Published in Protein Pept Lett on November 01, 2005
Cross-host evolution of severe acute respiratory syndrome coronavirus in palm civet and human. Proc Natl Acad Sci U S A (2005) 3.37
Systematic analysis of head-to-head gene organization: evolutionary conservation and potential biological relevance. PLoS Comput Biol (2006) 2.11
Using manifold embedding for assessing and predicting protein interactions from high-throughput experimental data. Bioinformatics (2010) 1.65
Construction of a chloroplast protein interaction network and functional mining of photosynthetic proteins in Arabidopsis thaliana. Cell Res (2008) 1.58
Comparison of normalization methods with microRNA microarray. Genomics (2008) 1.51
Analysis and prediction of the metabolic stability of proteins based on their sequential features, subcellular locations and interaction networks. PLoS One (2010) 1.51
Predicting protein interaction sites from residue spatial sequence profile and evolution rate. FEBS Lett (2005) 1.49
APIS: accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility. BMC Bioinformatics (2010) 1.44
Transcript-level annotation of Affymetrix probesets improves the interpretation of gene expression data. BMC Bioinformatics (2007) 1.35
Hierarchical modularity of nested bow-ties in metabolic networks. BMC Bioinformatics (2006) 1.33
Semantic search among heterogeneous biological databases based on gene ontology. Acta Biochim Biophys Sin (Shanghai) (2004) 1.30
Prediction of pharmacological and xenobiotic responses to drugs based on time course gene expression profiles. PLoS One (2009) 1.26
Modular co-evolution of metabolic networks. BMC Bioinformatics (2007) 1.23
DCGL: an R package for identifying differentially coexpressed genes and links from gene expression microarray data. Bioinformatics (2010) 1.23
Tumor clustering using nonnegative matrix factorization with gene selection. IEEE Trans Inf Technol Biomed (2009) 1.23
Metasample-based sparse representation for tumor classification. IEEE/ACM Trans Comput Biol Bioinform (2011) 1.23
A semi-supervised learning approach to predict synthetic genetic interactions by combining functional and topological properties of functional gene network. BMC Bioinformatics (2010) 1.21
Link-based quantitative methods to identify differentially coexpressed genes and gene pairs. BMC Bioinformatics (2011) 1.19
Combinatorial network of primary and secondary microRNA-driven regulatory mechanisms. Nucleic Acids Res (2009) 1.19
A HMM-based method to predict the transmembrane regions of beta-barrel membrane proteins. Comput Biol Chem (2003) 1.18
In silico discovery of human natural antisense transcripts. BMC Bioinformatics (2006) 1.16
Predicting protein-protein interactions from protein sequences using meta predictor. Amino Acids (2010) 1.16
Molecular pattern discovery based on penalized matrix decomposition. IEEE/ACM Trans Comput Biol Bioinform (2011) 1.15
Robust classification method of tumor subtype by using correlation filters. IEEE/ACM Trans Comput Biol Bioinform (2011) 1.15
miR-612 suppresses the invasive-metastatic cascade in hepatocellular carcinoma. J Exp Med (2013) 1.10
Identification and target prediction of miRNAs specifically expressed in rat neural tissue. BMC Genomics (2009) 1.10
Predicting protein-protein interactions from sequence using correlation coefficient and high-quality interaction dataset. Amino Acids (2009) 1.10
The prediction of interferon treatment effects based on time series microarray gene expression profiles. J Transl Med (2008) 1.10
Sequence-based prediction of protein-protein interactions by means of rotation forest and autocorrelation descriptor. Protein Pept Lett (2010) 1.10
Dynamic analysis of optimality in myocardial energy metabolism under normal and ischemic conditions. Mol Syst Biol (2006) 1.10
Proteomics characterization of the cytotoxicity mechanism of ganoderic acid D and computer-automated estimation of the possible drug target network. Mol Cell Proteomics (2007) 1.05
Assessing and predicting protein interactions by combining manifold embedding with multiple information integration. BMC Bioinformatics (2012) 1.04
Sys-BodyFluid: a systematical database for human body fluid proteome research. Nucleic Acids Res (2008) 1.02
DCGL v2.0: an R package for unveiling differential regulation from differential co-expression. PLoS One (2013) 1.02
