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Volume 7
2006
 
  
Communication Rajaiah Paramasivan, Ramamoorthy Sivaperumal, Kutty Jegadeeswaran Dhananjeyan, Velayutham Thenmozhi and Brij Kishore Tyagi
Prediction of 3-dimensional structure of salivary odorant-binding protein-2 of the mosquito Culex quinquefasciatus, the vector of human lymphatic filariasis
0001  
Article                Dipnarayan Saha, Anand M. Prasad, Thankeswaran P. Sujatha, Vajinder Kumar, Pradeep K. Jain, Sripad R. Bhat and Ramamurthy Srinivasan
In silico analysis of the Lateral Organ Junction (loj) gene and promoter of Arabidopsis thaliana
0002  
Article Kagan Tuncay, Lisa Ensman, Alaa Abi Haidar, Frank Stanley, Michael Trelinski and Peter Ortoleva
Transcriptional regulatory networks via gene ontology and expression data
0003  
Article Diederik W. J. Bosman, Evert-Jan Blom, Patrick J. Ogao, Oscar P. Kuipers and Jos B. T. M. Roerdink
MOVE: A Multi-level Ontology-based Visualization and Exploration framework for genomic networks
0004  
Article Yuchen Yang, Erwin Tantoso, Gek Huey Chua, Zhen Xuan Yeo, Felicia Soo Lee Ng, Sum Thai Wong, Cheuk Wang Chung and Kuo-Bin Li
In silico analysis of p53 using the P53 Knowledgebase: mutations, polymorphisms, microRNAs and pathways
0005  
Article Waiming Kong, Tsu Soo Tan, Lawrence Tham and Keng Wah Choo
Improved prediction of allergenicity by combination of multiple sequence motifs
0006  
Article Paras Chopra and Andreas Bender
Evolved cellular automata for protein secondary structure prediction imitate the determinants for folding observed in nature
0007  
Communication Pradeep Kota
GUIMACS - A Java based front end for GROMACS
0008  
 

