Metab2MeSH: annotating compounds with medical subject headings.

Data Mining Methods for Omics and Knowledge of Crude Medicinal Plants toward Big Data Biology. Comput Struct Biotechnol J (2013) 0.98

Recent progress in the development of metabolome databases for plant systems biology. Front Plant Sci (2013) 0.94

Metabolomics and diabetes: analytical and computational approaches. Diabetes (2015) 0.90

Network-based in silico drug efficacy screening. Nat Commun (2016) 0.87

MeSH ORA framework: R/Bioconductor packages to support MeSH over-representation analysis. BMC Bioinformatics (2015) 0.87

Metabolomics and Its Application to Acute Lung Diseases. Front Immunol (2016) 0.80

MetDisease--connecting metabolites to diseases via literature. Bioinformatics (2014) 0.76

MeSH Now: automatic MeSH indexing at PubMed scale via learning to rank. J Biomed Semantics (2017) 0.75

Aspergillus Secondary Metabolite Database, a resource to understand the Secondary metabolome of Aspergillus genus. Sci Rep (2017) 0.75

From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web-resources for mass spectral plant metabolomics. Gigascience (2017) 0.75

HMDB: a knowledgebase for the human metabolome. Nucleic Acids Res (2008) 11.23

PubChem: a public information system for analyzing bioactivities of small molecules. Nucleic Acids Res (2009) 11.05

ConceptGen: a gene set enrichment and gene set relation mapping tool. Bioinformatics (2009) 2.11

KNApSAcK family databases: integrated metabolite-plant species databases for multifaceted plant research. Plant Cell Physiol (2011) 1.82

A computational system to select candidate genes for complex human traits. Bioinformatics (2007) 1.60

Biomedical discovery acceleration, with applications to craniofacial development. PLoS Comput Biol (2009) 1.49

YMDB: the Yeast Metabolome Database. Nucleic Acids Res (2011) 1.48

TOXNET: an evolving web resource for toxicology and environmental health information. Toxicology (2001) 0.97

Defects in cAMP-pathway may initiate carcinogenesis in dividing nerve cells: a review. Apoptosis (2003) 0.95

Martini: using literature keywords to compare gene sets. Nucleic Acids Res (2009) 0.95

WENDI: A tool for finding non-obvious relationships between compounds and biological properties, genes, diseases and scholarly publications. J Cheminform (2010) 0.89

Ontology annotation treebrowser : an interactive tool where the complementarity of medical subject headings and gene ontology improves the interpretation of gene lists. Appl Bioinformatics (2006) 0.88

Compounds In Literature (CIL): screening for compounds and relatives in PubMed. Bioinformatics (2011) 0.87

Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data. Nucleic Acids Res (2005) 17.58

Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature (2009) 12.58

PRIDE: the proteomics identifications database. Proteomics (2005) 7.52

Computational Proteomics Analysis System (CPAS): an extensible, open-source analytic system for evaluating and publishing proteomic data and high throughput biological experiments. J Proteome Res (2006) 4.32

Human Proteinpedia enables sharing of human protein data. Nat Biotechnol (2008) 4.21

An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: sensitivity and specificity analysis. Proteomics (2005) 3.51

A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas. Mol Cell Proteomics (2011) 3.37

Selecting for functional alternative splices in ESTs. Genome Res (2002) 2.90

Medicine needs evolution. Science (2006) 2.83

Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together. Nucleic Acids Res (2006) 2.77

Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study. Nat Biotechnol (2006) 2.66

Differential protein expression profiling by iTRAQ-2DLC-MS/MS of lung cancer cells undergoing epithelial-mesenchymal transition reveals a migratory/invasive phenotype. J Proteome Res (2006) 2.43

The human proteome project: current state and future direction. Mol Cell Proteomics (2011) 2.34

The Beta-Carotene and Retinol Efficacy Trial: incidence of lung cancer and cardiovascular disease mortality during 6-year follow-up after stopping beta-carotene and retinol supplements. J Natl Cancer Inst (2004) 2.26

iTools: a framework for classification, categorization and integration of computational biology resources. PLoS One (2008) 2.18

The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome. Nat Biotechnol (2012) 2.14

ConceptGen: a gene set enrichment and gene set relation mapping tool. Bioinformatics (2009) 2.11

The Biomedical Resource Ontology (BRO) to enable resource discovery in clinical and translational research. J Biomed Inform (2010) 2.10

Michigan molecular interactions r2: from interacting proteins to pathways. Nucleic Acids Res (2008) 2.09

Characterization of KRAS rearrangements in metastatic prostate cancer. Cancer Discov (2011) 2.02

Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics. Genome Biol (2006) 1.98

