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ORCIDComputational Biology and Chemistry, Volume 32
Volume 32, Number 1, February 2008
- Jun Wu
, Yuejin Tan, Hongzhong Deng, Dazhi Zhu:
Relationship between degree-rank function and degree distribution of protein-protein interaction networks. 1-4 - Antônio Márcio Rodrigues, Antônio-Carlos G. Almeida, Antonio Fernando C. Infantosi, Hewerson Z. Teixeira, Mário A. Duarte:
Model and simulation of Na+/K+ pump phosphorylation in the presence of palytoxin. 5-16 - Alexander Bolshoy:
Revisiting the relationship between compositional sequence complexity and periodicity. 17-28 - Li-Yeh Chuang, Hsueh-Wei Chang, Chung-Jui Tu, Cheng-Hong Yang:
Improved binary PSO for feature selection using gene expression data. 29-38 - Elias Zintzaras, John P. A. Ioannidis:
Meta-analysis for ranked discovery datasets: Theoretical framework and empirical demonstration for microarrays. 39-47 - Stefan Zeiser, O. Rivera, Christina Kuttler, Burkhard A. Hense, R. Lasser, G. Winkler:
Oscillations of Hes7 caused by negative autoregulation and ubiquitination. 48-52 - Qi Shen, Wei-Min Shi, Wei Kong:
Hybrid particle swarm optimization and tabu search approach for selecting genes for tumor classification using gene expression data. 53-60
- Donggen Zhou, Siguang Li, Jian Wen, Xi Gong, Ling Xu, Yuping Luo:
Genome-wide computational analyses of microRNAs and their targets from Canis familiaris. 61-66 - Marco A. Ramos, Rosa E. Mares, Paloma D. Magaña, Joaquín E. Ortega, José M. Cornejo-Bravo:
In silico identification of the protein disulfide isomerase family from a protozoan parasite. 67-71 - Hyeoncheol Kim, Yiying Zhang, Yong-Seok Heo, Heung-Bum Oh, Su-Shing Chen:
Specificity rule discovery in HIV-1 protease cleavage site analysis. 72-79
Volume 32, Number 2, April 2008
- Ka-Lok Ng, Chien-Hung Huang, Hsueh-Chuan Liu, Hsiang-Chuan Liu:
Applications of domain-domain interactions in pathway study. 81-87 - Malakhat A. Turabekova, Bakhtiyor F. Rasulev, Mikhail G. Levkovich, Nasrulla D. Abdullaev, Jerzy Leszczynski:
Aconitum and Delphinium sp. alkaloids as antagonist modulators of voltage-gated Na+ channels: AM1/DFT electronic structure investigations and QSAR studies. 88-101 - Hajime Ogawa, Miki Nakano, Hirofumi Watanabe, E. B. Starikov, Stuart M. Rothstein, Shigenori Tanaka:
Molecular dynamics simulation study on the structural stabilities of polyglutamine peptides. 102-110 - Georgios Pampalakis, Maria Arampatzidou, Grigoris D. Amoutzias, Sofia Kossida, Georgia Sotiropoulou:
Identification and analysis of mammalian KLK6 orthologue genes for prediction of physiological substrates. 111-121 - Ömer Sinan Saraç, Özge Gürsoy-Yüzügüllü, Rengül Çetin-Atalay, Volkan Atalay:
Subsequence-based feature map for protein function classification. 122-130
- Matthias Dehmer, Frank Emmert-Streib:
Structural information content of networks: Graph entropy based on local vertex functionals. 131-138 - Victor M. Bolanos-Garcia:
The N-terminal, TPR-containing domain of the mitotic checkpoint protein BUBR1 does not bind fatty acids. 139-140 - Kh. Budhachandra, R. K. Brojen Singh, Gautam I. Menon:
Microtubule dynamics regulated by stathmin. 141-144 - Andrzej Galat:
Technical note. 145-146
- Eran Elhaik, Dan Graur, Kresimir Josic:
'Genome order index' should not be used for defining compositional constraints in nucleotide sequences. 147
Volume 32, Number 3, June 2008
- Bryan M. B. VanSchouwen, Heather L. Gordon, Stuart M. Rothstein, Yuto Komeiji, Kaori Fukuzawa, Shigenori Tanaka:
Water-mediated interactions in the CRP-cAMP-DNA complex: Does water mediate sequence-specific binding at the DNA primary-kink site? 149-158 - Jinhua Zhou, Tao Zhu, Chunxia Hu, Hongyu Li, Gang Chen, Gang Xu, Shixuan Wang, Jianfeng Zhou, Ding Ma:
Comparative genomics and function analysis on BI1 family. 159-162 - Krystian Kubica:
A pore creation in a triangular network model membrane. 163-166 - Christo Z. Christov, Tatyana G. Karabencheva, Alessio Lodola:
Relationship between chiroptical properties, structural changes and interactions in enzymes: A computational study on beta-lactamases from class A. 167-175 - Hongwei Wu, Fenglou Mao, Victor Olman, Ying Xu:
On application of directons to functional classification of genes in prokaryotes. 176-184 - Akinori Hirashima, Hongwei Huang:
Homology modeling, agonist binding site identification, and docking in octopamine receptor of Periplaneta americana. 185-190 - Amit Bafana, Tapan Chakrabarti:
Lateral gene transfer in phylogeny of azoreductase enzyme. 191-197 - Tatsunori Iwata, Kaori Fukuzawa, Katsuhisa Nakajima, Sachiko Aida-Hyugaji, Yuji Mochizuki, Hirofumi Watanabe, Shigenori Tanaka:
Theoretical analysis of binding specificity of influenza viral hemagglutinin to avian and human receptors based on the fragment molecular orbital method. 198-211
- Vineet Sangar, Victor I. Lesk, Arthur M. Lesk:
On the use of overlapping lattices for screening to find pairs of nearby points in two and three dimensions. 212-214 - Matthew E. Monroe, Jason L. Shaw, Don Simone Daly, Joshua N. Adkins, Richard D. Smith:
MASIC: A software program for fast quantitation and flexible visualization of chromatographic profiles from detected LC-MS(/MS) features. 215-217 - Hyung-Seok Choi, Jeong-Rae Kim, Sang-Woo Lee, Kwang-Hyun Cho:
Why have serine/threonine/tyrosine kinases been evolutionarily selected in eukaryotic signaling cascades? 218-221 - Nicole Davis, Natasha Biddlecom, David Hecht, Gary B. Fogel:
On the relationship between GC content and the number of predicted microRNA binding sites by MicroInspector. 222-226
- Yu-Yen Ou, M. Michael Gromiha, Shu-An Chen, Makiko Suwa:
TMBETADISC-RBF: Discrimination of beta-barrel membrane proteins using RBF networks and PSSM profiles. 227-231
Volume 32, Number 4, August 2008
- Antonio Mucherino, Susan Costantini, Daniela di Serafino, Marco D'Apuzzo, Angelo M. Facchiano, Giovanni Colonna:
Understanding the role of the topology in protein folding by computational inverse folding experiments. 233-239 - Wen Zhou, Xinjun Peng, Zhenglou Yan, Yifei Wang:
Accelerated stochastic simulation algorithm for coupled chemical reactions with delays. 240-242 - Zhihua Du, Yiwei Wang, Zhen Ji:
PK-means: A new algorithm for gene clustering. 243-247 - Andreas Alexander Albrecht, Alexandros Skaliotis, Kathleen Steinhöfel:
Stochastic protein folding simulation in the three-dimensional HP-model. 248-255 - Absalom Zamorano, César López-Camarillo, Esther Orozco, Christian Weber, Nancy Guillen, Laurence A. Marchat:
In silico analysis of EST and genomic sequences allowed the prediction of cis-regulatory elements for Entamoeba histolytica mRNA polyadenylation. 256-263 - Mugdha Khaladkar, Vandanaben Patel, Vivian Bellofatto, Jeffrey Wilusz, Jason Tsong-Li Wang:
Detecting conserved secondary structures in RNA molecules using constrained structural alignment. 264-272 - Hewerson Z. Teixeira, Antônio-Carlos G. Almeida, Antonio Fernando C. Infantosi, Antônio Márcio Rodrigues, Natália L. Costa, Mário A. Duarte:
Identifying essential conditions for refractoriness of Leão's spreading depression - Computational modeling. 273-281
- Gordon Blackshields, Mark A. Larkin, Iain M. Wallace, Andreas Wilm, Desmond G. Higgins:
Fast embedding methods for clustering tens of thousands of sequences. 282-286 - Zhihao Yang, Hongfei Lin, Yanpeng Li:
Exploiting the performance of dictionary-based bio-entity name recognition in biomedical literature. 287-291 - Werner Sandmann:
Discrete-time stochastic modeling and simulation of biochemical networks. 292-297 - Jing Hu, Changhui Yan:
A method for discovering transmembrane beta-barrel proteins in Gram-negative bacterial proteomes. 298-301
- K. Rao Raghuraj, Samavedham Lakshminarayanan:
Variable predictive model based classification algorithm for effective separation of protein structural classes. 302-306 - Purevjav Enkhbayar, Sodov Damdinsuren, Mitsuru Osaki, Norio Matsushima:
HELFIT: Helix fitting by a total least squares method. 307-310
Volume 32, Number 5, October 2008
- M. James C. Crabbe:
Climate change, global warming and coral reefs: Modelling the effects of temperature. 311-314 - Khashayar Khoshmanesh, Abbas Z. Kouzani, Saeid Nahavandi, Sara Baratchi, J. R. Kanwar:
At a glance: Cellular biology for engineers. 315-331
- Shigeru Takasaki:
Mitochondrial SNPs associated with Japanese centenarians, Alzheimer's patients, and Parkinson's patients. 332-337 - Massimo Pisu, Alessandro Concas, Sarah Fadda, Alberto Cincotti, Giacomo Cao:
A simulation model for stem cells differentiation into specialized cells of non-connective tissues. 338-344 - Tamir Caras, Ami Bachar, Zohar Pasternak:
Morphological variation in the oral disc of the scleractinian coral Favia speciosa (Dana) at Indonesia. 345-348 - Fernanda Barea, Simone Tessaro, Diego Bonatto:
In silico analyses of a new group of fungal and plant RecQ4-homologous proteins. 349-358 - Michael W. Towsey, Peter Timms, James M. Hogan, Sarah A. Mathews:
The cross-species prediction of bacterial promoters using a support vector machine. 359-366
- V. N. Azger Dusthackeer, V. N. Sameer Hassan, Vanaja Kumar:
Tape measure protein having MT3 motif facilitates phage entry into stationary phase cells of Mycobacterium tuberculosis. 367-369 - Suren A. Tatulian:
Determination of helix orientations in proteins. 370-374 - Dimitrij Surmeli, Oliver Ratmann, Hans-Werner Mewes, Igor V. Tetko:
FunCat functional inference with belief propagation and feature integration. 375-377 - R. Sreekanth, Vasantha Pattabhi, S. S. Rajan:
Characterization of alpha helices interacting with nucleic acids. 378-381 - Rajnikant Dixit, Upal Roy, Millind S. Patole, Yogesh S. Shouche:
Molecular and phylogenetic analysis of a novel family of fibrinogen-related proteins from mosquito Aedes albopictus cell line. 382-386
- A. Srinivas Reddy, H. S. Durga Amarnath, Raju S. Bapi, G. Madhavi Sastry, G. Narahari Sastry:
Protein ligand interaction database (PLID). 387-390
Volume 32, Number 6, December 2008
- Wentian Li, Young Ju Suh, Yaning Yang:
Exploring case-control genetic association tests using phase diagrams. 391-399 - Ahmed Ahmed, Christian J. Michel:
Plant microRNA detection using the circular code information. 400-405 - Sayed-Rzgar Hosseini, Mehdi Sadeghi, Hamid Pezeshk, Changiz Eslahchi, Mahnaz Habibi:
PROSIGN: A method for protein secondary structure assignment based on three-dimensional coordinates of consecutive Calpha atoms. 406-411 - Alexey V. Antonov, Hans-Werner Mewes:
Complex phylogenetic profiling reveals fundamental genotype-phenotype associations. 412-416 - Chenlei Leng:
Sparse optimal scoring for multiclass cancer diagnosis and biomarker detection using microarray data. 417-425 - Joon Jin Song, Weiguo Deng, Ho-Jin Lee, Deukwoo Kwon:
Optimal classification for time-course gene expression data using functional data analysis. 426-432 - Jun Lu, Liaofu Luo, Ying Zhang:
Distance conservation of transcription regulatory motifs in human promoters. 433-437
- Reiji Teramoto:
Prediction of Alzheimer's diagnosis using semi-supervised distance metric learning with label propagation. 438-441 - Amit Kumar Banerjee, K. Kiran, U. S. N. Murty, Ch. Venkateswarlu:
Classification and identification of mosquito species using artificial neural networks. 442-447 - Efendi N. Nasibov, Cagin Kandemir-Cavas:
Protein subcellular location prediction using optimally weighted fuzzy k-NN algorithm. 448-451 - T. G. Mamedov, Elsje Pienaar, Scott E. Whitney, J. R. TerMaat, G. Carvill, R. Goliath, A. Subramanian, Hendrik J. Viljoen:
A fundamental study of the PCR amplification of GC-rich DNA templates. 452-457 - Bobbie-Jo M. Webb-Robertson, Christopher S. Oehmen, Anuj R. Shah:
A feature vector integration approach for a generalized support vector machine pairwise homology algorithm. 458-461
- Degeng Wang:
Discrepancy between mRNA and protein abundance: Insight from information retrieval process in computers. 462-468
- Andrzej K. Konopka, M. James C. Crabbe:
Editors' note concerning an EST analysis pipeline by Zhu et al. (2006). 469
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