Volume 6 2006      Article                Atsushi Doi, Masao Nagasaki, Hiroshi Matsuno and Satoru Miyano Simulation based validation of the p53 transcriptional activity with hybrid functional Petri net 0001   Article Leszek Konieczny, Michal Brylinski and Irena Roterman Gauss-function-based model of hydrophobicity density in proteins 0002   Article Imtiaz A. Khan, Matthew Mort, Paul R. Buckland, Michael C. O’Donovan, David N. Cooper and Nadia A. Chuzhanova In silico discrimination of single nucleotide polymorphisms and pathological mutations in human gene promoter regions by means of local DNA sequence context and regularity 0003   Article Daniel R. Matute, Emiliano Barreto-Hernandez and Laurent Falquet Hunting for insect-specific protein domains 0004   Communication Anirban Dutta, Shashi Kr. Singh, Payel Ghosh, Runni Mukherjee, Sayak Mitter and Debashis Bandyopadhyay In silico identification of potential therapeutic targets in the human pathogen Helicobacter pylori 0005   Article Kazuharu Arakawa, Yoichi Nakayama and Masaru Tomita GPAC: Benchmarking the sensitivity of genome informatics analysis to genome annotation completeness 0006   Article Ralf Wessel, Volker Foos, Allan Aspelmeier, Martin Jürgens, Adolf Graessmann and Andreas Klein CorrXpression - identification of significant groups of genes and experiments by means of correspondence analysis and ratio analysis 0007   Article Workshop "GEOMETRY OF GENOME" Lokesh Kumar, Matthias Futschik and Hanspeter Herzel DNA motifs and sequence periodicities 0008   Article Daisuke Komura, Kunihiro Nishimura, Shumpei Ishikawa, Binaya Panda, Jing Huang, Hiroshi Nakamura, Sigeo Ihara, Michitaka Hirose, Keith W. Jones and Hiroyuki Aburatani Noise reduction from genotyping microarrays using probe level information 0009   Article Anna Gambin, Sławomir Lasota and Michał Rutkowski Analyzing stationary states of gene regulatory network using Petri nets 0010   Article Harpreet Kaur and G. P. S. Raghava Prediction of Cα-H···O and Cα-H···π interactions in proteins using recurrent neural network 0011   Communication Aswin Sai Narain Seshasayee Social behavior of the yeast protein-protein interaction network 0012   Article Christoph Bock and Jürgen Hesser Analysis and prediction of helix shift errors in homology modeling 0013   Article Satoshi Mizuta, Hikaru Munakata, Abulimiti Aimaiti, Ichitaro Oya, Kenji Oosawa and Toshio Shimizu Analysis of tandem repeats found in 44 prokaryotic genomes 0014   Article Tamanna Anwar, Sunil K. Lal and Asad U. Khan In silico analysis of genes nucleoprotein, neuraminidase and hemagglutinin: a comparative study on different strains of influenza A (bird flu) virus sub-type H5N1 0015   Article Patnala Kiranmayi and Pamarthi Maruthi Mohan Metal transportome of Neurospora crassa 0016   Article A. Bankhead III, Nancy S. Magnuson and Robert B. Heckendorn Gene knockout experiments to quantify a G2/M genetic network simulation for mammary cancer susceptibility 0017   Article Peter Gennemark, Bodil Nordlander, Stefan Hohmann and Dag Wedelin A simple mathematical model of adaptation to high osmolarity in yeast 0018   Article Achuthsankar S. Nair and T. Mahalakshmi Are categorical periodograms and indicator sequences of genomes spectrally equivalent? 0019   Communication Michael Bose and Robert D. Barber Prophage Finder: a prophage loci prediction tool for prokaryotic genome sequences 0020   Article B. Balamurugan, M.N.A. Md. Roshan, Daliah Michael, M. Ambaree, S. Divya, H. Keerthana, M. Seemanthini and K. Sekar SMS: Sequence, Motif and Structure - A database on the structural rigidity of peptide fragments in non-redundant proteins 0021   Communication Krishna R. Kalari, Melanie Casavant, Thomas B. Bair, Henry L. Keen, Josep M. Comeron, Thomas L. Casavant and Todd E. Scheetz First Exons and Introns - A survey of GC content and gene structure in the human genome 0022   Article Lorenz Bülow, Nils Ole Steffens, Claudia Galuschka, Martin Schindler and Reinhard Hehl AthaMap: from in silico data to real transcription factor binding sites 0023   Communication Francesco Piva and Giovanni Principato RANDNA: a random DNA sequence generator 0024   Article Steven E. Massey Basic faced alpha helices are widespread in the peptide extensions of the eukaryotic aminoacyl-tRNA synthetases 0025   Communication Meena Kishore Sakharkar, Pandjassarame Kangueane, Kishore Ramaji Sakharkar and Zhaowei Zhong Huge proteins in the human proteome and their participation in hereditary diseases 0026   Article Rainer Merkl AMIGOS: a method for the inspection of genomic organisation or structure and its application to characterise conserved gene arrangements 0027   Communication Gang Su, Binchen Mao and Jin Wang MACO: A gapped-alignment scoring tool for comparing transcription factor binding sites 0028   Article Saikat