High-coverage proteome analysis reveals the first insight of protein modification systems in the pathogenic spirochete Leptospira interrogans. Cell Res (2009) 1.01
Computational methods for protein-protein interaction and their application. Curr Protein Pept Sci (2005) 0.99
Prediction of inter-residue contacts map based on genetic algorithm optimized radial basis function neural network and binary input encoding scheme. J Comput Aided Mol Des (2005) 0.95
KDE Bioscience: platform for bioinformatics analysis workflows. J Biomed Inform (2005) 0.94
Large scale phosphoproteome profiles comprehensive features of mouse embryonic stem cells. Mol Cell Proteomics (2010) 0.94
A negative cooperativity mechanism of human CYP2E1 inferred from molecular dynamics simulations and free energy calculations. J Chem Inf Model (2011) 0.94
Localized-statistical quantification of human serum proteome associated with type 2 diabetes. PLoS One (2008) 0.93
A novel approach to extracting features from motif content and protein composition for protein sequence classification. Neural Netw (2005) 0.93
Gene expression data classification using consensus independent component analysis. Genomics Proteomics Bioinformatics (2008) 0.92
Completed local binary count for rotation invariant texture classification. IEEE Trans Image Process (2012) 0.92
Identifying modules of coexpressed transcript units and their organization of Saccharopolyspora erythraea from time series gene expression profiles. PLoS One (2010) 0.91
Molecular dynamics studies on the interactions of PTP1B with inhibitors: from the first phosphate-binding site to the second one. Protein Eng Des Sel (2009) 0.91
An improved kinetic model for the acetone-butanol-ethanol pathway of Clostridium acetobutylicum and model-based perturbation analysis. BMC Syst Biol (2011) 0.90
Prediction of protein B-factors using multi-class bounded SVM. Protein Pept Lett (2007) 0.90
Prediction of beta-turns with learning machines. Peptides (2003) 0.90
Small envelope protein E of SARS: cloning, expression, purification, CD determination, and bioinformatics analysis. Acta Pharmacol Sin (2003) 0.90
Systems perspectives on erythromycin biosynthesis by comparative genomic and transcriptomic analyses of S. erythraea E3 and NRRL23338 strains. BMC Genomics (2013) 0.89
Combining gene expression profiles and protein-protein interaction data to infer gene functions. J Biotechnol (2006) 0.89
Inferring protein-protein interacting sites using residue conservation and evolutionary information. Protein Pept Lett (2006) 0.89
3D structure modeling of cytochrome P450 2C19 and its implication for personalized drug design. Biochem Biophys Res Commun (2007) 0.89
Adipogenesis licensing and execution are disparately linked to cell proliferation. Cell Res (2009) 0.88
A new constrained independent component analysis method. IEEE Trans Neural Netw (2007) 0.88
Protein sumoylation sites prediction based on two-stage feature selection. Mol Divers (2009) 0.88
A gene selection algorithm based on the gene regulation probability using maximal likelihood estimation. Biotechnol Lett (2005) 0.88
Tumor classification by combining PNN classifier ensemble with neighborhood rough set based gene reduction. Comput Biol Med (2009) 0.88
Gene expression data classification using locally linear discriminant embedding. Comput Biol Med (2010) 0.87
Rig-I regulates NF-κB activity through binding to Nf-κb1 3'-UTR mRNA. Proc Natl Acad Sci U S A (2013) 0.87
Identification of probable genomic packaging signal sequence from SARS-CoV genome by bioinformatics analysis. Acta Pharmacol Sin (2003) 0.86
Identification of p27/KIP1 expression level as a candidate biomarker of response to rapalogs therapy in human cancer. J Mol Med (Berl) (2010) 0.86
Combinatorial network of transcriptional regulation and microRNA regulation in human cancer. BMC Syst Biol (2012) 0.86
Cancer classification using Rotation Forest. Comput Biol Med (2008) 0.86
Discovering multiple transcripts of human hepatocytes using massively parallel signature sequencing (MPSS). BMC Genomics (2007) 0.86
Induced fit for mRNA/TIS11d complex. J Chem Phys (2009) 0.86
DBH2H: vertebrate head-to-head gene pairs annotated at genomic and post-genomic levels. Database (Oxford) (2009) 0.85
