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ORCIDComputational Biology and Chemistry, Volume 33
Volume 33, Number 1, February 2009
- 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 Márcio 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, Stefania Favilla, Antonio 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 - Lorenzo Davia, Gabriele Grassi, Giuseppe Pontrelli, Romano Lapasin, Danilo Perin, Mario 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
- 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
- K. Scheibye-Alsing, Steve Hoffmann, A. Frankel, Peter Jensen, Peter F. Stadler, Y. Mang, Niels Tommerup, M. J. Gilchrist, A.-B. Nygård, Susanna Cirera, Claus B. Jørgensen, Merete Fredholm, Jan Gorodkin:
Sequence assembly. 121-136
- 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
- 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
- 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 A. 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
- 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
- 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 G. Nikolov, Olaf Wolkenhauer, Julio Vera:
A multi-level model accounting for the effects of JAK2-STAT5 signal modulation in erythropoiesis. 312-324
- 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
- Ren Zhang:
A rebuttal to the comments on the genome order index. 350
Volume 33, Number 5, October 2009
- 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
- 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
- M. James C. Crabbe:
Modelling effects of geoengineering options in response to climate change and global warming: Implications for coral reefs. 415-420
- 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
- 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
- Lixia Jin, Weiwu Fang:
On "A comment on 'Prediction of protein structural classes by a new measure of information discrepancy"'. 469-470
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