Volume 33, Number 1, February 2009

Research Articles

• 
  Zhaohua Gong, Chongyang Liu, Enmin Feng, Qingrui Zhang: Computational method for inferring objective function of glycerol metabolism in Klebsiella pneumoniae. 1-6
• 
  Karlien Vanden Branden, Sabine Verboven: Robust data imputation. 7-13
• 
  Antônio M. Rodrigues, Antônio-Carlos G. Almeida, Antonio Fernando C. Infantosi, Hewerson Z. Teixeira, Mário A. Duarte: Investigating the potassium interactions with the palytoxin induced channels in Na⁺/K⁺ pump. 14-21
• 
  Cristina Bondavalli, S. Favilla, A. Bodini: Quantitative versus qualitative modeling: A complementary approach in ecosystem study. 22-28
• 
  Olga V. Levtsova, Mikhail Yu. Antonov, D. Yu. Mordvintsev, Yu. N. Utkin, Konstantin V. Shaitan, M. P. Kirpichnikov: Steered molecular dynamics simulations of cobra cytotoxin interaction with zwitterionic lipid bilayer: No penetration of loop tips into membranes. 29-32
• 
  L. Davia, G. Grassi, G. Pontrelli, R. Lapasin, D. Perin, M. Grassi: Mathematical modelling of NABD release from endoluminal gel paved stent. 33-40
• 
  Hai-Feng Chen: Aggregation mechanism investigation of the GIFQINS cross-beta amyloid fibril. 41-45
• 
  Jeanice Kielbassa, Ralf H. Bortfeldt, Stefan Schuster, Ina Koch: Modeling of the U1 snRNP assembly pathway in alternative splicing in human cells using Petri nets. 46-61
• 
  Vesselin Baev, Evelina Daskalova, Ivan Nikiforov Minkov: Computational identification of novel microRNA homologs in the chimpanzee genome. 62-70
• 
  Ann Zahle Andersen, Ana Lúcia Carvalho, Ana Rute Neves, Helena Santos, Ursula Kummer, Lars Folke Olsen: The metabolic pH response in Lactococcus lactis: An integrative experimental and modelling approach. 71-83

Brief Communications

• 
  Wenwei Zhang, Yuping Luo, Xi Gong, Wenhong Zeng, Siguang Li: Computational identification of 48 potato microRNAs and their targets. 84-93
• 
  Shinuk Kim, Minsoo Choi, Kwang-Hyun Cho: Identifying the target mRNAs of microRNAs in colorectal cancer. 94-99
• 
  Hanlin Chen, Yanzhao Huang, Yi Xiao: A simple method of identifying symmetric substructures of proteins. 100-107
• 
  Jiyuan An, Yi-Ping Phoebe Chen: Finding rule groups to classify high dimensional gene expression datasets. 108-113
• 
  Hsueh-Wei Chang, Cheng-Hong Yang, Chang-Hsuan Ho, Cheng-Hao Wen, Li-Yeh Chuang: Generating SNP barcode to evaluate SNP-SNP interaction of disease by particle swarm optimization. 114-119

Volume 33, Number 2, April 2009

Review Article

• 
  K. Scheibye-Alsing, Steve Hoffmann, A. Frankel, Peter Jensen, Peter F. Stadler, Y. Mang, N. Tommerup, M. J. Gilchrist, A.-B. Nygård, Susanna Cirera, Claus B. Jørgensen, Merete Fredholm, Jan Gorodkin: Sequence assembly. 121-136

Research Articles

• 
  Elisa Maugini, Daniele Tronelli, Francesco Bossa, Stefano Pascarella: Structural adaptation of the subunit interface of oligomeric thermophilic and hyperthermophilic enzymes. 137-148
• 
  James Smith, Viktor Stein: SPORCalc: A development of a database analysis that provides putative metabolic enzyme reactions for ligand-based drug design. 149-159
• 
  Arneh Babakhani, Todd T. Talley, Palmer Taylor, James Andrew McCammon: A virtual screening study of the acetylcholine binding protein using a relaxed-complex approach. 160-170

Brief Communications

• 
  Kun-Nan Tsai, Shu-Hung Lin, Shin-Ru Shih, Jhih-Siang Lai, Chung-Ming Chen: Genomic splice site prediction algorithm based on nucleotide sequence pattern for RNA viruses. 171-175
• 
  Tomasz Zuk, Franciszek Rakowski, Jan P. Radomski: A model of influenza virus spread as a function of temperature and humidity. 176-180
• 
  Yung-fu Chen, Rung Ching Chen, Yung-Kuan Chan, Ren-Hao Pan, You-Cheng Hseu, Elong Lin: Design of multiplex PCR primers using heuristic algorithm for sequential deletion applications. 181-188

