Publications - Xavier
Role of dietary fiber in the recovery of the human gut microbiome and its metabolome.
Cell Host Microbe. 2021;:ePub - PMID: 33440171 - DOI: 10.1016/j.chom.2020.12.012
QRICH1 dictates the outcome of ER stress through transcriptional control of proteostasis.
Science. 2021;371(6524):ePub - PMID: 33384352 - DOI: 10.1126/science.abb6896
Sorting nexin 5 mediates virus-induced autophagy and immunity.
Nature. 2020;:ePub - PMID: 33328639 - DOI: 10.1038/s41586-020-03056-z
TFEB Transcriptional Responses Reveal Negative Feedback by BHLHE40 and BHLHE41.
Cell Rep. 2020;33(6):108371 - PMID: 33176151 - PMCID: PMC7686957 - DOI: 10.1016/j.celrep.2020.108371
A missense variant in SLC39A8 confers risk for Crohn's disease by disrupting manganese homeostasis and intestinal barrier integrity.
Proc Natl Acad Sci U S A. 2020;117(46):28930-28938 - PMID: 33139556 - PMCID: PMC7682327 - DOI: 10.1073/pnas.2014742117
USP15 Deubiquitinates CARD9 to Downregulate C-Type Lectin Receptor-Mediated Signaling.
Immunohorizons. 2020;4(10):670-678 - PMID: 33093067 - PMCID: PMC7758836 - DOI: 10.4049/immunohorizons.2000036
Multi-"-Omics" Profiling in Patients With Quiescent Inflammatory Bowel Disease Identifies Biomarkers Predicting Relapse.
Inflamm Bowel Dis. 2020;26(10):1524-1532 - PMID: 32766830 - PMCID: PMC7500522 - DOI: 10.1093/ibd/izaa183
The Human and Mouse Enteric Nervous System at Single-Cell Resolution.
Cell. 2020;182(6):1606-1622.e23 - PMID: 32888429 - DOI: 10.1016/j.cell.2020.08.003
Linking strain engraftment in fecal microbiota transplantation with maintenance of remission in Crohn's disease.
Gastroenterology. 2020;159(6):2193-2202.e5 - PMID: 32860788 - PMCID: PMC7725862 - DOI: 10.1053/j.gastro.2020.08.045
Whole exome sequencing analyses reveal gene-microbiota interactions in the context of IBD.
Gut. 2021;70(2):285-296 - PMID: 32651235 - DOI: 10.1136/gutjnl-2019-319706
Beth Cindy Levine (1960-2020).
Science. 2020;369(6502):378 - PMID: 32703867 - DOI: 10.1126/science.abd6216
Growth and the Microbiome - Integrating Global Health with Basic Science.
N Engl J Med. 2020;383(4):391-393 - PMID: 32706538 - DOI: 10.1056/NEJMe2017496
Cholesterol Metabolism by Uncultured Human Gut Bacteria Influences Host Cholesterol Level.
Cell Host Microbe. 2020;28(2):245-257.e6 - PMID: 32544460 - PMCID: PMC7435688 - DOI: 10.1016/j.chom.2020.05.013
Cell Type- and Stimulation-Dependent Transcriptional Programs Regulated by Atg16L1 and Its Crohn's Disease Risk Variant T300A.
Alterations in Fecal Microbiomes and Serum Metabolomes of Fatigued Patients With Quiescent Inflammatory Bowel Diseases.
Clin Gastroenterol Hepatol. 2020;:ePub - PMID: 32184182 - DOI: 10.1016/j.cgh.2020.03.013
Defining trained immunity and its role in health and disease.
Nat Rev Immunol. 2020;20(6):375-388 - PMID: 32132681 - PMCID: PMC7186935 - DOI: 10.1038/s41577-020-0285-6
Pathway paradigms revealed from the genetics of inflammatory bowel disease.
