Journal: J. Bioinformatics and Computational Biology

Volume 13, Issue 6

0 -- 0Jinyang Tang, Fei Wang. Detecting differentially expressed genes by smoothing effect of gene length on variance estimation
0 -- 0Wosley Arruda, Daniel S. Souza, Célia Ghedini Ralha, Maria Emilia M. T. Walter, Tainá Raiol, Marcelo M. Brigido, Peter F. Stadler. Knowledge-based reasoning to annotate noncoding RNA using multi-agent system
0 -- 0Alexei A. Sharov, David Schlessinger, Minoru S. H. Ko. ExAtlas: An interactive online tool for meta-analysis of gene expression data
0 -- 0Reza Mousavi, Mahdi Eftekhari, Mehdi Ghezelbash Haghighi. A new approach to human microRNA target prediction using ensemble pruning and rotation forest
0 -- 0Zengmiao Wang, Jun Wang, Changjing Wu, Minghua Deng. Estimation of isoform expression in RNA-seq data using a hierarchical Bayesian model
0 -- 0Haichun Li, Minghui Wang, Xiaoyi Xu. Prediction of kinase-substrate relations based on heterogeneous networks
0 -- 0Jing Zhou, Yuxuan Shui, Shengwen Peng, Xuhui Li, Hiroshi Mamitsuka, Shanfeng Zhu. MeSHSim: An R/Bioconductor package for measuring semantic similarity over MeSH headings and MEDLINE documents
0 -- 0Jian-Feng Yang, Xiao-Fan Ding, Xing Sun, Shui-Ying Tsang, Hong Xue. SAMSVM: A tool for misalignment filtration of SAM-format sequences with support vector machine
0 -- 0Binghua Wang, Minghui Wang, Yujie Jiang, Dongdong Sun, Xiaoyi Xu. A novel network-based computational method to predict protein phosphorylation on tyrosine sites
0 -- 0Murodzhon Akhmedov, Bülent Çatay, Mehmet Serkan Apaydin. Automating unambiguous NOE data usage in NVR for NMR protein structure-based assignments
0 -- 0Xing-Ming Zhao. Editorial - Data mining in bioinformatics
0 -- 0Kyung-Ah Sohn, Kyubum Wee. A comment on two-locus epistatic interaction models for genome-wide association studies

Volume 13, Issue 5

0 -- 0Edgar D. Coelho, André M. Santiago, Joel P. Arrais, José Luís Oliveira. Computational methodology for predicting the landscape of the human-microbial interactome region level influence
0 -- 0Chao Han, Jian Chen, Qingyao Wu, Shuai Mu, HuaQing Min. Sparse Markov chain-based semi-supervised multi-instance multi-label method for protein function prediction
0 -- 0Ali T. Abdallah, Matthias Fischer 0003, Peter Nürnberg, Michael Nothnagel, Peter Frommolt. CoNCoS: Copy number estimation in cancer with controlled support
0 -- 0Nam-Ninh Nguyen, Sriganesh Srihari, Hon Wai Leong, Ket Fah Chong. EnzDP: Improved enzyme annotation for metabolic network reconstruction based on domain composition profiles
0 -- 0Ming Fan, Bin Zheng, Lihua Li. A novel Multi-Agent Ada-Boost algorithm for predicting protein structural class with the information of protein secondary structure
0 -- 0Paul Horton, Christian Schönbach, Shoba Ranganathan, Siu-Ming Yiu. Introduction to selected papers from GIW/InCoB 2015
0 -- 0Westley Arthur Sherman, Durga Kuchibhatla, Vachiranee Limviphuvadh, Sebastian Maurer-Stroh, Birgit Eisenhaber, Frank Eisenhaber. HPMV: Human protein mutation viewer - relating sequence mutations to protein sequence architecture and function changes
0 -- 0Derui Wang, Jingyu Hou. Explore the hidden treasure in protein-protein interaction networks - An iterative model for predicting protein functions
0 -- 0Victoria E. Sánchez, Antonio M. Peinado, José L. Pérez-Córdoba, Ángel M. Gómez. A new signal characterization and signal-based Chou's PseAAC representation of protein sequences
0 -- 0Yoichi Takenaka, Shigeto Seno, Hideo Matsuda. Detecting shifts in gene regulatory networks during time-course experiments at single-time-point temporal resolution

