Published in Mol Cell Proteomics on August 27, 2013
Quantitative Imaging of Gut Microbiota Spatial Organization. Cell Host Microbe (2015) 1.84
Role of disease-associated tolerance in infectious superspreaders. Proc Natl Acad Sci U S A (2014) 1.56
Inflammatory bowel disease as a model for translating the microbiome. Immunity (2014) 1.39
Gut microbiota, metabolites and host immunity. Nat Rev Immunol (2016) 1.22
Microgeographic Proteomic Networks of the Human Colonic Mucosa and Their Association With Inflammatory Bowel Disease. Cell Mol Gastroenterol Hepatol (2016) 0.86
The Enteric Two-Step: nutritional strategies of bacterial pathogens within the gut. Cell Microbiol (2014) 0.85
Monitoring host responses to the gut microbiota. ISME J (2015) 0.84
The effect of microbial colonization on the host proteome varies by gastrointestinal location. ISME J (2015) 0.79
Host-Microbiota Interactions in the Pathogenesis of Antibiotic-Associated Diseases. Cell Rep (2016) 0.79
A metaproteomics approach to elucidate host and pathogen protein expression during catheter-associated urinary tract infections (CAUTIs). Mol Cell Proteomics (2015) 0.79
Metaproteomics reveals functional shifts in microbial and human proteins during a preterm infant gut colonization case. Proteomics (2015) 0.76
Development of an Integrated Pipeline for Profiling Microbial Proteins from Mouse Fecal Samples by LC-MS/MS. J Proteome Res (2016) 0.75
Elevated fecal peptidase D at onset of colitis in Galphai2-/- mice, a mouse model of IBD. PLoS One (2017) 0.75
Metaproteomics as a Complementary Approach to Gut Microbiota in Health and Disease. Front Chem (2017) 0.75
The effect of microbial challenge on the intestinal proteome of broiler chickens. Proteome Sci (2017) 0.75
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc (2009) 137.99
Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res (2008) 54.83
Diversity of the human intestinal microbial flora. Science (2005) 49.64
Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis (1999) 45.01
Microbial ecology: human gut microbes associated with obesity. Nature (2006) 36.98
Metagenomic analysis of the human distal gut microbiome. Science (2006) 29.76
Host-bacterial mutualism in the human intestine. Science (2005) 26.39
Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat Methods (2007) 25.29
Bacterial community variation in human body habitats across space and time. Science (2009) 24.84
Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics (2004) 19.05
Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res (2011) 18.50
The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med (2009) 16.02
The gut microbiota shapes intestinal immune responses during health and disease. Nat Rev Immunol (2009) 13.87
The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res (2012) 13.14
Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations. Nat Methods (2005) 6.73
Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal Chem (2003) 6.63
Gnotobiotic zebrafish reveal evolutionarily conserved responses to the gut microbiota. Proc Natl Acad Sci U S A (2004) 5.16
Trypsin cleaves exclusively C-terminal to arginine and lysine residues. Mol Cell Proteomics (2004) 4.79
Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla. Proc Natl Acad Sci U S A (2009) 4.09
Specificity of polysaccharide use in intestinal bacteroides species determines diet-induced microbiota alterations. Cell (2010) 3.70
Diet, gut microbiota and immune responses. Nat Immunol (2011) 3.66
Reversible microbial colonization of germ-free mice reveals the dynamics of IgA immune responses. Science (2010) 3.53
Shotgun metaproteomics of the human distal gut microbiota. ISME J (2008) 3.43
The human antimicrobial and chemotactic peptides LL-37 and alpha-defensins are expressed by specific lymphocyte and monocyte populations. Blood (2000) 3.09
Improving reproducibility and sensitivity in identifying human proteins by shotgun proteomics. Anal Chem (2004) 2.53
