Multi-omics analyses of the ulcerative colitis gut microbiome link Bacteroides vulgatus proteases with disease severity

Organ-level protein networks as a reference for the host effects of the microbiome

(2020) Robert H. Mills et al.   GENOME RESEARCH

Serine proteases at the cutting edge of IBD: Focus on gastrointestinal inflammation

(2020) Aicha Kriaa et al.   FASEB JOURNAL

Quantification of Cell-Substrate Adhesion Area and Cell Shape Distributions in MCF7 Cell Monolayers

(2020) Maciej Wakula et al.   Jove-Journal of Visualized Experiments

Novel fecal biomarkers that precede clinical diagnosis of ulcerative colitis.

(2020) Heather J. Galipeau et al.   GASTROENTEROLOGY

Chemically informed analyses of metabolomics mass spectrometry data with Qemistree

(2020) Anupriya Tripathi et al.   Nature Chemical Biology

Evaluating Metagenomic Prediction of the Metaproteome in a 4.5-Year Study of a Patient with Crohn's Disease

(2019) Robert H. Mills et al.   mSystems

Neutrophilic proteolysis in the cystic fibrosis lung correlates with a pathogenic microbiome

(2019) Robert A. Quinn et al.   Microbiome

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases

(2019) Jason Lloyd-Price et al.   NATURE

Associations of the fecal microbial proteome composition and proneness to diet-induced obesity

(2019) Hao Q. Tran et al.   MOLECULAR & CELLULAR PROTEOMICS

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

N-Terminomics/TAILS Profiling of Proteases and Their Substrates in Ulcerative Colitis

(2019) Marilyn H. Gordon et al.   ACS Chemical Biology

Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes

(2019) Marina García-López et al.   Frontiers in Microbiology

Alteration of Gut Microbiota in Inflammatory Bowel Disease (IBD): Cause or Consequence? IBD Treatment Targeting the Gut Microbiome

(2019) Israr Khan et al.   Pathogens

Good Gone Bad: One Toxin Away From Disease for Bacteroides fragilis

(2019) Ezequiel Valguarnera et al.   JOURNAL OF MOLECULAR BIOLOGY

Patient-Reported Outcomes and Endoscopic Appearance of Ulcerative Colitis—a Systematic Review and Meta-Analysis

(2018) Neeraj Narula et al.   Clinical Gastroenterology and Hepatology

Natural History of Adult Ulcerative Colitis in Population-based Cohorts: A Systematic Review

(2018) Mathurin Fumery et al.   Clinical Gastroenterology and Hepatology

Relationship between intestinal microbiota and ulcerative colitis: Mechanisms and clinical application of probiotics and fecal microbiota transplantation

(2018) Zhao-Hua Shen et al.   WORLD JOURNAL OF GASTROENTEROLOGY

Metaproteomics reveals associations between microbiome and intestinal extracellular vesicle proteins in pediatric inflammatory bowel disease

(2018) Xu Zhang et al.   Nature Communications

Functional Proteomic Profiling of Secreted Serine Proteases in Health and Inflammatory Bowel Disease

(2018) Alexandre Denadai-Souza et al.   Scientific Reports

Defining Host Responses during Systemic Bacterial Infection through Construction of a Murine Organ Proteome Atlas

(2018) John D. Lapek et al.   Cell Systems

Qiita: rapid, web-enabled microbiome meta-analysis

(2018) Antonio Gonzalez et al.   NATURE METHODS

Compositional and Temporal Changes in the Gut Microbiome of Pediatric Ulcerative Colitis Patients Are Linked to Disease Course

(2018) Melanie Schirmer et al.   Cell Host & Microbe

Isobaric Labeling Quantitative Metaproteomics for the Study of Gut Microbiome Response to Arsenic

(2018) Chih-Wei Liu et al.   JOURNAL OF PROTEOME RESEARCH

Gut microbiota composition and functional changes in inflammatory bowel disease and irritable bowel syndrome

(2018) Arnau Vich Vila et al.   Science Translational Medicine

Gut microbiome structure and metabolic activity in inflammatory bowel disease

(2018) Eric A. Franzosa et al.   Nature Microbiology

Roles for Intestinal Bacteria, Viruses, and Fungi in Pathogenesis of Inflammatory Bowel Diseases and Therapeutic Approaches

(2017) R. Balfour Sartor et al.   GASTROENTEROLOGY

Quantitative Temporal Viromics of an Inducible HIV-1 Model Yields Insight to Global Host Targets and Phospho-Dynamics Associated with Protein Vpr

(2017) John D. Lapek et al.   MOLECULAR & CELLULAR PROTEOMICS

A communal catalogue reveals Earth’s multiscale microbial diversity

(2017) Luke R. Thompson et al.   NATURE

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Regulation of intestinal permeability: The role of proteases

(2017) Hanne Van Spaendonk et al.   WORLD JOURNAL OF GASTROENTEROLOGY

Dynamics of the human gut microbiome in inflammatory bowel disease

(2017) Jonas Halfvarson et al.   Nature Microbiology

Lipocalin 2 Protects from Inflammation and Tumorigenesis Associated with Gut Microbiota Alterations

(2016) Alexander R. Moschen et al.   Cell Host & Microbe

The Sus operon: a model system for starch uptake by the human gut Bacteroidetes

(2016) Matthew H. Foley et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Comparative review of dipeptidyl peptidase-4 inhibitors and sulphonylureas