Volume 13, Issue 4

0 -- 0Lavinia Egidi, Giovanni Manzini. Multiple seeds sensitivity using a single seed with threshold
0 -- 0Natalia Novoselova, Junxi Wang, Frank Klawonn. Optimized leaf ordering with class labels for hierarchical clustering
0 -- 0El-Amine Zemali, Abdelmadjid Boukra. Resolving the multiple sequence alignment problem using biogeography-based optimization with multiple populations
0 -- 0Ming Li 0001, Limsoon Wong. John Wooley and JBCB
0 -- 0Kevin Lim, Zhenhua Li, Kwok Pui Choi, Limsoon Wong. A quantum leap in the reproducibility, precision, and sensitivity of gene expression profile analysis even when sample size is extremely small
0 -- 0Piotr Iwo Wójcik, Thérèse Ouellet, Margaret Balcerzak, Witold Dzwinel. Identification of biomarker genes for resistance to a pathogen by a novel method for meta-analysis of single-channel microarray datasets
0 -- 0Sayed-Amir Marashi, Zhaleh Hosseini. On correlated reaction sets and coupled reaction sets in metabolic networks
0 -- 0Christophe Guyeux, Jean-Marc Nicod, Laurent Philippe, Jacques M. Bahi. The study of unfoldable self-avoiding walks - Application to protein structure prediction software
0 -- 0Bo Liao, Sumei Ding, Haowen Chen, Zejun Li, Lijun Cai. Identifying human microRNA-disease associations by a new diffusion-based method
0 -- 0Jun Liu, Jiuqiang Han, Hongqiang Lv. ADPRtool: A novel predicting model for identification of ASP-ADP-Ribosylation sites of human proteins

Volume 13, Issue 3

0 -- 0Asako Komori, Yukihiro Maki, Isao Ono, Masahiro Okamoto. Investigating noise tolerance in an efficient engine for inferring biological regulatory networks
0 -- 0Zhanzhan Cheng, Shuigeng Zhou, Jihong Guan. Computationally predicting protein-RNA interactions using only positive and unlabeled examples
0 -- 0Tarini Shankar Ghosh, Varun Mehra, Sharmila S. Mande. Grid-Assembly: An oligonucleotide composition-based partitioning strategy to aid metagenomic sequence assembly
0 -- 0Xiaoli Li, Jie Zheng. Introduction to the CSBio2014 special issue
0 -- 0Yifan Nie, Wenge Rong, Yiyuan Zhang, Yuanxin Ouyang, Zhang Xiong. Embedding assisted prediction architecture for event trigger identification
0 -- 0Fan Zhang, Min Wu, Xuejuan Li, Xiao-Li Li, Chee Keong Kwoh, Jie Zheng. Predicting essential genes and synthetic lethality via influence propagation in signaling pathways of cancer cell fates
0 -- 0Anirban Dutta, Mohammed Monzoorul Haque, Tungadri Bose, Ch. V. Siva K. Reddy, Sharmila S. Mande. FQC: A novel approach for efficient compression, archival, and dissemination of fastq datasets
0 -- 0Marcus C. K. Ng, Simon Fong, Shirley W. I. Siu. PSOVina: The hybrid particle swarm optimization algorithm for protein-ligand docking

