Volume 28, Number 1, February 2004

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  Andrzej K. Konopka: All we need is truth. 1-2
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  Anne-Sophie Carpentier, Alessandra Riva, Pierre Tisseur, Gilles Didier, Alain Hénaut: The operons, a criterion to compare the reliability of transcriptome analysis tools: ICA is more reliable than ANOVA, PLS and PCA. 3-10
• 
  Jacek Blazewicz, Piotr Formanowicz, Marta Kasprzak, Wojciech T. Markiewicz, Aleksandra Swiercz: Tabu search algorithm for DNA sequencing by hybridization with isothermic libraries. 11-19
• 
  Mercè Llabrés, Francesc Rosselló: A new family of metrics for biopolymer contact structures. 21-37
• 
  Yasuhito Inoue, Masami Ikeda, Toshio Shimizu: Proteome-wide classification and identification of mammalian-type GPCRs by binary topology pattern. 39-49
• 
  Jun-Xiong Xia, Masami Ikeda, Toshio Shimizu: ConPred_elite: a highly reliable approach to transmembrane topology prediction. 51-60
• 
  Hideaki Nakamura: Prediction of peptide conformation using a scale-transformed entropy sampling algorithm. 61-66
• 
  Werner Baumgartner: Electrodiffusion near an ion channel and the effect of mobile buffer. 67-73
• 
  Emily A. Berry, Andrew R. Dalby, Zheng Rong Yang: Reduced bio basis function neural network for identification of protein phosphorylation sites: comparison with pattern recognition algorithms. 75-85
• 
  Cathy H. Wu, Hongzhan Huang, Anastasia N. Nikolskaya, Zhang-Zhi Hu, Winona C. Barker: The iProClass integrated database for protein functional analysis. 87-96

Volume 28, Number 2, April 2004

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  Lana Yeganova, Lawrence H. Smith, W. John Wilbur: Identification of related gene/protein names based on an HMM of name variations. 97-107
• 
  Alessandra Riva, Marie-Odile Delorme, Tony Chevalier, Nicolas Guilhot, Corinne Hénaut, Alain Hénaut: The difficult interpretation of transcriptome data: the case of the GATC regulatory network. 109-118
• 
  David Hernández, Robin Gras, Ron D. Appel: MoDEL: an efficient strategy for ungapped local multiple alignment. 119-128
• 
  Andrzej Galat: A note on clustering the functionally-related paralogues and orthologues of proteins: a case of the FK506-binding proteins (FKBPs). 129-140
• 
  Yi Wang, Kuo-Bin Li: An adaptive and iterative algorithm for refining multiple sequence alignment. 141-148
• 
  Chun-Ting Zhang, Ren Zhang: A nucleotide composition constraint of genome sequences. 149-153

Volume 28, Number 3, July 2004

• 
  Andrzej K. Konopka: Measuring quality of research: what do they mean and why they mean so?. 163
• 
  Thomas E. Turner, Santiago Schnell, Kevin Burrage: Stochastic approaches for modelling in vivo reactions. 165-178
• 
  Jing-Fa Xiao, Ze-Sheng Li, Miao Sun, Yuan Zhang, Chia-Chung Sun: Homology modeling and molecular dynamics study of GSK3/SHAGGY-like kinase. 179-188
• 
  Yong Deng, Qi Liu, Yi-Xue Li: Scoring hidden Markov models to discriminate -barrel membrane proteins. 189-194
• 
  Scott E. Whitney, Alugupally Sudhir, Michael Nelson, Hendrik J. Viljoen: Principles of rapid polymerase chain reactions: mathematical modeling and experimental verification. 195-209
• 
  S. Mohseni-Zadeh, Pierre Brézellec, Jean-Loup Risler: Cluster-C, an algorithm for the large-scale clustering of protein sequences based on the extraction of maximal cliques. 211-218
• 
  Bjarne Knudsen, Ebbe Sloth Andersen, Christian K. Damgaard, Jørgen Kjems, Jan Gorodkin: Evolutionary rate variation and RNA secondary structure prediction. 219-226
• 
  Stefano Allesina, Robert E. Ulanowicz: Cycling in ecological networks: Finn's index revisited . 227-233
• 
  Yongxi Tan, Leming M. Shi, Weida Tong, G. T. Gene Hwang, Charles Wang: Multi-class tumor classification by discriminant partial least squares using microarray gene expression data and assessment of classification models. 235-243

Volume 28, Number 4, October 2004

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  Pei-lin Mao, Tie-Fei Liu, Kelly Kueh, Ping Wu: Predicting the efficiency of UAG translational stop signal through studies of physicochemical properties of its composite mono- and dinucleotides. 245-256
• 
  Teresa M. Przytycka, Yi-Kuo Yu: Scale-free networks versus evolutionary drift. 257-264
• 
  W. Jim Zheng, Velin Z. Spassov, Lisa Yan, Paul K. Flook, Sándor Szalma: A hidden Markov model with molecular mechanics energy-scoring function for transmembrane helix prediction. 265-274
• 
  Ying Huang, Jun Cai, Liang Ji, Yanda Li: Classifying G-protein coupled receptors with bagging classification tree. 275-280
• 
  David I. Mester, Yefim I. Ronin, Eviatar Nevo, Abraham B. Korol: Fast and high precision algorithms for optimization in large-scale genomic problems. 281-290

Volume 28, Number 5-6, December 2004

• 
  William R. Taylor: A molecular model for transcription in the RNA world based on the ribosome large subunit. 313-319
• 
  Robert E. Ulanowicz: Quantitative methods for ecological network analysi. 321-339
• 
  Ernesto Pérez-Rueda, Julio Collado-Vides, Lorenzo Segovia: Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea. 341-350
• 
  Victor A. Simossis, Jaap Heringa: The influence of gapped positions in multiple sequence alignments on secondary structure prediction methods. 351-366
• 
  Jan Gorodkin: Comparing two K-category assignments by a K-category correlation coefficient. 367-374
• 
  Anna C. Tanczos, Rex A. Palmer, Brian S. Potter, José W. Saldanha, Brendan J. Howlin: Antagonist binding in the rat muscarinic receptor: A study by docking and X-ray crystallography. 375-385

• 
  Lawrence H. Smith, W. John Wilbur: Retrieving definitional content for ontology development. 387-391
• 
  Wentian Li, Dirk Holste: An unusual 500, 000 bases long oscillation of guanine and cytosine content in human chromosome 21. 393-399
• 
  Junwei Zhang, Masahiro Aizawa, Shinji Amari, Yoshio Iwasawa, Tatsuya Nakano, Kotoko Nakata: Development of KiBank, a database supporting structure-based drug design. 401-407
• 
  Zhang-Zhi Hu, Inderjeet Mani, Vincent Hermoso, Hongfang Liu, Cathy H. Wu: iProLINK: an integrated protein resource for literature mining. 409-416
• 
  Zhihua Du, Feng Lin: A hierarchical clustering algorithm for MIMD architecture. 417-419

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