A class of selective antibacterials derived from a protein kinase inhibitor pharmacophore. Proc Natl Acad Sci U S A (2009) 1.82

Metrics for the Human Proteome Project 2013-2014 and strategies for finding missing proteins. J Proteome Res (2013) 1.76

SNP Function Portal: a web database for exploring the function implication of SNP alleles. Bioinformatics (2006) 1.69

Metscape 2 bioinformatics tool for the analysis and visualization of metabolomics and gene expression data. Bioinformatics (2011) 1.69

Integrated expression profiling and ChIP-seq analyses of the growth inhibition response program of the androgen receptor. PLoS One (2009) 1.68

Meeting report: hazard assessment for nanoparticles--report from an interdisciplinary workshop. Environ Health Perspect (2007) 1.64

Metscape: a Cytoscape plug-in for visualizing and interpreting metabolomic data in the context of human metabolic networks. Bioinformatics (2010) 1.62

Intact-protein-based high-resolution three-dimensional quantitative analysis system for proteome profiling of biological fluids. Mol Cell Proteomics (2005) 1.59

Occurrence of autoantibodies to annexin I, 14-3-3 theta and LAMR1 in prediagnostic lung cancer sera. J Clin Oncol (2008) 1.55

State of the human proteome in 2013 as viewed through PeptideAtlas: comparing the kidney, urine, and plasma proteomes for the biology- and disease-driven Human Proteome Project. J Proteome Res (2013) 1.52

Systematic comparison of the human saliva and plasma proteomes. Proteomics Clin Appl (2009) 1.51

Fruits and vegetables are associated with lower lung cancer risk only in the placebo arm of the beta-carotene and retinol efficacy trial (CARET). Cancer Epidemiol Biomarkers Prev (2003) 1.51

An integrative approach to reveal driver gene fusions from paired-end sequencing data in cancer. Nat Biotechnol (2009) 1.47

Evolution in health and medicine Sackler colloquium: Making evolutionary biology a basic science for medicine. Proc Natl Acad Sci U S A (2009) 1.45

The gputools package enables GPU computing in R. Bioinformatics (2009) 1.44

Identification of novel alternative splice isoforms of circulating proteins in a mouse model of human pancreatic cancer. Cancer Res (2009) 1.40

Immunoassay and antibody microarray analysis of the HUPO Plasma Proteome Project reference specimens: systematic variation between sample types and calibration of mass spectrometry data. Proteomics (2005) 1.38

Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome Project. Proteomics (2005) 1.37

A first step toward completion of a genome-wide characterization of the human proteome. J Proteome Res (2012) 1.36

The biology/disease-driven human proteome project (B/D-HPP): enabling protein research for the life sciences community. J Proteome Res (2012) 1.35

Temporal quantitative proteomics by iTRAQ 2D-LC-MS/MS and corresponding mRNA expression analysis identify post-transcriptional modulation of actin-cytoskeleton regulators during TGF-beta-Induced epithelial-mesenchymal transition. J Proteome Res (2009) 1.29

Distinctive serum protein profiles involving abundant proteins in lung cancer patients based upon antibody microarray analysis. BMC Cancer (2005) 1.28

Deconvoluting the intestine: molecular evidence for a major role of the mesenchyme in the modulation of signaling cross talk. Physiol Genomics (2007) 1.27

Analysis of tumor-host interactions by gene expression profiling of lung adenocarcinoma xenografts identifies genes involved in tumor formation. Mol Cancer Res (2005) 1.27

The association between lung and prostate cancer risk, and serum micronutrients: results and lessons learned from beta-carotene and retinol efficacy trial. Cancer Epidemiol Biomarkers Prev (2003) 1.27

Proteomic characterization of novel alternative splice variant proteins in human epidermal growth factor receptor 2/neu-induced breast cancers. Cancer Res (2010) 1.25

Development and validation of sandwich ELISA microarrays with minimal assay interference. J Proteome Res (2008) 1.23

Ontology-based combinatorial comparative analysis of adverse events associated with killed and live influenza vaccines. PLoS One (2012) 1.21

Metabolic consequences of sepsis-induced acute lung injury revealed by plasma ¹H-nuclear magnetic resonance quantitative metabolomics and computational analysis. Am J Physiol Lung Cell Mol Physiol (2010) 1.21

Standard guidelines for the chromosome-centric human proteome project. J Proteome Res (2012) 1.20

Development of natural protein microarrays for diagnosing cancer based on an antibody response to tumor antigens. J Proteome Res (2004) 1.19

Do we want our data raw? Including binary mass spectrometry data in public proteomics data repositories. Proteomics (2005) 1.17

