Journal of Computational Biology, Volume 21 (original) (raw)

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Volume 21, Number 1, January 2014

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

Volume 21, Number 2, February 2014

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

Volume 21, Number 3, March 2014

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

Volume 21, Number 4, April 2014

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

Volume 21, Number 5, May 2014

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

Volume 21, Number 6, June 2014

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    John 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:
    Joint Variant and De Novo Mutation Identification on Pedigrees from High-Throughput Sequencing Data. 405-419
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    Wei Hu, John Hu:
    Prediction of siRNA Potency Using Sparse Logistic Regression. 420-427
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    Sebastian Klie, Zoran Nikoloski, Joachim Selbig:
    Biological Cluster Evaluation for Gene Function Prediction. 428-445
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    Vamsi Kundeti, Sanguthevar Rajasekaran, Hieu Dinh:
    Border Length Minimization Problem on a Square Array. 446-455
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    Nivit Gill, Shailendra Singh, Trilok Chand Aseri:
    Computational Disease Gene Prioritization: An Appraisal. 456-465
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    Abdul Arif Khan:
    In Silico Prediction of Escherichia coli Proteins Targeting the Host Cell Nucleus, with Special Reference to Their Role in Colon Cancer Etiology. 466-475
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    Correction: Journal of Computational Biology: 2014; 21/4: 303-319. 476

Volume 21, Number 7, July 2014

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    Jérôme Waldispühl, Charles W. O'Donnell, Sebastian Will, Srinivas Devadas, Rolf Backofen, Bonnie Berger:
    Simultaneous Alignment and Folding of Protein Sequences. 477-491
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    Md. Muksitul Haque, Michael K. Skinner, Lawrence B. Holder:
    Imbalanced Class Learning in Epigenetics. 492-507
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    Daniel 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. 508-519
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    Fabien de Montgolfier, Mathieu Raffinot, Irena Rusu:
    Easy Identification of Generalized Common and Conserved Nested Intervals. 520-533
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    Anna Zhukova, David James Sherman:
    Knowledge-based Generalization of Metabolic Models. 534-547
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    Wen-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. 548-567

Volume 21, Number 8, August 2014

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    Alexei 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. 569-577
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    Yu Zheng, Louxin Zhang:
    Are the Duplication Cost and Robinson-Foulds Distance Equivalent? 578-590
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    Hillary S. W. Han, Thomas J. X. Li, Christian M. Reidys:
    Combinatorics of _γ_-Structures. 591-608
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    Cuncong Zhong, Shaojie Zhang:
    Simultaneous Folding of Alternative RNA Structures with Mutual Constraints: An Application to Next-Generation Sequencing-based RNA Structure Probing. 609-621
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    Nikita Alexeev, Peter Zograf:
    Random Matrix Approach to the Distribution of Genomic Distance. 622-631
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    Ponne 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. 632-647

Volume 21, Number 9, September 2014

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    Benjamin M. M. Fu, Christian M. Reidys:
    Shapes of Interacting RNA Complexes. 649-664
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    Maria 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. 665-675
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    Jan Irvahn, Vladimir N. Minin:
    Phylogenetic Stochastic Mapping Without Matrix Exponentiation. 676-690
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    Yunzhang Huo, Ping Ji:
    Continuous-Time Markov Chain-Based Flux Analysis in Metabolism. 691-698
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    Alexandru Agapie, Anca Andreica, Marius Giuclea:
    Probabilistic Cellular Automata. 699-708
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    Albert Vexler, Xiwei Chen, Jihnhee Yu:
    Evaluations and Comparisons of Treatment Effects Based on Best Combinations of Biomarkers with Applications to Biomedical Studies. 709-721

Volume 21, Number 10, October 2014

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    Josh Voorkamp:
    Maximal Acyclic Agreement Forests. 723-731
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    Loni Philip Tabb, Wei Zhao, Jingyu Huang, Gail L. Rosen:
    Characterizing the Empirical Distribution of Prokaryotic Genome _n_-mers in the Presence of Nullomers. 732-740
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    Ziva Stepancic:
    Enhancing Gibbs Sampling Method for Motif Finding in DNA with Initial Graph Representation of Sequences. 741-752
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    Hari 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. 753-759
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    Alex Radu, Michael A. Charleston:
    Node Fingerprinting: An Efficient Heuristic for Aligning Biological Networks. 760-770
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    Peican Zhu, Jie Han:
    Asynchronous Stochastic Boolean Networks as Gene Network Models. 771-783

Volume 21, Number 11, November 2014

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

Volume 21, Number 12, December 2014

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

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