Volume 13, Issue 2

0 -- 0Prashant Singh Rana, Harish Sharma, Mahua Bhattacharya, Anupam Shukla. Quality assessment of modeled protein structure using physicochemical properties
0 -- 0Nicolas Loira, Anna Zhukova, David James Sherman. Pantograph: A template-based method for genome-scale metabolic model reconstruction
0 -- 0Changchuan Yin. Representation of DNA sequences in genetic codon context with applications in exon and intron prediction
0 -- 0Wenbin Chen, Matthew C. Schmidt, Wenhong Tian, Nagiza F. Samatova, Shaohong Zhang. An efficient algorithm for pairwise local alignment of protein interaction networks
0 -- 0Jun Wu, Xiaodong Zhao, Zongli Lin, Zhifeng Shao. An effective differential expression analysis of deep-sequencing data based on the Poisson log-normal model
0 -- 0Chern Han Yong, Limsoon Wong. From the static interactome to dynamic protein complexes: Three challenges
0 -- 0Farhad Hormozdiari, Eleazar Eskin. Memory efficient assembly of human genome
0 -- 0Chao Liu, Chi Zhang, Jing Su, Dongsheng Zhang, Sha Cao. Stresses drive a cancer's initiation, progression and metastasis: Critical comments on the book "Cancer Bioinformatics"
0 -- 0Scott E. Nixon, Dianelys González-Peña, Marcus A. Lawson, Robert H. McCusker, Alvaro G. Hernandez, Jason C. O'Connor, Robert Dantzer, Keith W. Kelley, Sandra L. Rodriguez-Zas. Analytical workflow profiling gene expression in murine macrophages
0 -- 0Mohammad-Hadi Foroughmand-Araabi, Bahram Goliaei, Kasra Alishahi, Mehdi Sadeghi, Sama Goliaei. Codon usage and protein sequence pattern dependency in different organisms: A Bioinformatics approach
0 -- 0Nimet Ilke Akçay, Rza Bashirov, Sükrü Tüzmen. Validation of signalling pathways: Case study of the p16-mediated pathway

Volume 13, Issue 1

0 -- 0Vitali A. Likhoshvai, Vladislav V. Kogai, Stanislav I. Fadeev, Tamara M. Khlebodarova. Alternative splicing can lead to chaos
0 -- 0Irina M. Larina, Lyudmila Kh. Pastushkova, Evgeny S. Tiys, Kirill S. Kireev, Alexey S. Kononikhin, Natalia L. Starodubtseva, Igor A. Popov, Marc-Antoine Custaud, Igor V. Dobrokhotov, Evgeny N. Nikolaev, Nikolay A. Kolchanov, Vladimir A. Ivanisenko. Permanent proteins in the urine of healthy humans during the Mars-500 experiment
0 -- 0Petr M. Ponomarenko, Mikhail P. Ponomarenko. Sequence-based prediction of transcription upregulation by auxin in plants
0 -- 0Vladimir P. Golubyatnikov, Tatyana A. Bukharina, Dagmara P. Furman. D. melanogaster mechanoreceptors: The central regulatory circuit
0 -- 0Sergey Matvienko, Nikolay Alemasov, Eduard Fomin. Interaction sorting method for molecular dynamics on multi-core SIMD CPU architecture
0 -- 0Alban Shoshi, Venus Ogultarhan, Tobias Hoppe, Benjamin Kormeier, Ulrich Müller, Ralf Hofestädt. Identifying adverse drug reactions and drug-induced diseases using network-based drug mapping
0 -- 0Ulyana Zubairova, Sergey Golushko, Aleksey Penenko, Sergey Nikolaev. A computational model of the effect of symplastic growth on cell mechanics in a linear leaf blade
0 -- 0Eduard Fomin. Reconstruction of sequence from its circular partial sums for cyclopeptide sequencing problem
0 -- 0L. A. Krasnobaeva, L. V. Yakushevich. Rotational dynamics of bases in the gene coding interferon alpha 17 (IFNA17)
0 -- 0Yuriy L. Orlov, Ralf Hofestädt, Nikolay A. Kolchanov. Introductory note for BGRS\SB-2014 special issue