(2016) C. F. Deacon et al.   DIABETES OBESITY & METABOLISM

Protease inhibition as new therapeutic strategy for GI diseases

(2016) Nathalie Vergnolle   GUT

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

(2016) Minoru Kanehisa et al.   JOURNAL OF MOLECULAR BIOLOGY

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

(2016) Mingxun Wang et al.   NATURE BIOTECHNOLOGY

Current best practice for disease activity assessment in IBD

(2016) Alissa J. Walsh et al.   Nature Reviews Gastroenterology & Hepatology

ClassyFire: automated chemical classification with a comprehensive, computable taxonomy

(2016) Yannick Djoumbou Feunang et al.   Journal of Cheminformatics

A multi-omic future for microbiome studies

(2016) Janet K. Jansson et al.   Nature Microbiology

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

Proteolytic Cleavage and Loss of Function of Biologic Agents That Neutralize Tumor Necrosis Factor in the Mucosa of Patients With Inflammatory Bowel Disease

(2015) Paolo Biancheri et al.   GASTROENTEROLOGY

Assessment of mucosal healing in inflammatory bowel disease: review

(2015) Parambir S. Dulai et al.   GASTROINTESTINAL ENDOSCOPY

Matrix Metalloproteinases in Inflammatory Bowel Disease: An Update

(2015) Shane O’Sullivan et al.   MEDIATORS OF INFLAMMATION

Gut biogeography of the bacterial microbiota

(2015) Gregory P. Donaldson et al.   NATURE REVIEWS MICROBIOLOGY

Searching molecular structure databases with tandem mass spectra using CSI:FingerID

(2015) Kai Dührkop et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Lysine Demethylase KDM4A Associates with Translation Machinery and Regulates Protein Synthesis

(2015) C. Van Rechem et al.   Cancer Discovery

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Systematic review: monotherapy with antitumour necrosis factor α agents versus combination therapy with an immunosuppressive for IBD

(2014) Parambir S Dulai et al.   GUT

ECM remodelling in IBD: innocent bystander or partner in crime? The emerging role of extracellular molecular events in sustaining intestinal inflammation

(2014) Elee Shimshoni et al.   GUT

A simple cage-autonomous method for the maintenance of the barrier status of germ-free mice during experimentation

(2014) G Hecht et al.   LABORATORY ANIMALS

An integrated catalog of reference genes in the human gut microbiome

(2014) Junhua Li et al.   NATURE BIOTECHNOLOGY

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

STRING v10: protein–protein interaction networks, integrated over the tree of life

(2014) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Preferential Packing of Acidic Glycosidases and Proteases into Bacteroides Outer Membrane Vesicles

(2014) W. Elhenawy et al.   mBio

Quantitative Proteomics Using Reductive Dimethylation for Stable Isotope Labeling

(2014) Andrew C. Tolonen et al.   Jove-Journal of Visualized Experiments

Inhibition of proteases as a novel therapeutic strategy in the treatment of metabolic, inflammatory and functional diseases of the gastrointestinal tract

(2013) Maciej Sałaga et al.   DRUG DISCOVERY TODAY

Global Substrate Profiling of Proteases in Human Neutrophil Extracellular Traps Reveals Consensus Motif Predominantly Contributed by Elastase

(2013) Anthony J. O’Donoghue et al.   PLoS One

A two-step database search method improves sensitivity in peptide sequence matches for metaproteomics and proteogenomics studies

(2013) Pratik Jagtap et al.   PROTEOMICS

Dipeptidyl peptidase-4 inhibitor anagliptin facilitates restoration of dextran sulfate sodium-induced colitis

(2013) Shunya Mimura et al.   SCANDINAVIAN JOURNAL OF GASTROENTEROLOGY

Enteric bacterial proteases in inflammatory bowel disease- pathophysiology and clinical implications

(2013) Ian M Carroll   WORLD JOURNAL OF GASTROENTEROLOGY

A novel significance score for gene selection and ranking

(2012) Yufei Xiao et al.   BIOINFORMATICS

Species Composition ofBacteroidalesOrder Bacteria in the Feces of Healthy People of Various Ages

(2012) Elena V. KULAGINA et al.   BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

Ulcerative colitis

(2012) Ingrid Ordás et al.   LANCET

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Fecal Lipocalin 2, a Sensitive and Broadly Dynamic Non-Invasive Biomarker for Intestinal Inflammation

(2012) Benoit Chassaing et al.   PLoS One

Integrated Metagenomics/Metaproteomics Reveals Human Host-Microbiota Signatures of Crohn's Disease

(2012) Alison R. Erickson et al.   PLoS One

Bacterial proteases in IBD and IBS

(2011) Natalie Steck et al.   GUT

PEAKS DB:De NovoSequencing Assisted Database Search for Sensitive and Accurate Peptide Identification

(2011) Jing Zhang et al.   MOLECULAR & CELLULAR PROTEOMICS

Proteome-wide systems analysis of a cellulosic biofuel-producing microbe

(2011) A. C. Tolonen et al.   Molecular Systems Biology

Reversed-phase chromatography with multiple fraction concatenation strategy for proteome profiling of human MCF10A cells

(2011) Yuexi Wang et al.   PROTEOMICS

MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data

(2010) Tomáš Pluskal et al.   BMC BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

A Tissue-Specific Atlas of Mouse Protein Phosphorylation and Expression

(2010) Edward L. Huttlin et al.   CELL

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Improved visualization of protein consensus sequences by iceLogo

(2009) Niklaas Colaert et al.   NATURE METHODS

Use of the noninvasive components of the mayo score to assess clinical response in Ulcerative Colitis

(2008) James D. Lewis et al.   INFLAMMATORY BOWEL DISEASES

Shotgun metaproteomics of the human distal gut microbiota

(2008) Nathan C Verberkmoes et al.   ISME Journal

The SCX/IMAC enrichment approach for global phosphorylation analysis by mass spectrometry

(2008) Judit Villén et al.   Nature Protocols