Journal: Computers & Chemistry

Volume 28, Issue 5-6

313 -- 319William R. Taylor. A molecular model for transcription in the RNA world based on the ribosome large subunit
321 -- 339Robert E. Ulanowicz. Quantitative methods for ecological network analysi
341 -- 350Ernesto Pérez-Rueda, Julio Collado-Vides, Lorenzo Segovia. Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea
351 -- 366Victor A. Simossis, Jaap Heringa. The influence of gapped positions in multiple sequence alignments on secondary structure prediction methods
367 -- 374Jan Gorodkin. Comparing two K-category assignments by a K-category correlation coefficient
375 -- 385Anna 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
387 -- 391Lawrence H. Smith, W. John Wilbur. Retrieving definitional content for ontology development
393 -- 399Wentian Li, Dirk Holste. An unusual 500, 000 bases long oscillation of guanine and cytosine content in human chromosome 21
401 -- 407Junwei Zhang, Masahiro Aizawa, Shinji Amari, Yoshio Iwasawa, Tatsuya Nakano, Kotoko Nakata. Development of KiBank, a database supporting structure-based drug design
409 -- 416Zhang-Zhi Hu, Inderjeet Mani, Vincent Hermoso, Hongfang Liu, Cathy H. Wu. iProLINK: an integrated protein resource for literature mining
417 -- 419Zhihua Du, Feng Lin. A hierarchical clustering algorithm for MIMD architecture

Volume 28, Issue 4

245 -- 256Pei-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
257 -- 264Teresa M. Przytycka, Yi-Kuo Yu. Scale-free networks versus evolutionary drift
265 -- 274W. 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
275 -- 280Ying Huang, Jun Cai, Liang Ji, Yanda Li. Classifying G-protein coupled receptors with bagging classification tree
281 -- 290David I. Mester, Yefim I. Ronin, Eviatar Nevo, Abraham B. Korol. Fast and high precision algorithms for optimization in large-scale genomic problems

Volume 28, Issue 3

163 -- 0Andrzej K. Konopka. Measuring quality of research: what do they mean and why they mean so?
165 -- 178Thomas E. Turner, Santiago Schnell, Kevin Burrage. Stochastic approaches for modelling in vivo reactions
179 -- 188Jing-Fa Xiao, Ze-Sheng Li, Miao Sun, Yuan Zhang, Chia-Chung Sun. Homology modeling and molecular dynamics study of GSK3/SHAGGY-like kinase
189 -- 194Yong Deng, Qi Liu, Yi-Xue Li. Scoring hidden Markov models to discriminate -barrel membrane proteins
195 -- 209Scott E. Whitney, Alugupally Sudhir, R. Michael Nelson, Hendrik J. Viljoen. Principles of rapid polymerase chain reactions: mathematical modeling and experimental verification
211 -- 218S. 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
219 -- 226Bjarne Knudsen, Ebbe Sloth Andersen, Christian K. Damgaard, J. Kjems, Jan Gorodkin. Evolutionary rate variation and RNA secondary structure prediction
227 -- 233Stefano Allesina, Robert E. Ulanowicz. Cycling in ecological networks: Finn s index revisited
235 -- 243Yongxi 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

Volume 28, Issue 2

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

Volume 28, Issue 1

1 -- 2Andrzej K. Konopka. All we need is truth
3 -- 10Anne-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
11 -- 19Jacek Blazewicz, Piotr Formanowicz, Marta Kasprzak, Wojciech T. Markiewicz, Aleksandra Swiercz. Tabu search algorithm for DNA sequencing by hybridization with isothermic libraries
21 -- 37Mercè Llabrés, Francesc Rosselló. A new family of metrics for biopolymer contact structures
39 -- 49Yasuhito Inoue, Masami Ikeda, Toshio Shimizu. Proteome-wide classification and identification of mammalian-type GPCRs by binary topology pattern
51 -- 60Jun-Xiong Xia, Masami Ikeda, Toshio Shimizu. ConPred_elite: a highly reliable approach to transmembrane topology prediction
61 -- 66Hideaki Nakamura. Prediction of peptide conformation using a scale-transformed entropy sampling algorithm
67 -- 73Werner Baumgartner. Electrodiffusion near an ion channel and the effect of mobile buffer
75 -- 85Emily 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
87 -- 96Cathy H. Wu, Hongzhan Huang, Anastasia N. Nikolskaya, Zhang-Zhi Hu, Winona C. Barker. The iProClass integrated database for protein functional analysis