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Journal of Bioinformatics and Computational Biology, Volume 14
Volume 14, Number 1, February 2016
- 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
- Monamorn Precharattana:
Stochastic modeling for dynamics of HIV-1 infection using cellular automata: A review. 1630001:1-1630001:17
- 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, Yuan-yuan 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
- Mikhail S. Gelfand:
Introduction to selected papers from MCCMB 2015. 1602003:1-1602003:2
- Igor V. Sharakhov
, Gleb N. Artemov
, Maria V. Sharakhova:
Chromosome evolution in malaria mosquitoes inferred from physically mapped genome assemblies. 1630003:1-1630003:17
- 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
- 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
- Muhammad Sardaraz
, Muhammad Tahir
, Ataul Aziz Ikram:
Advances in high throughput DNA sequence data compression. 1630002:1-1630002:18
- 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
- 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
- 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
- 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
- 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
- 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
- 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
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