Related references
Note: Only part of the references are listed.The Interplay Between Genetic Risk Factors and Proteolytic Dysregulation in the Pathophysiology of Inflammatory Bowel Disease
Nuria Sola Tapias et al.
JOURNAL OF CROHNS & COLITIS (2020)
M2IA: a web server for microbiome and metabolome integrative analysis
Yan Ni et al.
BIOINFORMATICS (2020)
Fecal Serine Protease Profiling in Inflammatory Bowel Diseases
Amin Jablaoui et al.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY (2020)
Network-based drug repurposing for novel coronavirus 2019-nCoV/SARS-CoV-2
Yadi Zhou et al.
CELL DISCOVERY (2020)
Targeted interplay between bacterial pathogens and host autophagy
Padhmanand Sudhakar et al.
AUTOPHAGY (2019)
Integrative analysis of Paneth cell proteomic and transcriptomic data from intestinal organoids reveals functional processes dependent on autophagy
Emily J. Jones et al.
DISEASE MODELS & MECHANISMS (2019)
SignalP 5.0 improves signal peptide predictions using deep neural networks
Jose Juan Almagro Armenteros et al.
NATURE BIOTECHNOLOGY (2019)
Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0
Laurent Heirendt et al.
NATURE PROTOCOLS (2019)
Benchmark and integration of resources for the estimation of human transcription factor activities
Luz Garcia-Alonso et al.
GENOME RESEARCH (2019)
The gut microbiome: Relationships with disease and opportunities for therapy
Juliana Durack et al.
JOURNAL OF EXPERIMENTAL MEDICINE (2019)
The Pfam protein families database in 2019
Sara El-Gebali et al.
NUCLEIC ACIDS RESEARCH (2019)
InterPro in 2019: improving coverage, classification and access to protein sequence annotations
Alex L. Mitchell et al.
NUCLEIC ACIDS RESEARCH (2019)
Host-microbiota interactions: from holobiont theory to analysis
Jean-Christophe Simon et al.
MICROBIOME (2019)
Metabolic Modeling of Human Gut Microbiota on a Genome Scale: An Overview
Partho Sen et al.
METABOLITES (2019)
The eukaryotic linear motif resource-2018 update
Marc Gouw et al.
NUCLEIC ACIDS RESEARCH (2018)
ProteomicsDB
Tobias Schmidt et al.
NUCLEIC ACIDS RESEARCH (2018)
Autophagy Caught in the Act: A Supramolecular FRET Pair Based on an Ultrastable Synthetic Host-Guest Complex Visualizes Autophagosome-Lysosome Fusion
Meng Li et al.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2018)
Autophagy Inhibition Mediates Apoptosis Sensitization in Cancer Therapy by Relieving FOXO3a Turnover
Brent E. Fitzwalter et al.
DEVELOPMENTAL CELL (2018)
KBase: The United States Department of Energy Systems Biology Knowledgebase
Adam P. Arkin et al.
NATURE BIOTECHNOLOGY (2018)
IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding
Balint Meszaros et al.
NUCLEIC ACIDS RESEARCH (2018)
Glucocorticoids promote apoptosis of proinflammatory monocytes by inhibiting ERK activity
Adrian Achuthan et al.
CELL DEATH & DISEASE (2018)
Whole Cell Cross-Linking to Discover Host-Microbe Protein Cognate Receptor/Ligand Pairs
Bart C. Weimer et al.
FRONTIERS IN MICROBIOLOGY (2018)
The Selective Autophagy Receptor Optineurin in Crohn's Disease
Markus Tschurtschenthaler et al.
FRONTIERS IN IMMUNOLOGY (2018)
Microbiome interactions shape host fitness
Alison L. Gould et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)
Gut microbiota: Role in pathogen colonization, immune responses, and inflammatory disease
Joseph M. Pickard et al.
IMMUNOLOGICAL REVIEWS (2017)
Genetic and Transcriptomic Bases of Intestinal Epithelial Barrier Dysfunction in Inflammatory Bowel Disease
Maaike Vancamelbeke et al.
