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ORCIDJournal of Bioinformatics and Computational Biology, Volume 12
Volume 12, Number 1, February 2014
- R. Rakshambikai, Narayanaswamy Srinivasan, Rupali A. Gadkari:
Repertoire of protein kinases Encoded in the genome of zebrafish shows remarkably Large Population of PIM kinases. - Peter Gennemark
, Dag Wedelin:
Odeion - a Software Module for Structural Identification of Ordinary differential equations. - Marco 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. - Christophe Guyeux, Nathalie M.-L. Côté, Jacques M. Bahi, Wojciech Bienia:
Is protein Folding Problem Really a NP-Complete One? First Investigations. - Eddy Taillefer, Jonathan Miller:
Exhaustive Computation of Exact duplications via Super and Non-Nested Local Maximal repeats. - Dorothy A. Hammond, Victor Olman, Ying Xu:
Functional Understanding of the Diverse exon-intron Structures of Human GPCR genes. - Belhassen Bayar, Nidhal Bouaynaya, Roman Shterenberg:
Probabilistic Non-Negative Matrix Factorization: Theory and Application to microarray Data Analysis. - Rishi 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. - Qingshan Ni, Lingyun Zou:
Accurate Discrimination of outer membrane proteins using secondary Structure Element Alignment and Support Vector Machine. - Slávka Jaromerská, Petr Praus, Young-Rae Cho:
Distance-Wise pathway Discovery from protein-protein Interaction Networks Weighted by Semantic Similarity. - Beibei 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.
- Ismael Sanchez-Osorio, Fernando Ramos, Pedro Mayorga, Edgar Dantan:
Foundations for Modeling the Dynamics of gene regulatory Networks: a Multilevel-Perspective Review.
Volume 12, Number 2, April 2014
- Anna Zhukova, David James Sherman:
Knowledge-based generalization of metabolic networks: A practical study. - Ekaterina M. Myasnikova, Konstantin Kozlov:
Statistical method for estimation of the predictive power of a gene circuit model. - Sulbha Choudhari, Ruchi Lohia, Andrey Grigoriev:
Comparative metagenome analysis of an Alaskan glacier. - Mikhail Krivozubov, Florian Goebels, Sergei A. Spirin:
Estimation of relative effectiveness of phylogenetic programs by machine learning. - Olga 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. - Yuri 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. - Nermin Pinar Karabulut, Murodzhon Akhmedov, Murat Cokol:
A drug similarity network for understanding drug mechanism of action. - Ramil R. Mintaev, Andrei V. Alexeevski, Larisa V. Kordyukova:
Co-evolution analysis to predict protein-protein interactions within influenza virus envelope. - Elizaveta A. Zagrijchuk, Marat A. Sabirov, David M. Holloway, Alexander V. Spirov:
In silico evolution of the hunchback gene indicates redundancy in cis-regulatory organization and spatial gene expression. - Burak Karacaören:
Admixture mapping of growth related traits in F2 mice dataset using ancestry informative markers.
Volume 12, Number 3, June 2014
- John C. Wooley, Ming Li, Limsoon Wong:
JBCB, the first decade.
- Jasmita Gill, Praapti Jayaswal, Dinakar M. Salunke:
Antigen exposure leads to rigidification of germline antibody combining site. - Ala 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. - Fei Xia, Guoqing Jin:
Fine-grained parallelism accelerating for RNA secondary structure prediction with pseudoknots based on FPGA. - Vitali A. Likhoshvai, Tamara M. Khlebodarova:
Mathematical modeling of bacterial cell cycle: The problem of coordinating genome replication with cell growth. - Emma Lindhardt, Peter Gennemark:
Automated analysis of routinely generated preclinical pharmacokinetic and pharmacodynamic data. - Branko Borstnik, Danilo Pumpernik:
The apparent enhancement of CpG transversions in primate lineage is a consequence of multiple replacements. - Ulisses Dias, Gustavo Rodrigues Galvão, Carla Negri Lintzmayer, Zanoni Dias:
A general heuristic for genome rearrangement problems. - Raquel Dias, Miguel G. Xavier, Fábio D. Rossi, Marcelo Veiga Neves, Timoteo Alberto Peters Lange, Adriana 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.
