Journal: J. Bioinformatics and Computational Biology

Volume 12, Issue 6

0 -- 0Junfang Chen, Pavlo Lutsik, Ruslan Akulenko, Jörn Walter, Volkhard Helms. AKSmooth: Enhancing low-coverage bisulfite sequencing data via kernel-based smoothing
0 -- 0Masaaki Kotera, Yosuke Nishimura, Zenichi Nakagawa, Ai Muto, Yuki Moriya, Shinobu Okamoto, Shuichi Kawashima, Toshiaki Katayama, Toshiaki Tokimatsu, Minoru Kanehisa, Susumu Goto. PIERO ontology for analysis of biochemical transformations: Effective implementation of reaction information in the IUBMB enzyme list
0 -- 0Tetsuo Shibuya, Chuan Yi Tang, Paul Horton, Kiyoshi Asai. Editorial
0 -- 0So Kobiki, Osamu Maruyama. ReSAPP: Predicting overlapping protein complexes by merging multiple-sampled partitions of proteins
0 -- 0Idoia Ochoa, Mikel Hernaez, Tsachy Weissman. Aligned genomic data compression via improved modeling
0 -- 0Jung-Hsien Chiang, Jiun-Huang Ju. Discovering novel protein-protein interactions by measuring the protein semantic similarity from the biomedical literature
0 -- 0Pawel Bednarz, Bartek Wilczynski. Supervised learning method for predicting chromatin boundary associated insulator elements
0 -- 0Dan He, Eleazar Eskin. IPED2X: A robust pedigree reconstruction algorithm for complicated pedigrees
0 -- 0Broto Chakrabarty, Nita Parekh. PRIGSA: Protein repeat identification by graph spectral analysis
0 -- 0Yutaka Ueno, Shuntaro Ito, Akihiko Konagaya. Implementing a modeling software for animated protein-complex interactions using a physics simulation library

Volume 12, Issue 5

0 -- 0Malik N. Akhtar, Bruce R. Southey, Per E. Andrén, Jonathan V. Sweedler, Sandra L. Rodriguez-Zas. Identification of best indicators of peptide-spectrum match using a permutation resampling approach
0 -- 0Abolfazl Rezvan, Sayed-Amir Marashi, Changiz Eslahchi. FCDECOMP: Decomposition of metabolic networks based on flux coupling relations
0 -- 0Harshal Inamdar, Avik Datta, Sunitha Manjari K, Rajendra Joshi. Rule-based integration of RNA-Seq analyses tools for identification of novel transcripts
0 -- 0Matthieu Willems, Nadia Tahiri, Vladimir Makarenkov. A new efficient algorithm for inferring explicit hybridization networks following the Neighbor-Joining principle
0 -- 0Chun Fang, Tamotsu Noguchi, Hayato Yamana. Analysis of evolutionary conservation patterns and their influence on identifying protein functional sites
0 -- 0Ghada Hany Badr, Isra Al-Turaiki, Marcel Turcotte, Hassan Mathkour. IncMD: Incremental trie-based structural motif discovery algorithm
0 -- 0Fahad Saeed, Hisham Al-Mubaid, Bhaskar DasGupta. Foreword
0 -- 0Hamed Tabatabaei Ghomi, Jared J. Thompson, Markus A. Lill. Are distance-dependent statistical potentials considering three interacting bodies superior to two-body statistical potentials for protein structure prediction?
0 -- 0Krishnendu Ghosh, John S. Schlipf. Formal modeling of a system of chemical reactions under uncertainty
0 -- 0Shang Gao, Ibrahim Karakira, Salim Afra, Ghada Naji, Reda Alhajj, Jia Zeng, Douglas J. Demetrick. Evaluating predictive performance of network biomarkers with network structures
0 -- 0Jing Ren, John Ellis, Jinyan Li. Influenza A HA's conserved epitopes and broadly neutralizing antibodies: A prediction method