Functional implications of structural predictions for alternative splice proteins expressed in Her2/neu-induced breast cancers. J Proteome Res (2011) 1.16

A functional annotation of subproteomes in human plasma. Proteomics (2005) 1.15

New and improved proteomics technologies for understanding complex biological systems: addressing a grand challenge in the life sciences. Proteomics (2012) 1.14

Proteomic interrogation of androgen action in prostate cancer cells reveals roles of aminoacyl tRNA synthetases. PLoS One (2009) 1.14

A cheminformatic toolkit for mining biomedical knowledge. Pharm Res (2007) 1.13

Quantitative proteomic profiling of prostate cancer reveals a role for miR-128 in prostate cancer. Mol Cell Proteomics (2009) 1.13

Microarrays of tumor cell derived proteins uncover a distinct pattern of prostate cancer serum immunoreactivity. Proteomics (2003) 1.13

Coupled global and targeted proteomics of human embryonic stem cells during induced differentiation. Mol Cell Proteomics (2008) 1.11

Mucin glycosylation is altered by pro-inflammatory signaling in pancreatic-cancer cells. J Proteome Res (2009) 1.11

Quantitative organellar proteomics analysis of rough endoplasmic reticulum from normal and acute pancreatitis rat pancreas. J Proteome Res (2010) 1.11

SRM targeted proteomics in search for biomarkers of HCV-induced progression of fibrosis to cirrhosis in HALT-C patients. Proteomics (2012) 1.11

Identification of alternatively spliced transcripts using a proteomic informatics approach. Methods Mol Biol (2011) 1.10

The relative merits of population-based and targeted prevention strategies. Milbank Q (2008) 1.10

Current perspective on the global and United States cancer burden attributable to lifestyle and environmental risk factors. Annu Rev Public Health (2013) 1.10

"Topological significance" analysis of gene expression and proteomic profiles from prostate cancer cells reveals key mechanisms of androgen response. PLoS One (2010) 1.10

Humoral response profiling reveals pathways to prostate cancer progression. Mol Cell Proteomics (2007) 1.09

Profiling of pathway-specific changes in gene expression following growth of human cancer cell lines transplanted into mice. Genome Biol (2003) 1.08

A wide range of protein isoforms in serum and plasma uncovered by a quantitative intact protein analysis system. Proteomics (2005) 1.08

Physical activity in relation to all-site and lung cancer incidence and mortality in current and former smokers. Cancer Epidemiol Biomarkers Prev (2004) 1.06

Systematically differentiating functions for alternatively spliced isoforms through integrating RNA-seq data. PLoS Comput Biol (2013) 1.04

A chromosome-centric human proteome project (C-HPP) to characterize the sets of proteins encoded in chromosome 17. J Proteome Res (2012) 1.03

HIV infection reveals widespread expansion of novel centromeric human endogenous retroviruses. Genome Res (2013) 1.03

Exploring the human plasma proteome. Proteomics (2005) 1.00

Untargeted LC-MS metabolomics of bronchoalveolar lavage fluid differentiates acute respiratory distress syndrome from health. J Proteome Res (2013) 1.00

LRpath analysis reveals common pathways dysregulated via DNA methylation across cancer types. BMC Genomics (2012) 0.99

The human proteome - a scientific opportunity for transforming diagnostics, therapeutics, and healthcare. Clin Proteomics (2012) 0.98

A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data. BMC Bioinformatics (2008) 0.98

A dominant function of IKK/NF-kappaB signaling in global lipopolysaccharide-induced gene expression. J Biol Chem (2006) 0.97

Cross-domain neurobiology data integration and exploration. BMC Genomics (2010) 0.96

Proteomics approaches to identify tumor antigen directed autoantibodies as cancer biomarkers. Dis Markers (2004) 0.96

The human proteome project: Current state and future direction. Mol Cell Proteomics (2011) 0.96

A mouse plasma peptide atlas as a resource for disease proteomics. Genome Biol (2008) 0.96

Immunology and genetics of type 1 diabetes. Mt Sinai J Med (2008) 0.95

Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles). Mol Cell Proteomics (2011) 0.94

Epigenetics: relevance and implications for public health. Annu Rev Public Health (2014) 0.94

The NIH National Center for Integrative Biomedical Informatics (NCIBI). J Am Med Inform Assoc (2011) 0.94

Identifying inhibitors of epithelial-mesenchymal transition by connectivity map-based systems approach. J Thorac Oncol (2011) 0.93

Humoral autoimmunity against the extracellular domain of the neuroendocrine autoantigen IA-2 heightens the risk of type 1 diabetes. Endocrinology (2010) 0.92