Journal of Bioinformatics and Computational Biology, Volume 11

Volume 11, Number 1, February 2013

Special Issue: Selected Papers from BGRS\SB-2012

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  Nikolay A. Kolchanov, Yuriy L. Orlov:
  Introductory Note for Bgrs-2012 Special Issue.

Review on Transcription Factors

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  Edgar Wingender:
  Criteria for an updated Classification of Human transcription factor DNA-binding Domains.

Motif Search in DNA

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  Ivan V. Kulakovskiy, Victor G. Levitsky, Dmitry Yu. Oshchepkov, Leonid Bryzgalov, Ilya E. Vorontsov, Vsevolod J. Makeev:
  From binding motifs in Chip-seq Data to Improved Models of transcription factor binding Sites.
• 
  Jan Grau, Jens Keilwagen, André Gohr, Ivan A. Paponov, Stefan Posch, Michael Seifert, Marc Strickert, Ivo Grosse:
  Dispom: a Discriminative de-novo Motif Discovery Tool Based on the Jstacs Library.

Motif Search in Proteins

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  Sebastian Maurer-Stroh, He Gao, Hao Han, Lies Baeten, Joost Schymkowitz, Frederic Rousseau, Louxin Zhang, Frank Eisenhaber:
  Motif Discovery with Data Mining in 3D protein Structure Databases: Discovery, Validation and Prediction of the U-Shape zinc binding ("Huf-zinc") Motif.
• 
  Seyed Shahriar Arab, Mohammadbagher Parsa Gharamaleki, Zaiddodine Pashandi, Rezvan Mobasseri:
  Putracer: a Novel Method for Identification of continuous-Domains in Multi-Domain proteins.

Networks

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  Carlo Maj, Ettore Mosca, Ivan Merelli, Giancarlo Mauri, Luciano Milanesi:
  Sensitivity Analysis for Studying the Relation between biochemical reactions and metabolic phenotypes.
• 
  Vitali A. Likhoshvai, Stanislav I. Fadeev, Vladislav V. Kogai, Tamara M. Khlebodarova:
  On the Chaos in gene Networks.

Network Application - Programming

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  Hang-mao Lee, Karl J. Dietz, Ralf Hofestädt:
  Computational Construction of Specialized Biological Networks.
• 
  Björn Sommer, Benjamin Kormeier, Pavel Demenkov, Patrizio Arrigo, Klaus Hippe, Özgür Ates, Alexey V. Kochetov, Vladimir A. Ivanisenko, Nikolay A. Kolchanov, Ralf Hofestädt:
  Subcellular Localization Charts: a New Visual Methodology for the Semi-Automatic Localization of protein-Related Data Sets.

Network Application in Plants

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  Ekaterina S. Novoselova, Victoria V. Mironova, Nadezda A. Omelyanchuk, Fedor V. Kazantsev, Vitali A. Likhoshvai:
  Mathematical Modeling of Auxin Transport in Protoxylem and Protophloem of Arabidopsis thaliana Root tips.
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  Victoria V. Mironova, Nadezda A. Omelyanchuk, Maria S. Savina, Petr M. Ponomarenko, Mikhail P. Ponomarenko, Vitali A. Likhoshvai, Nikolay A. Kolchanov:
  How Multiple Auxin Responsive Elements May Interact in plant promoters: a Reverse Problem solution.

Supercomputing and Metagenomics

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  Xiao Yang, Jaroslaw Zola, Srinivas Aluru:
  Large-Scale metagenomic sequence Clustering on Map-Reduce Clusters.

Volume 11, Number 2, April 2013

• 
  Limsoon Wong:
  An Introduction to some New Results in Bioinformatics and Computational Biology.

Research Papers

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  María M. Abad-Grau, Nuria Medina-Medina, Serafín Moral, Rosana Montes-Soldado, Sergio Torres-Sánchez, Fuencisla Matesanz:
  Increasing Power by using Haplotype Similarity in a Multimarker Transmission/disequilibrium Test.
• 
  Ahmed Hossain, Andrew R. Willan, Joseph Beyene:
  A Flexible nonparametric Approach to Find Candidate genes associated with disease in microarray Experiments.
• 
  Hiroshi Fujii, Tatsushi Ogata, Takehiko Shimada, Tomoko Endo, Hiroyuki Iketani, Tokurou Shimizu, Toshiya Yamamoto, Mitsuo Omura:
  Minimal Marker: an Algorithm and Computer Program for the Identification of Minimal Sets of Discriminating DNA Markers for Efficient Variety Identification.
• 
  Antonio Deiana, Andrea Giansanti:
  Tuning the Precision of Predictors to Reduce overestimation of protein Disorder over Large Datasets.
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  Alexandra Herzog, Björn Voss, Daniela Keilberg, Edina Hot, Lotte Søgaard-Andersen, Christoph Garbe, Ekaterina A. Kostina:
  A Strategy for Identifying Fluorescence Intensity Profiles of Single Rod-shaped Cells.
• 
  Céline Scornavacca, Wojciech Paprotny, Vincent Berry, Vincent Ranwez:
  Representing a Set of Reconciliations in a Compact Way.
• 
  Juan Antonio García-Martín, Peter Clote, Iván Dotú:
  Rnaifold: a Constraint Programming Algorithm for RNA inverse Folding and molecular Design.
• 
  Hadi Sabaa, Zhipeng Cai, Yining Wang, Randy Goebel, Stephen Moore, Guohui Lin:
  Whole genome Identity-by-Descent determination.

