Published in Nucleic Acids Res on January 01, 2006
Functional organization of the S. cerevisiae phosphorylation network. Cell (2009) 3.15
TSGene: a web resource for tumor suppressor genes. Nucleic Acids Res (2012) 2.90
PHOSIDA 2011: the posttranslational modification database. Nucleic Acids Res (2010) 2.61
Proteome-wide post-translational modification statistics: frequency analysis and curation of the swiss-prot database. Sci Rep (2011) 1.92
Deciphering a global network of functionally associated post-translational modifications. Mol Syst Biol (2012) 1.86
Post-translational modification: nature's escape from genetic imprisonment and the basis for dynamic information encoding. Wiley Interdiscip Rev Syst Biol Med (2012) 1.81
DbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications. Nucleic Acids Res (2012) 1.71
SysPTM: a systematic resource for proteomic research on post-translational modifications. Mol Cell Proteomics (2009) 1.51
Using bioinformatics to predict the functional impact of SNVs. Bioinformatics (2010) 1.49
FireDB--a database of functionally important residues from proteins of known structure. Nucleic Acids Res (2006) 1.45
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dbOGAP - an integrated bioinformatics resource for protein O-GlcNAcylation. BMC Bioinformatics (2011) 1.36
A systematic comparative and structural analysis of protein phosphorylation sites based on the mtcPTM database. Genome Biol (2007) 1.29
AntigenDB: an immunoinformatics database of pathogen antigens. Nucleic Acids Res (2009) 1.18
SysZNF: the C2H2 zinc finger gene database. Nucleic Acids Res (2008) 1.13
PlantPhos: using maximal dependence decomposition to identify plant phosphorylation sites with substrate site specificity. BMC Bioinformatics (2011) 1.10
Loss of post-translational modification sites in disease. Pac Symp Biocomput (2010) 1.08
Toward a complete in silico, multi-layered embryonic stem cell regulatory network. Wiley Interdiscip Rev Syst Biol Med (2010) 1.06
RegPhos: a system to explore the protein kinase-substrate phosphorylation network in humans. Nucleic Acids Res (2010) 1.03
RhesusBase: a knowledgebase for the monkey research community. Nucleic Acids Res (2012) 1.02
OKCAM: an ontology-based, human-centered knowledgebase for cell adhesion molecules. Nucleic Acids Res (2008) 1.01
Genome-scale modeling of the protein secretory machinery in yeast. PLoS One (2013) 0.96
FMM: a web server for metabolic pathway reconstruction and comparative analysis. Nucleic Acids Res (2009) 0.94
A systematic framework for molecular dynamics simulations of protein post-translational modifications. PLoS Comput Biol (2013) 0.94
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Incorporating substrate sequence motifs and spatial amino acid composition to identify kinase-specific phosphorylation sites on protein three-dimensional structures. BMC Bioinformatics (2013) 0.92
A comprehensive resource for integrating and displaying protein post-translational modifications. BMC Res Notes (2009) 0.91
Carboxylator: incorporating solvent-accessible surface area for identifying protein carboxylation sites. J Comput Aided Mol Des (2011) 0.91
Charge environments around phosphorylation sites in proteins. BMC Struct Biol (2008) 0.91
Rampant purifying selection conserves positions with posttranslational modifications in human proteins. Mol Biol Evol (2011) 0.91
dbPTM 2016: 10-year anniversary of a resource for post-translational modification of proteins. Nucleic Acids Res (2015) 0.90
RegPhos 2.0: an updated resource to explore protein kinase-substrate phosphorylation networks in mammals. Database (Oxford) (2014) 0.90
Software for automated interpretation of mass spectrometry data from glycans and glycopeptides. Analyst (2013) 0.89
Characterization and identification of protein O-GlcNAcylation sites with substrate specificity. BMC Bioinformatics (2014) 0.88
Graphlet kernels for prediction of functional residues in protein structures. J Comput Biol (2010) 0.88
dbSNO 2.0: a resource for exploring structural environment, functional and disease association and regulatory network of protein S-nitrosylation. Nucleic Acids Res (2014) 0.87
topPTM: a new module of dbPTM for identifying functional post-translational modifications in transmembrane proteins. Nucleic Acids Res (2013) 0.87
AMS 3.0: prediction of post-translational modifications. BMC Bioinformatics (2010) 0.86
ProGlycProt: a repository of experimentally characterized prokaryotic glycoproteins. Nucleic Acids Res (2011) 0.85
