Enrichment and identification of small proteins in a simplified human gut microbiome.

[1]  S. Müller,et al.  The Simplified Human Intestinal Microbiota (SIHUMIx) Shows High Structural and Functional Resistance against Changing Transit Times in In Vitro Bioreactors , 2019, Microorganisms.

[2]  S. Fuchs,et al.  Challenges and promise at the interface of metaproteomics and genomics: an overview of recent progress in metaproteogenomic data analysis , 2019, Expert review of proteomics.

[3]  Bonnie L Bassler,et al.  Bacterial quorum sensing in complex and dynamically changing environments , 2019, Nature Reviews Microbiology.

[4]  Philipp T Kaulich,et al.  Depletion of High-Molecular-Mass Proteins for the Identification of Small Proteins and Short Open Reading Frame Encoded Peptides in Cellular Proteomes. , 2019, Journal of proteome research.

[5]  N. Jehmlich,et al.  Disease Development Is Accompanied by Changes in Bacterial Protein Abundance and Functions in a Refined Model of Dextran Sulfate Sodium (DSS)-Induced Colitis. , 2019, Journal of proteome research.

[6]  Robert D. Finn,et al.  A new genomic blueprint of the human gut microbiota , 2019, Nature.

[7]  Georgios A. Pavlopoulos,et al.  Large-Scale Analyses of Human Microbiomes Reveal Thousands of Small, Novel Genes , 2019, Cell.

[8]  Martin Eisenacher,et al.  The PRIDE database and related tools and resources in 2019: improving support for quantification data , 2018, Nucleic Acids Res..

[9]  Christopher S. Hughes,et al.  Single-pot, solid-phase-enhanced sample preparation for proteomics experiments , 2018, Nature Protocols.

[10]  E. Allen-Vercoe,et al.  Using bioreactors to study the effects of drugs on the human microbiota. , 2018, Methods.

[11]  Gerben Menschaert,et al.  An update on sORFs.org: a repository of small ORFs identified by ribosome profiling , 2017, Nucleic Acids Res..

[12]  J. Casadesús,et al.  Interactions between Bacteria and Bile Salts in the Gastrointestinal and Hepatobiliary Tracts , 2017, Front. Med..

[13]  N. Jehmlich,et al.  Differential sensitivity of total and active soil microbial communities to drought and forest management , 2017, Global change biology.

[14]  M. von Bergen,et al.  Interactions between bile salts, gut microbiota, and hepatic innate immunity , 2017, Immunological reviews.

[15]  Evgenia Shishkova,et al.  Now, More Than Ever, Proteomics Needs Better Chromatography. , 2016, Cell systems.

[16]  Liam Cassidy,et al.  Combination of Bottom-up 2D-LC-MS and Semi-top-down GelFree-LC-MS Enhances Coverage of Proteome and Low Molecular Weight Short Open Reading Frame Encoded Peptides of the Archaeon Methanosarcina mazei. , 2016, Journal of proteome research.

[17]  P. Straight,et al.  Bacterial Communities: Interactions to Scale , 2016, Front. Microbiol..

[18]  P. Straight,et al.  Multifaceted Interfaces of Bacterial Competition , 2016, Journal of bacteriology.

[19]  Manolis Kellis,et al.  Improved Identification and Analysis of Small Open Reading Frame Encoded Polypeptides. , 2016, Analytical chemistry.

[20]  Chongle Pan,et al.  Microbial metaproteomics for characterizing the range of metabolic functions and activities of human gut microbiota , 2015, Proteomics.

[21]  K. Kehn-Hall,et al.  The Use of Nanotrap Particles in the Enhanced Detection of Rift Valley Fever Virus Nucleoprotein , 2015, PloS one.

[22]  Y. Wolf,et al.  Small proteins can no longer be ignored. , 2014, Annual review of biochemistry.

[23]  Jingfa Xiao,et al.  Small proteins: untapped area of potential biological importance , 2013, Front. Genet..

[24]  P. Stadler,et al.  Identification of new protein coding sequences and signal peptidase cleavage sites of Helicobacter pylori strain 26695 by proteogenomics. , 2013, Journal of proteomics.

