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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