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Volume 8
Article John A. Bumpus, Mark Trax, Ashley Reisdorph, Cindi Boyd, Damien Gilbert, Sara Techau and Roy Ventullo
An in silico analysis of cytochrome c from Phanerochaete chrysosporium: its amino acid sequence and characterization of gene structural elements
Article Aylan Farid Arenas, Andrés J. Gutierrez Escobara and Jorge Enrique Gómez-Marin
Evolutionary origin of the protozoan parasites histone-like proteins (HU)
Article Zhuofei Xu, Yanjie Chao, Youhui Si, Jian Wang, Meilin Jin, Aizhen Guo, Ping Qian, Rui Zhou and Huanchun Chen
The GTP binding sites interacted with RNA-dependent RNA polymerase of classical swine fever virus in de novo initiation
Article Simon J. Furney, Stephen F. Madden, Tomasz A. Kisiel, Desmond G. Higgins and Nuria Lopez-Bigas
Distinct patterns in the regulation and evolution of human cancer genes
Communication Longlong Yang, John R. Walker, John B. Hogenesch and Russell S. Thomas
NetAtlas: A Cytoscape Plugin to Examine Signaling Networks Based on Tissue Gene Expression
Article Takeru Nakazato, Toru Takinaka, Hironori Mizuguchi, Hideo Matsuda, Hidemasa Bono and Minoru Asogawa
BioCompass: A novel functional inference tool that utilizes MeSH hierarchy to analyze groups of genes
Communication Antony Le Béchec, Pierre Zindy, Thomas Sierocinski, Dimitri Petritis, Audrey Bihouée, Nolwenn Le Meur, Jean Léger and Nathalie Théret
M@IA: A modular open-source application for microarray workflow and integrative datamining

Review Qing Yan
Bioinformatics databases and tools in virology research: an overview
Communication Passoupathy Rajendrakumar, Akshaya Kumar Biswal, Sena M. Balachandran and Raman M. Sundaram
In silico analysis of microsatellites in organellar genomes of major cereals for understanding their phylogenetic relationships
Article Adaya Cohen, Samuel Bocobza, Isana Veksler, Idan Gabdank, Danny Barash, Asaph Aharoni, Michal Shapira and Klara Kedem
Computational identification of three-way junctions in folded RNAs: a case study in Arabidopsis
Communication Manish Kumar, Varun Thakur and Gajendra P. S. Raghava
COPid: Composition based protein identification
Article Aarti Garg and Gajendra P. S. Raghava
A machine learning based method for the prediction of secretory proteins using amino acid composition, their order and similarity-search
Article Preti Jain, Puneet Wadhwa, Ramazan Aygun and Gopi Podila
Vector-G: Multi-modular SVM-based heterotrimeric G-protein prediction
Article Jií Kléma, Sylvain Blachon, Arnaud Soulet, Bruno Crémilleux and Olivier Gandrillon
Constraint-based knowledge discovery from SAGE data
Article Claudia Pommerenke, Inga Gabriel, Boyke Bunk, Richard Münch, Isam Haddad, Petra Tielen, Irene Wagner-Döbler and Dieter Jahn
ROSY - a flexible and universal database and bioinformatics tool platform for Roseobacter related species
Communication Kuljeet Singh Sandhu, Sunil Pandey, Souvik Maiti and Beena Pillai
GASCO: Genetic Algorithm Simulation for Codon Optimization
Article Babita Sharma
Structure and mechanism of a transmission blocking vaccine candidate protein Pfs25 from P. falciparum: A molecular modeling and docking study
Article Palakkad Krishnan Unni Vinod and Kareenhalli V. Venkatesh
A steady state model for the transcriptional regulation of filamentous growth in Saccharomyces cerevisiae
Article Sachin Pundhir, Hemant Vijayvargiya and Anil Kumar
PredictBias: a server for the identification of genomic and pathogenicity islands in prokaryotes
Article Oruganty Krishnadev and Narayanaswamy Srinivasan
A data integration approach to predict host - pathogen protein-protein interactions: application to recognize protein interactions between human and a malarial parasite
Article Siya Ram, Ram Lakhan Singh and Rishi Shanker
In silico comparison of real-time PCR probes for detection of pathogens
Article Sudha Anand, Anand Anbarasu and Rao Sethumadhavan
Influence of C-H···π hydrogen bonds in interleukins
Article Dipankar Sengupta, Deeptak Verma and Pradeep Kumar Naik
Docking-MM-GB/SA and ADME screening of HIV-1 NNRTI inhibitor: Nevirapine and its analogues