[25]  M. R. Hemm,et al.  The Escherichia coli CydX Protein Is a Member of the CydAB Cytochrome bd Oxidase Complex and Is Required for Cytochrome bd Oxidase Activity , 2013, Journal of bacteriology.

[26]  J. Yates,et al.  Protein analysis by shotgun/bottom-up proteomics. , 2013, Chemical reviews.

[27]  A. Kostic,et al.  Exploring host-microbiota interactions in animal models and humans. , 2013, Genes & development.

[28]  P. Turnbaugh,et al.  Xenobiotics Shape the Physiology and Gene Expression of the Active Human Gut Microbiome , 2013, Cell.

[29]  K. Jahreis,et al.  Characterization of the Interaction Between the Small Regulatory Peptide SgrT and the EIICBGlc of the Glucose-Phosphotransferase System of E. coli K-12 , 2012, Metabolites.

[30]  H. Flint,et al.  Role of the gut microbiota in nutrition and health , 2018, British Medical Journal.

[31]  G. Storz,et al.  Conserved small protein associates with the multidrug efflux pump AcrB and differentially affects antibiotic resistance , 2012, Proceedings of the National Academy of Sciences.

[32]  V. Tremaroli,et al.  Functional interactions between the gut microbiota and host metabolism , 2012, Nature.

[33]  Gerald A Tuskan,et al.  Discovery and annotation of small proteins using genomics, proteomics, and computational approaches. , 2011, Genome research.

[34]  A. Darzi,et al.  Gut microbiome-host interactions in health and disease , 2011, Genome Medicine.

[35]  Manolis Kellis,et al.  Optimization of parameters for coverage of low molecular weight proteins , 2010, Analytical and bioanalytical chemistry.

[36]  Ruedi Aebersold,et al.  The pros and cons of peptide-centric proteomics , 2010, Nature Biotechnology.

[37]  M. Metzker.  Sequencing technologies — the next generation , 2010, Nature Reviews Genetics.

[38]  M. Mann,et al.  Universal sample preparation method for proteome analysis , 2009, Nature Methods.

[39]  Ming Yi,et al.  bioDBnet: the biological database network , 2009, Bioinform..

[40]  William Stafford Noble,et al.  Semi-supervised learning for peptide identification from shotgun proteomics datasets , 2007, Nature Methods.

[41]  Ruedi Aebersold,et al.  The Implications of Proteolytic Background for Shotgun Proteomics*S , 2007, Molecular & Cellular Proteomics.

[42]  Michael K. Coleman,et al.  Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae. , 2006, Journal of proteome research.

[43]  H. Schägger.  Tricine–SDS-PAGE , 2006, Nature Protocols.

[44]  T. Macdonald,et al.  Immunity, Inflammation, and Allergy in the Gut , 2005, Science.

[45]  Jue Chen,et al.  ATP-binding cassette transporters in bacteria. , 2004, Annual review of biochemistry.

[46]  S. Gallagher,et al.  Staining Proteins in Gels , 2003, Current protocols in immunology.

[47]  M. Kanehisa,et al.  SSDB: Sequence Similarity Database in KEGG , 2001 .

[48]  K. Postle,et al.  TolC, a macromolecular periplasmic ‘chunnel’ , 2000, Nature Structural Biology.

[49]  Ann M Stock,et al.  Two-component signal transduction. , 2000, Annual review of biochemistry.

[50]  G. Montelione,et al.  RNA binding by the novel helical domain of the influenza virus NS1 protein requires its dimer structure and a small number of specific basic amino acids. , 1999, RNA.

[51]  C. Sensen,et al.  Complete DNA sequence of yeast chromosome XI , 1994, Nature.

[52]  H. Weintraub,et al.  The MyoD DNA binding domain contains a recognition code for muscle-specific gene activation , 1990, Cell.

[53]  J. Vaughan,et al.  [28] Assay of growth hormone-releasing factor , 1986 .

[54]  D. Wessel,et al.  A method for the quantitative recovery of protein in dilute solution in the presence of detergents and lipids. , 1984, Analytical biochemistry.

[55]  J. Vaughan,et al.  [38] Assay of corticotropin releasing factor , 1983 .

[56]  E. Stellwag,et al.  Purification and characterization of bile salt hydrolase from Bacteroides fragilis subsp. fragilis. , 1976, Biochimica et biophysica acta.