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ORCIDJournal of Computational Biology, Volume 21
Volume 21, Number 1, January 2014
- Jakub Kovác:
On the Complexity of Rearrangement Problems under the Breakpoint Distance. 1-15 - Stefano Beretta
, Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Raffaella Rizzi:
Modeling Alternative Splicing Variants from RNA-Seq Data with Isoform Graphs. 16-40 - Conrad J. Burden, Paul C. Leopardi, Sylvain Forêt:
The Distribution of Word Matches Between Markovian Sequences with Periodic Boundary Conditions. 41-63 - Aïda Ouangraoua, Mathieu Raffinot:
On the Identification of Conflicting Contiguities in Ancestral Genome Reconstruction. 64-79 - Chuanxi Li, Rujing Wang, Peng Chen, He Huang, Yaru Su:
Interaction Relation Ontology Learning. 80-88 - Pawel Górecki, Oliver Eulenstein:
DrML: Probabilistic Modeling of Gene Duplications. 89-98
Volume 21, Number 2, February 2014
- Francesco Bartolucci, Silvia Pandolfi:
A New Constant Memory Recursion for Hidden Markov Models. 99-117 - 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 - Junshan Wang, Ajay Jasra, Maria De Iorio:
Computational Methods for a Class of Network Models. 141-161 - Wajdi Dhifli, Rabie Saidi, Engelbert Mephu Nguifo:
Smoothing 3D Protein Structure Motifs Through Graph Mining and Amino Acid Similarities. 162-172 - 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
- Chaozhi Zheng, Mary K. Kuhner, Elizabeth A. Thompson:
Joint Inference of Identity by Descent Along Multiple Chromosomes from Population Samples. 185-200 - Yang Ding, William Andrew Lorenz, Iván Dotú, Evan Senter, Peter Clote:
Computing the Probability of RNA Hairpin and Multiloop Formation. 201-218 - Heewook Lee, Ellen Popodi, Patricia L. Foster, Haixu Tang:
Detection of Structural Variants Involving Repetitive Regions in the Reference Genome. 219-233 - Mu-Fen Hsieh, Sing-Hoi Sze:
Finding Alignments of Conserved Graphlets in Protein Interaction Networks. 234-246 - Dariusz Plewczynski, Anna Philips, Marcin von Grotthuss, Leszek Rychlewski, Krzysztof Ginalski:
HarmonyDOCK: The Structural Analysis of Poses in Protein-Ligand Docking. 247-256 - Guillermo Peris, Andrés Marzal:
Statistical Significance of Normalized Global Alignment. 257-268 - Andrew F. Neuwald:
A Bayesian Sampler for Optimization of Protein Domain Hierarchies. 269-286
Volume 21, Number 4, April 2014
- Andrew F. Neuwald:
Evaluating, Comparing, and Interpreting Protein Domain Hierarchies. 287-302 - Lavanya Kannan, Ward C. Wheeler:
Exactly Computing the Parsimony Scores on Phylogenetic Networks Using Dynamic Programming. 303-319 - Xun Wang, Ying Miao, Minquan Cheng:
Finding Motifs in DNA Sequences Using Low-Dispersion Sequences. 320-329 - Matteo Comin, Montse Farreras:
Parallel Continuous Flow: A Parallel Suffix Tree Construction Tool for Whole Genomes. 330-344 - Seyoung Kim, Eric P. Xing:
Exploiting Genome Structure in Association Analysis. 345-360 - Robert Hochberg, Treena Larrew Milam:
Data Structures for Parsimony Correlation and Biosequence Co-Evolution. 361-369
Volume 21, Number 5, May 2014
- Andrea Califano, Manolis Kellis, Gustavo Stolovitzky:
RECOMB/ISCB Systems Biology, Regulatory Genomics, and DREAM 2013 Special Issue. 371-372 - Patrick K. O'Neill, Robert Forder, Ivan Erill:
Informational Requirements for Transcriptional Regulation. 373-384 - Zhiyong Wang, Jinbo Xu, Xinghua Shi:
Finding Alternative Expression Quantitative Trait Loci by Exploring Sparse Model Space. 385-393 - Arnon Mazza, Irit Gat-Viks, Roded Sharan:
Elucidating Influenza Inhibition Pathways via Network Reconstruction. 394-404
Volume 21, Number 6, June 2014
- 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 - Wei Hu, John Hu:
Prediction of siRNA Potency Using Sparse Logistic Regression. 420-427 - Sebastian Klie, Zoran Nikoloski, Joachim Selbig:
Biological Cluster Evaluation for Gene Function Prediction. 428-445 - Vamsi Kundeti, Sanguthevar Rajasekaran, Hieu Dinh:
Border Length Minimization Problem on a Square Array. 446-455 - Nivit Gill, Shailendra Singh, Trilok Chand Aseri:
Computational Disease Gene Prioritization: An Appraisal. 456-465 - 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 - Correction: Journal of Computational Biology: 2014; 21/4: 303-319. 476
Volume 21, Number 7, July 2014
- Jérôme Waldispühl, Charles W. O'Donnell, Sebastian Will, Srinivas Devadas, Rolf Backofen, Bonnie Berger:
Simultaneous Alignment and Folding of Protein Sequences. 477-491 - Md. Muksitul Haque, Michael K. Skinner, Lawrence B. Holder:
Imbalanced Class Learning in Epigenetics. 492-507 - 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 - Fabien de Montgolfier, Mathieu Raffinot, Irena Rusu:
Easy Identification of Generalized Common and Conserved Nested Intervals. 520-533 - Anna Zhukova, David James Sherman:
Knowledge-based Generalization of Metabolic Models. 534-547 - 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
- 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 - Yu Zheng, Louxin Zhang:
Are the Duplication Cost and Robinson-Foulds Distance Equivalent? 578-590 - Hillary S. W. Han, Thomas J. X. Li, Christian M. Reidys:
Combinatorics of γ-Structures. 591-608 - 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 - Nikita Alexeev, Peter Zograf:
Random Matrix Approach to the Distribution of Genomic Distance. 622-631 - 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
- Benjamin M. M. Fu, Christian M. Reidys:
Shapes of Interacting RNA Complexes. 649-664 - 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 - Jan Irvahn, Vladimir N. Minin:
Phylogenetic Stochastic Mapping Without Matrix Exponentiation. 676-690 - Yunzhang Huo, Ping Ji:
Continuous-Time Markov Chain-Based Flux Analysis in Metabolism. 691-698 - Alexandru Agapie, Anca Andreica, Marius Giuclea:
Probabilistic Cellular Automata. 699-708 - 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
- Josh Voorkamp:
Maximal Acyclic Agreement Forests. 723-731 - 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 - Ziva Stepancic:
Enhancing Gibbs Sampling Method for Motif Finding in DNA with Initial Graph Representation of Sequences. 741-752 - 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 - Alex Radu, Michael A. Charleston:
Node Fingerprinting: An Efficient Heuristic for Aligning Biological Networks. 760-770 - Peican Zhu, Jie Han:
Asynchronous Stochastic Boolean Networks as Gene Network Models. 771-783
Volume 21, Number 11, November 2014
- 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 - Amir Carmel, Noa Musa-Lempel, Dekel Tsur, Michal Ziv-Ukelson:
The Worst Case Complexity of Maximum Parsimony. 799-808 - Bogumil Konopka, Tomasz Golda, Malgorzata Kotulska:
Evaluating the Significance of Protein Functional Similarity Based on Gene Ontology. 809-822 - José Santos Reyes, Pablo Villot, Martín Diéguez:
Emergent Protein Folding Modeled with Evolved Neural Cellular Automata Using the 3D HP Model. 823-845 - Nha Nguyen, An P. N. Vo, Kyoung-Jae Won:
A Wavelet Approach to Detect Enriched Regions and Explore Epigenomic Landscapes. 846-854 - Katrin Illner, Christiane Fuchs, Fabian J. Theis:
Bayesian Blind Source Separation for Data with Network Structure. 855-865
Volume 21, Number 12, December 2014
- Changchuan Yin, Xuemeng E. Yin, Jiasong Wang:
A Novel Method for Comparative Analysis of DNA Sequences by Ramanujan-Fourier Transform. 867-879 - Eman Badr, Lenwood S. Heath:
Identifying Splicing Regulatory Elements with de Bruijn Graphs. 880-897 - Alexia Kakourou, Werner Vach, Bart J. A. Mertens:
Combination Approaches Improve Predictive Performance of Diagnostic Rules for Mass-Spectrometry Proteomic Data. 898-914 - William Y. C. Chen, Qiang-Hui Guo, Lisa Hui Sun, Jian Wang:
Zigzag Stacks and m-Regular Linear Stacks. 915-935 - Huda Amin Maghawry, Mostafa G. M. Mostafa, Tarek F. Gharib:
A New Protein Structure Representation for Efficient Protein Function Prediction. 936-946 - 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 - 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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