Published in Comput Biol Chem on February 01, 2003
PRED-TMBB: a web server for predicting the topology of beta-barrel outer membrane proteins. Nucleic Acids Res (2004) 2.76
A Hidden Markov Model method, capable of predicting and discriminating beta-barrel outer membrane proteins. BMC Bioinformatics (2004) 1.90
Predicting transmembrane beta-barrels in proteomes. Nucleic Acids Res (2004) 1.83
A new decoding algorithm for hidden Markov models improves the prediction of the topology of all-beta membrane proteins. BMC Bioinformatics (2005) 1.49
Evaluation of methods for predicting the topology of beta-barrel outer membrane proteins and a consensus prediction method. BMC Bioinformatics (2005) 1.41
T-cell epitope vaccine design by immunoinformatics. Open Biol (2013) 1.20
HHomp--prediction and classification of outer membrane proteins. Nucleic Acids Res (2009) 1.16
OMPdb: a database of {beta}-barrel outer membrane proteins from Gram-negative bacteria. Nucleic Acids Res (2010) 1.04
TMB-Hunt: an amino acid composition based method to screen proteomes for beta-barrel transmembrane proteins. BMC Bioinformatics (2005) 1.03
TOPPER: topology prediction of transmembrane protein based on evidential reasoning. ScientificWorldJournal (2013) 0.85
Positively selected codons in immune-exposed loops of the vaccine candidate OMP-P1 of Haemophilus influenzae. J Mol Evol (2007) 0.84
transFold: a web server for predicting the structure and residue contacts of transmembrane beta-barrels. Nucleic Acids Res (2006) 0.83
Recent applications of Hidden Markov Models in computational biology. Genomics Proteomics Bioinformatics (2004) 0.76
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
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
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
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
In silico discovery of human natural antisense transcripts. BMC Bioinformatics (2006) 1.16
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
The prediction of interferon treatment effects based on time series microarray gene expression profiles. J Transl Med (2008) 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
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
Development, characterization, and cross-species/genera transferability of SSR markers for rubber tree (Hevea brasiliensis). Plant Cell Rep (2010) 0.95
A negative cooperativity mechanism of human CYP2E1 inferred from molecular dynamics simulations and free energy calculations. J Chem Inf Model (2011) 0.94
Large scale phosphoproteome profiles comprehensive features of mouse embryonic stem cells. Mol Cell Proteomics (2010) 0.94
KDE Bioscience: platform for bioinformatics analysis workflows. J Biomed Inform (2005) 0.94
Localized-statistical quantification of human serum proteome associated with type 2 diabetes. PLoS One (2008) 0.93
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
Identifying modules of coexpressed transcript units and their organization of Saccharopolyspora erythraea from time series gene expression profiles. PLoS One (2010) 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 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
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
Protein sumoylation sites prediction based on two-stage feature selection. Mol Divers (2009) 0.88
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
Induced fit for mRNA/TIS11d complex. J Chem Phys (2009) 0.86
Discovering multiple transcripts of human hepatocytes using massively parallel signature sequencing (MPSS). BMC Genomics (2007) 0.86
Combinatorial network of transcriptional regulation and microRNA regulation in human cancer. BMC Syst Biol (2012) 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
DBH2H: vertebrate head-to-head gene pairs annotated at genomic and post-genomic levels. Database (Oxford) (2009) 0.85
[Analysis of the survival in patients after surgical resection of thoracic esophageal cancer]. Zhonghua Zhong Liu Za Zhi (2009) 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
Analysis of gene expression profile in gastric cancer cells stimulated with Helicobacter pylori isogenic strains. J Med Microbiol (2004) 0.84
Exploring mitochondrial evolution and metabolism organization principles by comparative analysis of metabolic networks. Genomics (2010) 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
A 3D model of SARS_CoV 3CL proteinase and its inhibitors design by virtual screening. Acta Pharmacol Sin (2003) 0.84