Predicting contact map using radial basis function neural network with conformational energy function. Int J Bioinform Res Appl (2008) 0.85
An algorithm for finding functional modules and protein complexes in protein-protein interaction networks. J Biomed Biotechnol (2008) 0.85
Reversal of coenzyme specificity and improvement of catalytic efficiency of Pichia stipitis xylose reductase by rational site-directed mutagenesis. Biotechnol Lett (2009) 0.85
A 3D model of SARS_CoV 3CL proteinase and its inhibitors design by virtual screening. Acta Pharmacol Sin (2003) 0.84
t-LSE: a novel robust geometric approach for modeling protein-protein interaction networks. PLoS One (2013) 0.84
A high-throughput approach for subcellular proteome: identification of rat liver proteins using subcellular fractionation coupled with two-dimensional liquid chromatography tandem mass spectrometry and bioinformatic analysis. Mol Cell Proteomics (2004) 0.84
Analysis of gene expression profile in gastric cancer cells stimulated with Helicobacter pylori isogenic strains. J Med Microbiol (2004) 0.84
Predicting key long-range interaction sites by B-factors. Protein Pept Lett (2008) 0.84
Large number of phosphotransferase genes in the Clostridium beijerinckii NCIMB 8052 genome and the study on their evolution. BMC Bioinformatics (2010) 0.84
Exploring mitochondrial evolution and metabolism organization principles by comparative analysis of metabolic networks. Genomics (2010) 0.84
Scoring hidden Markov models to discriminate beta-barrel membrane proteins. Comput Biol Chem (2004) 0.84
Graphical representation for DNA sequences via joint diagonalization of matrix pencil. IEEE J Biomed Health Inform (2013) 0.83
The discovery of novel protein-coding features in mouse genome based on mass spectrometry data. Genomics (2011) 0.83
Predicting Hub Genes Associated with Cervical Cancer through Gene Co-Expression Networks. IEEE/ACM Trans Comput Biol Bioinform (2015) 0.83
ChIP-PIT: Enhancing the Analysis of ChIP-Seq Data Using Convex-Relaxed Pair-Wise Interaction Tensor Decomposition. IEEE/ACM Trans Comput Biol Bioinform (2016) 0.82
Prediction of protein-protein interactions based on protein-protein correlation using least squares regression. Curr Protein Pept Sci (2014) 0.82
Crosstissue coexpression network of aging. OMICS (2011) 0.82
Negatively cooperative binding properties of human cytochrome P450 2E1 with monocyclic substrates. Curr Drug Metab (2012) 0.81
A method of tumor classification based on wavelet packet transforms and neighborhood rough set. Comput Biol Med (2010) 0.81
Concurrent quantification of proteome and phosphoproteome to reveal system-wide association of protein phosphorylation and gene expression. Mol Cell Proteomics (2009) 0.81
cGRNB: a web server for building combinatorial gene regulatory networks through integrated engineering of seed-matching sequence information and gene expression datasets. BMC Syst Biol (2013) 0.81
GalNAc-transferase specificity prediction based on feature selection method. Peptides (2008) 0.81
Identifying protein-protein interfacial residues in heterocomplexes using residue conservation scores. Int J Biol Macromol (2006) 0.81
Comparisons of graph-structure clustering methods for gene expression data. Acta Biochim Biophys Sin (Shanghai) (2006) 0.80
Predicting protein oxidation sites with feature selection and analysis approach. J Biomol Struct Dyn (2012) 0.80
A hybrid forward algorithm for RBF neural network construction. IEEE Trans Neural Netw (2006) 0.80
Exploration of conformational transition in the aryl-binding site of human FXa using molecular dynamics simulations. J Mol Model (2011) 0.80
Prediction of prokaryotic promoters based on prediction of transcriptional units. Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao (Shanghai) (2003) 0.80
Selection of reprogramming factors of induced pluripotent stem cells based on the protein interaction network and functional profiles. Protein Pept Lett (2012) 0.80
Molecular dynamics studies on the conformational transitions of adenylate kinase: a computational evidence for the conformational selection mechanism. Biomed Res Int (2013) 0.79
A comparison of computational methods for identifying virulence factors. PLoS One (2012) 0.79
A protein interaction network analysis for yeast integral membrane protein. Protein Pept Lett (2008) 0.79