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.
- 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.
- Alexander Bolshoy:
Revisiting the relationship between compositional sequence complexity and periodicity.
- Li-Yeh Chuang, Hsueh-Wei Chang, Chung-Jui Tu, Cheng-Hong Yang:
Improved binary PSO for feature selection using gene expression data.
- Elias Zintzaras, John P. A. Ioannidis:
Meta-analysis for ranked discovery datasets: Theoretical framework and empirical demonstration for microarrays.
- S. Zeiser, O. Rivera, Christina Kuttler, Burkhard A. Hense, R. Lasser, G. Winkler:
Oscillations of Hes7 caused by negative autoregulation and ubiquitination.
- 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.
- Donggen Zhou, Siguang Li, Jian Wen, Xi Gong, Ling Xu, Yuping Luo:
Genome-wide computational analyses of microRNAs and their targets from Canis familiaris.
- 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.
- Hyeoncheol Kim, Yiying Zhang, Yong-Seok Heo, Heung-Bum Oh, Su-Shing Chen:
Specificity rule discovery in HIV-1 protease cleavage site analysis.
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.
- 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.
- 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.
- Georgios Pampalakis, Maria Arampatzidou, Grigoris Amoutzias, Sofia Kossida, Georgia Sotiropoulou:
Identification and analysis of mammalian KLK6 orthologue genes for prediction of physiological substrates.
- Ömer Sinan Saraç, Özge Gürsoy-Yüzügüllü, Rengül Çetin-Atalay, Volkan Atalay:
Subsequence-based feature map for protein function classification.
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?
- 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.
- Krystian Kubica:
A pore creation in a triangular network model membrane.
- 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.
- Hongwei Wu, Fenglou Mao, Victor Olman, Ying Xu:
On application of directons to functional classification of genes in prokaryotes.
- Akinori Hirashima, Hongwei Huang:
Homology modeling, agonist binding site identification, and docking in octopamine receptor of Periplaneta americana.
- Amit Bafana, Tapan Chakrabarti:
Lateral gene transfer in phylogeny of azoreductase enzyme.
- 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.
- 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.
- 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.
- 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?
- 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.
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.
- Wen Zhou, Xinjun Peng, Zhenglou Yan, Yifei Wang:
Accelerated stochastic simulation algorithm for coupled chemical reactions with delays.
- Zhihua Du, Yiwei Wang, Zhen Ji:
PK-means: A new algorithm for gene clustering.
- Andreas Alexander Albrecht, Alexandros Skaliotis, Kathleen Steinhöfel:
Stochastic protein folding simulation in the three-dimensional HP-model.
- 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.
- Mugdha Khaladkar, Vandanaben Patel, Vivian Bellofatto, Jeffrey Wilusz, Jason Tsong-Li Wang:
Detecting conserved secondary structures in RNA molecules using constrained structural alignment.
- 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.
Volume 32, Number 5, October 2008
- Shigeru Takasaki:
Mitochondrial SNPs associated with Japanese centenarians, Alzheimer's patients, and Parkinson's patients.
- Massimo Pisu, Alessandro Concas, Sarah Fadda, Alberto Cincotti, Giacomo Cao:
A simulation model for stem cells differentiation into specialized cells of non-connective tissues.
- Tamir Caras, Ami Bachar, Zohar Pasternak:
Morphological variation in the oral disc of the scleractinian coral Favia speciosa (Dana) at Indonesia.
- Fernanda Barea, Simone Tessaro, Diego Bonatto:
In silico analyses of a new group of fungal and plant RecQ4-homologous proteins.
- Michael W. Towsey, Peter Timms, James M. Hogan, Sarah A. Mathews:
The cross-species prediction of bacterial promoters using a support vector machine.
- 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.
- Suren A. Tatulian:
Determination of helix orientations in proteins.
- Dimitrij Surmeli, Oliver Ratmann, Hans-Werner Mewes, Igor V. Tetko:
FunCat functional inference with belief propagation and feature integration.
- R. Sreekanth, Vasantha Pattabhi, S. S. Rajan:
Characterization of alpha helices interacting with nucleic acids.
- 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.
Volume 32, Number 6, December 2008
- Wentian Li, Young Ju Suh, Yaning Yang:
Exploring case-control genetic association tests using phase diagrams.
- Ahmed Ahmed, Christian J. Michel:
Plant microRNA detection using the circular code information.
- 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.
- Alexey V. Antonov, Hans-Werner Mewes:
Complex phylogenetic profiling reveals fundamental genotype-phenotype associations.
- Chenlei Leng:
Sparse optimal scoring for multiclass cancer diagnosis and biomarker detection using microarray data.
- Joon Jin Song, Weiguo Deng, Ho-Jin Lee, Deukwoo Kwon:
Optimal classification for time-course gene expression data using functional data analysis.
- Jun Lu, Liaofu Luo, Ying Zhang:
Distance conservation of transcription regulatory motifs in human promoters.
- Reiji Teramoto:
Prediction of Alzheimer's diagnosis using semi-supervised distance metric learning with label propagation.
- Amit Kumar Banerjee, K. Kiran, U. S. N. Murty, Ch. Venkateswarlu:
Classification and identification of mosquito species using artificial neural networks.
- Efendi N. Nasibov, Cagin Kandemir-Cavas:
Protein subcellular location prediction using optimally weighted fuzzy k-NN algorithm.
- 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.
- 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.
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- Degeng Wang:
Discrepancy between mRNA and protein abundance: Insight from information retrieval process in computers.