Published in Mol Endocrinol on August 17, 2012
Guidelines for the design, analysis and interpretation of 'omics' data: focus on human endometrium. Hum Reprod Update (2013) 0.89
The proteomics big challenge for biomarkers and new drug-targets discovery. Int J Mol Sci (2012) 0.79
Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science (1995) 88.48
An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J Am Soc Mass Spectrom (1994) 45.51
Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis (1999) 45.01
The Pfam protein families database. Nucleic Acids Res (2011) 33.46
Mass spectrometry-based proteomics. Nature (2003) 28.94
Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res (2011) 18.50
TANDEM: matching proteins with tandem mass spectra. Bioinformatics (2004) 17.41
Electrospray ionization for mass spectrometry of large biomolecules. Science (1989) 16.50
Open mass spectrometry search algorithm. J Proteome Res (2004) 15.25
InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res (2011) 13.45
A common open representation of mass spectrometry data and its application to proteomics research. Nat Biotechnol (2004) 11.42
Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles. Neoplasia (2007) 10.74
The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol (2007) 10.24
A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Mol Syst Biol (2005) 9.81
The BioGRID Interaction Database: 2011 update. Nucleic Acids Res (2010) 8.46
The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol (2007) 8.24
Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biol (2007) 8.03
Shotgun sequence assembly and recent segmental duplications within the human genome. Nature (2004) 7.91
Reverse phase protein array: validation of a novel proteomic technology and utility for analysis of primary leukemia specimens and hematopoietic stem cells. Mol Cancer Ther (2006) 7.73
PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows. EMBO Rep (2008) 6.10
Mass spectrometry-based metabolomics. Mass Spectrom Rev (2006) 5.23
Petabyte-scale innovations at the European Nucleotide Archive. Nucleic Acids Res (2008) 5.21
Analysis and validation of proteomic data generated by tandem mass spectrometry. Nat Methods (2007) 5.10
A guided tour of the Trans-Proteomic Pipeline. Proteomics (2010) 5.09
Current two-dimensional electrophoresis technology for proteomics. Proteomics (2004) 4.87
mzML--a community standard for mass spectrometry data. Mol Cell Proteomics (2010) 4.81
CORUM: the comprehensive resource of mammalian protein complexes--2009. Nucleic Acids Res (2009) 4.71
TOPP--the OpenMS proteomics pipeline. Bioinformatics (2007) 4.37
The need for guidelines in publication of peptide and protein identification data: Working Group on Publication Guidelines for Peptide and Protein Identification Data. Mol Cell Proteomics (2004) 4.15
The proteomics standards initiative. Proteomics (2003) 3.78
Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: the Amsterdam principles. J Proteome Res (2009) 3.77
Development and validation of a spectral library searching method for peptide identification from MS/MS. Proteomics (2007) 3.74
The model organism as a system: integrating 'omics' data sets. Nat Rev Mol Cell Biol (2006) 3.69
Proteomic profiling of the NCI-60 cancer cell lines using new high-density reverse-phase lysate microarrays. Proc Natl Acad Sci U S A (2003) 3.66
Ligand induction of a transcriptionally active thyroid hormone receptor coactivator complex. Proc Natl Acad Sci U S A (1996) 3.61
Guidelines for the next 10 years of proteomics. Proteomics (2006) 3.61
Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions. Genome Biol (2001) 3.58
A novel experimental design for comparative two-dimensional gel analysis: two-dimensional difference gel electrophoresis incorporating a pooled internal standard. Proteomics (2003) 3.57
Reporting protein identification data: the next generation of guidelines. Mol Cell Proteomics (2006) 3.50
Self-assembling protein microarrays. Science (2004) 3.37
Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. Nat Methods (2012) 3.17
