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ORCIDJournal of Computational Biology, Volume 23
Volume 23, Number 1, January 2016
- Feilong Deng, Shi-Yi Chen:
dbHT-Trans: An Efficient Tool for Filtering the Protein-Encoding Transcripts Assembled by RNA-Seq According to Search for Homologous Proteins. 1-9 - Sabeur Aridhi
, Haïtham Sghaier, Manel Zoghlami, Mondher Maddouri, Engelbert Mephu Nguifo:
Prediction of Ionizing Radiation Resistance in Bacteria Using a Multiple Instance Learning Model. 10-20 - Christopher Girdlestone, Steven Hayward:
The DynDom3D Webserver for the Analysis of Domain Movements in Multimeric Proteins. 21-26 - Cesar M. Camilo, Gustavo M. A. Lima, Fernando V. Maluf, Rafael V. C. Guido, Igor Polikarpov:
HTP-OligoDesigner: An Online Primer Design Tool for High-Throughput Gene Cloning and Site-Directed Mutagenesis. 27-29 - Fabio Vandin, Benjamin J. Raphael, Eli Upfal:
On the Sample Complexity of Cancer Pathways Identification. 30-41 - Ya-Chun Hsiao, Li-Yu Daisy Liu:
A Stepwise Approach of Finding Dependent Variables via Coefficient of Intrinsic Dependence. 42-55 - Yucheng Hu, John S. Lowengrub:
Collective Properties of a Transcription Initiation Model Under Varying Environment. 56-66
Volume 23, Number 2, February 2016
- Yaron Orenstein, Bonnie Berger:
Efficient Design of Compact Unstructured RNA Libraries Covering All k-mers. 67-79 - Leyla Rohani, Derrick J. Morton, Xiao-Qian Wang, Jaideep Chaudhary:
Relative Stability of Wild-Type and Mutant p53 Core Domain: A Molecular Dynamic Study. 80-89 - Daniele Pepe, Jin Hwan Do:
Comparison of Perturbed Pathways in Two Different Cell Models for Parkinson's Disease with Structural Equation Model. 90-101 - Xiaoling Peng, Gang Li, Zhenqiu Liu:
Zero-Inflated Beta Regression for Differential Abundance Analysis with Metagenomics Data. 102-110 - Xiujun (Sylvia) Zhu, Monnie McGee:
Metagenomic Classification Using an Abstraction Augmented Markov Model. 111-122 - Haiou Li, Lu Sun, Sheng Luo, Xiaoyan Xia, Qiang Lyu:
Modeling Protein Loop Structure by Cyclic Coordinate Descent-based Approach. 123-136
Volume 23, Number 3, March 2016
- Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi:
LSG: An External-Memory Tool to Compute String Graphs for Next-Generation Sequencing Data Assembly. 137-149 - Pavel Avdeyev, Shuai Jiang, Sergey Aganezov Jr., Fei Hu, Max A. Alekseyev:
Reconstruction of Ancestral Genomes in Presence of Gene Gain and Loss. 150-164 - Ilan Y. Smoly, Amir Carmel, Yonat Shemer-Avni, Esti Yeger Lotem, Michal Ziv-Ukelson:
Algorithms for Regular Tree Grammar Network Search and Their Application to Mining Human-viral Infection Patterns. 165-179 - Deeparnab Chakrabarty, Sampath Kannan, Kevin Tian:
Detecting Character Dependencies in Stochastic Models of Evolution. 180-191 - Zhenqiu Liu, Shili Lin, Nan Deng, Dermot P. B. McGovern, Steven T. Piantadosi:
Sparse Inverse Covariance Estimation with L0 Penalty for Network Construction with Omics Data. 192-202 - Stefan Canzar, Khaled M. Elbassioni, Mitchell Jones, Julián Mestre:
Resolving Conflicting Predictions from Multimapping Reads. 203-217 - Benjamin Drinkwater, Michael A. Charleston:
RASCAL: A Randomized Approach for Coevolutionary Analysis. 218-227
Volume 23, Number 4, April 2016
- Shi-Yi Chen, Feilong Deng, Ying Huang, Xianbo Jia, Yi-Ping Liu, Song-Jia Lai:
bioOTU: An Improved Method for Simultaneous Taxonomic Assignments and Operational Taxonomic Units Clustering of 16s rRNA Gene Sequences. 229-238 - Arfa Anjum, Seema Jaggi, Eldho Varghese, Shwetank Lall, Arpan Bhowmik, Anil Rai:
Identification of Differentially Expressed Genes in RNA-seq Data of Arabidopsis thaliana: A Compound Distribution Approach. 239-247 - Jose Nelson Perez Castillo, Miguel Gutierrez, Nelson Enrique Vera Parra:
Computational Performance Assessment of k-mer Counting Algorithms. 248-255 - Abdoulaye Sarr, Anya Désilles, Alexandra Fronville, Vincent Rodin:
A Viability Approach for Robustness Measurement, Organizational Autopoiesis, and Cell Turnover in a Multicellular System. 256-269 - Pablo Mier, Miguel A. Andrade-Navarro:
FastaHerder2: Four Ways to Research Protein Function and Evolution with Clustering and Clustered Databases. 270-278 - Michael Laimighofer, Jan Krumsiek, Florian A. Büttner, Fabian J. Theis:
Unbiased Prediction and Feature Selection in High-Dimensional Survival Regression. 279-290 - Daniel Lobo, Jennifer Hammelman, Michael Levin:
MoCha: Molecular Characterization of Unknown Pathways. 291-297
Volume 23, Number 5, May 2016
- Teresa M. Przytycka:
Preface. 299 - Huichao Gong, Sai Zhang, Jiangdian Wang, Haipeng Gong, Jianyang Zeng:
Constructing Structure Ensembles of Intrinsically Disordered Proteins from Chemical Shift Data. 300-310 - Mark A. Hallen, Bruce Randall Donald:
comets (Constrained Optimization of Multistate Energies by Tree Search): A Provable and Efficient Protein Design Algorithm to Optimize Binding Affinity and Specificity with Respect to Sequence. 311-321 - Yifeng Li, Chih-Yu Chen, Wyeth W. Wasserman:
Deep Feature Selection: Theory and Application to Identify Enhancers and Promoters. 322-336 - Mingfu Shao, Bernard M. E. Moret:
A Fast and Exact Algorithm for the Exemplar Breakpoint Distance. 337-346 - Leena Salmela, Kristoffer Sahlin, Veli Mäkinen, Alexandru I. Tomescu:
Gap Filling as Exact Path Length Problem. 347-361 - Rasmus Fonseca, Henry van den Bedem, Julie Bernauer:
Probing RNA Native Conformational Ensembles with Structural Constraints. 362-371 - Seunghak Lee, Aurélie C. Lozano, Prabhanjan Kambadur, Eric P. Xing:
An Efficient Nonlinear Regression Approach for Genome-wide Detection of Marginal and Interacting Genetic Variations. 372-389 - Arnon Mazza, Allon Wagner, Eytan Ruppin, Roded Sharan:
Functional Alignment of Metabolic Networks. 390-399 - Sumudu P. Leelananda, Robert L. Jernigan, Andrzej Kloczkowski:
Predicting Designability of Small Proteins from Graph Features of Contact Maps. 400-411
Volume 23, Number 6, June 2016
- Jonathan D. Jou, Swati Jain, Ivelin Georgiev, Bruce Randall Donald:
BWM*: A Novel, Provable, Ensemble-based Dynamic Programming Algorithm for Sparse Approximations of Computational Protein Design. 413-424 - Emre Sefer, Geet Duggal, Carl Kingsford:
Deconvolution of Ensemble Chromatin Interaction Data Reveals the Latent Mixing Structures in Cell Subpopulations. 425-438 - Yichao Zhou, Yuexin Wu, Jianyang Zeng:
Computational Protein Design Using AND/OR Branch-and-Bound Search. 439-451 - Sharma V. Thankachan, Sriram P. Chockalingam, Yongchao Liu, Alberto Apostolico, Srinivas Aluru:
ALFRED: A Practical Method for Alignment-Free Distance Computation. 452-460 - Ilan Ben-Bassat, Benny Chor:
CRISPR Detection From Short Reads Using Partial Overlap Graphs. 461-471 - Sharma V. Thankachan, Alberto Apostolico, Srinivas Aluru:
A Provably Efficient Algorithm for the k-Mismatch Average Common Substring Problem. 472-482 - Stefano Bonissone, Pavel A. Pevzner:
Immunoglobulin Classification Using the Colored Antibody Graph. 483-494 - Shuo Yang, Shai Carmi, Itsik Pe'er:
Rapidly Registering Identity-by-Descent Across Ancestral Recombination Graphs. 495-507 - David Manescu, Uri Keich:
A Symmetric Length-Aware Enrichment Test. 508-525 - Surojit Biswas, Meredith McDonald, Derek S. Lundberg, Jeffery L. Dangl, Vladimir Jojic:
Learning Microbial Interaction Networks from Metagenomic Count Data. 526-535
Volume 23, Number 7, July 2016
- Zhi-Zhong Chen, Fei Deng, Chao Shen, Yiji Wang, Lusheng Wang:
Better ILP-Based Approaches to Haplotype Assembly. 537-552 - Louxin Zhang:
On Tree-Based Phylogenetic Networks. 553-565 - Jiawen Chen, Zhong-Ru Xie, Yinghao Wu:
Elucidating the Functional Roles of Spatial Organization in Cross-Membrane Signal Transduction by a Hybrid Simulation Method. 566-584 - Boxin Guan, Changsheng Zhang, Jiaxu Ning:
EDGA: A Population Evolution Direction-Guided Genetic Algorithm for Protein-Ligand Docking. 585-596 - Yi Wang, Shuangshuang Wang, Dongjie Zhou, Shuai Yang, Yongchao Xu, Chao Yang, Long Yang:
CsSNP: A Web-Based Tool for the Detecting of Comparative Segments SNPs. 597-602 - Fabrizio Serra, Chiara Romualdi, Federico Fogolari:
Similarity Measures Based on the Overlap of Ranked Genes Are Effective for Comparison and Classification of Microarray Data. 603-614 - Anas Al-Okaily, Chun-Hsi Huang:
ET-Motif: Solving the Exact (l, d)-Planted Motif Problem Using Error Tree Structure. 615-623
Volume 23, Number 8, August 2016
- Jira Jindalertudomdee, Morihiro Hayashida, Tatsuya Akutsu:
Enumeration Method for Structural Isomers Containing User-Defined Structures Based on Breadth-First Search Approach. 625-640 - Eli Goz, Tamir Tuller:
Evidence of a Direct Evolutionary Selection for Strong Folding and Mutational Robustness Within HIV Coding Regions. 641-650 - Ravi Prabhakar More, Hemant J. Purohit:
The Identification of Discriminating Patterns from 16S rRNA Gene to Generate Signature for Bacillus Genus. 651-661 - Metodi Traykov, Slav Angelov, Nicola Yanev:
A New Heuristic Algorithm for Protein Folding in the HP Model. 662-668 - Duo Chen, Jiasong Wang, Ming Yan, Forrest Sheng Bao:
A Complex Prime Numerical Representation of Amino Acids for Protein Function Comparison. 669-677 - Enrique J. deAndrés-Galiana, Juan Luis Fernández Martínez, Stephen T. Sonis:
Design of Biomedical Robots for Phenotype Prediction Problems. 678-692 - Yuandi Wang, Jinyu Cong:
An Improved Model of Nonuniform Coleochaete Cell Division. 693-709
Volume 23, Number 9, September 2016
- Sergey Pirogov, Alexander Rybko, Anastasia S. Kalinina, Mikhail S. Gelfand:
Recombination Processes and Nonlinear Markov Chains. 711-717 - Paola Bonizzoni, Riccardo Dondi, Gunnar W. Klau, Yuri Pirola, Nadia Pisanti, Simone Zaccaria:
On the Minimum Error Correction Problem for Haplotype Assembly in Diploid and Polyploid Genomes. 718-736 - Yuchao Pan, Yuxi Dong, Jingtian Zhou, Mark Hallen, Bruce Randall Donald, Jianyang Zeng, Wei Xu:
cOSPREY: A Cloud-Based Distributed Algorithm for Large-Scale Computational Protein Design. 737-749 - Andy S. Alic, Ignacio Blanquer:
MuffinInfo: HTML5-Based Statistics Extractor from Next-Generation Sequencing Data. 750-755 - Kerstin Gärtner, Andreas Futschik:
Improved Versions of Common Estimators of the Recombination Rate. 756-768 - Eduard Fomin:
A Simple Approach to the Reconstruction of a Set of Points from the Multiset of n2 Pairwise Distances in n2 Steps for the Sequencing Problem: I. Theory. 769-775 - Martin McGrane, Michael A. Charleston:
Biological Network Edit Distance. 776-788
Volume 23, Number 10, October 2016
- Eliza O'Reilly, François Baccelli, Gustavo de Veciana, Haris Vikalo:
End-to-End Optimization of High-Throughput DNA Sequencing. 789-800 - Sergio Gálvez, Adis Ferusic, Francisco José Esteban, Pilar Hernández, Juan Antonio Caballero, Gabriel Dorado:
Speeding-up Bioinformatics Algorithms with Heterogeneous Architectures: Highly Heterogeneous Smith-Waterman (HHeterSW). 801-809 - Troy Hernandez, Jie Yang:
Descriptive Statistics of the Genome: Phylogenetic Classification of Viruses. 810-820 - Shufang Zhao, Yichao He, Xinlu Zhang, Wen Xu, Weili Wu, Suogang Gao:
Group Testing with Multiple Inhibitor Sets and Error-Tolerant and Its Decoding Algorithms. 821-829 - Yucheng Hu, Gongrong Yang:
Sequence Evolution Under Constraints: Lessons Learned from Sudoku. 830-840 - Morgan Madec, François Pêcheux, Yves Gendrault, Elise Rosati, Christophe Lallement, Jacques Haiech:
GeNeDA: An Open-Source Workflow for Design Automation of Gene Regulatory Networks Inspired from Microelectronics. 841-855
Volume 23, Number 11, November 2016
- Christopher L. Barrett, Thomas J. X. Li, Christian M. Reidys:
RNA Secondary Structures Having a Compatible Sequence of Certain Nucleotide Ratios. 857-873 - Strahil Ristov:
A Fast and Simple Pattern Matching with Hamming Distance on Large Alphabets. 874-876 - Wenchuan Guo, Zhenqiu Liu, Shujie Ma:
Nonparametric Regularized Regression for Phenotype-Associated Taxa Selection and Network Construction with Metagenomic Count Data. 877-890 - Mariana Buongermino Pereira, Mikael Wallroth, Erik Kristiansson, Marina Axelson-Fisk:
HattCI: Fast and Accurate attC site Identification Using Hidden Markov Models. 891-902 - Somaye Hashemifar, Qixing Huang, Jinbo Xu:
Joint Alignment of Multiple Protein-Protein Interaction Networks via Convex Optimization. 903-911 - Lamiaa A. Amar, Nahla A. Belal, Shaheera Rashwan:
Comparing Unlabeled Pedigree Graphs via Covering with Bipartite and Path. 912-922
Volume 23, Number 12, December 2016
- Manca Bizjak, Nikolaj Zimic, Miha Mraz, Miha Moskon:
Computational Framework for Modeling Multiple Noncooperative Transcription Factor Binding and Its Application to the Analysis of Nuclear Factor Kappa B Oscillatory Response. 923-933 - Eduard Fomin:
A Simple Approach to the Reconstruction of a Set of Points from the Multiset of n2 Pairwise Distances in n2 Steps for the Sequencing Problem: II. Algorithm. 934-942 - Qiang-Hui Guo, Lisa Hui Sun, Jian Wang:
Enumeration of Extended m-Regular Linear Stacks. 943-956 - Enrique J. deAndrés-Galiana, Juan Luis Fernández Martínez, Leorey N. Saligan, Stephen T. Sonis:
Impact of Microarray Preprocessing Techniques in Unraveling Biological Pathways. 957-968 - Sean B. Johnston, Ronald T. Raines:
PTENpred: A Designer Protein Impact Predictor for PTEN-related Disorders. 969-975 - Stefano Pirrò, Antonella Minutolo, Andrea Galgani, Marina Potestà, Vittorio Colizzi, Carla Montesano:
Bioinformatics Prediction and Experimental Validation of MicroRNAs Involved in Cross-Kingdom Interaction. 976-989
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