UbiSite: incorporating two-layered machine learning method with substrate motifs to predict ubiquitin-conjugation site on lysines. BMC Syst Biol (2016) 0.85
An evidence-based knowledgebase of pulmonary arterial hypertension to identify genes and pathways relevant to pathogenesis. Mol Biosyst (2014) 0.84
Immunome knowledge base (IKB): an integrated service for immunome research. BMC Immunol (2009) 0.83
PTM-Switchboard--a database of posttranslational modifications of transcription factors, the mediating enzymes and target genes. Nucleic Acids Res (2008) 0.83
A two-layered machine learning method to identify protein O-GlcNAcylation sites with O-GlcNAc transferase substrate motifs. BMC Bioinformatics (2015) 0.82
Characterization and identification of ubiquitin conjugation sites with E3 ligase recognition specificities. BMC Bioinformatics (2015) 0.81
EuLoc: a web-server for accurately predict protein subcellular localization in eukaryotes by incorporating various features of sequence segments into the general form of Chou's PseAAC. J Comput Aided Mol Des (2013) 0.81
Sequence alignment reveals possible MAPK docking motifs on HIV proteins. PLoS One (2010) 0.81
Web resources for mass spectrometry-based proteomics. Genomics Proteomics Bioinformatics (2015) 0.81
Functional analyses of endometriosis-related polymorphisms in the estrogen synthesis and metabolism-related genes. PLoS One (2012) 0.80
Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data. BMC Bioinformatics (2014) 0.80
ViralPhos: incorporating a recursively statistical method to predict phosphorylation sites on virus proteins. BMC Bioinformatics (2013) 0.80
CAPIH: a Web interface for comparative analyses and visualization of host-HIV protein-protein interactions. BMC Microbiol (2009) 0.80
Prediction of protein modification sites of pyrrolidone carboxylic acid using mRMR feature selection and analysis. PLoS One (2011) 0.80
Critical role of glycosylation in determining the length and structure of T cell epitopes. Immunome Res (2009) 0.79
Investigation and identification of protein γ-glutamyl carboxylation sites. BMC Bioinformatics (2011) 0.78
Mouse chromosome 17 candidate modifier genes for thrombosis. Mamm Genome (2010) 0.78
dbCPG: A web resource for cancer predisposition genes. Oncotarget (2016) 0.77
KinView: a visual comparative sequence analysis tool for integrated kinome research. Mol Biosyst (2016) 0.76
Absolute protein quantification of the yeast chaperome under conditions of heat shock. Proteomics (2016) 0.76
Baking a mass-spectrometry data PIE with McMC and simulated annealing: predicting protein post-translational modifications from integrated top-down and bottom-up data. Bioinformatics (2011) 0.76
dbPSP: a curated database for protein phosphorylation sites in prokaryotes. Database (Oxford) (2015) 0.76
dbPAF: an integrative database of protein phosphorylation in animals and fungi. Sci Rep (2016) 0.75
Prediction of post-translational modification sites using multiple kernel support vector machine. PeerJ (2017) 0.75
PathwayBooster: a tool to support the curation of metabolic pathways. BMC Bioinformatics (2015) 0.75
jEcho: an Evolved weight vector to CHaracterize the protein's posttranslational modification mOtifs. Interdiscip Sci (2015) 0.75
A new scheme to discover functional associations and regulatory networks of E3 ubiquitin ligases. BMC Syst Biol (2016) 0.75
Comparative analysis of housekeeping and tissue-specific driver nodes in human protein interaction networks. BMC Bioinformatics (2016) 0.75
A gene browser of colorectal cancer with literature evidence and pre-computed regulatory information to identify key tumor suppressors and oncogenes. Sci Rep (2016) 0.75
PChopper: high throughput peptide prediction for MRM/SRM transition design. BMC Bioinformatics (2011) 0.75
UbiNet: an online resource for exploring the functional associations and regulatory networks of protein ubiquitylation. Database (Oxford) (2016) 0.75
SUMOhunt: Combining Spatial Staging between Lysine and SUMO with Random Forests to Predict SUMOylation. ISRN Bioinform (2013) 0.75
Well-positioned nucleosomes punctuate polycistronic pol II transcription units and flank silent VSG gene arrays in Trypanosoma brucei. Epigenetics Chromatin (2017) 0.75
Large-scale analysis of the evolutionary histories of phosphorylation motifs in the human genome. Gigascience (2015) 0.75
ProKware: integrated software for presenting protein structural properties in protein tertiary structures. Nucleic Acids Res (2006) 0.75