Laser capture microdissection of mouse intestine: characterizing mRNA and protein expression, and profiling intermediary metabolism in specified cell populations. Methods Enzymol (2002) 2.17
Microbiota restoration: natural and supplemented recovery of human microbial communities. Nat Rev Microbiol (2010) 1.89
Complex interactions among diet, gastrointestinal transit, and gut microbiota in humanized mice. Gastroenterology (2013) 1.86
Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn's disease. PLoS One (2012) 1.84
Effective recovery of bacterial DNA and percent-guanine-plus-cytosine-based analysis of community structure in the gastrointestinal tract of broiler chickens. Appl Environ Microbiol (1998) 1.56
IMG/M-HMP: a metagenome comparative analysis system for the Human Microbiome Project. PLoS One (2012) 1.20
Community dynamics in the mouse gut microbiota: a possible role for IRF9-regulated genes in community homeostasis. PLoS One (2010) 0.92
Effect of column degradation on the reversed-phase high-performance liquid chromatographic separation of peptides and proteins. J Chromatogr (1987) 0.91
Host-bacterial mutualism in the human intestine. Science (2005) 26.39
Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome. J Proteome Res (2003) 11.96
Large-scale characterization of HeLa cell nuclear phosphoproteins. Proc Natl Acad Sci U S A (2004) 10.78
A proteomics approach to understanding protein ubiquitination. Nat Biotechnol (2003) 10.51
A tissue-specific atlas of mouse protein phosphorylation and expression. Cell (2010) 8.65
Microbiota-liberated host sugars facilitate post-antibiotic expansion of enteric pathogens. Nature (2013) 4.43
Optimization and use of peptide mass measurement accuracy in shotgun proteomics. Mol Cell Proteomics (2006) 4.25
Specificity of polysaccharide use in intestinal bacteroides species determines diet-induced microbiota alterations. Cell (2010) 3.70
Intensity-based protein identification by machine learning from a library of tandem mass spectra. Nat Biotechnol (2004) 3.30
Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae. J Proteome Res (2007) 3.13
A function for cyclin D1 in DNA repair uncovered by protein interactome analyses in human cancers. Nature (2011) 2.82
BRCA1-dependent ubiquitination of gamma-tubulin regulates centrosome number. Mol Cell Biol (2004) 2.46
The phosphoproteomes of Plasmodium falciparum and Toxoplasma gondii reveal unusual adaptations within and beyond the parasites' boundaries. Cell Host Microbe (2011) 2.25
Transcriptional role of cyclin D1 in development revealed by a genetic-proteomic screen. Nature (2010) 2.20
The impact of peptide abundance and dynamic range on stable-isotope-based quantitative proteomic analyses. J Proteome Res (2008) 2.11
Eating for two: how metabolism establishes interspecies interactions in the gut. Cell Host Microbe (2011) 2.06
A hybrid two-component system protein of a prominent human gut symbiont couples glycan sensing in vivo to carbohydrate metabolism. Proc Natl Acad Sci U S A (2006) 1.90
Complex interactions among diet, gastrointestinal transit, and gut microbiota in humanized mice. Gastroenterology (2013) 1.86
Enhanced analysis of metastatic prostate cancer using stable isotopes and high mass accuracy instrumentation. J Proteome Res (2006) 1.82
Bacteroides in the infant gut consume milk oligosaccharides via mucus-utilization pathways. Cell Host Microbe (2011) 1.77
Genetically dictated change in host mucus carbohydrate landscape exerts a diet-dependent effect on the gut microbiota. Proc Natl Acad Sci U S A (2013) 1.69
The Parkinson's disease-associated DJ-1 protein is a transcriptional co-activator that protects against neuronal apoptosis. Hum Mol Genet (2005) 1.66
Identification of beta-secretase (BACE1) substrates using quantitative proteomics. PLoS One (2009) 1.52
Characterization of mouse spleen cells by subtractive proteomics. Mol Cell Proteomics (2005) 1.51
