Computational 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 M. 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
  
• S. 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, Jose 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 Amoutzias, Sofia Kossida, Georgia Sotiropoulou:
  Identification and analysis of mammalian KLK6 orthologue genes for prediction of physiological substrates. 111-121
  
• Omer Sinan Sarac, 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, G. I. Menon:
  Microtubule dynamics regulated by stathmin. 141-144
  
• A. 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 M. Rodrigues, Natália L. Costa, Mário A. Duarte:
  Identifying essential conditions for refractoriness of Leão's spreading depression - Computational modeling. 273-281
  

• Gordon Blackshields, Mark 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
  
• K. Khoshmanesh, Abbas Z. Kouzani, Saeid Nahavandi, S. 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 C_alpha 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 Nasibov, Cagin Kandemir-Cavas:
  Protein subcellular location prediction using optimally weighted fuzzy k-NN algorithm. 448-451
  
• T. G. Mamedov, E. 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