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers (1983) 99.69
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res (2003) 52.80
The PSIPRED protein structure prediction server. Bioinformatics (2000) 20.58
Sequence and structure-based prediction of eukaryotic protein phosphorylation sites. J Mol Biol (1999) 15.63
Ensembl 2005. Nucleic Acids Res (2005) 15.13
The Protein Information Resource. Nucleic Acids Res (2003) 11.17
The importance of intrinsic disorder for protein phosphorylation. Nucleic Acids Res (2004) 8.23
The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema. Nucleic Acids Res (2005) 7.81
Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins. BMC Bioinformatics (2004) 4.44
KinasePhos: a web tool for identifying protein kinase-specific phosphorylation sites. Nucleic Acids Res (2005) 3.28
The RESID Database of Protein Modifications as a resource and annotation tool. Proteomics (2004) 3.11
InterPro: an integrated documentation resource for protein families, domains and functional sites. Brief Bioinform (2002) 2.66
The Swiss-Prot variant page and the ModSNP database: a resource for sequence and structure information on human protein variants. Hum Mutat (2004) 1.97
O-GLYCBASE version 4.0: a revised database of O-glycosylated proteins. Nucleic Acids Res (1999) 1.81
Annotation of post-translational modifications in the Swiss-Prot knowledge base. Proteomics (2004) 1.76
Incorporating hidden Markov models for identifying protein kinase-specific phosphorylation sites. J Comput Chem (2005) 1.45
RVP-net: online prediction of real valued accessible surface area of proteins from single sequences. Bioinformatics (2003) 1.42
Reduced bio basis function neural network for identification of protein phosphorylation sites: comparison with pattern recognition algorithms. Comput Biol Chem (2004) 1.39
miRTarBase: a database curates experimentally validated microRNA-target interactions. Nucleic Acids Res (2010) 5.72
MicroRNA-122, a tumor suppressor microRNA that regulates intrahepatic metastasis of hepatocellular carcinoma. Hepatology (2009) 4.36
miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions. Nucleic Acids Res (2013) 4.19
Target RNA-directed trimming and tailing of small silencing RNAs. Science (2010) 3.98
miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes. Nucleic Acids Res (2006) 3.59
MicroRNA-122 plays a critical role in liver homeostasis and hepatocarcinogenesis. J Clin Invest (2012) 3.46
Mbd3/NURD complex regulates expression of 5-hydroxymethylcytosine marked genes in embryonic stem cells. Cell (2011) 3.19
miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes. Nucleic Acids Res (2007) 3.05
Fungal small RNAs suppress plant immunity by hijacking host RNA interference pathways. Science (2013) 2.99
VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology. Nucleic Acids Res (2009) 2.71
KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns. Nucleic Acids Res (2007) 2.69
Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence. Genome Res (2010) 2.56
RegRNA: an integrated web server for identifying regulatory RNA motifs and elements. Nucleic Acids Res (2006) 2.43
Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. Nucleic Acids Res (2012) 2.32
Flow-Dependent Regulation of Kruppel-Like Factor 2 Is Mediated by MicroRNA-92a. Circulation (2011) 2.29
miRExpress: analyzing high-throughput sequencing data for profiling microRNA expression. BMC Bioinformatics (2009) 2.22
TET1 suppresses cancer invasion by activating the tissue inhibitors of metalloproteinases. Cell Rep (2012) 2.20
Arabidopsis Argonaute 2 regulates innate immunity via miRNA393(∗)-mediated silencing of a Golgi-localized SNARE gene, MEMB12. Mol Cell (2011) 2.01
Clusters of nucleotide substitutions and insertion/deletion mutations are associated with repeat sequences. PLoS Biol (2011) 1.95
miR-103/107 promote metastasis of colorectal cancer by targeting the metastasis suppressors DAPK and KLF4. Cancer Res (2012) 1.77
RNAcentral: A vision for an international database of RNA sequences. RNA (2011) 1.73
DbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications. Nucleic Acids Res (2012) 1.71
PlantPAN: Plant promoter analysis navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene groups. BMC Genomics (2008) 1.68
Long-term, efficient inhibition of microRNA function in mice using rAAV vectors. Nat Methods (2012) 1.67
