Journal of Bioinformatics and Computational Biology, Volume 14

Volume 14, Number 1, February 2016

Special Issue - Selected Papers from CSBio2015

• 
  Weerayuth Kittichotirat, Worrawat Engchuan, Wanwipa Vongsangnak, Asawin Meechai:
  Preface to selected papers from the 6th International Conference on Computational Systems-Biology and Bioinformatics (CSBio2015). 1602001:1-1602001:2
• 
  Jonathan Behaegel, Jean-Paul Comet, Gilles Bernot, Emilien Cornillon, Franck Delaunay:
  A hybrid model of cell cycle in mammals. 1640001:1-1640001:17
• 
  Shuzhi Yu, Fanchang Hao, Hon Wai Leong:
  An O(n3) algorithm for sorting signed genomes by reversals, transpositions, transreversals and block-interchanges. 1640002:1-1640002:17
• 
  Bingxin Lu, Hon Wai Leong:
  GI-SVM: A sensitive method for predicting genomic islands based on unannotated sequence of a single genome. 1640003:1-1640003:16

Regular Paper: Review Paper

• 
  Monamorn Precharattana:
  Stochastic modeling for dynamics of HIV-1 infection using cellular automata: A review. 1630001:1-1630001:17

Regular Paper: Research Paper

• 
  Wenlei Wu, Weibin Sun, Tingzhe Sun:
  Modeling the heterogeneity of p53 dynamics in DNA damage response. 1650001:1-1650001:18
• 
  Jakub Bielecki, Ewelina Lipiec:
  Basis set dependence using DFT/B3LYP calculations to model the Raman spectrum of thymine. 1650002:1-1650002:15
• 
  Prantik Chatterjee, Nikhil Ranjan Pal:
  Discovery of synergistic genetic network: A minimum spanning tree-based approach. 1650003:1-1650003:19
• 
  Jiao Chen, Tianhong Pan, Tianqing Pu, Biao Huang, Dorothy Yu Huang, Weiping Zhang, Stephan Gabos, Can Jin:
  Predicting GHS toxicity using RTCA and discrete-time Fourier transform. 1650004:1-1650004:20
• 
  Ludi Jiang, Jiahua Chen, Yusu He, Yanling Zhang, Gongyu Li:
  A method to predict different mechanisms for blood-brain barrier permeability of CNS activity compounds in Chinese herbs using support vector machine. 1650005:1-1650005:14
• 
  Cong Pian, Jin Zhang, Yuanyuan Chen, Zhi Chen, Qin Li, Qiang Li, Liang-Yun Zhang:
  OP-Triplet-ELM: Identification of real and pseudo microRNA precursors using extreme learning machine with optimal features. 1650006:1-1650006:14

Volume 14, Number 2, April 2016

Special Issue - Selected Papers from MCCMB 2015

• 
  Mikhail S. Gelfand:
  Introduction to selected papers from MCCMB 2015. 1602003:1-1602003:2

Review Paper

• 
  Igor V. Sharakhov, Gleb N. Artemov, Maria V. Sharakhova:
  Chromosome evolution in malaria mosquitoes inferred from physically mapped genome assemblies. 1630003:1-1630003:17

