Volume 31, Number 1, February 2007

• 
  Andrea Sackmann, Dorota Formanowicz, Piotr Formanowicz, Ina Koch, Jacek Blazewicz: An analysis of the Petri net based model of the human body iron homeostasis process. 1-10
• 
  Howard A. Levine, Marit Nilsen-Hamilton: A mathematical analysis of SELEX. 11-35
• 
  Christian J. Michel: Codon phylogenetic distance. 36-43
• 
  Majid Kazemian, Behzad Moshiri, Hamid Nikbakht, Caro Lucas: A new expertness index for assessment of secondary structure prediction engines. 44-47
• 
  Zhenqiang Su, Huixiao Hong, Roger Perkins, Xueguang Shao, Wensheng Cai, Weida Tong: Consensus analysis of multiple classifiers using non-repetitive variables: Diagnostic application to microarray gene expression data. 48-56
• 
  Andrey A. Toropov, Emilio Benfenati: SMILES as an alternative to the graph in QSAR modelling of bee toxicity. 57-60

Brief Communication

• 
  Xiaofeng Ji, Hanlin Chen, Yi Xiao: Hidden symmetries in the primary sequences of beta-barrel family. 61-63

Volume 31, Number 2, April 2007

• 
  Fang Liu, Baolin Wu: Multi-group cancer outlier differential gene expression detection. 65-71
• 
  D. Yu. Mordvintsev, Ya. L. Polyak, D. A. Kuzmin, Olga V. Levtsova, Ye. V. Tourleigh, Yu. N. Utkin, Konstantin V. Shaitan, V. I. Tsetlin: Computer modeling of binding of diverse weak toxins to nicotinic acetylcholine receptors. 72-81
• 
  N. S. Gomathi, H. Sameer, Vanaja Kumar, S. Balaji, V. N. Azger Dustackeer, P. R. Narayanan: In silico analysis of mycobacteriophage Che12 genome: Characterization of genes required to lysogenise Mycobacterium tuberculosis. 82-91
• 
  Raad Z. Gharaibeh, Anthony Fodor, Cynthia Gibas: Software Note: Using probe secondary structure information to enhance Affymetrix GeneChip background estimates. 92-98
• 
  H. H. Haeri, S. M. Hashemianzadeh, M. Monajjemi: A kinetic Monte Carlo simulation study of inositol 1, 4, 5-trisphosphate receptor (IP3R) calcium release channel. 99-109
• 
  Jack Xiao-Dong Yang, Roderick V. N. Melnik: Effect of internal viscosity on Brownian dynamics of DNA molecules in shear flow. 110-114
• 
  Armando Hernandez-Mendoza, Carmen Quinto, Lorenzo Segovia, Ernesto Pérez-Rueda: Ligand-binding prediction in the resistance-nodulation-cell division (RND) proteins. 115-123

Brief Communications

• 
  Wei-Bo Jin, Fang-Li Wu, Dong Kong, Ai-Guang Guo: HBV-encoded microRNA candidate and its target. 124-126
• 
  Andrey A. Toropov, Danuta Leszczynska, Jerzy Leszczynski: Predicting water solubility and octanol water partition coefficient for carbon nanotubes based on the chiral vector. 127-128
• 
  Yuan Zhang, Nan Zheng, Yang Zhong: Computational characterization and design of SARS coronavirus receptor recognition and antibody neutralization. 129-133
• 
  Yuan Zhang, Nan Zheng, Peng Nan, Ying Cao, Masami Hasegawa, Yang Zhong: Computational simulation of interactions between SARS coronavirus spike mutants and host species-specific receptors. 134-137
• 
  Anuj R. Shah, Christopher S. Oehmen, Jill Harper, Bobbie-Jo M. Webb-Robertson: Integrating subcellular location for improving machine learning models of remote homology detection in eukaryotic organisms. 138-142

Database Note

• 
  Lam C. Tsoi, W. Jim Zheng: A method of microarray data storage using array data type. 143-147

Technical Comment

• 
  Ying Wang, Enmin Feng, Ruisheng Wang: A clustering algorithm based on two distance functions for MEC model. 148-150

Volume 31, Number 3, June 2007

• 
  William R. Taylor: Protein knots and fold complexity: Some new twists. 151-162
• 
  Bjørn Altermark, Steinar Thorvaldsen, Elin Moe, Arne O. Smalås, Nils Willassen: Sequence comparison and environmental adaptation of a bacterial endonuclease. 163-172
• 
  Nadezhda M. Belonogova, Tatiana I. Axenovich: Optimal peeling order for pedigrees with incomplete genotypic information. 173-177
• 
  Arief Gusnanto, Brian Tom, Philippa Burns, Iain Macaulay, Daphne C. Thijssen-Timmer, Marloes R. Tijssen, Cordelia Langford, Nicholas Watkins, Willem Ouwehand, Carlo Berzuini, Frank Dudbridge: Improving the power to detect differentially expressed genes in comparative microarray experiments by including information from self-self hybridizations. 178-185
• 
  Zhili Zuo, Chen Gang, Hanjun Zou, Puah Chum Mok, Weiliang Zhu, Kaixian Chen, Hualiang Jiang: Why does beta-secretase zymogen possess catalytic activity? Molecular modeling and molecular dynamics simulation studies. 186-195
• 
  Susan Costantini, Giovanni Colonna, Angelo M. Facchiano: Simulation of conformational changes occurring when a protein interacts with its receptor. 196-206
• 
  Atsushi Inouchi, Shuichi Shinohara, Hiroshi Inoue, Kenji Kita, Mitsuo Itakura: Identification of specific sequence motifs in the upstream region of 242 human miRNA genes. 207-214