Review Papers

• 
  Hufeng Zhou, Jingjing Jin, Limsoon Wong:
  Progress in Computational Studies of Host-pathogen Interactions.
• 
  Sriganesh Srihari, Hon Wai Leong:
  A Survey of Computational Methods for protein Complex Prediction from protein Interaction Networks.
• 
  Clemens Kühn, Peter Gennemark:
  Modeling yeast Osmoadaptation at Different Levels of Resolution.

Volume 11, Number 3, June 2013

Special Issue: Selected Papers from the Second IEEE Conference on Healthcare Informatics, Imaging, and Systems Biology (HISB 2012)

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  Spencer Angus Thomas, Yaochu Jin:
  Evolving Connectivity between Genetic oscillators and Switches using Evolutionary Algorithms.
• 
  Min Li, Jianxin Wang, Huan Wang, Yi Pan:
  Identification of Essential proteins from Weighted protein-protein Interaction Networks.
• 
  Jaehyun An, Kwangsoo Kim, SungMin Rhee, Heejoon Chae, Kenneth P. Nephew, Sun Kim:
  Genome-Wide Analysis and Modeling of DNA methylation susceptibility in 30 Breast Cancer Cell Lines by using CPG Flanking Sequences.
• 
  Yuanning Liu, Yaping Chang, Chao Zhang, Qingkai Wei, Jingbo Chen, Hui-Ling Chen, Dong Xu:
  Influence of mRNA Features on siRNA Interference Efficacy.
• 
  Qinmin Hu, Jimmy Xiangji Huang:
  Enhancing genomics Information Retrieval through Dimensional Analysis.
• 
  Qiang Lou, Zoran Obradovic:
  Classifying Temporal microarray Data by Selecting Informative genes.
• 
  Alberto Cozzini, Ajay Jasra, Giovanni Montana:
  Model-Based Clustering with gene Ranking using penalized Mixtures of heavy-tailed Distributions.
• 
  Golnaz Taheri, Mahnaz Habibi, Limsoon Wong, Changiz Eslahchi:
  Disruption of protein complexes.

Volume 11, Number 4, August 2013

Research Papers

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  Manoj Kumar Yadav, Saurabh Kumar Pandey, D. Swati:
  Drug Target prioritization in Plasmodium falciparum through metabolic Network Analysis, and inhibitor Designing using Virtual Screening and docking Approach.
• 
  Willem P. A. Ligtenberg, Dragan Bosnacki, Peter A. J. Hilbers:
  Reconn: a Cytoscape Plug-in for Exploring and Visualizing Reactome.
• 
  Zhanyu Ma, Andrew E. Teschendorff:
  A variational Bayes beta Mixture Model for Feature Selection in DNA methylation Studies.
• 
  Mark C. Evans, Agnes C. Paquet, Wei Huang, Laura Napolitano, Arne Frantzell, Jonathan Toma, Eric W. Stawiski, Matthew Bidwell Goetz, Christos J. Petropoulos, Jeannette M. Whitcomb, Eoin Coakley, Mojgan Haddad:
  A Case-Based Reasoning System for Genotypic Prediction of HIV-1 Co-receptor tropism.
• 
  Lin He, Xi Han, Bin Ma:
  De novo sequencing with Limited Number of Post-Translational Modifications per peptide.
• 
  Jingyu Hou, Yongqing Jiang:
  Dynamically Searching for a Domain for protein Function Prediction.
• 
  Yipu Zhang, Hongwei Huo, Qiang Yu:
  A Heuristic Cluster-Based EM Algorithm for the Planted (L, d) Problem.
• 
  Jingli Wu, Binbin Liang:
  A Fast and Accurate Algorithm for Diploid Individual Haplotype Reconstruction.

