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Volume 9
Article Keya Sau and Arpan Deb
Temperature influences synonymous codon and amino acid usage biases in the phages infecting extremely thermophilic prokaryotes
Article Klaus Ecker, Jens Lichtenberg and Lonnie Welch
The SiteSeeker motif discovery tool
Article Jukka Kohonen, Sarish Talikota, Jukka Corander, Petri Auvinen and Elja Arjas
A Naive Bayes classifier for protein function prediction
Article Prabha Garg, Virag Sharma, Pradeep Chaudhari and Nilanjan Roy
SubCellProt: Predicting protein subcellular localization using machine learning approaches
Article Tiratha Raj Singh and Kamal Raj Pardasani
In silico analysis of evolutionary patterns in restriction endonucleases

Communication Wei Zhang, R. Stephanie Huang, Shiwei Duan and M. Eileen Dolan
Gene set enrichment analyses revealed differences in gene expression patterns between males and females
Review Jane Synnergren, Björn Olsson and Jonas Gamalielsson
Classification of information fusion methods in systems biology
Article Ashesh Nandy, Ambarnil Ghosh and Papiya Nandy
Numerical characterization of protein sequences and application to voltage-gated sodium channel α subunit phylogeny
Article Daniela Wieser and Mahesan Niranjan
Remote homology detection using a kernel method that combines sequence and secondary-structure similarity scores
Article Mahmud Tareq Hassan Khan and Ingebrigt Sylte
Determinants for psychrophilic and thermophilic features of metallopeptidases of the M4 family
Article Alessio Soggiu, Osvaldo Marullo, Paola Roncada and Enrico Capobianco
Empowering spot detection in 2DE images by wavelet denoising
Article Firoz Ahmed, Manish Kumar and Gajendra P. S. Raghava
Prediction of polyadenylation signals in human DNA sequences using nucleotide frequencies
Article Andrés Julián Gutiérrez Escobar and Dolly Montoya Castaño
Evolutionary analysis for functional divergence of the Spo0A protein: the key sporulation control element
Article Isam Haddad, Karsten Hiller, Eliane Frimmersdorf, Beatrice Benkert, Dietmar Schomburg and Dieter Jahn
An emergent self-organizing map based analysis pipeline for comparative metabolome studies
Article Raghuraj Rao, Kyaw Tun, Yuko Makita, Samavedham Lakshminarayanan and Pawan K. Dhar
Amino-acid Residue Association models for large scale protein-protein interaction prediction
Article Aditya Rao, Sri Jyothsna Yeleswarapu, Gudladona Raghavendra, Rajgopal Srinivasan and Gopalakrishnan Bulusu
PlasmoID: A P. falciparum protein information discovery tool
Communication Leonid V. Omelyanchuk, Julya A. Pertseva and John M. Saul
Evolutionary origin of the tumor suppressor Hyperplastic discs protein
Article Kirsti Laurila and Harri Lähdesmäki
Systematic analysis of disease-related regulatory mutation classes reveals distinct effects on transcription factor binding
Communication Debmalya Barh and Anil Kumar
In silico identification of candidate drug and vaccine targets from various pathways in Neisseria gonorrhoeae
Article Asami Suzuki, Takako Takai-Igarashi, Yukihiro Numabe and Hiroshi Tanaka
Development of a database and ontology for pathogenic pathways in periodontitis
Article Sajib Chakraborty, T. M. Zaved Waise, Faizule Hassan, Yearul Kabir, Mark A. Smith and Mohammad Arif
Assessment of the evolutionary origin and possibility of CRISPR-Cas (CASS) mediated RNA interference pathway in Vibrio cholerae O395
Article Vladislav Victorovich Khrustalev
HIV1 V3 loop hypermutability is enhanced by the guanine usage bias in the part of env gene coding for it
Article Xiaomin Wu, Gang Yang, Yuangang Zu, Zhiwei Yang and Lijun Zhou
Conformational dynamics and thermal stabilities of the αβ-tubulin dimer: a molecular dynamics simulation study
Article Klaus Ecker and Lonnie Welch
A concept for ab initio prediction of cis-regulatory modules
Article Sofia Khan and Mauno Vihinen
Evaluation of accuracy and applicability of protein models: retrospective analysis of biological and biomedical predictions
Communication David B. Whyte, Gopakumar Gopalakrishnan Nair, Achuthsankar S. Nair and Oommen V. Oommen
GEN-SNiP: an online tool to find polymorphisms in a genome
Article Kinshuk C. Nayak
Mutational bias and gene expression level shape codon usage in Thermobifida fusca YX
Article Nielsen Q. Fernandez-Becker and Alan C. Moss
In silico analysis of T-bet activity in peripheral blood mononuclear cells in patients with inflammatory bowel disease (IBD)
Article Pralay Mitra, Riddhiman Dhar and Debnath Pal
Interface of apoptotic protein complexes has distinct properties
Article Yunkai Liu, Sujuan Ye and Alexandre M. Erkine
Analysis of Saccharomyces cerevisiae genome for the distributions of stress-response elements potentially affecting gene expression by transcriptional interference
Article Anton Dormer, Vasti Pauleus, Mondy Sevian, Clarissa Dacil and Peta-Gaye Smile
Challenges in the use of in silico tools for predicting peptides binding to HLA-Class II molecules of HCV E1, E2, and P7
Communication Shubha Gopal, Vanishree Srinivas, Farhan Zameer and Jürgen Kreft
Prediction of proteins putatively involved in the thiol:disulfide redox metabolism of a bacterium (Listeria): the CXXC motif as query sequence

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