Volume 12, Issue 4

0 -- 0Junbo Duan, Ji-Gang Zhang, Mingxi Wan, Hong-Wen Deng, Yu-Ping Wang. Population clustering based on copy number variations detected from next generation sequencing data
0 -- 0Apichat Suratanee, Kitiporn Plaimas. Identification of inflammatory bowel disease-related proteins using a reverse k-nearest neighbor search
0 -- 0Ross D. King, Chuan Lu. An investigation into eukaryotic pseudouridine synthases
0 -- 0Mun-Ho Choi, Seung-Ho Kang, Hyeong-Seok Lim. An improved preprocessing algorithm for haplotype inference by pure parsimony
0 -- 0Christos Lampros, Thomas Simos, Themis P. Exarchos, Konstantinos P. Exarchos, Costas Papaloukas, Dimitrios I. Fotiadis. Assessment of optimized Markov models in protein fold classification
0 -- 0Imhoi Koo, Sen Yao, Xiang Zhang, Seongho Kim. Comparative analysis of false discovery rate methods in constructing metabolic association networks
0 -- 0Fumiya Shida, Satoshi Mizuta. Measurement of word frequencies in genomic DNA sequences based on partial alignment and fuzzy set
0 -- 0Alireza Vazifedoost, Maseud Rahgozar, Behzad Moshiri, Mehdi Sadeghi, Hon Nian Chua, See-Kiong Ng, Limsoon Wong. Using data fusion for scoring reliability of protein-protein interactions

Volume 12, Issue 3

0 -- 0Frank Eisenhaber. Unix interfaces, Kleisli, bucandin structure, etc. - The heroic beginning of bioinformatics in Singapore
0 -- 0Emma Lindhardt, Peter Gennemark. Automated analysis of routinely generated preclinical pharmacokinetic and pharmacodynamic data
0 -- 0John C. Wooley, Ming Li, Limsoon Wong. JBCB, the first decade
0 -- 0R. Dias, Miguel G. Xavier, Fabio D. Rossi, Marcelo Veiga Neves, T. A. P. Lange, A. Giongo, César Augusto Fonticielha De Rose, E. W. Triplett. MPI-blastn and NCBI-TaxCollector: Improving metagenomic analysis with high performance classification and wide taxonomic attachment
0 -- 0Jasmita Gill, Praapti Jayaswal, Dinakar M. Salunke. Antigen exposure leads to rigidification of germline antibody combining site
0 -- 0Ala Qabaja, Tamer N. Jarada, Abdallah M. ElSheikh, Reda Alhajj. Prediction of gene-based drug indications using compendia of public gene expression data and PubMed abstracts
0 -- 0Ulisses Dias, Gustavo Rodrigues Galvão, Carla Negri Lintzmayer, Zanoni Dias. A general heuristic for genome rearrangement problems
0 -- 0Branko Borstnik, Danilo Pumpernik. The apparent enhancement of CpG transversions in primate lineage is a consequence of multiple replacements
0 -- 0Vitali A. Likhoshvai, Tamara M. Khlebodarova. Mathematical modeling of bacterial cell cycle: The problem of coordinating genome replication with cell growth
0 -- 0Frank Eisenhaber, Westley Arthur Sherman. 10 years for the Journal of Bioinformatics and Computational Biology (2003-2013) - A retrospective
0 -- 0Fei Xia, Guoqing Jin. Fine-grained parallelism accelerating for RNA secondary structure prediction with pseudoknots based on FPGA

