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ORCIDComputational Biology and Chemistry, Volume 30
Volume 30, Number 1, February 2006
- Gabriel Frey, Christian J. Michel:
An analytical model of gene evolution with six mutation parameters: An application to archaeal circular codes. 1-11 - David I. Mester, Yefim I. Ronin, M. A. Korostishevsky, V. L. Pikus, A. E. Glazman, Abraham B. Korol:
Multilocus consensus genetic maps (MCGM): Formulation, algorithms, and results. 12-20 - Wenjiang J. Fu, Jianbo Hu, Thomas Spencer
, Raymond J. Carroll, Guoyao Wu:
Statistical models in assessing fold change of gene expression in real-time RT-PCR experiments. 21-26 - Weichuan Yu, Baolin Wu, Ning Lin, Kathy Stone, Kenneth R. Williams, Hongyu Zhao:
Detecting and aligning peaks in mass spectrometry data with applications to MALDI. 27-38 - James M. McCollum, Gregory D. Peterson, Chris D. Cox, Michael L. Simpson, Nagiza F. Samatova:
The sorting direct method for stochastic simulation of biochemical systems with varying reaction execution behavior. 39-49 - Sayed-Amir Marashi, Hani Goodarzi, Mehdi Sadeghi, Changiz Eslahchi, Hamid Pezeshk:
Importance of RNA secondary structure information for yeast donor and acceptor splice site predictions by neural networks. 50-57
- Ashok Reddy Dinasarapu, B. V. L. S. Prasad, Chanchal K. Mitra:
Comparative analysis of core promoter region: Information content from mono and dinucleotide substitution matrices. 58-62 - Li Shen, Eng Chong Tan:
Reducing multiclass cancer classification to binary by output coding and SVM. 63-71
- Haijun Liu, Dong Xu, Jianlin Shao, Yifei Wang:
An RNA folding algorithm including pseudoknots based on dynamic weighted matching. 72-76 - Ernesto Picardi, Carla Quagliariello:
EdiPy: A resource to simulate the evolution of plant mitochondrial genes under the RNA editing. 77-80 - Tao Zhu, Jianfeng Zhou, Yuming An, Jinhua Zhou, Hongyu Li, Gang Xu, Ding Ma:
Construction and characterization of a rock-cluster-based EST analysis pipeline. 81-86
Volume 30, Number 2, April 2006
- Gabriel Frey, Christian J. Michel:
Identification of circular codes in bacterial genomes and their use in a factorization method for retrieving the reading frames of genes. 87-101 - Elsje Pienaar, Melanie Theron, Michael Nelson, Hendrik J. Viljoen:
A quantitative model of error accumulation during PCR amplification. 102-111 - Juraj Kotulic Bunta, Aatto Laaksonen, Miroslav Pinak, Toshiyuki Nemoto:
DNA strand break: Structural and electrostatic properties studied by molecular dynamics simulation. 112-119 - Ch. Surendhar Reddy, K. Vijayasarathy, E. Srinivas, G. Madhavi Sastry, G. Narahari Sastry:
Homology modeling of membrane proteins: A critical assessment. 120-126 - Qiwen Dong, Xiaolong Wang, Lei Lin, Zhiming Xu:
Domain boundary prediction based on profile domain linker propensity index. 127-133 - Takuma Tsukahara, Sun Kim, Milton W. Taylor:
REFINEMENT: A search framework for the identification of interferon-responsive elements in DNA sequences - a case study with ISRE and GAS. 134-147
- Yiyu Cheng, Yi Wang, Xuewei Wang:
A causal relationship discovery-based approach to identifying active components of herbal medicine. 148-154 - M. James C. Crabbe, David J. Smith:
Modelling variations in corallite morphology of Galaxea fascicularis coral colonies with depth and light on coastal fringing reefs in the Wakatobi Marine National Park (S.E. Sulawesi, Indonesia). 155-159 - Marcos J. Araúzo-Bravo, Shandar Ahmad, Akinori Sarai:
Dimensionality of amino acid space and solvent accessibility prediction with neural networks. 160-168
Volume 30, Number 3, June 2006
- Shigeru Takasaki, Yoshihiro Kawamura, Akihiko Konagaya:
Selecting effective siRNA sequences based on the self-organizing map and statistical techniques. 169-178 - Özlem Demir, Isil Aksan Kurnaz:
An integrated model of glucose and galactose metabolism regulated by the GAL genetic switch. 179-192 - Yinglei Lai:
A statistical method for estimating the proportion of differentially expressed genes. 193-202 - Sujun Li, Boshu Liu, Rong Zeng, Yudong Cai, Yixue Li:
Predicting O-glycosylation sites in mammalian proteins by using SVMs. 203-208 - Jeyaraman Srividhya, Santiago Schnell:
Why substrate depletion has apparent first-order kinetics in enzymatic digestion. 209-214
- Alexander J. Marchut, Carol K. Hall:
Spontaneous formation of annular structures observed in molecular dynamics simulations of polyglutamine peptides. 215-218 - John Eargle, Zaida Luthey-Schulten:
Visualizing the dual space of biological molecules. 219-226 - Angshuman Bagchi, Tapash Chandra Ghosh:
Structural study of two proteins SigE and ORF1 to predict their roles in the biochemical oxidation of sulfur anions via the global sulfur oxidation operon (sox). 227-232 - Guoqing Zhang, Zhi-Wei Cao, Qing-ming Luo, Yu-Dong Cai, Yixue Li:
Operon prediction based on SVM. 233-240
Volume 30, Number 4, August 2006
- Sourav Roy, Santiago Schnell, Predrag Radivojac:
Unraveling the nature of the segmentation clock: Intrinsic disorder of clock proteins and their interaction map. 241-248 - Jan Gorodkin, Jakob Hull Havgaard, Milena Ensterö, Milena Sawera, Peter Jensen, M. Öhman, Merete Fredholm:
MicroRNA sequence motifs reveal asymmetry between the stem arms. 249-254 - Michal Brylinski, Leszek Konieczny, Irena Roterman:
Hydrophobic collapse in (in silico) protein folding. 255-267 - Anshul Dubey, Matthew J. Realff, Jay H. Lee, Andreas S. Bommarius:
Identifying the interacting positions of a protein using Boolean learning and support vector machines. 268-279 - Tiina Manninen, Marja-Leena Linne, Keijo Ruohonen:
Developing Itô stochastic differential equation models for neuronal signal transduction pathways. 280-291 - Hasan Ogul, Ü. Erkan Mumcuoglu:
SVM-based detection of distant protein structural relationships using pairwise probabilistic suffix trees. 292-299
- Riqiang Deng, Mingsong Huang, Jinwen Wang, Yuansen Huang, Jie Yang, Jinghua Feng, Xunzhang Wang:
PTreeRec: Phylogenetic Tree Reconstruction based on genome BLAST distance. 300-302
- Yoko Watanabe, Hideyuki Tsuboi, Michihisa Koyama, Momoji Kubo, Carlos Adriel Del Carpio, Ewa Broclawik, Eiichiro Ichiishi, Masahiro Kohno, Akira Miyamoto:
Molecular dynamics study on the ligand recognition by tandem SH3 domains of p47phox, regulating NADPH oxidase activity. 303-312
Volume 30, Number 5, October 2006
- Jacek Blazewicz, Fred W. Glover, Marta Kasprzak, Wojciech T. Markiewicz, Ceyda Oguz, Dietrich Rebholz-Schuhmann, Aleksandra Swiercz:
Dealing with repetitions in sequencing by hybridization. 313-320 - Yinglei Lai:
On the identification of differentially expressed genes: Improving the generalized F-statistics for Affymetrix microarray gene expression data. 321-326 - Saliha Durmus Tekir, Tunahan Çakir, Kutlu Ö. Ülgen:
Analysis of enzymopathies in the human red blood cells by constraint-based stoichiometric modeling approaches. 327-338 - Maria Stepanova, Feng Lin, Valerie C.-L. Lin:
Establishing a statistic model for recognition of steroid hormone response elements. 339-347 - Andrzej Galat:
Involvement of some large immunophilins and their ligands in the protection and regeneration of neurons: A hypothetical mode of action. 348-359 - Inge Jonassen, Daniel Klose, William R. Taylor:
Protein model refinement using structural fragment tessellation. 360-366 - Tongliang Zhang, Yongsheng Ding, Kuo-Chen Chou:
Prediction of protein subcellular location using hydrophobic patterns of amino acid sequence. 367-371 - Chin-Fu Chen, Xin Feng, Jack Szeto:
Identification of critical genes in microarray experiments by a Neuro-Fuzzy approach. 372-381
- Tatiana I. Axenovich, Yurii S. Aulchenko:
Solution for underflow problem in linkage and segregation analysis. 382-385 - Minghui Li, Xiaolong Wang, Lei Lin, Tao Liu:
Effect of example weights on prediction of protein-protein interactions. 386-392
- Kanaka Durga Kedarisetti, Lukasz A. Kurgan, Scott Dick:
A comment on "Prediction of protein structural classes by a new measure of information discrepancy". 393-394
Volume 30, Number 6, December 2006
- Baohong Zhang, Xiaoping Pan, Qinglian Wang, George P. Cobb, Todd A. Anderson:
Computational identification of microRNAs and their targets. 395-407 - Liang-Tsung Huang, M. Michael Gromiha, Shiow-Fen Hwang, Shinn-Ying Ho:
Knowledge acquisition and development of accurate rules for predicting protein stability changes. 408-415 - Ioannis K. Valavanis, Pantelis G. Bagos, Ioannis Z. Emiris:
beta-Barrel transmembrane proteins: Geometric modelling, detection of transmembrane region, and structural properties. 416-424 - Xutao Deng, Huimin Geng, Dhundy Bastola, Hesham H. Ali:
Link test - A statistical method for finding prostate cancer biomarkers. 425-433 - Andrey A. Toropov, Karel Nesmerak Jr., Ivan Raska Jr., Karel Waisser, Karel Palat:
QSPR modeling of the half-wave potentials of benzoxazines by optimal descriptors calculated with the SMILES. 434-437 - Jeong-Rae Kim, Kwang-Hyun Cho:
The multi-step phosphorelay mechanism of unorthodox two-component systems in E. coli realizes ultrasensitivity to stimuli while maintaining robustness to noises. 438-444
- Shi-Hua Zhang, Xue-Mei Ning, Xiang-Sun Zhang:
Identification of functional modules in a PPI network by clique percolation clustering. 445-451
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