Proteomic profiling of gamma-secretase substrates and mapping of substrate requirements. PLoS Biol (2008) 1.45
Production of α-galactosylceramide by a prominent member of the human gut microbiota. PLoS Biol (2013) 1.42
Integrative analysis of the microbiome and metabolome of the human intestinal mucosal surface reveals exquisite inter-relationships. Microbiome (2013) 1.32
Functional genomic studies of the intestinal response to a foodborne enteropathogen in a humanized gnotobiotic mouse model. J Biol Chem (2007) 1.25
The dynamic state of protein turnover: It's about time. Trends Cell Biol (2011) 1.24
Development of a multilocus sequence typing method for analysis of Lactobacillus plantarum strains. Microbiology (2006) 1.22
A randomized placebo-controlled comparison of 2 prebiotic/probiotic combinations in preterm infants: impact on weight gain, intestinal microbiota, and fecal short-chain fatty acids. J Pediatr Gastroenterol Nutr (2009) 1.20
Tannase activity by lactic acid bacteria isolated from grape must and wine. Int J Food Microbiol (2004) 1.16
Lifestyle of Lactobacillus plantarum in the mouse caecum. Environ Microbiol (2009) 1.15
Effects of sialic acid substitutions on recognition by Sambucus nigra agglutinin and Maackia amurensis hemagglutinin. Anal Biochem (2002) 1.14
Allelic diversity and population structure in Oenococcus oeni as determined from sequence analysis of housekeeping genes. Appl Environ Microbiol (2004) 1.13
A refined palate: bacterial consumption of host glycans in the gut. Glycobiology (2013) 1.11
Prognostic significance of von willebrand factor in cirrhosis: a possible mechanism. Hepatology (2013) 1.09
Prioritization of a plant polysaccharide over a mucus carbohydrate is enforced by a Bacteroides hybrid two-component system. Mol Microbiol (2012) 1.02
Rapid evolution of binding specificities and expression patterns of inhibitory CD33-related Siglecs in primates. FASEB J (2013) 1.01
Assessing enzyme activities using stable isotope labeling and mass spectrometry. Mol Cell Proteomics (2007) 0.98
Catch-and-release reagents for broadscale quantitative proteomics analyses. J Proteome Res (2007) 0.98
Molecular analysis of model gut microbiotas by imaging mass spectrometry and nanodesorption electrospray ionization reveals dietary metabolite transformations. Anal Chem (2012) 0.97
SILVER helps assign peptides to tandem mass spectra using intensity-based scoring. J Am Soc Mass Spectrom (2004) 0.92
Genetic dissection of Flaviviridae host factors through genome-scale CRISPR screens. Nature (2016) 0.92
Assessing subunit dependency of the Plasmodium proteasome using small molecule inhibitors and active site probes. ACS Chem Biol (2014) 0.90
Updated molecular knowledge about histamine biosynthesis by bacteria. Crit Rev Food Sci Nutr (2008) 0.90
Mechanistic insight into polysaccharide use within the intestinal microbiota. Gut Microbes (2011) 0.88
The role of students as teachers: four years' experience of a large-scale, peer-led programme. Med Teach (2010) 0.88
The intestinal microbiota and viral susceptibility. Front Microbiol (2011) 0.88
Molecular methods for the detection of biogenic amine-producing bacteria on foods. Int J Food Microbiol (2007) 0.86
The Enteric Two-Step: nutritional strategies of bacterial pathogens within the gut. Cell Microbiol (2014) 0.85
Microbiology: Genetic pot luck. Nature (2010) 0.83
Synthetic small interfering RNA down-regulates caspase-3 and affects apoptosis, IL-1 β, and viability of porcine proximal tubular cells. J Cell Biochem (2011) 0.82
PCR detection of foodborne bacteria producing the biogenic amines histamine, tyramine, putrescine, and cadaverine. J Food Prot (2006) 0.79
The cyclin D1-CDK4 oncogenic interactome enables identification of potential novel oncogenes and clinical prognosis. Cell Cycle (2014) 0.79
Improved multiplex-PCR method for the simultaneous detection of food bacteria producing biogenic amines. FEMS Microbiol Lett (2005) 0.78