Chakrabarti, Gowri Manohari, Ganesan Pugalenthi and Ramanathan Sowdhamini SSToSS - Sequence-Structural Templates of Single-member Superfamilies 0029   Article Gordon Blackshields, Iain M. Wallace, Mark Larkin and Desmond G. Higgins Analysis and comparison of benchmarks for multiple sequence alignment 0030   Communication Chan-Eng Chong, Boon-San Lim, Sheila Nathan and Rahmah Mohamed In silico analysis of Burkholderia pseudomallei genome sequence for potential drug targets 0031   Communication Andrés J. Gutiérrez Escobar, Aylan Farid Arenas and Jorge Enrique Gómez-Marin Molecular evolution of serine/arginine splicing factors family (SR) by positive selection 0032   Article Chandrashekar S. Reddy, Arunachalam Manonmani, Meenakshi Babu and Ramanathan Sowdhamini Enhanced structure prediction of gene products containing class III adenylyl cyclase domains 0033   Article Alessandra C. Faria-Campos, Sérgio V. A. Campos, Francisco Prosdocimi, Glaura C. Franco, Glória R. Franco and J. Miguel Ortega Efficient secondary database driven annotation using model organism sequences 0034   Communication Pratip Shil, Niraj Dudani and Pandit B. Vidyasagar ISHAN: sequence homology analysis package 0035   Article Mamoun Ahram, Zoi I. Litou, Ruihua Fang and Ghaith Al-Tawallbeh Estimation of membrane proteins in the human proteome 0036   Article Melissa J. Davis, Fasheng Zhang, Zheng Yuan and Rohan D. Teasdale MemO: A consensus approach to the annotation of a protein's membrane organization 0037   Opinion Paras Chopra and Akhil Kamma Engineering life through Synthetic Biology 0038   Communication Junichi Sugahara, Nozomu Yachie, Yasuhiko Sekine, Akiko Soma, Motomu Matsui, Masaru Tomita and Akio Kanai SPLITS: a new program for predicting split and intron-containing tRNA genes at the genome level 0039   Article Mark Doderer, Kihoon Yoon, John Salinas and Stephen Kwek Protein subcellular localization prediction using a hybrid of similarity search and error-correcting output code techniques that produces interpretable results 0040   Article P. Nataraj Sekhar, P. B. Kavi Kishor, L. Ananda Reddy, P. Mondal, A. K. Dash, M. Kar, S. Mohanty and S. C. Sabat In silico modeling and hydrogen peroxide binding study of rice catalase 0041   Article Vito Librando, Danilo Gullotto and Zelica Minniti Automated molecular library generation of proteic fragments by virtual proteolysis for molecular modelling studies 0042   Article Abdelouahab Chikhi, Abderrahmane Bensegueni, Abderrahmane Boulahrouf and Mustapha Bencharif Theoretical study of Escherichia coli peptide deformylase inhibition by several drugs 0043   Article Alfonso Benítez-Páez Sequence analysis of the Receptor Activity-Modifying Proteins family, new putative peptides and structural conformation inference 0044   Article Nitesh Kumar Singh, S. Mahalaxmi Selvam and Paulsharma Chakravarthy T-iDT : Tool for identification of Drug Target in bacteria and validation by Mycobacterium tuberculosis 0045   Article Jorge Andrade, Lisa Berglund, Mathias Uhlén and Jacob Odeberg Using Grid technology for computationally intensive applied bioinformatics analyses 0046   Article Adrian E. H. Png, Keng Wah Choo, Cheryl I. P. Lee, Siew Hong Leong and Oi Lian Kon Primer design for whole genome amplification using genetic algorithms 0047   Article Shinsuke Dohkan, Asako Koike and Toshihisa Takagi Improving the performance of an SVM-based method for predicting protein-protein interactions 0048   Article Tae-Min Kim and Myeong Ho Jung Identification of transcriptional regulators using binding site enrichment analysis 0049   Article Najl V. Valeyev, A Kristina Downing, Andrei I. Skorinkin, Iain D. Campbell and Nikolai V. Kotov A calcium dependent de-adhesion mechanism regulates the direction and rate of cell migration: a mathematical model 0050   Article Kevin Bleakley, Véronique Giudicelli, Yan Wu, Marie-Paule Lefranc and Gérard Biau IMGT standardization for statistical analyses of T cell receptor junctions: the TRAV-TRAJ example 0051   Article Michal Brylinski, Marek Kochanczyk, Leszek Konieczny and Irena Roterman Sequence-structure-function relation characterized in silico 0052   Communication Saju Joy, Parvathy S. Nair, Ramkumar Hariharan and M. Radhakrishna Pillai Detailed comparison of the protein-ligand docking efficiencies of GOLD, a commercial package and Arguslab, a licensable freeware 0053   Article B. Jayashree, Ramu Punna, P. Prasad, Kassahun Bantte, C. Tom Hash, Subhash Chandra, David A. Hoisington and Rajeev K. Varshney A database of simple sequence repeats from cereal and legume expressed sequence tags mined in silico: survey and evaluation 0054   Communication Nobuaki Kono, Kazuharu Arakawa and Masaru Tomita MEGU: Pathway mapping web-service based on KEGG and SVG 0055

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