Article Jiayu Wen, Tancred Frickey, Georg F. Weiller
Computational prediction of candidate miRNAs and their targets from Medicago truncatula non-protein-coding transcripts
Article Kanagarajadurai K. and Ramanathan Sowdhamini
Sequence and structural analyses of interleukin-8-like chemokine superfamily
Communication Vibhuti Sharma, Preeti Gupta and Aparna Dixit
In silico identification of putative drug targets from different metabolic pathways of Aeromonas hydrophila
Communication Kenji Akiyama, Eisuke Chikayama, Hiroaki Yuasa, Yukihisa Shimada, Takayuki Tohge, Kazuo Shinozaki, Masami Yokota Hirai, Tetsuya Sakurai, Jun Kikuchi and Kazuki Saito
PRIMe: a Web site that assembles tools for metabolomics and transcriptomics
Article Masami Kamasawa and Jun-ichi Horiuchi
Identification and characterization of polyadenylation signal (PAS) variants in human genomic sequences based on modified EST clustering
Article Sabah Khalid, Mohsin Khan, Chandrasekhar Babu Gorle, Karl Fraser, Ping Wang, Xiaohui Liu and Suling Li
MaXlab: A novel application for the cross comparison and integration of biological signatures from microarray studies
Communication Bram Sebastian and Samuel E. Aggrey
Specificity and sensitivity of PROMIR, ERPIN and MIR-ABELA in predicting pre-microRNAs in the chicken genome
Article Yury V. Kondrakhin, Ruslan N. Sharipov, Alexander E. Kel and Fedor A. Kolpakov
Identification of differentially expressed genes by meta-analysis of microarray data on breast cancer
Article Sher-ullah S. S. Khoyratty, Manoel T. Souza Jr. and Yasmina Jaufeerally-Fakim
Structural analysis of catalase from two Musa accessions, FHIA18 and Williams and from Ravenala madagascariensis
Article Sudha Jayaraman and Kavita Shah
Comparative studies on inhibitors of HIV-protease – a target for drug design
Article Neha S. Gandhi, Kathy Young, John R. Warmington and Ricardo L. Mancera
Characterization of sequence and structural features of the Candida krusei enolase
Article Andrea Brancale, Chrisanthy Vlachaki and Dimitrios Vlachakis
Molecular modelling study of the 3D structure of the Bovine Viral Diarrhea Virus (BVDV) helicase
Article Natarajan Vidya, Bagavathkumar Vadivukkarasi, Gopalakrishnan Manivannan and Krishnan Anbarasu
Molecular modeling and docking studies of glutamate racemase in Vibrio vulnificus CMCP6
Article Lan Khuyen Nguyen and Don Kulasiri
On multiple regulatory mechanisms in the tryptophan operon system in Escherichia coli: in silico study of perturbation dynamics
Communication Ananyo Choudhury and Ansuman Lahiri
TRABAS: A database for transcription regulation by ABA signaling
Article Biju Thomas and Rathanam Boopathy
Essential amino acids for the stability of human butyrylcholinesterase as predicted by CUPSAT server
Article Diane A. Flasch, Ellen K. Rebman, Emily H. Olfson, Khanh K. Nguyen, Lucasz E. Geirut, Megan C. Garland, Christi M. Lindorfer and Howard M. Laten
Analysis of insertional sites of the SIRE1 retroelement family from Glycine max using GenBank BAC-end sequences
Article Sandeep Joseph, Kelly Robbins, Wensheng Zhang and Romdhane Rekaya
Effects of misdiagnosis in input data on the identification of differential expression genes in incipient Alzheimer patients
Article T. Sobha Rani and Raju S. Bapi
Analysis of n-gram based promoter recognition methods and application to whole genome promoter prediction
Article Ieva Mitašiūnaitė, Christophe Rigotti, Stéphane Schicklin, Laurène Meyniel, Jean-François Boulicaut and Olivier Gandrillon
Extracting signature motifs from promoter sets of differentially expressed genes
Article Ambrish Roy, Narayanaswamy Srinivasan and Venkatraman S. Gowri
Molecular and structural basis of drift in the functions of closely-related homologous enzyme domains: Implications for function annotation based on homology searches and structural genomics
Article Aparna B. Ganesh, Hannah Rajasingh and Sharmila S. Mande
Mathematical modeling of regulation of type III secretion system in Salmonella enterica serovar Typhimurium by SirA

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