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In Silico Biology, Volume 9
Volume 9, Numbers 1-2, 2009
- Keya Sau, Arpan Deb
:
Temperature Influences Synonymous Codon and Amino Acid Usage Biases in the Phages Infecting Extremely Thermophilic Prokaryotes. 1-9 - Klaus Ecker, Jens Lichtenberg, Lonnie R. Welch:
The SiteSeeker Motif Discovery Tool. 11-22 - Jukka Kohonen, Sarish Talikota, Jukka Corander, Petri Auvinen, Elja Arjas:
A Naive Bayes Classifier for Protein Function Prediction. 23-34 - Prabha Garg
SubCellProt: Predicting Protein Subcellular Localization Using Machine Learning Approaches. 35-44 - Tiratha Raj Singh, Kamal Raj Pardasani
In silico Analysis of Evolutionary Patterns in Restriction Endonucleases. 45-53
- T. Sobha Rani, Raju S. Bapi
Analysis of n-Gram based Promoter Recognition Methods and Application to Whole Genome Promoter Prediction. S1-S16 - Ieva Mitasiunaite, Christophe Rigotti, Stéphane Schicklin, Laurène Meyniel, Jean-François Boulicaut, Olivier Gandrillon:
Extracting Signature Motifs from Promoter Sets of Differentially Expressed Genes. S17-S39 - Ambrish Roy, Narayanaswamy Srinivasan, 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. S41-S55 - Aparna B. Ganesh, Hannah Rajasingh, Sharmila S. Mande:
Mathematical Modeling of Regulation of Type III Secretion System in Salmonella enterica Serovar Typhimurium by SirA. S57-S72
Volume 9, Number 3, 2009
- Wei Zhang, Rong Stephanie Huang
Gene Set Enrichment Analyses Revealed Differences in Gene Expression Patterns between Males and Females. 55-63 - Jane Synnergren, Björn Olsson
Classification of Information Fusion Methods in Systems Biology. 65-76 - Ashesh Nandy, Ambarnil Ghosh, Papiya Nandy:
Numerical Characterization of Protein Sequences and Application to Voltage-Gated Sodium Channel α Subunit Phylogeny. 77-87 - Daniela Wieser, Mahesan Niranjan
Remote Homology Detection Using a Kernel Method that Combines Sequence and Secondary-Structure Similarity Scores. 89-103 - Mahmud Tareq Hassan Khan, Ingebrigt Sylte
Determinants for Psychrophilic and Thermophilic Features of Metallopeptidases of the M4 Family. 105-124 - Alessio Soggiu
Empowering Spot Detection in 2DE Images by Wavelet Denoising. 125-133 - Firoz Ahmed
Prediction of Polyadenylation Signals in Human DNA Sequences using Nucleotide Frequencies. 135-148
Volume 9, Number 4, 2009
- Andrés Julián Gutiérrez Escobar, Dolly Montoya Castaño:
Evolutionary Analysis for the Functional Divergence of the Spo0A Protein: The Key Sporulation Control Element. 149-162 - Isam Haddad, Karsten Hiller
An Emergent Self-Organizing Map Based Analysis Pipeline for Comparative Metabolome Studies. 163-178 - K. Rao Raghuraj, Kyaw Tun, Yuko Makita, Samavedham Lakshminarayanan
Amino-Acid Residue Association Models for Large Scale Protein-Protein Interaction Prediction. 179-194 - Aditya Rao, Sri Jyothsna Yeleswarapu, Gudladona Raghavendra, Rajgopal Srinivasan, Gopalakrishnan Bulusu
PlasmoID: A P. falciparum Information Discovery Tool. 195-202 - Leonid V. Omelyanchuk, Julya A. Pertseva, John M. Saul:
Evolutionary Origin of the Tumor Suppressor Hyperplastic Discs Protein. 203-207 - Kirsti Laurila, Harri Lähdesmäki:
Systematic Analysis of Disease-Related Regulatory Mutation Classes Reveals Distinct Effects on Transcription Factor Binding. 209-224 - Debmalya Barh
In silico Identification of Candidate Drug and Vaccine Targets from Various Pathways in Neisseria gonorrhoeae. 225-231 - Asami Suzuki, Takako Takai-Igarashi, Yukihiro Numabe, Hiroshi Tanaka:
Development of a Database and Ontology for Pathogenic Pathways in Periodontitis. 233-243 - Sajib Chakraborty, T. M. Zaved Waise, Faizule Hassan, Yearul Kabir, Mark A. Smith, Mohammad Arif:
Assessment of the Evolutionary Origin and Possibility of CRISPR-Cas (CASS) Interference Pathway in Vibrio cholerae O395. 245-254 - Vladislav Victorovich Khrustalev:
HIV1 V3 Loop Hypermutability is Enhanced by the Guanine Usage Bias in the Part of env Gene Coding for it. 255-269 - Xiaomin Wu, Gang Yang
Conformational Dynamics and Thermal Stabilities of the αβ-Tubulin Dimer: A Molecular Dynamics Simulation Study. 271-284
Volume 9, Numbers 5-6, 2009
- Klaus H. Ecker, Lonnie R. Welch:
A Concept for ab initio Prediction of cis-regulatory Modules. 285-306 - Sofia Khan, Mauno Vihinen
Evaluation of Accuracy and Applicability of Protein Models: Retrospective Analysis of Biological and Biomedical Predictions. 307-331 - David B. Whyte, Gopakumar Gopalakrishnan Nair
GEN-SNiP: An Online Tool to Find Polymorphisms in a Genome. 333-336 - Kinshuk C. Nayak:
Mutational Bias and Gene Expression Level Shape Codon Usage in Thermobifida fusca YX. 337-353 - Nielsen Q. Fernandez-Becker, Alan C. Moss
In silico Analysis of T-bet Activity in Peripheral Blood Mononuclear Cells in Patients with Inflammatory Bowel Disease (IBD). 355-363 - Pralay Mitra, Riddhiman Dhar, Debnath Pal
Interface of Apoptotic Protein Complexes Has Distinct Properties. 365-378 - Yunkai Liu, Sujuan Ye, Alexandre M. Erkine:
Analysis of Saccharomyces cerevisiae Genome for the Distributions of Stress-Response Elements Potentially Affecting Gene Expression by Transcriptional Interference. 379-389 - Anton Dormer, Cathelina V. Pauleus, Mondy N. Syverin, Clarissa Dacil, 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. 391-406 - Shubha Gopal, Vanishree Srinivas, Farhan Zameer, Jürgen Kreft:
Prediction of Proteins Putatively Involved in the Thiol: Disulfide Redox Metabolism of a Bacterium (Listeria): The CXXC Motif as Query Sequence. 407-414
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