Research Papers

• 
  Anastasia S. Kalinina, Alexandra L. Suvorikova, Vladimir G. Spokoiny, Mikhail S. Gelfand:
  Detection of homologous recombination in closely related strains. 1641001:1-1641001:12
• 
  Ekaterina Khrameeva, Geoffrey Fudenberg, Mikhail S. Gelfand, Leonid A. Mirny:
  History of chromosome rearrangements reflects the spatial organization of yeast chromosomes. 1641002:1-1641002:12
• 
  Anna S. Ershova, Ivan Rusinov, Mikhail O. Vasiliev, Sergei A. Spirin, Anna S. Karyagina:
  Restriction-Modification systems interplay causes avoidance of GATC site in prokaryotic genomes. 1641003:1-1641003:19
• 
  Nikita G. Shiliaev, Olga M. Selivanova, Oxana V. Galzitskaya:
  Search for conserved amino acid residues of the α-crystallin proteins of vertebrates. 1641004:1-1641004:16
• 
  Alexander V. Spirov, Ekaterina M. Myasnikova, David M. Holloway:
  Sequential construction of a model for modular gene expression control, applied to spatial patterning of the Drosophila gene hunchback. 1641005:1-1641005:24
• 
  Oxana A. Volkova, Yury V. Kondrakhin, Ivan S. Yevshin, Tagir F. Valeev, Ruslan N. Sharipov:
  Assessment of translational importance of mammalian mRNA sequence features based on Ribo-Seq and mRNA-Seq data. 1641006:1-1641006:15
• 
  Olga Zanegina, Evgeniy Aksianov, Andrei V. Alexeevski, Anna S. Karyagina, Sergei A. Spirin:
  Conserved features of complexes of TATA-box binding proteins with DNA. 1641007:1-1641007:18
• 
  Dmitry A. Suplatov, Nina Popova, Sergey A. Zhumatiy, Vladimir V. Voevodin, Vytas K. Svedas:
  Parallel workflow manager for non-parallel bioinformatic applications to solve large-scale biological problems on a supercomputer. 1641008:1-1641008:15
• 
  Elena V. Zemlyanskaya, Daniil S. Wiebe, Nadezda A. Omelyanchuk, Victor G. Levitsky, Victoria V. Mironova:
  Meta-analysis of transcriptome data identified TGTCNN motif variants associated with the response to plant hormone auxin in Arabidopsis thaliana L.. 1641009:1-1641009:16

Volume 14, Number 3, June 2016

Special Issue - Selected Papers from BICOB2015

• 
  Fahad Saeed, Nurit Haspel, Hisham Al-Mubaid:
  Introduction to the selected papers from the 7th International Conference on Bioinformatics and Computational Biology (BICoB 2015). 1602002:1-1602002:3
• 
  Christopher Ochs, Yehoshua Perl, Michael Halper, James Geller, Jane Lomax:
  Quality assurance of the gene ontology using abstraction networks. 1642001:1-1642001:22
• 
  Bahar Akbal-Delibas, Roshanak Farhoodi, Marc Pomplun, Nurit Haspel:
  Accurate refinement of docked protein complexes using evolutionary information and deep learning. 1642002:1-1642002:16
• 
  Gareth B. Ferneyhough, Corey M. Thibeault, Sergiu M. Dascalu, Frederick C. Harris Jr.:
  ModFossa: A library for modeling ion channels using Python. 1642003:1-1642003:16
• 
  Michael A. DeJesus, Thomas R. Ioerger:
  Normalization of transposon-mutant library sequencing datasets to improve identification of conditionally essential genes. 1642004:1-1642004:20
• 
  Jucheol Moon, Harris T. Lin, Oliver Eulenstein:
  Consensus properties and their large-scale applications for the gene duplication problem. 1642005:1-1642005:17

Regular Paper: Review Paper

• 
  Muhammad Sardaraz, Muhammad Tahir, Ataul Aziz Ikram:
  Advances in high throughput DNA sequence data compression. 1630002:1-1630002:18

Regular Papers: Research Papers

• 
  Matthias Gerstgrasser, Sarah Nicholls, Michael Stout, Katherine Smart, Chris Powell, Theodore Kypraios, Dov J. Stekel:
  A Bayesian approach to analyzing phenotype microarray data enables estimation of microbial growth parameters. 1650007:1-1650007:23
• 
  Archana Chowdhury, Pratyusha Rakshit, Amit Konar:
  Prediction of protein-protein interaction network using a multi-objective optimization approach. 1650008:1-1650008:34
• 
  Yanga Byun, Kyungsook Han:
  An efficient algorithm for planar drawing of RNA structures with pseudoknots of any type. 1650009:1-1650009:23
• 
  Sudip Mandal, Abhinandan Khan, Goutam Saha, Rajat Kumar Pal:
  Reverse engineering of gene regulatory networks based on S-systems and Bat algorithm. 1650010:1-1650010:22
• 
  Wajid Arshad Abbasi, Fayyaz ul Amir Afsar Minhas:
  Issues in performance evaluation for host-pathogen protein interaction prediction. 1650011:1-1650011:17
• 
  Tingfang Wu, Xun Wang, Zheng Zhang, Faming Gong, Tao Song, Zhihua Chen, Pan Zhang, Yang Zhao:
  NES-REBS: A novel nuclear export signal prediction method using regular expressions and biochemical properties. 1650013:1-1650013:18

