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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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