Hippocampal synaptic metaplasticity requires the activation of NR2B-containing NMDA receptors. Brain Res Bull (2010) 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
Scoring hidden Markov models to discriminate beta-barrel membrane proteins. Comput Biol Chem (2004) 0.84
The discovery of novel protein-coding features in mouse genome based on mass spectrometry data. Genomics (2011) 0.83
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
Prediction of protein secondary structure using improved two-level neural network architecture. Protein Pept Lett (2005) 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
Exploration of conformational transition in the aryl-binding site of human FXa using molecular dynamics simulations. J Mol Model (2011) 0.80
Predicting protein oxidation sites with feature selection and analysis approach. J Biomol Struct Dyn (2012) 0.80
Comparisons of graph-structure clustering methods for gene expression data. Acta Biochim Biophys Sin (Shanghai) (2006) 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
Cancer classification from the gene expression profiles by Discriminant Kernel-PLS. J Bioinform Comput Biol (2010) 0.79
[Analysis and application of SNP and haplotype in the human genome]. Yi Chuan Xue Bao (2005) 0.79
Putative hAPN receptor binding sites in SARS_CoV spike protein. Acta Pharmacol Sin (2003) 0.79
Analyses of copy number variation of GK rat reveal new putative type 2 diabetes susceptibility loci. PLoS One (2010) 0.79
Autoinhibitory mechanism for the mutation-induced impaired FGF9 signaling. J Chem Inf Model (2012) 0.78
Global transcriptome analysis profiles metabolic pathways in traditional herb Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao. BMC Genomics (2015) 0.78
Structural flexibility and interactions of PTP1B's S-loop. Interdiscip Sci (2009) 0.78
Structural basis for the mutation-induced dysfunction of human CYP2J2: a computational study. J Chem Inf Model (2013) 0.78
Computational studies on the substrate interactions of influenza A virus PB2 subunit. PLoS One (2012) 0.78
Sorting out inherent features of head-to-head gene pairs by evolutionary conservation. BMC Bioinformatics (2010) 0.78
π-π Stacking mediated drug-drug interactions in human CYP2E1. Proteins (2013) 0.77
Support vector machine for predicting alpha-turn types. Peptides (2003) 0.77
Comparison of a proteomic approach with a microarray-based approach to detect exons in the mouse genome. Nat Genet (2006) 0.77
Splice blocking of zygotic sox31 leads to developmental arrest shortly after Mid-Blastula Transition and induces apoptosis in zebrafish. FEBS Lett (2011) 0.76
MPSS: an integrated database system for surveying a set of proteins. Bioinformatics (2005) 0.76
Modeling the effects of cell cycle M-phase transcriptional inhibition on circadian oscillation. PLoS Comput Biol (2008) 0.75
EcoBrowser: a web-based tool for visualizing transcriptome data of Escherichia coli. BMC Res Notes (2011) 0.75
Network analysis of the protein chain tertiary structures of heterocomplexes. Protein Pept Lett (2006) 0.75
Detecting the determinism of EEG time series using a nonlinear forecasting method. Conf Proc IEEE Eng Med Biol Soc (2005) 0.75
Use of ANN and Complexity Measures in Cognitive EEG Discrimination. Conf Proc IEEE Eng Med Biol Soc (2005) 0.75
Partition dataset according to amino acid type improves the prediction of deleterious non-synonymous SNPs. Biochem Biophys Res Commun (2012) 0.75
Molecular dynamics simulations of dipolar fluids in orientationally ordered phases. Phys Rev E Stat Nonlin Soft Matter Phys (2007) 0.75
[Confocal scanning microscopy for biomedicine]. Zhongguo Yi Liao Qi Xie Za Zhi (2005) 0.75
[Construction of a proteomic map database]. Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao (Shanghai) (2002) 0.75
Efficacy of tranexamic acid plus drain-clamping to reduce blood loss in total knee arthroplasty: A meta-analysis. Medicine (Baltimore) (2017) 0.75
EMMA: an efficient massive mapping algorithm using improved approximate mapping filtering. Acta Biochim Biophys Sin (Shanghai) (2006) 0.75
A new nucleotide-composition based fingerprint of SARS-CoV with visualization analysis. Med Chem (2005) 0.75
[Fluoroscopic image capturing and DICOM storage application in the cardio-catheter room]. Zhongguo Yi Liao Qi Xie Za Zhi (2005) 0.75
Association between alcohol, smoking and HLA-DQA1*0201 genotype in psoriasis. Acta Biochim Biophys Sin (Shanghai) (2004) 0.75