INFLAMMATORY BOWEL DISEASES (2017)
Targeting the Mucosal Barrier: How Pathogens Modulate the Cellular Polarity Network
Travis R. Ruch et al.
COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY (2017)
Structural host- microbiota interaction networks
Emine Guven-Maiorov et al.
PLOS COMPUTATIONAL BIOLOGY (2017)
Perturbed human sub-networks by Fusobacterium nucleatum candidate virulence proteins
Andreas Zanzoni et al.
MICROBIOME (2017)
Gastrointestinal functionality in animal nutrition and health: New opportunities for sustainable animal production
P. Celi et al.
ANIMAL FEED SCIENCE AND TECHNOLOGY (2017)
PSORTdb: expanding the bacteria and archaea protein subcellular localization database to better reflect diversity in cell envelope structures
Michael A. Peabody et al.
NUCLEIC ACIDS RESEARCH (2016)
Death in the intestinal epithelium-basic biology and implications for inflammatory bowel disease
J. Magarian Blander
FEBS JOURNAL (2016)
OmniPath: guidelines and gateway for literature-curated signaling pathway resources
Denes Turei et al.
NATURE METHODS (2016)
Functional Characterization of Inflammatory Bowel Disease-Associate Gut Dysbiosis in Gnotobiotic Mice
Hiroko Nagao-Kitamoto et al.
CELLULAR AND MOLECULAR GASTROENTEROLOGY AND HEPATOLOGY (2016)
NetCooperate: a network-based tool for inferring host-microbe and microbe-microbe cooperation
Roie Levy et al.
BMC BIOINFORMATICS (2015)
Tissue-based map of the human proteome
Mathias Uhlen et al.
SCIENCE (2015)
Computational approaches for prediction of pathogen-host protein-protein interactions
Esmaeil Nourani et al.
FRONTIERS IN MICROBIOLOGY (2015)
The impact of Docker containers on the performance of genomic pipelines
Paolo Di Tommaso et al.
PEERJ (2015)
SUMO1 promotes Aβ production via the modulation of autophagy
Sun-Jung Cho et al.
AUTOPHAGY (2015)
ComPPI: a cellular compartment-specific database for protein-protein interaction network analysis
Daniel V. Veres et al.
NUCLEIC ACIDS RESEARCH (2015)
ViRBase: a resource for virus-host ncRNA-associated interactions
Yanhui Li et al.
NUCLEIC ACIDS RESEARCH (2015)
MatrixDB, the extracellular matrix interaction database: updated content, a new navigator and expanded functionalities
G. Launay et al.
NUCLEIC ACIDS RESEARCH (2015)
Dysbiosis of Gut Fungal Microbiota is Associated With Mucosal Inflammation in Crohn's Disease
Qiurong Li et al.
JOURNAL OF CLINICAL GASTROENTEROLOGY (2014)
The eukaryotic linear motif resource ELM: 10 years and counting
Holger Dinkel et al.
NUCLEIC ACIDS RESEARCH (2014)
PATRIC, the bacterial bioinformatics database and analysis resource
Alice R. Wattam et al.
NUCLEIC ACIDS RESEARCH (2014)
Metabolic Resource Allocation in Individual Microbes Determines Ecosystem Interactions and Spatial Dynamics
William R. Harcombe et al.
CELL REPORTS (2014)
Key hub and bottleneck genes differentiate the macrophage response to virulent and attenuated Mycobacterium bovis
Kate E. Killick et al.
FRONTIERS IN IMMUNOLOGY (2014)
PHISTO: pathogen-host interaction search tool
Saliha Durmus Tekir et al.
BIOINFORMATICS (2013)
Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE)
Evan O. Paull et al.
BIOINFORMATICS (2013)
Teaching the bioinformatics of signaling networks: an integrated approach to facilitate multi-disciplinary learning
Tamas Korcsmaros et al.
BRIEFINGS IN BIOINFORMATICS (2013)
The Human Gut Microbiome and Body Metabolism: Implications for Obesity and Diabetes
Sridevi Devaraj et al.