Volume 12, Issue 2

0 -- 0Ramil R. Mintaev, Andrei V. Alexeevski, Larisa V. Kordyukova. Co-evolution analysis to predict protein-protein interactions within influenza virus envelope
0 -- 0Elizaveta A. Zagrijchuk, Marat A. Sabirov, David M. Holloway, Alexander V. Spirov. hunchback gene indicates redundancy in cis-regulatory organization and spatial gene expression
0 -- 0Olga N. Rogacheva, Vasiliy E. Stefanov, Boris F. Shchegolev, Elena A. Vershinina, Elena V. Savvateeva-Popova. Role of arginine 209 in the conformational transition of the protein kinase A regulatory subunit RIα A-domain
0 -- 0Ekaterina Myasnikova, Konstantin Kozlov. Statistical method for estimation of the predictive power of a gene circuit model
0 -- 0Burak Karacaören. 2 mice dataset using ancestry informative markers
0 -- 0Yuri A. Purtov, Olga A. Glazunova, Sergey S. Antipov, Viktoria O. Pokusaeva, Eugeny E. Fesenko, Elena V. Preobrazhenskaya, Konstantin S. Shavkunov, Maria N. Tutukina, Viktor I. Lukyanov, Olga N. Ozoline. Promoter islands as a platform for interaction with nucleoid proteins and transcription factors
0 -- 0Nermin Pinar Karabulut, Murodzhon Akhmedov, Murat Cokol. A drug similarity network for understanding drug mechanism of action
0 -- 0Sulbha Choudhari, Ruchi Lohia, Andrey Grigoriev. Comparative metagenome analysis of an Alaskan glacier
0 -- 0Mikhail Krivozubov, Florian Goebels, Sergei A. Spirin. Estimation of relative effectiveness of phylogenetic programs by machine learning
0 -- 0Anna Zhukova, David J. Sherman. Knowledge-based generalization of metabolic networks: A practical study

Volume 12, Issue 1

0 -- 0Peter Gennemark, Dag Wedelin. Odeion - a Software Module for Structural Identification of Ordinary differential equations
0 -- 0Christophe Guyeux, Nathalie M.-L. Côté, Jacques M. Bahi, Wojciech Bienia. Is protein Folding Problem Really a NP-Complete One? First Investigations
0 -- 0Qingshan Ni, Lingyun Zou. Accurate Discrimination of outer membrane proteins using secondary Structure Element Alignment and Support Vector Machine
0 -- 0Beibei Ru, Peter A. C. 't Hoen, Fulei Nie, Hao Lin, Feng-Biao Guo, Jian Huang. Phd7faster: Predicting Clones Propagating Faster from the pH.D.-7 phage Display peptide Library
0 -- 0Rishi Mukhopadhyay, Stephanie Jimenez Irausquin, Chris Schmidt, Homayoun Valafar. Dynafold: a Dynamic Programming Approach to protein Backbone Structure determination from Minimal Sets of residual Dipolar couplings
0 -- 0Belhassen Bayar, Nidhal Bouaynaya, Roman Shterenberg. Probabilistic Non-Negative Matrix Factorization: Theory and Application to microarray Data Analysis
0 -- 0Eddy Taillefer, Jonathan Miller. Non-Nested Local Maximal repeats
0 -- 0Dorothy A. Hammond, Victor Olman, Ying Xu. Functional Understanding of the Diverse exon-intron Structures of Human GPCR genes
0 -- 0Marco Mernberger, Daniel Moog, Simone Stork, Stefan Zauner, Uwe G. Maier, Eyke Hüllermeier. Protein Sub-Cellular Localization Prediction for Special compartments via Optimized Time Series Distances
0 -- 0Slávka Jaromerská, Petr Praus, Young-Rae Cho. Distance-Wise pathway Discovery from protein-protein Interaction Networks Weighted by Semantic Similarity
0 -- 0R. Rakshambikai, Narayanaswamy Srinivasan, Rupali A. Gadkari. Repertoire of protein kinases Encoded in the genome of zebrafish shows remarkably Large Population of PIM kinases
0 -- 0Ismael Sanchez-Osorio, Fernando Ramos, Pedro Mayorga, Edgar Dantan. Foundations for Modeling the Dynamics of gene regulatory Networks: a Multilevel-Perspective Review