ProbID: a probabilistic algorithm to identify peptides through sequence database searching using tandem mass spectral data. Proteomics (2002) 3.01
Analysis of the human endogenous coregulator complexome. Cell (2011) 2.97
Aptamers as therapeutic and diagnostic agents. J Biotechnol (2000) 2.89
Submit your interaction data the IMEx way: a step by step guide to trouble-free deposition. Proteomics (2007) 2.74
The development of the DIGE system: 2D fluorescence difference gel analysis technology. Anal Bioanal Chem (2005) 2.64
A novel protein complex that interacts with the vitamin D3 receptor in a ligand-dependent manner and enhances VDR transactivation in a cell-free system. Genes Dev (1998) 2.63
A perspective on the use of iTRAQ reagent technology for protein complex and profiling studies. J Exp Bot (2006) 2.50
Human Protein Reference Database and Human Proteinpedia as discovery tools for systems biology. Methods Mol Biol (2009) 2.47
Next-generation high-density self-assembling functional protein arrays. Nat Methods (2008) 2.46
Statistical and computational methods for comparative proteomic profiling using liquid chromatography-tandem mass spectrometry. Mol Cell Proteomics (2005) 2.24
Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics. Physiol Genomics (2008) 2.23
Historical review: a brief history and personal retrospective of seven-transmembrane receptors. Trends Pharmacol Sci (2004) 2.22
Regulation of gene expression by a metabolic enzyme. Science (2004) 2.15
Dissection of the insulin signaling pathway via quantitative phosphoproteomics. Proc Natl Acad Sci U S A (2008) 2.11
Statistical design of quantitative mass spectrometry-based proteomic experiments. J Proteome Res (2009) 2.02
Stable isotope labeling by amino acids in cell culture for quantitative proteomics. Methods Mol Biol (2007) 1.96
LabKey Server: an open source platform for scientific data integration, analysis and collaboration. BMC Bioinformatics (2011) 1.94
Quantitative proteomics reveals posttranslational control as a regulatory factor in primary hematopoietic stem cells. Blood (2006) 1.92
High-throughput microarray-based enzyme-linked immunosorbent assay (ELISA). Biotechniques (1999) 1.80
Dopamine activation of an orphan of the steroid receptor superfamily. Science (1991) 1.78
neXtProt: a knowledge platform for human proteins. Nucleic Acids Res (2011) 1.77
Phosphoproteomics reveals new ERK MAP kinase targets and links ERK to nucleoporin-mediated nuclear transport. Nat Struct Mol Biol (2009) 1.64
Proteomic identification and functional validation of activins and bone morphogenetic protein 11 as candidate novel muscle mass regulators. Mol Endocrinol (2008) 1.59
Protein identification in the post-genome era: the rapid rise of proteomics. Q Rev Biophys (1997) 1.55
CPFP: a central proteomics facilities pipeline. Bioinformatics (2010) 1.53
Much room for improvement in deposition rates of expression microarray datasets. Nat Methods (2008) 1.51
Array-based ELISAs for high-throughput analysis of human cytokines. Biotechniques (2001) 1.48
Utility of reverse phase protein arrays: applications to signalling pathways and human body arrays. Brief Funct Genomic Proteomic (2002) 1.42
Profiling of cancer cells using protein microarrays: discovery of novel radiation-regulated proteins. Cancer Res (2001) 1.39
Printing protein arrays from DNA arrays. Nat Methods (2008) 1.39
Estradiol in vivo regulation of brain mitochondrial proteome. J Neurosci (2007) 1.36
Large-scale phosphosite quantification in tissues by a spike-in SILAC method. Nat Methods (2011) 1.34
Literature curation of protein interactions: measuring agreement across major public databases. Database (Oxford) (2010) 1.33
Quantitative phosphoproteomic analysis reveals cAMP/vasopressin-dependent signaling pathways in native renal thick ascending limb cells. Proc Natl Acad Sci U S A (2010) 1.33
Identification of coexpressed gene clusters in a comparative analysis of transcriptome and proteome in mouse tissues. Proc Natl Acad Sci U S A (2005) 1.28
Tranche distributed repository and ProteomeCommons.org. Methods Mol Biol (2011) 1.25
Two-dimensional difference gel electrophoresis. Nat Protoc (2006) 1.24