Volume 33, Number 3, June 2009

Research Articles

• 
  Roderic C. E. Green, Alfred E. Thumser, David C. Povey, José W. Saldanha, Brian S. Potter, Rex A. Palmer, Brendan J. Howlin: A comparative study of the single crystal X-ray determination and molecular modelling of the binding of oligomycin to ATP Synthase. 189-195
• 
  Andrew Shelenkov, Eugene V. Korotkov: Search of regular sequences in promoters from eukaryotic genomes. 196-204
• 
  Georgios Kalantzis: Hybrid stochastic simulations of intracellular reaction-diffusion systems. 205-215
• 
  Pooja Jain, Jonathan M. Garibaldi, Jonathan D. Hirst: Supervised machine learning algorithms for protein structure classification. 216-223

Brief Communications

• 
  Jacek Blazewicz, Marcin Bryja, Marek Figlerowicz, Piotr Gawron, Marta Kasprzak, Edward Kirton, Darren Platt, Jakub Przybytek, Aleksandra Swiercz, Lukasz Szajkowski: Whole genome assembly from 454 sequencing output via modified DNA graph concept. 224-230
• 
  Dagmara P. Furman, Tatyana A. Bukharina: The gene network determining development of Drosophila melanogaster mechanoreceptors. 231-234
• 
  Boris Vishnepolsky, Malak Pirtskhalava: ALIGN_MTX - An optimal pairwise textual sequence alignment program, adapted for using in sequence-structure alignment. 235-238
• 
  Tiratha Raj Singh, Kamal Raj Pardasani: Ambush hypothesis revisited: Evidences for phylogenetic trends. 239-244

Volume 33, Number 4, August 2009

Research Articles

• 
  Emmanuel Benard, Christian J. Michel: Computation of direct and inverse mutations with the SEGM web server (Stochastic Evolution of Genetic Motifs): An application to splice sites of human genome introns. 245-252
• 
  Simon Scarle: Implications of the Turing completeness of reaction-diffusion models, informed by GPGPU simulations on an XBox 360: Cardiac arrhythmias, re-entry and the Halting problem. 253-260
• 
  Sarath Chandra Janga, Ernesto Pérez-Rueda: Plasticity of transcriptional machinery in bacteria is increased by the repertoire of regulatory families. 261-268
• 
  Dan V. Nicolau Jr., Judith P. Armitage, Philip K. Maini: Directional persistence and the optimality of run-and-tumble chemotaxis. 269-274
• 
  Tamar Nov Klaiman, Sergey Hosid, Alexander Bolshoy: Upstream curved sequences in E. coli are related to the regulation of transcription initiation. 275-282
• 
  Leonidas Kapsokalivas, Xiangchao Gan, Andreas Alexander Albrecht, Kathleen Steinhöfel: Population-based local search for protein folding simulation in the MJ energy model and cubic lattices. 283-294
• 
  Vladislav Victorovich Khrustalev, Eugene Victorovich Barkovsky: Mutational pressure is a cause of inter- and intragenomic differences in GC-content of simplex and varicello viruses. 295-302
• 
  Bin Liu, Xiaolong Wang, Lei Lin, Qiwen Dong, Xuan Wang: Exploiting three kinds of interface propensities to identify protein binding sites. 303-311
• 
  Xin Lai, Svetoslav Nikolov, Olaf Wolkenhauer, Julio Vera: A multi-level model accounting for the effects of JAK2-STAT5 signal modulation in erythropoiesis. 312-324

Brief Communications

• 
  Yi He, Rui Zhou, Yanzhao Huang, Yi Xiao: Foldable subunits of helix protein. 325-328
• 
  Manoj Tyagi, Aurélie Bornot, Bernard O. Offmann, Alexandre G. de Brevern: Protein short loop prediction in terms of a structural alphabet. 329-333
• 
  Lishuang Li, Rongpeng Zhou, Degen Huang: Two-phase biomedical named entity recognition using CRFs. 334-338
• 
  Tomasz Zuk, Franciszek Rakowski, Jan P. Radomski: Probabilistic model of influenza virus transmissibility at various temperature and humidity conditions. 339-343
• 
  Xiaofeng Song, Yan Hao: Adaptive evolution of rotavirus VP7 and NSP4 genes in different species. 344-349

