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ORCIDJournal of Computational Biology, Volume 19
Volume 19, Number 1, January 2012
- Hugo Devillers, Sophie Schbath
:
Separating Significant Matches from Spurious Matches in DNA Sequences. 1-12 - Afshin Fayyaz Movaghar, Guillaume Launay, Sophie Schbath, Jean-François Gibrat, François Rodolphe:
Statistical Significance of Threading Scores. 13-29 - Guy Karlebach, Ron Shamir:
Constructing Logical Models of Gene Regulatory Networks by Integrating Transcription Factor-DNA Interactions with Expression Data: An Entropy-Based Approach. 30-41 - Xiguo Yuan, David J. Miller, Junying Zhang, David M. Herrington, Yue Wang:
An Overview of Population Genetic Data Simulation. 42-54 - Ritsuko Onuki, Ryo Yamada, Rui Yamaguchi, Minoru Kanehisa, Tetsuo Shibuya:
Population Model-Based Inter-Diplotype Similarity Measure for Accurate Diplotype Clustering. 55-67 - Li-Yeh Chuang, Cheng-Huei Yang, Jung-Chike Li, Cheng-Hong Yang:
A Hybrid BPSO-CGA Approach for Gene Selection and Classification of Microarray Data. 68-82 - Pawel Winter, Rasmus Fonseca:
Adjustable Chain Trees for Proteins. 83-99
Volume 19, Number 2, February 2012
- Andrea Califano, Manolis Kellis, Gustavo Stolovitzky:
Preface: RECOMB Systems Biology, Regulatory Genomics, and DREAM 2011 Special Issue. 101 - Emanuel J. V. Gonçalves, Rui Pereira, Isabel Rocha, Miguel Rocha:
Optimization Approaches for the In Silico Discovery of Optimal Targets for Gene Over/Underexpression. 102-114 - Roee Amit:
Anti-Cooperative and Cooperative Protein-Protein Interactions between TetR Isoforms on Synthetic Enhancers. 115-125 - Thomas Sakoparnig, Tobias Kockmann, Renato Paro, Christian Beisel, Niko Beerenwinkel:
Binding Profiles of Chromatin-Modifying Proteins Are Predictive for Transcriptional Activity and Promoter-Proximal Pausing. 126-138 - Nnamdi E. Ihuegbu, Gary D. Stormo, Jeremy Buhler:
Fast, Sensitive Discovery of Conserved Genome-Wide Motifs. 139-147 - Carlo Cosentino, Luca Salerno, Antonio Passanti, Alessio Merola, Declan G. Bates, Francesco Amato:
Structural Bistability of the GAL Regulatory Network and Characterization of its Domains of Attraction. 148-162 - Yael Silberberg, Assaf Gottlieb, Martin Kupiec, Eytan Ruppin, Roded Sharan:
Large-Scale Elucidation of Drug Response Pathways in Humans. 163-174 - Xinyi Yang, Jennifer E. Dent, Christine Nardini:
An S-System Parameter Estimation Method (SPEM) for Biological Networks. 175-187 - Federica Eduati, Barbara Di Camillo, Michael Karbiener, Marcel Scheideler, Davide Corà, Michele Caselle, Gianna Toffolo:
Dynamic Modeling of miRNA-mediated Feed-Forward Loops. 188-199 - Alexandra Dana, Tamir Tuller:
Efficient Manipulations of Synonymous Mutations for Controlling Translation Rate: An Analytical Approach. 200-231 - Liram Vardi, Eytan Ruppin, Roded Sharan:
A Linearized Constraint-Based Approach for Modeling Signaling Networks. 232-240 - Yi Wang, Henry C. M. Leung, Siu-Ming Yiu, Francis Y. L. Chin:
MetaCluster 4.0: A Novel Binning Algorithm for NGS Reads and Huge Number of Species. 241-249
Volume 19, Number 3, March 2012
- Kai Song, Ze Zhang, Tuopeng Tong, Fang Wu:
Classifier Assessment and Feature Selection for Recognizing Short Coding Sequences of Human Genes. 251-260 - Alberto Ceselli, Sandro Luciano Fornili, Giovanni Righini:
Algorithms for the Design of Maximum Hydropathic Complementarity Molecules. 261-270 - Olivier David, Catherine Larédo, Raphaël Leblois, Brigitte Schaeffer, Nicolas Vergne:
Coalescent-Based DNA Barcoding: Multilocus Analysis and Robustness. 271-278 - Paolo Carnevali, Jonathan Baccash, Aaron L. Halpern, Igor Nazarenko, Geoffrey B. Nilsen, Krishna P. Pant, Jessica C. Ebert, Anushka Brownley, Matt Morenzoni, Vitali Karpinchyk, Bruce Martin, Dennis G. Ballinger, Radoje Drmanac:
Computational Techniques for Human Genome Resequencing Using Mated Gapped Reads. 279-292 - Ethan M. Jewett, Noah A. Rosenberg:
iGLASS: An Improvement to the GLASS Method for Estimating Species Trees from Gene Trees. 293-315
- Nikita A. Sakhanenko, David J. Galas:
Probabilistic Logic Methods and Some Applications to Biology and Medicine. 316-336
Volume 19, Number 4, April 2012
- Banu Dost, Nuno Bandeira, Xiangqian Li, Zhouxin Shen, Steve Briggs, Vineet Bafna:
Accurate Mass Spectrometry Based Protein Quantification via Shared Peptides. 337-348 - Sébastien Li-Thiao-Té, Benno Schwikowski:
Feature Detection with Controlled Error Rates in LC/MS Images. 349-364 - Thomas K. F. Wong, Siu-Ming Yiu:
Structural Alignment of RNA with Triple Helix Structure. 365-378 - Aleksandar Stojmirovic, Yi-Kuo Yu:
Information Flow in Interaction Networks II: Channels, Path Lengths, and Potentials. 379-403 - Yen Hung Chen:
The k Partition-Distance Problem. 404-417 - Serena Arima, Luca Tardella:
Improved Harmonic Mean Estimator for Phylogenetic Model Evidence. 418-438 - Arvind Gupta, Ján Manuch, Ladislav Stacho, Xiaohong Zhao:
Algorithm for Haplotype Inference via Galled-Tree Networks with Simple Galls. 439-454
Volume 19, Number 5, May 2012
- Anton Bankevich, Sergey Nurk, Dmitry Antipov, Alexey A. Gurevich, Mikhail Dvorkin, Alexander S. Kulikov, Valery M. Lesin, Sergey I. Nikolenko, Son K. Pham, Andrey D. Prjibelski, Alex Pyshkin, Alexander Sirotkin, Nikolay Vyahhi, Glenn Tesler, Max A. Alekseyev, Pavel A. Pevzner:
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing. 455-477 - Deepayan Sarkar, Steve Goldstein, David C. Schwartz, Michael A. Newton:
Statistical Significance of Optical Map Alignments. 478-492 - Genki Terashi, Tetsuo Shibuya, Mayuko Takeda-Shitaka:
LB3D: A Protein Three-Dimensional Substructure Search Program Based on the Lower Bound of a Root Mean Square Deviation Value. 493-503 - Nimrod Bar-Yaakov, Zehava Grossman, Nathan Intrator:
Using Iterative Ridge Regression to Explore Associations Between Conditioned Variables. 504-518 - Mikael Falconnet, Sarah Behrens:
Accurate Estimations of Evolutionary Times in the Context of Strong CpG Hypermutability. 519-531 - Michiaki Hamada, Kiyoshi Asai:
A Classification of Bioinformatics Algorithms from the Viewpoint of Maximizing Expected Accuracy (MEA). 532-549 - Sarah Behrens, Cyril Nicaud, Pierre Nicodème:
An Automaton Approach for Waiting Times in DNA Evolution. 550-562 - Maysson Al-Haj Ibrahim, Sabah A. Jassim, Michael Anthony Cawthorne, Kenneth Langlands:
A Topology-Based Score for Pathway Enrichment. 563-573
Volume 19, Number 6, June 2012
- Ting Chen, Paul Marjoram, Fengzhu Sun, Xianghong Jasmine Zhou:
Preface: Special Issue. 575-576 - Derek Aguiar, Sorin Istrail:
HapCompass: A Fast Cycle Basis Algorithm for Accurate Haplotype Assembly of Sequence Data. 577-590 - Md. Shamsuzzoha Bayzid, Tandy J. Warnow:
Estimating Optimal Species Trees from Incomplete Gene Trees Under Deep Coalescence. 591-605 - Zachary Frazier, Frank Alber:
A Computational Approach to Increase Time Scales in Brownian Dynamics-Based Reaction-Diffusion Modeling. 606-618 - Qinghui Gao, Christine Ho, Yingmin Jia, Jingyi Jessica Li, Haiyan Huang:
Biclustering of Linear Patterns In Gene Expression Data. 619-631 - Laura J. Helmkamp, Ethan M. Jewett, Noah A. Rosenberg:
Improvements to a Class of Distance Matrix Methods for Inferring Species Trees from Gene Trees. 632-649 - Paul Joyce, Alan Genz, Erkan Ozge Buzbas:
Efficient Simulation and Likelihood Methods for Non-Neutral Multi-Allele Models. 650-661 - Marcus Kinsella, Vineet Bafna:
Combinatorics of the Breakage-Fusion-Bridge Mechanism. 662-678 - Yinglei Lai:
Change-Point Analysis of Paired Allele-Specific Copy Number Variation Data. 679-693 - Ofer Lavi, Gideon Dror, Ron Shamir:
Network-Induced Classification Kernels for Gene Expression Profile Analysis. 694-709 - Wenyuan Li, Chao Dai, Chun-Chi Liu, Xianghong Jasmine Zhou:
Algorithm to Identify Frequent Coupled Modules from Two-Layered Network Series: Application to Study Transcription and Splicing Coupling. 710-730 - Li Luo, Yun Zhu, Momiao Xiong:
A Novel Genome-Information Content-Based Statistic for Genome-Wide Association Analysis Designed for Next-Generation Sequencing Data. 731-744 - Ioanna Manolopoulou, Brent C. Emerson:
Phylogeographic Ancestral Inference Using the Coalescent Model on Haplotype Trees. 745-755 - Mary Sara McPeek:
BLUP Genotype Imputation for Case-Control Association Testing with Related Individuals and Missing Data. 756-765 - Shengyu Ni, Martin Vingron:
R2KS: A Novel Measure for Comparing Gene Expression Based on Ranked Gene Lists. 766-775 - Dhruv Grover, Juan Nunez-Iglesias:
Betamax: Towards Optimal Sampling Strategies for High-Throughput Screens. 776-784 - Tiago Rito, Charlotte M. Deane, Gesine Reinert:
The Importance of Age and High Degree, in Protein-Protein Interaction Networks. 785-795 - Sophie Schbath, Véronique Martin, Matthias Zytnicki, Julien Fayolle, Valentin Loux, Jean-François Gibrat:
Mapping Reads on a Genomic Sequence: An Algorithmic Overview and a Practical Comparative Analysis. 796-813 - Mingjie Wang, Yuzhen Ye, Haixu Tang:
A de Bruijn Graph Approach to the Quantification of Closely-Related Genomes in a Microbial Community. 814-825 - Jialin Xu, Yu Zhang:
A Generalized Linear Model for Peak Calling in ChIP-Seq Data. 826-838 - Zhiyuan Zhai, Gesine Reinert, Kai Song, Michael S. Waterman, Yihui Luan, Fengzhu Sun:
Normal and Compound Poisson Approximations for Pattern Occurrences in NGS Reads. 839-854 - Jing Zhang, C.-C. Jay Kuo, Liang Chen:
VERSE: A Varying Effect Regression for Splicing Elements Discovery. 855-865
Volume 19, Number 7, July 2012
- Hillary S. W. Han, Christian M. Reidys:
The 5′-3′ Distance of RNA Secondary Structures. 867-878 - Pawel Gniewek, Andrzej Kolinski, Dominik Gront:
Optimization of Profile-to-Profile Alignment Parameters for One-Dimensional Threading. 879-886 - Torben Tvedebrink, Poul Svante Eriksen, Helle Smidt Mogensen, Niels Morling:
Identifying Contributors of DNA Mixtures by Means of Quantitative Information of STR Typing. 887-902 - Yichao He, Haiyan Tian, Xinlu Zhang, Zhiwei Wang, Suogang Gao:
Nonadaptive Algorithms for Threshold Group Testing with Inhibitors and Error-Tolerance. 903-910 - Fabio Cunial, Alberto Apostolico:
Phylogeny Construction with Rigid Gapped Motifs. 911-927 - Jørgen E. Andersen, Fenix W. D. Huang, Robert C. Penner, Christian M. Reidys:
Topology of RNA-RNA Interaction Structures. 928-943
Volume 19, Number 8, August 2012
- Eyal Cohen, Benny Chor:
Detecting Phylogenetic Signals in Eukaryotic Whole Genome Sequences. 945-956 - Gangman Yi, Michael R. Thon, Sing-Hoi Sze:
Supervised Protein Family Classification and New Family Construction. 957-967 - Elias August:
Using Noise for Model-Testing. 968-977 - Matthew Sperrin, Thomas Jaki:
Recovering Independent Associations in Genetics: A Comparison. 978-987
Volume 19, Number 9, September 2012
- Hamid Bolouri, Walter L. Ruzzo:
Integration of 198 ChIP-seq Datasets Reveals Human cis-Regulatory Regions. 989-997 - Bonnie Kirkpatrick, Yakir Reshef, Hilary K. Finucane, Haitao Jiang, Binhai Zhu, Richard M. Karp:
Comparing Pedigree Graphs. 998-1014 - Miguel González, Cristina Gutiérrez, Rodrigo Martínez:
Expectation-Maximization Algorithm for Determining Natural Selection of Y-Linked Genes Through Two-Sex Branching Processes. 1015-1026 - Min Wu, Xiaoli Li, Chee Keong Kwoh, See-Kiong Ng, Limsoon Wong:
Discovery of Protein Complexes with Core-Attachment Structures from Tandem Affinity Purification (TAP) Data. 1027-1042 - Mahmud Shahriar Hossain, Monika Akbar, Nicholas F. Polys:
Narratives in the Network: Interactive Methods for Mining Cell Signaling Networks. 1043-1059 - Christina Schindler, Wolfgang B. Fischer:
Sequence Alignment of Viral Channel Proteins with Cellular Ion Channels. 1060-1072 - Yun Cui, Jesper Jansson, Wing-Kin Sung:
Polynomial-Time Algorithms for Building a Consensus MUL-Tree. 1073-1088
Volume 19, Number 10, October 2012
- Tomoya Mori, Takeyuki Tamura, Daiji Fukagawa, Atsuhiro Takasu, Etsuji Tomita, Tatsuya Akutsu:
A Clique-Based Method Using Dynamic Programming for Computing Edit Distance Between Unordered Trees. 1089-1104 - Hillary S. W. Han, Christian M. Reidys:
A Phase Transition in Energy-Filtered RNA Secondary Structures. 1105-1119 - Azadeh Saffarian, Mathieu Giraud, Antoine de Monte, Hélène Touzet:
RNA Locally Optimal Secondary Structures. 1120-1133 - Markus E. Nebel, Frank Weinberg:
Algebraic and Combinatorial Properties of Common RNA Pseudoknot Classes with Applications. 1134-1150 - Huwaida S. Rabie, Ian W. Saunders:
A Simulation Study to Assess a Variable Selection Method for Selecting Single Nucleotide Polymorphisms Associated with Disease. 1151-1161 - Rajat Shuvro Roy, Kevin C. Chen, Anirvan M. Sengupta, Alexander Schliep:
SLIQ: Simple Linear Inequalities for Efficient Contig Scaffolding. 1162-1175 - Narendra M. Dixit, Piyush Srivastava, Nisheeth K. Vishnoi:
A Finite Population Model of Molecular Evolution: Theory and Computation. 1176-1202 - Rasmus Fonseca, Pawel Winter:
Bounding Volumes for Proteins: A Comparative Study. 1203-1213
Volume 19, Number 11, November 2012
- I-Lin Lu, Hsiuying Wang:
Protein-specific Scoring Method for Ligand Discovery. 1215-1226 - Céline Scornavacca, Simone Linz, Benjamin Albrecht:
A First Step Toward Computing All Hybridization Networks For Two Rooted Binary Phylogenetic Trees. 1227-1242 - M. Veselsky:
Order of Precedence and Age of Y-DNA Haplotypes. 1243-1250 - Martin Ehler, Frank Filbir, Hrushikesh Narhar Mhaskar:
Locally Learning Biomedical Data Using Diffusion Frames. 1251-1264
Volume 19, Number 12, December 2012
- Michiaki Hamada:
Direct Updating of an RNA Base-Pairing Probability Matrix with Marginal Probability Constraints. 1265-1276 - Hiroshi Toyoizumi, Hideo Tsubouchi:
Estimating the Number of Double-Strand Breaks Formed During Meiosis from Partial Observation. 1277-1283 - Jia-Hao Fan, Jianer Chen, Sing-Hoi Sze:
Identifying Complexes from Protein Interaction Networks According to Different Types of Neighborhood Density. 1284-1294 - R. Reyes, Daniel Gamermann, Arnau Montagud, David Fuente, Julián Triana, Javier F. Urchueguía Schölzel, Pedro Fernández de Córdoba:
Automation on the Generation of Genome-Scale Metabolic Models. 1295-1306 - Young Hwan Chang, Joe W. Gray, Claire J. Tomlin:
Optimization-based Inference for Temporally Evolving Networks with Applications in Biology. 1307-1323 - Baikang Pei, Dong-Guk Shin:
Reconstruction of Biological Networks by Incorporating Prior Knowledge into Bayesian Network Models. 1324-1334
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