Software/Algorithm Notes

• 
  Weichuan Yu, Junfeng Liu, Chris Colangelo, Erol Gulcicek, Hongyu Zhao: A new protocol of analyzing isotope-coded affinity tag data from high-resolution LC-MS spectrometry. 215-221
• 
  Mudita Singhal, Kelly Domico: CABIN: Collective Analysis of Biological Interaction Networks. 222-225
• 
  Lingyi Lu, Ziliang Qian, Yu-Dong Cai, Yixue Li: ECS: An automatic enzyme classifier based on functional domain composition. 226-232
• 
  Guang-Zheng Zhang, Kyungsook Han: Hepatitis C virus contact map prediction based on binary encoding strategy. 233-238

Volume 31, Number 4, August 2007

• 
  Shinuk Kim, Junil Kim, Kwang-Hyun Cho: Inferring gene regulatory networks from temporal expression profiles under time-delay and noise. 239-245
• 
  Hae-Seok Eo, Jae Pil Choi, Seung-Jae Noh, Cheol-Goo Hur, Won Kim: A combined approach for the classification of G protein-coupled receptors and its application to detect GPCR splice variants. 246-256
• 
  Jianmiao Fan, Kagan Tuncay, Peter J. Ortoleva: Chromosome segregation in Escherichia coli division: A free energy-driven string model. 257-264
• 
  Joon Jin Song, Ho-Jin Lee, Jeffrey S. Morris, Sanghoon Kang: Clustering of time-course gene expression data using functional data analysis. 265-274
• 
  Yee Leng Yap, Xue Wu Zhang, David Smith, Richie Soong, Jeffrey Hill: Molecular gene expression signature patterns for gastric cancer diagnosis. 275-287

Algorithm note

• 
  Ying Wang, Enmin Feng, Ruisheng Wang, Dan Zhang: The haplotype assembly model with genotype information and iterative local-exhaustive search algorithm. 288-293

Brief communication

• 
  M. James C. Crabbe: Global warming and coral reefs: Modelling the effect of temperature on Acropora palmata colony growth. 294-297

Database note

• 
  Sanghoon Moon, Yanga Byun, Kyungsook Han: FSDB: A frameshift signal database. 298-302

Erratum

• 
  Ernesto Estrada, Eugenio Uriarte: Erratum to "Folding degrees of azurins and pseudoazurins. Implications for structure and function" [Computational Biology and Chemistry 29 (2005) 345-353]. 303

Volume 31, Numbers 5-6, October 2007

• 
  Abhishek Tiwari, Arvind K. T. Sekhar: Workflow based framework for life science informatics. 305-319

Regular Articles

• 
  Sabine Verboven, Karlien Vanden Branden, Peter Goos: Sequential imputation for missing values. 320-327
• 
  MunJu Kim, Songjoon Baek, Sung Hoon Jung, Kwang-Hyun Cho: Dynamical characteristics of bacteria clustering by self-generated attractants. 328-334
• 
  Aaron M. Fluitt, Elsje Pienaar, Hendrik J. Viljoen: Ribosome kinetics and aa-tRNA competition determine rate and fidelity of peptide synthesis. 335-346
• 
  Soohee Han, Yeoin Yoon, Kwang-Hyun Cho: Inferring biomolecular interaction networks based on convex optimization. 347-354
• 
  Dong He, Dao Zhou, Yanhong Zhou: Identifying transcription factor targets using enhanced Bayesian classifier. 355-360
• 
  Mingyi Wang, Zuozhou Chen, Sylvie Cloutier: A hybrid Bayesian network learning method for constructing gene networks. 361-372

Brief Communications

• 
  Sukjoon Yoon, William J. Welsh, Heeyoung Jung, Young Do Yoo: CSSP2: An improved method for predicting contact-dependent secondary structure propensity. 373-377
• 
  Kui Chen, Xiaohang Huang: Structural analysis of SNARE motifs from sea perch, Lateolabrax japonicus by computerized approaches. 378-383
• 
  Roghayeh Zarei, Shahriar Arab, Mehdi Sadeghi: A method for protein accessibility prediction based on residue types and conformational states. 384-388

Software Note

• 
  Susan Costantini, Giovanni Colonna, Angelo M. Facchiano: PreSSAPro: A software for the prediction of secondary structure by amino acid properties. 389-392