MicrobioLink: An Integrated Computational Pipeline to Infer Functional Effects of Microbiome–Host Interactions

The interplay between genetic risk factors and proteolytic dysregulation in the pathophysiology of inflammatory bowel disease

(2020) Núria Solà Tapias et al.   Journal of Crohns & Colitis

Fecal Serine Protease Profiling in Inflammatory Bowel Diseases

(2020) Amin Jablaoui et al.   Frontiers in Cellular and Infection Microbiology

M2IA: a web server for microbiome and metabolome integrative analysis

(2020) Yan Ni et al.   BIOINFORMATICS

Network-based drug repurposing for novel coronavirus 2019-nCoV/SARS-CoV-2

(2020) Yadi Zhou et al.   Cell Discovery

Host-microbiota interactions: from holobiont theory to analysis

(2019) Jean-Christophe Simon et al.   Microbiome

Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0

(2019) Laurent Heirendt et al.   Nature Protocols

SignalP 5.0 improves signal peptide predictions using deep neural networks

(2019) José Juan Almagro Armenteros et al.   NATURE BIOTECHNOLOGY

Integrative analysis of Paneth cell proteomic and transcriptomic data from intestinal organoids reveals functional processes dependent on autophagy

(2019) Emily J. Jones et al.   Disease Models & Mechanisms

Targeted interplay between bacterial pathogens and host autophagy

(2019) Padhmanand Sudhakar et al.   Autophagy

Benchmark and integration of resources for the estimation of human transcription factor activities

(2019) Luz Garcia-Alonso et al.   GENOME RESEARCH

Autophagy Caught in the Act: A Supramolecular FRET Pair Based on an Ultrastable Synthetic Host-Guest Complex Visualizes Autophagosome-Lysosome Fusion

(2018) Meng Li et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Autophagy Inhibition Mediates Apoptosis Sensitization in Cancer Therapy by Relieving FOXO3a Turnover

(2018) Brent E. Fitzwalter et al.   DEVELOPMENTAL CELL

KBase: The United States Department of Energy Systems Biology Knowledgebase

(2018) Adam P Arkin et al.   NATURE BIOTECHNOLOGY

IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding

(2018) Bálint Mészáros et al.   NUCLEIC ACIDS RESEARCH

Glucocorticoids promote apoptosis of proinflammatory monocytes by inhibiting ERK activity

(2018) Adrian Achuthan et al.   Cell Death & Disease

Whole Cell Cross-Linking to Discover Host–Microbe Protein Cognate Receptor/Ligand Pairs

(2018) Bart C. Weimer et al.   Frontiers in Microbiology

The Selective Autophagy Receptor Optineurin in Crohn’s Disease

(2018) Markus Tschurtschenthaler et al.   Frontiers in Immunology

The gut microbiome: Relationships with disease and opportunities for therapy

(2018) Juliana Durack et al.   JOURNAL OF EXPERIMENTAL MEDICINE

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

InterPro in 2019: improving coverage, classification and access to protein sequence annotations

(2018) Alex L Mitchell et al.   NUCLEIC ACIDS RESEARCH

Microbiome interactions shape host fitness

(2018) Alison L. Gould et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gut microbiota: Role in pathogen colonization, immune responses, and inflammatory disease

(2017) Joseph M. Pickard et al.   IMMUNOLOGICAL REVIEWS

Genetic and Transcriptomic Bases of Intestinal Epithelial Barrier Dysfunction in Inflammatory Bowel Disease

(2017) Maaike Vancamelbeke et al.   INFLAMMATORY BOWEL DISEASES

The eukaryotic linear motif resource – 2018 update

(2017) Marc Gouw et al.   NUCLEIC ACIDS RESEARCH

ProteomicsDB

(2017) Tobias Schmidt et al.   NUCLEIC ACIDS RESEARCH

Targeting the Mucosal Barrier: How Pathogens Modulate the Cellular Polarity Network

(2017) Travis R. Ruch et al.   Cold Spring Harbor Perspectives in Biology

Structural host-microbiota interaction networks

(2017) Emine Guven-Maiorov et al.   PLoS Computational Biology

Perturbed human sub-networks by Fusobacterium nucleatum candidate virulence proteins

(2017) Andreas Zanzoni et al.   Microbiome

Death in the intestinal epithelium-basic biology and implications for inflammatory bowel disease

(2016) J. Magarian Blander   FEBS Journal

OmniPath: guidelines and gateway for literature-curated signaling pathway resources

(2016) Dénes Türei et al.   NATURE METHODS

NetCooperate: a network-based tool for inferring host-microbe and microbe-microbe cooperation

(2015) Roie Levy et al.   BMC BIOINFORMATICS

PSORTdb: expanding the bacteria and archaea protein subcellular localization database to better reflect diversity in cell envelope structures

(2015) Michael A. Peabody et al.   NUCLEIC ACIDS RESEARCH

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

Computational approaches for prediction of pathogen-host protein-protein interactions