 
2007
 
Communication Tarcísio de Souza Peres, Fernando Ferreira Costa and Fernando Lopes Alberto
LyM: A tool to reach the best factor in gene expression comparison
0009  
Article Skarlas Lambros, Ioannidis Panos and Likothanassis Spiridon
Coding potential prediction in Wolbachia using artificial neural networks
0010  
Communication King-Hwa Ling, Shu-San Loo, Rozita Rosli, Mariana Nor Shamsudin, Rahmah Mohamed and Kiew-Lian Wan
In silico identification and characterization of a putative phosphatidylinositol 4-phosphate 5-kinase (PIP5K) gene in Eimeria tenella
0011  
Article Kalyan Gayen, Manish Gupta and and Kareenhalli V. Venkatesh
Elementary mode analysis to study the preculturing effect on the metabolic state of Lactobacillus rhamnosus during growth on mixed substrates
0012  
Communication Yoshiteru Negishi, Hiyoyuki Nakamura, Nozomu Yachie, Rintaro Saito and Masaru Tomita
eXpanda: an integrated platform for network analysis and visualization
0013  
Article J. Lynn Fink and Nicholas Hamilton
DomainDraw: A macromolecular feature drawing program
0014  
Communication Daniel Gerlach, Matthias Wolf, Thomas Dandekar, Tobias Müller, Andreas Pokorny and Sven Rahmann
Deep metazoan phylogeny
0015  
Article Ahmed Ahmed, Gabriel Frey and Christian J. Michel
Frameshift signals in genes associated with the circular code
0016  
Article Aruna Ranganath, K. C. Shet and N. Vidyavathi
Efficient shape descriptors for feature extraction in 3D protein structures
0017  
Article Sukanta Mondal, Rajasekaran Mohan Babu, Rajasekaran Bhavna and Suryanarayanarao Ramakumar
In silico detection of binding mode of J-superfamily conotoxin pl14a with Kv1.6 channel
0018  
Article Bharath Srinivasan and Hemalatha Balaram
ISN1 nucleotidases and HAD superfamily protein fold: in silico sequence and structure analysis
0019  
Article Jiqiang Yao, Hong Lin, Harshavardhan Doddapaneni and Edwin L. Civerolo
nWayComp: A Genome-wide Sequence Comparison Tool for Multiple Strains/Species of Phylogeny-related Microorganisms
0020  
Article Atul Grover and Prakash C. Sharma
Microsatellite motifs with moderate GC content are clustered around genes on Arabidopsis thaliana chromosome 2
0021  
Article Rozana Othman, Habibah Abdul Wahab, Rohana Yusof and Noorsaadah Abd Rahman
Analysis of secondary structure predictions of Dengue virus type 2 NS2B/NS3 against crystal structure to evaluate the predictive power of the in silico methods
0022  
Article Susan Idicula-Thomas and Petety V. Balaji
Correlation between the structural stability and aggregation propensity of proteins
0023  
Article Abinash Padhi, Bindhu Verghese, Subhendu K. Otta, Binu Varghese and Karri Ramu
Positive Darwinian selection on crustacean hyperglycemic hormone (CHH) of the green shore crab, Carcinus maenas
0024  
Article Sudipto Saha and Gajendra P. S. Raghava
Prediction of neurotoxins based on their function and source
0025  
Communication Boon-San Lim, Chan-Eng Chong, Zulkiflie Zamrod, Sheila Nathan and Rahmah Mohamed
Genome-wide prediction and annotation of Burkholderia pseudomallei AraC/XylS family transcription regulator
0026  
Communication Anjali Bajpai, Settu Sridhar, Hemakumar M. Reddy and Rachel A. Jesudasan
BRM-Parser: A tool for comprehensive analysis of BLAST and RepeatMasker results
0027  
Article Sudipto Saha and Gajendra P. S. Raghava
BTXpred: Prediction of Bacterial Toxins
0028  
Article Rengaraj Rajesh, Kasinathan Gunasekaran, Subramanian Muthukumaravel, Kothandapani Balaraman and Purusothaman Jambulingam
In silico analysis of voltage-gated sodium channel in relation to DDT resistance in vector mosquitoes
0029  
Article Ashutosh Ranjan, Ambrish Sharan Vidyarthi and Raju Poddar
Evaluation of codon bias perspectives in phage therapy of Mycobacterium tuberculosis by multivariate analysis
0030  
Article Bangaly Kaba, Nicolas Pinet, Gaëlle Lelandais, Alain Sigayret and Anne Berry
Clustering gene expression data using graph separators
0031  
Article Deepak Perumal, Chu Sing Lim, Kishore R. Sakharkar and Meena K. Sakharkar
Differential genome analyses of metabolic enzymes in Pseudomonas aeruginosa for drug target identification
0032  
Article Sylvain Blachon, Ruggero G. Pensa, Jérémy Besson, Céline Robardet, Jean-François Boulicaut and Olivier Gandrillon
Clustering formal concepts to discover biologically relevant knowledge from gene expression data
0033  
Article Jiayu Wen, Brian J. Parker and Georg F. Weiller
In silico identification and characterization of mRNA-like noncoding transcripts in Medicago truncatula
0034  
Article Matteo Ramazzotti, Matteo Brilli, Renato Fani, Giampaolo Manao and Donatella Degl'Innocenti
The CAI Analyser Package: inferring gene expressivity from raw genomic data
0035  
Article Li Liao and Zhongwei Li
Correlation between gene silencing activity and structural features of antisense oligodeoxynucleotides and target RNA
0036  
Article Olav Zimmermann, Longhui Wang and Ulrich H. E. Hansmann
BETTY: Prediction of β-strand type from sequence
0037  
Communication Soma Marla and Vinay Kumar Singh
PGV- Prokaryotic Genome Viewer
0038  
Article Gargi Sen, Saubashya Sur, Debadin Bose, Uttam Mondal, Teal Furnholm, Asim Bothra, Louis Tisa and Arnab Sen
Analysis of codon usage patterns and predicted highly expressed genes for six phytopathogenic Xanthomonas genomes shows a high degree of conservation
0039  


Special Issue: 5th International Conference on Bioinformatics of Genome Regulation and Structure (BGRS 2006)
  