Volume 14, Number 4, August 2016

Selected Paper from CCC2015

• 
  Jin Li, Chengzhen Xu, Lei Wang, Hong Liang, Weixing Feng, Zhongxi Cai, Ying Wang, Wang Cong, Yunlong Liu:
  PSRna: Prediction of small RNA secondary structures based on reverse complementary folding method. 1643001:1-1643001:18

Research Papers

• 
  Yaou Zhao, Mingyan Jiang, Yuehui Chen:
  Inferring gene regulatory networks using a time-delayed mass action model. 1650012:1-1650012:17
• 
  Worrawat Engchuan, Asawin Meechai, Sissades Tongsima, Narumol Doungpan, Jonathan H. Chan:
  Gene-set activity toolbox (GAT): A platform for microarray-based cancer diagnosis using an integrative gene-set analysis approach. 1650015:1-1650015:22
• 
  Xiaoling Wang, Jingshi Han, Kui Li, Guoqing Wang, Mudong Hao:
  Multi-layer composite mechanical modeling for the inhomogeneous biofilm mechanical behavior. 1650014:1-1650014:14
• 
  Ruifeng Hu, Xiaobo Sun:
  lncRNATargets: A platform for lncRNA target prediction based on nucleic acid thermodynamics. 1650016:1-1650016:10
• 
  Chang-Chang Cao, Xiao Sun:
  Ehapp2: Estimate haplotype frequencies from pooled sequencing data with prior database information. 1650017:1-1650017:15
• 
  Nolen Joy Perualila-Tan, Ziv Shkedy, Willem Talloen, Hinrich W. H. Göhlmann, Marijke Van Moerbeke, Adetayo Kasim:
  Weighted similarity-based clustering of chemical structures and bioactivity data in early drug discovery. 1650018:1-1650018:22
• 
  Artem Petrov, Vladimir Arzhanik, Gennady Makarov, Oleg V. Koliasnikov:
  A novel Arg H52/Tyr H33 conservative motif in antibodies: A correlation between sequence of antibodies and antigen binding. 1650019:1-1650019:17
• 
  Daniel Cerqueda-García, Luisa I. Falcón:
  Metabolic potential of microbial mats and microbialites: Autotrophic capabilities described by an in silico stoichiometric approach from shared genomic resources. 1650020:1-1650020:15
• 
  Javier González, Alberto Muñoz, Gabriel Martos:
  Asymmetric latent semantic indexing for gene expression experiments visualization. 1650023:1-1650023:18

Volume 14, Number 5, October 2016

Special Issue - Selected Papers from GIW 2016

• 
  Shuigeng Zhou, Yi-Ping Phoebe Chen, Hiroshi Mamitsuka:
  Introduction to the special issue on GIW 2016. 1602004:1-1602004:3
• 
  Fangzhou Shen, Jian Li, Ying Zhu, Zhuo Wang:
  Systematic investigation of metabolic reprogramming in different cancers based on tissue-specific metabolic models. 1644001:1-1644001:18
• 
  Jinwoo Park, Benjamin Hur, SungMin Rhee, Sangsoo Lim, Min-Su Kim, Kwangsoo Kim, Wonshik Han, Sun Kim:
  Information theoretic sub-network mining characterizes breast cancer subtypes in terms of cancer core mechanisms. 1644002:1-1644002:23
• 
  Kento Kodama, Hiroto Saigo:
  KDSNP: A kernel-based approach to detecting high-order SNP interactions. 1644003:1-1644003:16
• 
  Wilson Wen Bin Goh, Limsoon Wong:
  Spectra-first feature analysis in clinical proteomics - A case study in renal cancer. 1644004:1-1644004:18
• 
  Sohee Oh, Ik-Soo Huh, Seung Yeoun Lee, Taesung Park:
  Analysis of multiple related phenotypes in genome-wide association studies. 1644005:1-1644005:23
• 
  Jungsoo Gim, Sungho Won, Taesung Park:
  Conditional estimation of local pooled dispersion parameter in small-sample RNA-Seq data improves differential expression test. 1644006:1-1644006:13

