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Journal 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
Large Local Analysis of the Unaligned Genome and Its Application. 19-29 - Guilherme P. Telles, Nalvo F. Almeida
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
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
Probabilistic Inference of Viral Quasispecies Subject to Recombination. 113-123 - Nurcan Tuncbag
Simultaneous Reconstruction of Multiple Signaling Pathways via the Prize-Collecting Steiner Forest Problem. 124-136 - Lu He, Fabio Vandin, Gopal Pandurangan
Ballast: A Ball-based Algorithm for Structural Motifs. 137-151 - Andrew S. Parker, Yoonjoo Choi
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
A Robust Method for Transcript Quantification with RNA-Seq Data. 167-187 - Stefan Canzar
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
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
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
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
Pathset Graphs: A Novel Approach for Comprehensive Utilization of Paired Reads in Genome Assembly. 359-371
Volume 20, Number 5, May 2013
- Andrea Califano
Preface: RECOMB Systems Biology, Regulatory Genomics, and DREAM 2012 Special Issue. 373-374
- Yaron Orenstein
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
Optimal Sparsity Criteria for Network Inference. 398-408 - Christopher L. Poirel, Richard R. Rodrigues, Katherine C. Chen, John J. Tyson
Top-Down Network Analysis to Drive Bottom-Up Modeling of Physiological Processes. 409-418
Volume 20, Number 6, June 2013
- Emmanuel Faure
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
On Topological RNA Interaction Structures. 495-513 - Yalu Wen
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
Model Discrimination in Dynamic Molecular Systems: Application to Parotid De-differentiation Network. 524-539 - Henry C. M. Leung, Siu-Ming Yiu, John Parkinson
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
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
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
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
Graphics Processing Unit-Accelerated Quantitative Trait Loci Detection. 672-686 - Carl Nettelblad
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
Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products. 714-737 - Mukul S. Bansal
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
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
3D Chromosome Modeling with Semi-Definite Programming and Hi-C Data. 831-846 - Shijian Chen, Anqi Wang
SEME: A Fast Mapper of Illumina Sequencing Reads with Statistical Evaluation. 847-860 - Itamar Eskin, Farhad Hormozdiari, Lucía Conde
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
Using Structural and Evolutionary Information to Detect and Correct Pyrosequencing Errors in Noncoding RNAs. 905-919 - Mohammad Javad Sadeh, Giusi Moffa
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
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
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
Calculating Sample Size Estimates for RNA Sequencing Data. 970-978 - Paul D. W. Kirk, Aviva Witkover, Charles R. M. Bangham
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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