(2015) Esmaeil Nourani et al.   Frontiers in Microbiology

The impact of Docker containers on the performance of genomic pipelines

(2015) Paolo Di Tommaso et al.   PeerJ

SUMO1 promotes Aβ production via the modulation of autophagy

(2014) Sun-Jung Cho et al.   Autophagy

ComPPI: a cellular compartment-specific database for protein–protein interaction network analysis

(2014) Daniel V. Veres et al.   NUCLEIC ACIDS RESEARCH

ViRBase: a resource for virus–host ncRNA-associated interactions

(2014) Yanhui Li et al.   NUCLEIC ACIDS RESEARCH

MatrixDB, the extracellular matrix interaction database: updated content, a new navigator and expanded functionalities

(2014) G. Launay et al.   NUCLEIC ACIDS RESEARCH

Metabolic Resource Allocation in Individual Microbes Determines Ecosystem Interactions and Spatial Dynamics

(2014) William R. Harcombe et al.   Cell Reports

Key Hub and Bottleneck Genes Differentiate the Macrophage Response to Virulent and Attenuated Mycobacterium bovis

(2014) Kate E. Killick et al.   Frontiers in Immunology

PHISTO: pathogen–host interaction search tool

(2013) Saliha Durmuş Tekir et al.   BIOINFORMATICS

Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE)

(2013) Evan O. Paull et al.   BIOINFORMATICS

Teaching the bioinformatics of signaling networks: an integrated approach to facilitate multi-disciplinary learning

(2013) T. Korcsmaros et al.   BRIEFINGS IN BIOINFORMATICS

The Human Gut Microbiome and Body Metabolism: Implications for Obesity and Diabetes

(2013) S. Devaraj et al.   CLINICAL CHEMISTRY

Dysbiosis of Gut Fungal Microbiota is Associated With Mucosal Inflammation in Crohn’s Disease

(2013) Qiurong Li et al.   JOURNAL OF CLINICAL GASTROENTEROLOGY

Salmonella Pathogenicity and Host Adaptation in Chicken-Associated Serovars

(2013) S. L. Foley et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

The eukaryotic linear motif resource ELM: 10 years and counting

(2013) Holger Dinkel et al.   NUCLEIC ACIDS RESEARCH

PATRIC, the bacterial bioinformatics database and analysis resource

(2013) Alice R. Wattam et al.   NUCLEIC ACIDS RESEARCH

Identification of Novel Predictor Classifiers for Inflammatory Bowel Disease by Gene Expression Profiling

(2013) Trinidad Montero-Meléndez et al.   PLoS One

Complex regulation of autophagy in cancer – Integrated approaches to discover the networks that hold a double-edged sword

(2013) János Kubisch et al.   SEMINARS IN CANCER BIOLOGY

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

(2013) Ian M Carroll   WORLD JOURNAL OF GASTROENTEROLOGY

The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum

(2013) Rasmus Agren et al.   PLoS Computational Biology

Phenotype–Genotype Profiles in Crohnʼs Disease Predicted by Genetic Markers in Autophagy-Related Genes (GOIA Study II)

(2012) Cecília Durães et al.   INFLAMMATORY BOWEL DISEASES

iELM--a web server to explore short linear motif-mediated interactions

(2012) R. J. Weatheritt et al.   NUCLEIC ACIDS RESEARCH

Effects of Gut Microbes on Nutrient Absorption and Energy Regulation

(2012) Rosa Krajmalnik-Brown et al.   NUTRITION IN CLINICAL PRACTICE

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

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

Infection Strategies of Bacterial and Viral Pathogens through Pathogen–Human Protein–Protein Interactions

(2012) Saliha Durmuş Tekir et al.   Frontiers in Microbiology

Role of Small RNAs in Host-Microbe Interactions

(2010) Surekha Katiyar-Agarwal et al.   Annual Review of Phytopathology

HPIDB - a unified resource for host-pathogen interactions

(2010) Ranjit Kumar et al.   BMC BIOINFORMATICS

The Human-Bacterial Pathogen Protein Interaction Networks of Bacillus anthracis, Francisella tularensis, and Yersinia pestis

(2010) Matthew D. Dyer et al.   PLoS One

A Primer on Metagenomics

(2010) John C. Wooley et al.   PLoS Computational Biology

Prediction of HIV-1 virus-host protein interactions using virus and host sequence motifs

(2009) Perry Evans et al.   BMC Medical Genomics

Interaction networks for systems biology

(2008) Samuel Bader et al.   FEBS LETTERS

E2F1 regulates autophagy and the transcription of autophagy genes

(2008) S Polager et al.   ONCOGENE

Impaired Autophagy of an Intracellular Pathogen Induced by a Crohn's Disease Associated ATG16L1 Variant

(2008) Petric Kuballa et al.   PLoS One

The Landscape of Human Proteins Interacting with Viruses and Other Pathogens

(2008) Matthew D. Dyer et al.   PLoS Pathogens

Activation of an IL-6:STAT3-dependent transcriptome in pediatric-onset inflammatory bowel disease

(2007) Rebecca Carey et al.   INFLAMMATORY BOWEL DISEASES