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    Journal: Journal of Computational Biology

    Volume 21, Issue 9

    649 -- 664Benjamin M. M. Fu, Christian M. Reidys. Shapes of Interacting RNA Complexes
    665 -- 675Maria Brigida Ferraro, Marco Savarese, Giuseppina Di Fruscio, Vincenzo Nigro, Mario Rosario Guarracino. Prediction of Rare Single-Nucleotide Causative Mutations for Muscular Diseases in Pooled Next-Generation Sequencing Experiments
    676 -- 690Jan Irvahn, Vladimir N. Minin. Phylogenetic Stochastic Mapping Without Matrix Exponentiation
    691 -- 698Yunzhang Huo, Ping Ji. Continuous-Time Markov Chain-Based Flux Analysis in Metabolism
    699 -- 708Alexandru Agapie, Anca Andreica, Marius Giuclea. Probabilistic Cellular Automata
    709 -- 721Albert Vexler, Xiwei Chen, Jihnhee Yu. Evaluations and Comparisons of Treatment Effects Based on Best Combinations of Biomarkers with Applications to Biomedical Studies

    Volume 21, Issue 8

    569 -- 577Alexei A. Sharov, Akira Nishiyama, Yong Qian, Dawood B. Dudekula, Dan L. Longo, David Schlessinger, Minoru S. H. Ko. Chromatin Properties of Regulatory DNA Probed by Manipulation of Transcription Factors
    578 -- 590Yu Zheng, Louxin Zhang. Are the Duplication Cost and Robinson-Foulds Distance Equivalent?
    591 -- 608Hillary S. W. Han, Thomas J. X. Li, Christian M. Reidys. γ-Structures
    609 -- 621Cuncong Zhong, Shaojie Zhang. Simultaneous Folding of Alternative RNA Structures with Mutual Constraints: An Application to Next-Generation Sequencing-based RNA Structure Probing
    622 -- 631Nikita Alexeev, Peter Zograf. Random Matrix Approach to the Distribution of Genomic Distance
    632 -- 647Ponne Saravanaraman, Raj Kumar Chinnadurai, Rathanam Boopathy. A New Role for the Nonpathogenic Nonsynonymous Single-Nucleotide Polymorphisms of Acetylcholinesterase in the Treatment of Alzheimer's Disease: A Computational Study

    Volume 21, Issue 7

    477 -- 491Jérôme Waldispühl, Charles W. O'Donnell, Sebastian Will, Srinivas Devadas, Rolf Backofen, Bonnie Berger. Simultaneous Alignment and Folding of Protein Sequences
    492 -- 507Md. Muksitul Haque, Michael K. Skinner, Lawrence B. Holder. Imbalanced Class Learning in Epigenetics
    508 -- 519Daniel Gamermann, Arnau Montagud, J. Alberto Conejero, Javier F. Urchueguía, Pedro Fernández de Córdoba. New Approach for Phylogenetic Tree Recovery Based on Genome-Scale Metabolic Networks
    520 -- 533Fabien de Montgolfier, Mathieu Raffinot, Irena Rusu. Easy Identification of Generalized Common and Conserved Nested Intervals
    534 -- 547Anna Zhukova, David James Sherman. Knowledge-based Generalization of Metabolic Models
    548 -- 567Wen-Shyong Tzou, Ying-Tsang Lo, Tun-Wen Pai, Chin-Hua Hu, Chung-Hao Li. Stochastic Simulation of Notch Signaling Reveals Novel Factors That Mediate the Differentiation of Neural Stem Cells

    Volume 21, Issue 6

    405 -- 419John G. Cleary, Ross Braithwaite, Kurt Gaastra, Brian S. Hilbush, Stuart Inglis, Sean A. Irvine, Alan Jackson, Richard Littin, Sahar Nohzadeh-Malakshah, Mehul Rathod, David Ware, Len Trigg, Francisco M. de la Vega. De Novo Mutation Identification on Pedigrees from High-Throughput Sequencing Data
    420 -- 427Wei Hu, John Hu. Prediction of siRNA Potency Using Sparse Logistic Regression
    428 -- 445Sebastian Klie, Zoran Nikoloski, Joachim Selbig. Biological Cluster Evaluation for Gene Function Prediction
    446 -- 455Vamsi Kundeti, Sanguthevar Rajasekaran, Hieu Dinh. Border Length Minimization Problem on a Square Array
    456 -- 465Nivit Gill, Shailendra Singh, Trilok C. Aseri. Computational Disease Gene Prioritization: An Appraisal
    466 -- 475Abdul Arif Khan. Escherichia coli Proteins Targeting the Host Cell Nucleus, with Special Reference to Their Role in Colon Cancer Etiology
    476 -- 0. Correction: Journal of Computational Biology: 2014; 21/4: 303-319