Volume 11, Number 5, October 2013

Special Issue: Selected Papers from BICoB 2013

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  Bhaskar DasGupta, Hisham Al-Mubaid, Fahad Saeed:
  Foreword to the Special Issue on Selected Papers from the 5th International Conference on Bioinformatics and Computational Biology (Bicob 2013).
• 
  Anna Fowler, Vilas Menon, Nicholas A. Heard:
  Dynamic Bayesian Clustering.
• 
  Ashis Kumer Biswas, Baoju Zhang, Xiaoyong Wu, Jean X. Gao:
  Cnctdiscriminator: Coding and noncoding transcript Discriminator - an Excursion through Hypothesis Learning and Ensemble Learning Approaches.
• 
  Christina Rose Kyrtsos, John S. Baras:
  Studying the Role of APOE in Alzheimer's disease Pathogenesis using a Systems Biology Model.
• 
  Joseph G. Makin, Srini Narayanan:
  A Hybrid-System Model of the coagulation Cascade: Simulation, sensitivity, and Validation.
• 
  Wen-Chieh Chang, Pawel Górecki, Oliver Eulenstein:
  Exact solutions for species Tree Inference from discordant gene Trees.

Regular Papers: Research Papers

• 
  Fethullah Karabiber:
  A Peak Alignment Algorithm with Novel Improvements in Application to Electropherogram Analysis.
• 
  Pradip Ghanty, Nikhil R. Pal, Rajani K. Mudi:
  Prediction of protein secondary Structure using Probability Based Features and a Hybrid System.
• 
  Ulisses Dias, Zanoni Dias:
  Heuristics for the Transposition Distance Problem.

Regular Papers: Review Paper

• 
  Shuigeng Zhou, Ruiqi Liao, Jihong Guan:
  When Cloud Computing Meets Bioinformatics: a Review.

Regular Papers: Critical Comments

• 
  Francisco M. Couto, Helena Sofia Pinto:
  The Next Generation of Similarity Measures that Fully Explore the Semantics in Biomedical Ontologies.

Volume 11, Number 6, December 2013

Special Issue: Selected Papers from GIW2013

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  Frank Eisenhaber, Wing-Kin Sung, Limsoon Wong:
  The 24th International Conference on genome Informatics, Giw2013, in Singapore.
• 
  Venkata Rajesh Yella, Manju Bansal:
  Dna Structural Features and Architecture of promoter Regions Play a Role in gene Responsiveness of S. Cerevisiae.
• 
  Yuta Taniguchi, Yasuhiro Yamada, Osamu Maruyama, Satoru Kuhara, Daisuke Ikeda:
  The Purity Measure for genomic Regions leads to Horizontally Transferred genes.
• 
  Jing-Doo Wang:
  Comparing Virus Classification using genomic Materials According to Different Taxonomic Levels.
• 
  Yu-Lun Chen, Chien-Ming Chen, Tun-Wen Pai, Hon-Wai Leong, Ket Fah Chong:
  Homologous synteny Block Detection Based on Suffix Tree Algorithms.
• 
  Sebastian Maurer-Stroh, Vithiagaran Gunalan, Wing-Cheong Wong, Frank Eisenhaber:
  A Simple Shortcut to Unsupervised Alignment-Free phylogenetic genome Groupings, even from Unassembled sequencing reads.
• 
  Meiyappan Lakshmanan, Bevan Kai-Sheng Chung, Chengcheng Liu, Seon-Won Kim, Dong-Yup Lee:
  Cofactor Modification Analysis: a Computational Framework to Identify cofactor specificity Engineering targets for strain Improvement.
• 
  Yang Zhao, Morihiro Hayashida, Jira Jindalertudomdee, Hiroshi Nagamochi, Tatsuya Akutsu:
  Breadth-First Search Approach to Enumeration of Tree-like Chemical Compounds.
• 
  Claudiu Mihaila, Sophia Ananiadou:
  Recognising Discourse Causality Triggers in the Biomedical Domain.
• 
  Igor I. Titov, Pavel S. Vorozheykin:
  Ab initio Human miRNA and Pre-miRNA Prediction.
• 
  Henry Han, Xiaoli Li, See-Kiong Ng, Zhou Ji:
  Multi-Resolution-Test for Consistent phenotype Discrimination and biomarker Discovery in Translational Bioinformatics.
• 
  Jianmin Ma, Frank Eisenhaber, Sebastian Maurer-Stroh:
  Automatic phylogenetic Classification of bacterial beta-Lactamase Sequences including Structural and Antibiotic substrate Preference Information.
• 
  Yitzhak Friedman, Michal Linial:
  Mirror2.0: a Platform for Assessing the Joint Action of microRNAs in Cell regulation.