Editorial              Sergei N. Rodin and Nikolay A. Kolchanov
- Preface -
0040  
Article Yuriy L. Orlov, J. Zhou, Leonard L. Lipovich, Atif Shahab and Vladimir A. Kuznetsov
Quality assessment of the Affymetrix U133A&B probesets by target sequence mapping and expression data analysis
0041  
Article Sergey A. Lashin, Valentin V. Suslov, Nikolay A. Kolchanov and Yury G. Matushkin
Simulation of coevolution in community by using the "Evolutionary Constructor" program
0042  
Article Jury Sergeevich Bukin, Tatyana Anatoljevna Pudovkina, Dmitry Jurjevich Sherbakov and Tatyana Jakovlevna Sitnikova
Genetic flows in a structured one-dimensional population: simulation and real data on Baikalian polychaetes M. godlewskii
0043  
Article Lev Rubanov and Vassily Lyubetsky
RNAmodel Web Server: Modeling Classic Attenuation in Bacteria
0044  
Article Andrei S. Rodin and Sergei N. Rodin
Translation of both complementary strands might govern early evolution of the genetic code
0045  
Article Sergey S. Pintus, Eduard S. Fomin, Ivan S. Oshurkov and Vladimir A. Ivanisenko
Phylogenetic analysis of the p53 and p63/p73 gene families
0046  
Article Konstantin V. Gunbin, Dmitrij A. Afonnikov and Nikolay A. Kolchanov
The evolution of the Hh-signalling pathway genes: a computer-assisted study
0047  
      

Further regular articles:
      
Article Kunal Jaiswal
Prediction of ubiquitin proteins using artificial neural networks and hidden Markov models
0048  
Communication Shu Chen, Arunkumar Chinnaswamy, Subhra K. Biswas, Andrew B. Goryachev, Choon-Kong Yap, Koi-Yau Lam, Cheng-Pei Tay, Hong-Sang Low, Alexandra Pokhilko, Toh Da-Jun and Santosh K. Mishra
Cell Interaction Knowledgebase: An online database for innate immune cells, cytokines and chemokines
0049  
Article Yiannis A. I. Kourmpetis, Ate van der Burgt, Marco C. A. M. Bink, Cajo J. F. ter Braak and Roeland C. H. J. van Ham
The use of multiple hierarchically independent Gene Ontology terms in gene function prediction and genome annotation
0050  
Article Sangeeta Kundu and Debjani Roy
Structural considerations for designing adenosine analogs as selective inhibitors of Trichomonas sp. glyceraldehyde-3-phosphate dehydrogenase
0051  
Article Jochen Farwer, Martin J. Packer and Christopher A. Hunter
PREDICTOR: A web-based tool for the prediction of atomic structure from sequence for double helical DNA with up to 150 base pairs
0052  
Article Jayavel Sridhar and Ziauddin Ahamed Rafi
Identification of novel genomic islands associated with small RNAs
0053  
Article Martin Stephan, Friedrich Möller, Thomas Wiehe and Jürgen Kleffe
Self-Alignments to detect mutually exclusive exon usage
0054  
Article Euna Jeong, Masao Nagasaki, Ayumu Saito and Satoru Miyano
Cell System Ontology: Representation for modeling, visualizing, and simulating biological pathways
0055  
Article Amitava Karmaker and Stephen Kwek
CGHsweep: An algorithm for analyzing chromosomal aberrations in genome using aCGH Profiles
0056  
Article Abhishek Tiwari and Sunil K. Panigrahi
HBAT: A complete package for analysing strong and weak hydrogen bonds in macromolecular crystal structures
0057  


Supplement: Workshop "Storage and Annotation of Reaction Kinetics Data"
  
Editorial              Isabel Rojas and Ulrike Wittig
Workshop on "Storage and Annotation of Reaction Kinetics Data", Villa Bosch in Heidelberg, May 21-23, 2007
– Preface –
01  
Article Manuel Cánovas*, Vicente Bernal, Ángel Sevilla and José L. Iborra
Role of wet experiment design in data generation: from in vivo to in silico and back
02  
Article Edgar Wingender, Jennifer Hogan, Frank Schacherer, Anatolij P. Potapov and Olga Kel-Margoulis
Integrating pathway data for systems pathology
03  
Article Carel van Gend, Riaan Conradie, Franco B. du Preez and Jacky L. Snoep
Data and model integration using JWS Online
04  
Article Isabel Rojas, Martin Golebiewski, Renate Kania, Olga Krebs, Saqib Mir, Andreas Weidemann and Ulrike Wittig
Storing and annotating of kinetic data
05  
Article Kirill Degtyarenko, Marcus Ennis and John S. Garavelli
"Good annotation practice" for chemical data in biology
06  
Article Carsten Kettner
Good publication practice as a perequisite for comparable enzyme data?
07  
Article Ursula Kummer
Usage of reaction kinetics data stored in databases - a modeler's point of view
08  
Article Simon Borger, Jannis Uhlendorf, Anselm Helbig and Wolfram Liebermeister
Integration of enzyme kinetic data from various sources
09  
Article Akira Funahashi, Akiya Jouraku, Yukiko Matsuoka and Hiroaki Kitano
Integration of CellDesigner and SABIO-RK
10  







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