Research Papers

• 
  Bin Yang, Sanrong Liu, Wei Zhang:
  Reverse engineering of gene regulatory network using restricted gene expression programming. 1650021:1-1650021:17
• 
  Darlington S. Mapiye, Alan Christoffels, Junaid Gamieldien:
  Identification of phenotype-relevant differentially expressed genes in breast cancer demonstrates enhanced quantile discretization protocol's utility in multi-platform microarray data integration. 1650022:1-1650022:18
• 
  Mani Mehraei, Rza Bashirov, Sükrü Tüzmen:
  Target-based drug discovery for β-globin disorders: drug target prediction using quantitative modeling with hybrid functional Petri nets. 1650026:1-1650026:18
• 
  Ashis Kumer Biswas, Jean X. Gao:
  PR2S2Clust: Patched RNA-seq read segments' structure-oriented clustering. 1650027:1-1650027:25
• 
  Deyong He, Ling Huang, Yaping Xu, Xiaoliang Pan, Lijun Liu:
  Computational analysis and enzyme assay of inhibitor response to disease single nucleotide polymorphisms (SNPs) in lipoprotein lipase. 1650028:1-1650028:15
• 
  Wilson Wen Bin Goh, Limsoon Wong:
  Evaluating feature-selection stability in next-generation proteomics. 1650029:1-1650029:23

Volume 14, Number 6, December 2016

Special Issue: Selected Papers from InCoB2016

• 
  Chandra Verma, Peter J. Bond:
  Introductory note for JBCB special issue. 1602005:1-1602005:2
• 
  Ruchishree Konhar, Manish Debnath, Jean Valrie Marbaniang, Devendra Kumar Biswal, Pramod Tandon:
  Age estimation for the genus Cymbidium (Orchidaceae: Epidendroideae) with implementation of fossil data calibration using molecular markers (ITS2 & matK) and phylogeographic inference from ancestral area reconstruction. 1660001:1-1660001:17
• 
  Varsha Embar, Adam Handen, Madhavi K. Ganapathiraju:
  Is the average shortest path length of gene set a reflection of their biological relatedness? 1660002:1-1660002:8

Regular Papers: Research Papers

• 
  Nada Abidi, Raimo Franke, Peter Findeisen, Frank Klawonn:
  Alignment of time-resolved data from high throughput experiments. 1650030:1-1650030:16
• 
  Ana Brândusa Pavel, Cristian Ioan Vasile:
  Identifying cancer type specific oncogenes and tumor suppressors using limited size data. 1650031:1-1650031:16
• 
  Beichuan Deng, Seongho Kim, Hengguang Li, Elisabeth Heath, Xiang Zhang:
  Global peak alignment for comprehensive two-dimensional gas chromatography mass spectrometry using point matching algorithms. 1650032:1-1650032:18
• 
  Li Gu, Lichun Xue, Qi Song, Fengji Wang, Huaqin He, Zhongyi Zhang:
  Classification of the fragrant styles and evaluation of the aromatic quality of flue-cured tobacco leaves by machine-learning methods. 1650033:1-1650033:18
• 
  Naim Al Mahi, Munni Begum:
  A two-step integrated approach to detect differentially expressed genes in RNA-Seq data. 1650034:1-1650034:18
• 
  Kiri Choi, Lucian P. Smith, J. Kyle Medley, Herbert M. Sauro:
  phraSED-ML: A paraphrased, human-readable adaptation of SED-ML. 1650035:1-1650035:11