The 3'-to-5' exoribonuclease Nibbler shapes the 3' ends of microRNAs bound to Drosophila Argonaute1. Curr Biol (2011) 1.66
Identifying transcriptional start sites of human microRNAs based on high-throughput sequencing data. Nucleic Acids Res (2011) 1.64
Dicer partner proteins tune the length of mature miRNAs in flies and mammals. Cell (2012) 1.57
microRNA: a master regulator of cellular processes for bioengineering systems. Annu Rev Biomed Eng (2010) 1.44
Performance of ZDOCK and ZRANK in CAPRI rounds 13-19. Proteins (2010) 1.39
An enhanced computational platform for investigating the roles of regulatory RNA and for identifying functional RNA motifs. BMC Bioinformatics (2013) 1.32
RNALogo: a new approach to display structural RNA alignment. Nucleic Acids Res (2008) 1.31
miRTar: an integrated system for identifying miRNA-target interactions in human. BMC Bioinformatics (2011) 1.30
MicroRNA-regulated, systemically delivered rAAV9: a step closer to CNS-restricted transgene expression. Mol Ther (2010) 1.30
Hypoxia-responsive miRNAs target argonaute 1 to promote angiogenesis. J Clin Invest (2013) 1.30
sRNAMap: genomic maps for small non-coding RNAs, their regulators and their targets in microbial genomes. Nucleic Acids Res (2008) 1.26
Sterol regulatory element binding protein 2 activation of NLRP3 inflammasome in endothelium mediates hemodynamic-induced atherosclerosis susceptibility. Circulation (2013) 1.25
Let-7b is a novel regulator of hepatitis C virus replication. Cell Mol Life Sci (2012) 1.22
ViTa: prediction of host microRNAs targets on viruses. Nucleic Acids Res (2006) 1.21
Functional network analysis of the transcriptomes of mesenchymal stem cells derived from amniotic fluid, amniotic membrane, cord blood, and bone marrow. Stem Cells (2007) 1.20
Target RNA-directed tailing and trimming purifies the sorting of endo-siRNAs between the two Drosophila Argonaute proteins. RNA (2010) 1.19
Incorporating structural characteristics for identification of protein methylation sites. J Comput Chem (2009) 1.16
Incorporating support vector machine for identifying protein tyrosine sulfation sites. J Comput Chem (2009) 1.16
Histone demethylase RBP2 promotes lung tumorigenesis and cancer metastasis. Cancer Res (2013) 1.14
A systematic review of microRNA expression profiling studies in human gastric cancer. Cancer Med (2014) 1.14
Differentially expressed genes in radioresistant nasopharyngeal cancer cells: gp96 and GDF15. Mol Cancer Ther (2007) 1.11
Molecular characterization of adenocarcinoma and squamous carcinoma of the uterine cervix using microarray analysis of gene expression. Int J Cancer (2006) 1.11
Decreased expression of microRNA-199b increases protein levels of SET (protein phosphatase 2A inhibitor) in human choriocarcinoma. Cancer Lett (2009) 1.10
dbSNO: a database of cysteine S-nitrosylation. Bioinformatics (2012) 1.07
Using functional signatures to identify repositioned drugs for breast, myelogenous leukemia and prostate cancer. PLoS Comput Biol (2012) 1.06
Microarray meta-analysis database (M(2)DB): a uniformly pre-processed, quality controlled, and manually curated human clinical microarray database. BMC Bioinformatics (2010) 1.05
Novel poly-silicon nanowire field effect transistor for biosensing application. Biosens Bioelectron (2008) 1.05
SNOSite: exploiting maximal dependence decomposition to identify cysteine S-nitrosylation with substrate site specificity. PLoS One (2011) 1.04
RegPhos: a system to explore the protein kinase-substrate phosphorylation network in humans. Nucleic Acids Res (2010) 1.03
Computational identification of riboswitches based on RNA conserved functional sequences and conformations. RNA (2009) 1.02
Identification and characterization of two amino acids critical for the substrate inhibition of human dehydroepiandrosterone sulfotransferase (SULT2A1). Mol Pharmacol (2007) 1.01
Promoter polymorphisms of DNMT3B and the risk of head and neck squamous cell carcinoma in Taiwan: a case-control study. Oral Oncol (2006) 1.00
Small molecule amiloride modulates oncogenic RNA alternative splicing to devitalize human cancer cells. PLoS One (2011) 0.99
Mixed sequence reader: a program for analyzing DNA sequences with heterozygous base calling. ScientificWorldJournal (2012) 0.99
Poly-silicon nanowire field-effect transistor for ultrasensitive and label-free detection of pathogenic avian influenza DNA. Biosens Bioelectron (2009) 0.99
PEAT: an intelligent and efficient paired-end sequencing adapter trimming algorithm. BMC Bioinformatics (2015) 0.99
