Volume 9 2008   Article Keya Sau and Arpan Deb Temperature influences synonymous codon and amino acid usage biases in the phages infecting extremely thermophilic prokaryotes 0001   Article Klaus Ecker, Jens Lichtenberg and Lonnie Welch The SiteSeeker motif discovery tool 0002   Article Jukka Kohonen, Sarish Talikota, Jukka Corander, Petri Auvinen and Elja Arjas A Naive Bayes classifier for protein function prediction 0003   Article Prabha Garg, Virag Sharma, Pradeep Chaudhari and Nilanjan Roy SubCellProt: Predicting protein subcellular localization using machine learning approaches 0004   Article Tiratha Raj Singh and Kamal Raj Pardasani In silico analysis of evolutionary patterns in restriction endonucleases 0005       2009   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 0006   Review Jane Synnergren, Björn Olsson and Jonas Gamalielsson Classification of information fusion methods in systems biology 0007   Article Ashesh Nandy, Ambarnil Ghosh and Papiya Nandy Numerical characterization of protein sequences and application to voltage-gated sodium channel α subunit phylogeny 0008   Article Daniela Wieser and Mahesan Niranjan Remote homology detection using a kernel method that combines sequence and secondary-structure similarity scores 0009   Article Mahmud Tareq Hassan Khan and Ingebrigt Sylte Determinants for psychrophilic and thermophilic features of metallopeptidases of the M4 family 0010   Article Alessio Soggiu, Osvaldo Marullo, Paola Roncada and Enrico Capobianco Empowering spot detection in 2DE images by wavelet denoising 0011   Article Firoz Ahmed, Manish Kumar and Gajendra P. S. Raghava Prediction of polyadenylation signals in human DNA sequences using nucleotide frequencies 0012   Article Andrés Julián Gutiérrez Escobar and Dolly Montoya Castaño Evolutionary analysis for functional divergence of the Spo0A protein: the key sporulation control element 0013   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 0014   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 0015   Article Aditya Rao, Sri Jyothsna Yeleswarapu, Gudladona Raghavendra, Rajgopal Srinivasan and Gopalakrishnan Bulusu PlasmoID: A P. falciparum protein information discovery tool 0016   Communication Leonid V. Omelyanchuk, Julya A. Pertseva and John M. Saul Evolutionary origin of the tumor suppressor Hyperplastic discs protein 0017   Article Kirsti Laurila and Harri Lähdesmäki Systematic analysis of disease-related regulatory mutation classes reveals distinct effects on transcription factor binding 0018   Communication Debmalya Barh and Anil Kumar In silico identification of candidate drug and vaccine targets from various pathways in Neisseria gonorrhoeae 0019   Article Asami Suzuki, Takako Takai-Igarashi, Yukihiro Numabe and Hiroshi Tanaka Development of a database and ontology for pathogenic pathways in periodontitis 0020   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 0021   Article Vladislav Victorovich Khrustalev HIV1 V3 loop hypermutability is enhanced by the guanine usage bias in the part of env gene coding for it 0022   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 0023   Article Klaus Ecker and Lonnie Welch A concept for ab initio prediction of cis-regulatory modules 0024   Article Sofia Khan and Mauno Vihinen Evaluation of accuracy and applicability of protein models: retrospective analysis of biological and biomedical predictions 0025   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 0026   Article Kinshuk C. Nayak Mutational bias and gene expression level shape codon usage in Thermobifida fusca YX 0027   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) 0028   Article Pralay Mitra, Riddhiman Dhar and Debnath Pal Interface of apoptotic protein complexes has distinct properties 0029   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 0030   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 0031   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 0032

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