Single step generation of protein arrays from DNA by cell-free expression and in situ immobilisation (PISA method). Nucleic Acids Res (2001) 1.17
Phosphoproteomic profiling reveals vasopressin-regulated phosphorylation sites in collecting duct. J Am Soc Nephrol (2010) 1.13
Systematic mapping of posttranslational modifications in human estrogen receptor-alpha with emphasis on novel phosphorylation sites. Mol Cell Proteomics (2008) 1.11
Supporting tool suite for production proteomics. Bioinformatics (2011) 1.08
In vitro selection of nucleoprotein enzymes. Nat Biotechnol (2001) 1.05
The HUPO proteomics standards initiative--easing communication and minimizing data loss in a changing world. Brief Bioinform (2007) 1.04
PMAP: databases for analyzing proteolytic events and pathways. Nucleic Acids Res (2008) 1.03
Exon level integration of proteomics and microarray data. BMC Bioinformatics (2008) 1.03
Protein markers for insulin-producing beta cells with higher glucose sensitivity. PLoS One (2010) 0.99
Transcriptomine, a web resource for nuclear receptor signaling transcriptomes. Physiol Genomics (2012) 0.99
High-performance peptide identification by tandem mass spectrometry allows reliable automatic data processing in proteomics. Proteomics (2004) 0.98
Getting started in computational mass spectrometry-based proteomics. PLoS Comput Biol (2009) 0.98
Integrated quantitative analysis of the phosphoproteome and transcriptome in tamoxifen-resistant breast cancer. J Biol Chem (2010) 0.98
Quantitative analysis of mTRAQ-labeled proteome using full MS scans. J Proteome Res (2010) 0.96
Protein pathway activation mapping of brain metastasis from lung and breast cancers reveals organ type specific drug target activation. J Proteome Res (2011) 0.94
Hormonal regulation and identification of chicken progesterone receptor phosphorylation sites. J Biol Chem (1990) 0.93
Proteomic analysis of pathways involved in estrogen-induced growth and apoptosis of breast cancer cells. PLoS One (2011) 0.93
Identification of proteins associated with ligand-activated estrogen receptor α in human breast cancer cell nuclei by tandem affinity purification and nano LC-MS/MS. Proteomics (2010) 0.92
Exploring salivary proteomes in edentulous patients with type 2 diabetes. Mol Biosyst (2012) 0.92
Protein microarray on-demand: a novel protein microarray system. PLoS One (2008) 0.91
Much room for improvement in deposition rates of expression microarray datasets. Nat Methods (2008) 1.51
Feed-forward inhibition of androgen receptor activity by glucocorticoid action in human adipocytes. Chem Biol (2012) 1.47
GEMS (Gene Expression MetaSignatures), a Web resource for querying meta-analysis of expression microarray datasets: 17beta-estradiol in MCF-7 cells. Cancer Res (2009) 1.44
Re-expression of GATA2 cooperates with peroxisome proliferator-activated receptor-gamma depletion to revert the adipocyte phenotype. J Biol Chem (2009) 1.24
Combined deletion of Fxr and Shp in mice induces Cyp17a1 and results in juvenile onset cholestasis. J Clin Invest (2010) 1.17
Nuclear Receptor Signaling Atlas (www.nursa.org): hyperlinking the nuclear receptor signaling community. Nucleic Acids Res (2006) 1.07
Transcriptomine, a web resource for nuclear receptor signaling transcriptomes. Physiol Genomics (2012) 0.99
Hierarchical affinities and a bipartite interaction model for estrogen receptor isoforms and full-length steroid receptor coactivator (SRC/p160) family members. J Biol Chem (2003) 0.91
Coactivators and corepressors: what's in a name? Mol Endocrinol (2008) 0.88
Activation of NF-κB protein prevents the transition from juvenile ovary to testis and promotes ovarian development in zebrafish. J Biol Chem (2012) 0.81
Research resource: Tissue-specific transcriptomics and cistromics of nuclear receptor signaling: a web research resource. Mol Endocrinol (2010) 0.78
Androgen receptor agonism promotes an osteogenic gene program in preadipocytes. Biochem Biophys Res Commun (2013) 0.76
Signals from NURSA. Mol Endocrinol (2009) 0.75
Molecular endocrinology: A portal for enhanced access and utility of the nuclear receptor signaling atlas (NURSA) web resource. Mol Endocrinol (2009) 0.75