- Frank Eisenhaber, Westley Arthur Sherman:
10 years for the Journal of Bioinformatics and Computational Biology (2003-2013) - A retrospective. - Frank Eisenhaber:
Unix interfaces, Kleisli, bucandin structure, etc. - The heroic beginning of bioinformatics in Singapore.
Volume 12, Number 4, August 2014
- Alireza 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. - Ross D. King, Chuan Lu:
An investigation into eukaryotic pseudouridine synthases. - Christos Lampros, Thomas Simos, Themis P. Exarchos, Konstantinos P. Exarchos, Costas Papaloukas, Dimitrios I. Fotiadis:
Assessment of optimized Markov models in protein fold classification. - Apichat Suratanee, Kitiporn Plaimas:
Identification of inflammatory bowel disease-related proteins using a reverse k-nearest neighbor search. - Imhoi Koo, Sen Yao, Xiang Zhang, Seongho Kim:
Comparative analysis of false discovery rate methods in constructing metabolic association networks. - Fumiya Shida, Satoshi Mizuta:
Measurement of word frequencies in genomic DNA sequences based on partial alignment and fuzzy set. - Mun-Ho Choi, Seung-Ho Kang, Hyeong-Seok Lim:
An improved preprocessing algorithm for haplotype inference by pure parsimony. - Junbo 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.
Volume 12, Number 5, October 2014
- Fahad Saeed, Hisham Al-Mubaid, Bhaskar DasGupta:
Foreword. - Malik 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. - Krishnendu Ghosh, John S. Schlipf:
Formal modeling of a system of chemical reactions under uncertainty. - Chun Fang, Tamotsu Noguchi, Hayato Yamana:
Analysis of evolutionary conservation patterns and their influence on identifying protein functional sites.
- Hamed 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? - Jing Ren, John T. Ellis, Jinyan Li:
Influenza A HA's conserved epitopes and broadly neutralizing antibodies: A prediction method. - Matthieu Willems, Nadia Tahiri, Vladimir Makarenkov:
A new efficient algorithm for inferring explicit hybridization networks following the Neighbor-Joining principle. - Shang Gao, Ibrahim Karakira, Salim Afra, Ghada Naji, Reda Alhajj, Jia Zeng, Douglas J. Demetrick:
Evaluating predictive performance of network biomarkers with network structures. - Harshal Inamdar, Avik Datta, Sunitha Manjari K, Rajendra Joshi:
Rule-based integration of RNA-Seq analyses tools for identification of novel transcripts. - Ghada Hany Badr, Isra Al-Turaiki, Marcel Turcotte, Hassan Mathkour:
IncMD: Incremental trie-based structural motif discovery algorithm. - Abolfazl Rezvan, Sayed-Amir Marashi, Changiz Eslahchi:
FCDECOMP: Decomposition of metabolic networks based on flux coupling relations.
Volume 12, Number 6, December 2014
- Tetsuo Shibuya, Chuan Yi Tang, Paul Horton, Kiyoshi Asai:
Editorial.
- Masaaki 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. - Idoia Ochoa, Mikel Hernaez, Tsachy Weissman:
Aligned genomic data compression via improved modeling. - Yutaka Ueno, Shuntaro Ito, Akihiko Konagaya:
Implementing a modeling software for animated protein-complex interactions using a physics simulation library. - So Kobiki, Osamu Maruyama:
ReSAPP: Predicting overlapping protein complexes by merging multiple-sampled partitions of proteins. - Junfang Chen, Pavlo Lutsik, Ruslan Akulenko, Jörn Walter, Volkhard Helms:
AKSmooth: Enhancing low-coverage bisulfite sequencing data via kernel-based smoothing. - Pawel Bednarz, Bartek Wilczynski:
Supervised learning method for predicting chromatin boundary associated insulator elements. - Dan He, Eleazar Eskin:
IPED2X: A robust pedigree reconstruction algorithm for complicated pedigrees. - Jung-Hsien Chiang, Jiun-Huang Ju:
Discovering novel protein-protein interactions by measuring the protein semantic similarity from the biomedical literature. - Broto Chakrabarty, Nita Parekh:
PRIGSA: Protein repeat identification by graph spectral analysis.
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