C. M. Leung, Siu-Ming Yiu, John Parkinson, Francis Y. L. Chin:
IDBA-MT: De Novo Assembler for Metatranscriptomic Data Generated from Next-Generation Sequencing Technology. 540-550
Volume 20, Number 8, August 2013
- Hoyt A. Koepke, Elizabeth Thompson:
Efficient Identification of Equivalences in Dynamic Graphs and Pedigree Structures. 551-570 - Mitsunori Kayano, Seiya Imoto, Rui Yamaguchi, Satoru Miyano:
Multi-omics Approach for Estimating Metabolic Networks Using Low-Order Partial Correlations. 571-582 - Steven Flygare, Michael Campbell, Robert Mars Ross, Barry Moore, Mark Yandell:
ImagePlane: An Automated Image Analysis Pipeline for High-Throughput Screens Using the Planarian Schmidtea mediterranea. 583-592 - Emanuele Giaquinta, Laura Pozzi:
An Effective Exact Algorithm and a New Upper Bound for the Number of Contacts in the Hydrophobic-Polar Two-Dimensional Lattice Model. 593-609 - Lyamine Hedjazi, Marie-Véronique Le Lann, Tatiana Kempowsky, Florence Dalenc, Joseph Aguilar-Martin, Gilles Favre:
Symbolic Data Analysis to Defy Low Signal-to-Noise Ratio in Microarray Data for Breast Cancer Prognosis. 610-620
Volume 20, Number 9, September 2013
- Emanuele Giaquinta, Szymon Grabowski, Esko Ukkonen:
Fast Matching of Transcription Factor Motifs Using Generalized Position Weight Matrix Models. 621-630 - Janusz Dutkowski, Jerzy Tiuryn:
A Probabilistic Model of Neutral and Selective Dynamics of Protein Network Evolution. 631-642 - Sandro Andreotti, Knut Reinert, Stefan Canzar:
The Duplication-Loss Small Phylogeny Problem: From Cherries to Trees. 643-659 - Hervé Seligmann:
Triplex DNA: RNA, 3′-to-5′ Inverted RNA and Protein Coding in Mitochondrial Genomes. 660-671 - Guillaume Chapuis, Olivier Filangi, Jean-Michel Elsen, Dominique Lavenier, Pascale Le Roy:
Graphics Processing Unit-Accelerated Quantitative Trait Loci Detection. 672-686 - Carl Nettelblad, Behrang Mahjani, Sverker Holmgren:
Fast and Accurate Detection of Multiple Quantitative Trait Loci. 687-702 - Xiayu Rao, Dejian Lai, Xuelin Huang:
A New Method for Quantitative Real-Time Polymerase Chain Reaction Data Analysis. 703-711
Volume 20, Number 10, October 2013
- Fengzhu Sun:
Preface: Research in Computational Molecular Biology (RECOMB 2013). 713 - Sergey Nurk, Anton Bankevich, Dmitry Antipov, Alexey A. Gurevich, Anton I. Korobeynikov, Alla L. Lapidus, Andrey D. Prjibelski, Alex Pyshkin, Alexander Sirotkin, Yakov Sirotkin, Ramunas Stepanauskas, Scott R. Clingenpeel, Tanja Woyke, Jeffrey S. McLean, Roger Lasken, Glenn Tesler, Max A. Alekseyev, Pavel A. Pevzner:
Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products. 714-737 - Mukul S. Bansal, Eric J. Alm, Manolis Kellis:
Reconciliation Revisited: Handling Multiple Optima when Reconciling with Duplication, Transfer, and Loss. 738-754 - William A. Bryant, Ali A. Faruqi, John W. Pinney:
Analysis of Metabolic Evolution in Bacteria Using Whole-Genome Metabolic Models. 755-764 - Fei Guo, Shuai Cheng Li, Wenji Ma, Lusheng Wang:
Detecting Protein Conformational Changes in Interactions via Scaling Known Structures. 765-779 - Dan He, Zhanyong Wang, Buhm Han, Laxmi Parida, Eleazar Eskin:
IPED: Inheritance Path-based Pedigree Reconstruction Algorithm Using Genotype Data. 780-791 - Yufeng Wu:
An Algorithm for Constructing Parsimonious Hybridization Networks with Multiple Phylogenetic Trees. 792-804 - Dong Xu, Hua Li, Yang Zhang:
Protein Depth Calculation and the Use for Improving Accuracy of Protein Fold Recognition. 805-816 - Emrah Kostem, Eleazar Eskin:
Efficiently Identifying Significant Associations in Genome-wide Association Studies. 817-830
Volume 20, Number 11, November 2013
- ZhiZhuo Zhang, Guoliang Li, Kim-Chuan Toh, Wing-Kin Sung:
3D Chromosome Modeling with Semi-Definite Programming and Hi-C Data. 831-846 - Shijian Chen, Anqi Wang, Lei M. Li:
SEME: A Fast Mapper of Illumina Sequencing Reads with Statistical Evaluation. 847-860 - Itamar Eskin, Farhad Hormozdiari, Lucía Conde, Jacques Riby, Christine F. Skibola, Eleazar Eskin, Eran Halperin:
eALPS: Estimating Abundance Levels in Pooled Sequencing Using Available Genotyping Data. 861-877 - Lei Deng, Jihong Guan, Xiaoming Wei, Yuan Yi, Qiangfeng Cliff Zhang, Shuigeng Zhou:
Boosting Prediction Performance of Protein-Protein Interaction Hot Spots by Using Structural Neighborhood Properties. 878-891 - Kriti Puniyani, Eric P. Xing:
NP-MuScL: Unsupervised Global Prediction of Interaction Networks from Multiple Data Sources. 892-904 - Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl:
Using Structural and Evolutionary Information to Detect and Correct Pyrosequencing Errors in Noncoding RNAs. 905-919 - Mohammad Javad Sadeh, Giusi Moffa, Rainer Spang:
Considering Unknown Unknowns: Reconstruction of Nonconfoundable Causal Relations in Biological Networks. 920-932 - Raheleh Salari, Syed Shayon Saleh, Dorna Kashef Haghighi, David Khavari, Daniel E. Newburger, Robert B. West, Arend Sidow, Serafim Batzoglou:
Inference of Tumor Phylogenies with Improved Somatic Mutation Discovery. 933-944
Volume 20, Number 12, December 2013
- Dima Blokh, Danny Segev, Roded Sharan:
The Approximability of Shortest Path-Based Graph Orientations of Protein-Protein Interaction Networks. 945-957 - Avraham A. Melkman, Tatsuya Akutsu:
An Improved Satisfiability Algorithm for Nested Canalyzing Functions and its Application to Determining a Singleton Attractor of a Boolean Network. 958-969 - Steven N. Hart, Terry M. Therneau, Yuji Zhang, Gregory A. Poland, Jean-Pierre A. Kocher:
Calculating Sample Size Estimates for RNA Sequencing Data. 970-978 - Paul D. W. Kirk, Aviva Witkover, Charles R. M. Bangham, Sylvia Richardson, Alexandra M. Lewin, Michael P. H. Stumpf:
Balancing the Robustness and Predictive Performance of Biomarkers. 979-989 - Yuval Nov, Alexander Fulton, Karl-Erich Jaeger:
Optimal Scanning of All Single-Point Mutants of a Protein. 990-997
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