    Volume 21, Issue 5

    371 -- 372Andrea Califano, Manolis Kellis, Gustavo Stolovitzky. RECOMB/ISCB Systems Biology, Regulatory Genomics, and DREAM 2013 Special Issue
    373 -- 384Patrick K. O'Neill, Robert Forder, Ivan Erill. Informational Requirements for Transcriptional Regulation
    385 -- 393Zhiyong Wang, Jinbo Xu, Xinghua Shi. Finding Alternative Expression Quantitative Trait Loci by Exploring Sparse Model Space
    394 -- 404Arnon Mazza, Irit Gat-Viks, Roded Sharan. Elucidating Influenza Inhibition Pathways via Network Reconstruction

    Volume 21, Issue 4

    287 -- 302Andrew F. Neuwald. Evaluating, Comparing, and Interpreting Protein Domain Hierarchies
    303 -- 319Lavanya Kannan, Ward C. Wheeler. Exactly Computing the Parsimony Scores on Phylogenetic Networks Using Dynamic Programming
    320 -- 329Xun Wang, Ying Miao, Minquan Cheng. Finding Motifs in DNA Sequences Using Low-Dispersion Sequences
    330 -- 344Matteo Comin, Montse Farreras. Parallel Continuous Flow: A Parallel Suffix Tree Construction Tool for Whole Genomes
    345 -- 360Seyoung Kim, Eric P. Xing. Exploiting Genome Structure in Association Analysis
    361 -- 369Robert Hochberg, Treena Larrew Milam. Data Structures for Parsimony Correlation and Biosequence Co-Evolution

    Volume 21, Issue 3

    185 -- 200Chaozhi Zheng, Mary K. Kuhner, Elizabeth A. Thompson. Joint Inference of Identity by Descent Along Multiple Chromosomes from Population Samples
    201 -- 218Yang Ding, William Andrew Lorenz, Iván Dotú, Evan Senter, Peter Clote. Computing the Probability of RNA Hairpin and Multiloop Formation
    219 -- 233Heewook Lee, Ellen Popodi, Patricia L. Foster, Haixu Tang. Detection of Structural Variants Involving Repetitive Regions in the Reference Genome
    234 -- 246Mu-Fen Hsieh, Sing-Hoi Sze. Finding Alignments of Conserved Graphlets in Protein Interaction Networks
    247 -- 256Dariusz Plewczynski, Anna Philips, Marcin von Grotthuss, Leszek Rychlewski, Krzysztof Ginalski. HarmonyDOCK: The Structural Analysis of Poses in Protein-Ligand Docking
    257 -- 268Guillermo Peris, Andrés Marzal. Statistical Significance of Normalized Global Alignment
    269 -- 286Andrew F. Neuwald. A Bayesian Sampler for Optimization of Protein Domain Hierarchies

    Volume 21, Issue 2

    99 -- 117Francesco Bartolucci, Silvia Pandolfi. A New Constant Memory Recursion for Hidden Markov Models
    118 -- 140David J. Galas, Nikita A. Sakhanenko, Alexander Skupin, Tomasz M. Ignac. Describing the Complexity of Systems: Multivariable "Set Complexity" and the Information Basis of Systems Biology
    141 -- 161Junshan Wang, Ajay Jasra, Maria De Iorio. Computational Methods for a Class of Network Models
    162 -- 172Wajdi Dhifli, Rabie Saidi, Engelbert Mephu Nguifo. Smoothing 3D Protein Structure Motifs Through Graph Mining and Amino Acid Similarities
    173 -- 183Nissan Levtov, Sandeep Amberkar, Zakharia M. Frenkel, Lars Kaderali, Zeev Volkovich. Detecting Non-Uniform Clusters in Large-Scale Interaction Graphs