CLINICAL CHEMISTRY (2013)
Phenotype-Genotype Profiles in Crohn's Disease Predicted by Genetic Markers in Autophagy-Related Genes (GOIA Study II)
Cecilia Duraes et al.
INFLAMMATORY BOWEL DISEASES (2013)
Salmonella Pathogenicity and Host Adaptation in Chicken-Associated Serovars
Steven L. Foley et al.
MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS (2013)
Identification of Novel Predictor Classifiers for Inflammatory Bowel Disease by Gene Expression Profiling
Trinidad Montero-Melendez et al.
PLOS ONE (2013)
Complex regulation of autophagy in cancer - Integrated approaches to discover the networks that hold a double-edged sword
Janos Kubisch et al.
SEMINARS IN CANCER BIOLOGY (2013)
Enteric bacterial proteases in inflammatory bowel disease-pathophysiology and clinical implications
Ian M. Carroll et al.
WORLD JOURNAL OF GASTROENTEROLOGY (2013)
The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum
Rasmus Agren et al.
PLOS COMPUTATIONAL BIOLOGY (2013)
Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut
Almut Heinken et al.
GUT MICROBES (2013)
The plant microbiome
Thomas R. Turner et al.
GENOME BIOLOGY (2013)
iELM-a web server to explore short linear motif-mediated interactions
Robert J. Weatheritt et al.
NUCLEIC ACIDS RESEARCH (2012)
Effects of Gut Microbes on Nutrient Absorption and Energy Regulation
Rosa Krajmalnik-Brown et al.
NUTRITION IN CLINICAL PRACTICE (2012)
Integrated Metagenomics/Metaproteomics Reveals Human Host-Microbiota Signatures of Crohn's Disease
Alison R. Erickson et al.
PLOS ONE (2012)
Infection strategies of bacterial and viral pathogens through pathogen-human protein-protein interactions
Saliha Durmus Tekir et al.
FRONTIERS IN MICROBIOLOGY (2012)
Role of commensal gut bacteria in inflammatory bowel diseases
Gunnar Loh et al.
GUT MICROBES (2012)
Role of Small RNAs in Host-Microbe Interactions
Surekha Katiyar-Agarwal et al.
ANNUAL REVIEW OF PHYTOPATHOLOGY, VOL 48 (2010)
HPIDB - a unified resource for host-pathogen interactions
Ranjit Kumar et al.
BMC BIOINFORMATICS (2010)
The Human-Bacterial Pathogen Protein Interaction Networks of Bacillus anthracis, Francisella tularensis, and Yersinia pestis
Matthew D. Dyer et al.
PLOS ONE (2010)
A Primer on Metagenomics
John C. Wooley et al.
PLOS COMPUTATIONAL BIOLOGY (2010)
Prediction of HIV-1 virus-host protein interactions using virus and host sequence motifs
Perry Evans et al.
BMC MEDICAL GENOMICS (2009)
Interaction networks for systems biology
Samuel Bader et al.
FEBS LETTERS (2008)
Activation of an IL-6:STAT3-dependent transcriptome in pediatric-onset inflammatory bowel disease
Rebecca Carey et al.
INFLAMMATORY BOWEL DISEASES (2008)
E2F1 regulates autophagy and the transcription of autophagy genes
S. Polager et al.
ONCOGENE (2008)
Impaired Autophagy of an Intracellular Pathogen Induced by a Crohn's Disease Associated ATG16L1 Variant
Petric Kuballa et al.
PLOS ONE (2008)
The landscape of human proteins interacting with viruses and other pathogens
Matthew D. Dyer et al.
PLOS PATHOGENS (2008)
DOMINE: a database of protein domain interactions
Balaji Raghavachari et al.
NUCLEIC ACIDS RESEARCH (2008)
Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis
John D. Rioux et al.
NATURE GENETICS (2007)
Non-classical protein secretion in bacteria
JD Bendtsen et al.
BMC MICROBIOLOGY (2005)