Diet posttranslationally modifies the mouse gut microbial proteome to modulate renal function

Clostridium difficile Modulates the Gut Microbiota by Inducing the Production of Indole, an Interkingdom Signaling and Antimicrobial Molecule

(2019) Charles Darkoh et al.   mSystems

Chronic Kidney Disease Diagnosis and Management

(2019) Teresa K. Chen et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Dietary methionine restriction modulates renal response and attenuates kidney injury in mice

(2018) Diana Cooke et al.   FASEB JOURNAL

SearchGUI: A Highly Adaptable Common Interface for Proteomics Search and de Novo Engines

(2018) Harald Barsnes et al.   JOURNAL OF PROTEOME RESEARCH

Impacts of Indoxyl Sulfate and p-Cresol Sulfate on Chronic Kidney Disease and Mitigating Effects of AST-120

(2018) Wen-Chih Liu et al.   Toxins

Species-level functional profiling of metagenomes and metatranscriptomes

(2018) Eric A. Franzosa et al.   NATURE METHODS

Diet, gut microbiome and indoxyl sulphate in chronic kidney disease patients

(2018) Chih-Yu Yang et al.   NEPHROLOGY

A real-time PCR assay for accurate quantification of the individual members of the Altered Schaedler Flora microbiota in gnotobiotic mice

(2017) João Carlos Gomes-Neto et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Microbiome Helper: a Custom and Streamlined Workflow for Microbiome Research

(2017) André M. Comeau et al.   mSystems

Impaired renal function and dysbiosis of gut microbiota contribute to increased trimethylamine-N-oxide in chronic kidney disease patients

(2017) Kai-Yu Xu et al.   Scientific Reports

Modulation of a Circulating Uremic Solute via Rational Genetic Manipulation of the Gut Microbiota

(2016) A. Sloan Devlin et al.   Cell Host & Microbe

Fast and Accurate Protein False Discovery Rates on Large-Scale Proteomics Data Sets with Percolator 3.0

(2016) Matthew The et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Transcription factor DecR (YbaO) controls detoxification of L-cysteine in Escherichia coli

(2016) Tomohiro Shimada et al.   MICROBIOLOGY-SGM

PyQuant: A Versatile Framework for Analysis of Quantitative Mass Spectrometry Data

(2016) Christopher J. Mitchell et al.   MOLECULAR & CELLULAR PROTEOMICS

OpenMS: a flexible open-source software platform for mass spectrometry data analysis

(2016) Hannes L Röst et al.   NATURE METHODS

Indoxyl Sulfate—Review of Toxicity and Therapeutic Strategies

(2016) Sheldon Leong et al.   Toxins

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

The Altered Schaedler Flora: Continued Applications of a Defined Murine Microbial Community

(2015) Meghan Wymore Brand et al.   ILAR JOURNAL

Transient Kinetic Analysis of Hydrogen Sulfide Oxidation Catalyzed by Human Sulfide Quinone Oxidoreductase

(2015) Tatiana V. Mishanina et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

PeptideShaker enables reanalysis of MS-derived proteomics data sets

(2015) Marc Vaudel et al.   NATURE BIOTECHNOLOGY

H 2 S: A Novel Gasotransmitter that Signals by Sulfhydration

(2015) Bindu D. Paul et al.   TRENDS IN BIOCHEMICAL SCIENCES

Fat, fibre and cancer risk in African Americans and rural Africans

(2015) Stephen J. D. O’Keefe et al.   Nature Communications

Quantitative H2S-mediated protein sulfhydration reveals metabolic reprogramming during the integrated stress response

(2015) Xing-Huang Gao et al.   eLife

Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys

(2015) William Walters et al.   mSystems

The Influence of Dietary Protein Intake on Mammalian Tryptophan and Phenolic Metabolites

(2015) Ruben Poesen et al.   PLoS One

MultiNotch MS3 Enables Accurate, Sensitive, and Multiplexed Detection of Differential Expression across Cancer Cell Line Proteomes

(2014) Graeme C. McAlister et al.   ANALYTICAL CHEMISTRY

STAMP: statistical analysis of taxonomic and functional profiles

(2014) Donovan H. Parks et al.   BIOINFORMATICS

Cystathionine γ-lyase deficiency mediates neurodegeneration in Huntington’s disease

(2014) Bindu D. Paul et al.   NATURE

MS-GF+ makes progress towards a universal database search tool for proteomics

(2014) Sangtae Kim et al.   Nature Communications

The Impact of Diet and Lifestyle on Gut Microbiota and Human Health

(2014) Michael Conlon et al.   Nutrients

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

Tryptophan Catabolites from Microbiota Engage Aryl Hydrocarbon Receptor and Balance Mucosal Reactivity via Interleukin-22

(2013) Teresa Zelante et al.   IMMUNITY

iFASP: Combining Isobaric Mass Tagging with Filter-Aided Sample Preparation

(2013) Gary S. McDowell et al.   JOURNAL OF PROTEOME RESEARCH

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

A novel model of adenine-induced tubulointerstitial nephropathy in mice

(2013) Ting Jia et al.   BMC Nephrology

SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data

(2012) Evguenia Kopylova et al.   BIOINFORMATICS

Chronic kidney disease alters intestinal microbial flora

(2012) Nosratola D. Vaziri et al.   KIDNEY INTERNATIONAL

A cross-platform toolkit for mass spectrometry and proteomics

(2012) Matthew C Chambers et al.   NATURE BIOTECHNOLOGY

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

(2012) Xochitl C Morgan et al.   GENOME BIOLOGY

Dietary cystine level affects metabolic rate and glycaemic control in adult mice

(2011) Amany K. Elshorbagy et al.   JOURNAL OF NUTRITIONAL BIOCHEMISTRY

H2S: A Universal Defense Against Antibiotics in Bacteria

(2011) K. Shatalin et al.   SCIENCE

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

Evaluation of extraction processes for intracellular metabolite profiling of mammalian cells: matching extraction approaches to cell type and metabolite targets

(2010) Christopher A. Sellick et al.   Metabolomics

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

H2S Signals Through Protein S-Sulfhydration

(2009) A. K. Mustafa et al.   Science Signaling