    Volume 21, Issue 12

    867 -- 879Changchuan Yin, Xuemeng E. Yin, Jiasong Wang. A Novel Method for Comparative Analysis of DNA Sequences by Ramanujan-Fourier Transform
    880 -- 897Eman Badr, Lenwood S. Heath. Identifying Splicing Regulatory Elements with de Bruijn Graphs
    898 -- 914Alexia Kakourou, Werner Vach, Bart J. A. Mertens. Combination Approaches Improve Predictive Performance of Diagnostic Rules for Mass-Spectrometry Proteomic Data
    915 -- 935William Y. C. Chen, Qiang-Hui Guo, Lisa H. Sun, Jian Wang. m-Regular Linear Stacks
    936 -- 946Huda Amin Maghawry, Mostafa G. M. Mostafa, Tarek F. Gharib. A New Protein Structure Representation for Efficient Protein Function Prediction
    947 -- 963Laurent Noé, Donald E. K. Martin. k-Mer Distances
    964 -- 974Lizhen Liu, Xuemin Dai, Hanshi Wang, Wei Song, Jingli Lu. A Weighted Multipath Measurement Based on Gene Ontology for Estimating Gene Products Similarity

    Volume 21, Issue 11

    785 -- 798Takanori Hasegawa, Tomoya Mori, Rui Yamaguchi, Seiya Imoto, Satoru Miyano, Tatsuya Akutsu. An Efficient Data Assimilation Schema for Restoration and Extension of Gene Regulatory Networks Using Time-Course Observation Data
    799 -- 808Amir Carmel, Noa Musa-Lempel, Dekel Tsur, Michal Ziv-Ukelson. The Worst Case Complexity of Maximum Parsimony
    809 -- 822Bogumil Konopka, Tomasz Golda, Malgorzata Kotulska. Evaluating the Significance of Protein Functional Similarity Based on Gene Ontology
    823 -- 845José Santos Reyes, Pablo Villot, Martín Diéguez. Emergent Protein Folding Modeled with Evolved Neural Cellular Automata Using the 3D HP Model
    846 -- 854Nha Nguyen, An P. N. Vo, Kyoung-Jae Won. A Wavelet Approach to Detect Enriched Regions and Explore Epigenomic Landscapes
    855 -- 865Katrin Illner, Christiane Fuchs, Fabian J. Theis. Bayesian Blind Source Separation for Data with Network Structure

    Volume 21, Issue 10

    723 -- 731Josh Voorkamp. Maximal Acyclic Agreement Forests
    732 -- 740Loni Philip Tabb, Wei Zhao, Jingyu Huang, Gail L. Rosen. n-mers in the Presence of Nullomers
    741 -- 752Ziva Stepancic. Enhancing Gibbs Sampling Method for Motif Finding in DNA with Initial Graph Representation of Sequences
    753 -- 759Hari Ram, Alok Kumar, Lebin Thomas, Ved Pal Singh. In silico Approach to Study Adaptive Divergence in Nucleotide Composition of the 16S rRNA Gene Among Bacteria Thriving Under Different Temperature Regimes
    760 -- 770Alex Radu, Michael A. Charleston. Node Fingerprinting: An Efficient Heuristic for Aligning Biological Networks
    771 -- 783Peican Zhu, Jie Han. Asynchronous Stochastic Boolean Networks as Gene Network Models

    Volume 21, Issue 1

    1 -- 15Jakub Kovác. On the Complexity of Rearrangement Problems under the Breakpoint Distance
    16 -- 40Stefano Beretta, Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Raffaella Rizzi. Modeling Alternative Splicing Variants from RNA-Seq Data with Isoform Graphs
    41 -- 63Conrad J. Burden, Paul Leopardi, Sylvain Forêt. The Distribution of Word Matches Between Markovian Sequences with Periodic Boundary Conditions
    64 -- 79Aïda Ouangraoua, Mathieu Raffinot. On the Identification of Conflicting Contiguities in Ancestral Genome Reconstruction
    80 -- 88Chuanxi Li, Rujing Wang, Peng Chen, He Huang, Yaru Su. Interaction Relation Ontology Learning
    89 -- 98Pawel Górecki, Oliver Eulenstein. DrML: Probabilistic Modeling of Gene Duplications
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