Protein metal binding residue prediction based on neural networks. Int J Neural Syst (2005) 0.97
Usage of case-based reasoning, neural network and adaptive neuro-fuzzy inference system classification techniques in breast cancer dataset classification diagnosis. J Med Syst (2010) 0.97
Secreted stress-induced phosphoprotein 1 activates the ALK2-SMAD signaling pathways and promotes cell proliferation of ovarian cancer cells. Cell Rep (2012) 0.97
Hdac6 regulates Tip60-p400 function in stem cells. Elife (2013) 0.96
A computational approach for identifying microRNA-target interactions using high-throughput CLIP and PAR-CLIP sequencing. BMC Genomics (2013) 0.96
Ultrasensitive detection of dopamine using a polysilicon nanowire field-effect transistor. Chem Commun (Camb) (2008) 0.96
Molecular signature of clinical severity in recovering patients with severe acute respiratory syndrome coronavirus (SARS-CoV). BMC Genomics (2005) 0.95
Prenatally diagnosed balanced chromosome rearrangements: eight years' experience. J Reprod Med (2006) 0.95
Global analyses of small interfering RNAs derived from Bamboo mosaic virus and its associated satellite RNAs in different plants. PLoS One (2010) 0.94
FMM: a web server for metabolic pathway reconstruction and comparative analysis. Nucleic Acids Res (2009) 0.94
RNAMST: efficient and flexible approach for identifying RNA structural homologs. Nucleic Acids Res (2006) 0.93
Transcribed pseudogene ψPPM1K generates endogenous siRNA to suppress oncogenic cell growth in hepatocellular carcinoma. Nucleic Acids Res (2013) 0.92
A novel role of CPEB3 in regulating EGFR gene transcription via association with Stat5b in neurons. Nucleic Acids Res (2010) 0.92
Hysteroscopic management of cesarean scar pregnancy after unsuccessful methotrexate treatment. J Minim Invasive Gynecol (2005) 0.92
A comprehensive resource for integrating and displaying protein post-translational modifications. BMC Res Notes (2009) 0.91
The concentration of inhibin B in follicular fluid: relation to oocyte maturation and embryo development. Hum Reprod (2002) 0.90
RegPhos 2.0: an updated resource to explore protein kinase-substrate phosphorylation networks in mammals. Database (Oxford) (2014) 0.90
CRP represses the CRISPR/Cas system in Escherichia coli: evidence that endogenous CRISPR spacers impede phage P1 replication. Mol Microbiol (2014) 0.90
Change in amniotic fluid levels of multiple anti-angiogenic proteins before development of preeclampsia and intrauterine growth restriction. J Clin Endocrinol Metab (2010) 0.89
MicroRNA and messenger RNA analyses of mesenchymal stem cells derived from teeth and the Wharton jelly of umbilical cord. Stem Cells Dev (2011) 0.89
Identifying the combination of genetic factors that determine susceptibility to cervical cancer. IEEE Trans Inf Technol Biomed (2004) 0.89
N-Ace: using solvent accessibility and physicochemical properties to identify protein N-acetylation sites. J Comput Chem (2010) 0.88
Sulphonation of dehydroepiandrosterone and neurosteroids: molecular cloning, expression, and functional characterization of a novel zebrafish SULT2 cytosolic sulphotransferase. Biochem J (2003) 0.88
Label-free biosensing of a gene mutation using a silicon nanowire field-effect transistor. Biosens Bioelectron (2009) 0.88
Intra- and inter-individual variance of gene expression in clinical studies. PLoS One (2012) 0.88
Meconium peritonitis in utero---the value of prenatal diagnosis in determining neonatal outcome. Taiwan J Obstet Gynecol (2008) 0.88
Tumor stress-induced phosphoprotein1 (STIP1) as a prognostic biomarker in ovarian cancer. PLoS One (2013) 0.87
Analyses of placental gene expression in pregnancy-related hypertensive disorders. Taiwan J Obstet Gynecol (2011) 0.87
Identification of differential gene expression between intestinal and diffuse gastric cancer using cDNA microarray. Oncol Rep (2006) 0.87
Modeling neurogenesis impairment in Down syndrome with induced pluripotent stem cells from Trisomy 21 amniotic fluid cells. Exp Cell Res (2012) 0.87
Analysis of functional groups of differentially expressed genes in the peripheral blood of patients with cervical cancer undergoing concurrent chemoradiation treatment. Radiat Res (2008) 0.87
Characterization of a de novo unbalanced Y;autosome translocation in a 45,X mentally retarded male and literature review. Fertil Steril (2008) 0.87
The activation of directional stem cell motility by green light-emitting diode irradiation. Biomaterials (2012) 0.87