Technical Note

• 
  Ren Zhang: A rebuttal to the comments on the genome order index. 350

Volume 33, Number 5, October 2009

Research Articles

• 
  Steinar Thorvaldsen, Elinor Ytterstad: Environmental adaptation of proteins: Regression models with simple physicochemical properties. 351-356
• 
  Gordon M. Crippen: A statistical measure of association and a series expansion of chain conformations. 357-360
• 
  Gheorghe Craciun, Casian Pantea, Grzegorz A. Rempala: Algebraic methods for inferring biochemical networks: A maximum likelihood approach. 361-367

Brief Communications

• 
  Shigeru Takasaki: Selecting effective siRNA target sequences by using Bayes' theorem. 368-372
• 
  Anup Som: ML or NJ-MCL? A comparison between two robust phylogenetic methods. 373-378
• 
  Roger S. Holmes, Erwin Goldberg: Computational analyses of mammalian lactate dehydrogenases: Human, mouse, opossum and platypus LDHs. 379-385
• 
  Antonino Lauria, Mario Ippolito, Anna Maria Almerico: Principal component analysis on molecular descriptors as an alternative point of view in the search of new Hsp90 inhibitors. 386-390
• 
  Yan-Qiong Zhang, Dong-Liang Chen, Hai-Feng Tian, Bao-Hong Zhang, Jian-Fan Wen: Genome-wide computational identification of microRNAs and their targets in the deep-branching eukaryote Giardia lamblia. 391-396
• 
  Ruth V. Spriggs, Susan Jones: RNA-binding residues in sequence space: Conservation and interaction patterns. 397-403
• 
  Mark A. Plummer, Scott M. Plummer: Modeling the folding and hydrogen production of Clostridium acetobutylicum and Clostridium saccharobutylium mutants using electrostatic potential surfaces and molecular dynamics. 404-407
• 
  Joon Jin Song, Yuan Ren, Fenglan Yan: Classification for high-throughput data with an optimal subset of principal components. 408-413

Volume 33, Number 6, December 2009

Review Article

• 
  M. James C. Crabbe: Modelling effects of geoengineering options in response to climate change and global warming: Implications for coral reefs. 415-420

Research Articles

• 
  T. Murlidharan Nair: On selecting mRNA isoform features for profiling prostate cancer. 421-428
• 
  Hiroaki Ohdaira, Hiroki Nakagawa, Kenichi Yoshida: Profiling of molecular pathways regulated by microRNA 601. 429-433
• 
  Giuseppe Fiume, Annalisa Rossi, Emanuela Di Salle, Carmen Spatuzza, Massimo Mallardo, Giuseppe Scala, Ileana Quinto: Computational analysis and in vivo validation of a microRNA encoded by the IBTK gene, a regulator of B-lymphocytes differentiation and survival. 434-439
• 
  Philipp Weil, Franziska Hoffgaard, Kay Hamacher: Estimating sufficient statistics in co-evolutionary analysis by mutual information. 440-444
• 
  Tienhsiung Ku, Peiyu Lu, Chenhsiung Chan, Tsusheng Wang, Szuming Lai, Pingchiang Lyu, Naiwan Hsiao: Predicting melting temperature directly from protein sequences. 445-450

Brief Communications

• 
  Melanie Füllbeck, Nina Gebhardt, Julia Hossbach, Peter T. Daniel, Robert Preissner: Computer-assisted identification of small-molecule Bcl-2 modulators. 451-456
• 
  Alla Bulashevska, Martin Stein, David Jackson, Roland Eils: Prediction of small molecule binding property of protein domains with Bayesian classifiers based on Markov chains. 457-460
• 
  Efendi N. Nasibov, Cagin Kandemir-Cavas: Efficiency analysis of KNN and minimum distance-based classifiers in enzyme family prediction. 461-464
• 
  Dagmara P. Furman, Eugenia A. Oshchepkova, Dmitry Yu. Oshchepkov, Marina Yu. Shamanina, Viatcheslav A. Mordvinov: Promoters of the genes encoding the transcription factors regulating the cytokine gene expression in macrophages contain putative binding sites for aryl hydrocarbon receptor. 465-468

Technical note

• 
  Lixia Jin, Weiwu Fang: On "A comment on 'Prediction of protein structural classes by a new measure of information discrepancy"'. 469-470