Nature. 2020;578(7796):527-539 - PMID: 32103191 - DOI: 10.1038/s41586-020-2025-2
Global chemical effects of the microbiome include new bile-acid conjugations.
Nature. 2020;579(7797):123-129 - PMID: 32103176 - PMCID: PMC7252668 - DOI: 10.1038/s41586-020-2047-9
Growth effects of N-acylethanolamines on gut bacteria reflect altered bacterial abundances in inflammatory bowel disease.
Nat Microbiol. 2020;5(3):486-497 - PMID: 31959971 - PMCID: PMC7047597 - DOI: 10.1038/s41564-019-0655-7
Comprehensive analysis of chromosomal mobile genetic elements in the gut microbiome reveals phylum-level niche-adaptive gene pools.
PLoS One. 2019;14(12):e0223680 - PMID: 31830054 - PMCID: PMC6907783 - DOI: 10.1371/journal.pone.0223680
Transcriptional Atlas of Intestinal Immune Cells Reveals that Neuropeptide α-CGRP Modulates Group 2 Innate Lymphoid Cell Responses.
Immunity. 2019;51(4):696-708.e9 - PMID: 31618654 - PMCID: PMC6991097 - DOI: 10.1016/j.immuni.2019.09.004
Distinct Tissue-Specific Roles for the Disease-Associated Autophagy Genes ATG16L2 and ATG16L1.
J Immunol. 2019;203(7):1820-1829 - PMID: 31451676 - PMCID: PMC6761021 - DOI: 10.4049/jimmunol.1800419
Use of narrative concepts in the EHR to validate genetic determinants of treatment response in a virtual inflammatory bowel disease cohort.
Clin Gastroenterol Hepatol. 2020;18(8):1890-1892 - PMID: 31404664 - DOI: 10.1016/j.cgh.2019.08.005
Cytokine release and gastrointestinal symptoms after gluten challenge in celiac disease.
Therapeutic Opportunities in Inflammatory Bowel Disease: Mechanistic Dissection of Host-Microbiome Relationships.
Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences.
Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis.
Cell. 2019;178(3):714-730.e22 - PMID: 31348891 - PMCID: PMC6662628 - DOI: 10.1016/j.cell.2019.06.029
Microbial genes and pathways in inflammatory bowel disease.
Nat Rev Microbiol. 2019;17(8):497-511 - PMID: 31249397 - PMCID: PMC6759048 - DOI: 10.1038/s41579-019-0213-6
Ruminococcus gnavus, a member of the human gut microbiome associated with Crohn's disease, produces an inflammatory polysaccharide.
Proc Natl Acad Sci U S A. 2019;116(26):12672-12677 - PMID: 31182571 - PMCID: PMC6601261 - DOI: 10.1073/pnas.1904099116
Akkermansia muciniphila induces intestinal adaptive immune responses during homeostasis.
Science. 2019;364(6446):1179-1184 - PMID: 31221858 - PMCID: PMC6645389 - DOI: 10.1126/science.aaw7479
Correction: Insights into the genetic epidemiology of Crohn's and rare diseases in the Ashkenazi Jewish population.
PLoS Genet. 2019;15(5):e1008190 - PMID: 31145742 - PMCID: PMC6542503 - DOI: 10.1371/journal.pgen.1008190
Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases.
Nature. 2019;569(7758):655-662 - PMID: 31142855 - PMCID: PMC6650278 - DOI: 10.1038/s41586-019-1237-9
Induction of the metal transporter ZIP8 by interferon gamma in intestinal epithelial cells: Potential role of metal dyshomeostasis in Crohn's disease.
Biochem Biophys Res Commun. 2019;515(2):325-331 - PMID: 31151823 - DOI: 10.1016/j.bbrc.2019.05.137
Meiotic gatekeeper STRA8 suppresses autophagy by repressing Nr1d1 expression during spermatogenesis in mice.
PLoS Genet. 2019;15(5):e1008084 - PMID: 31059511 - PMCID: PMC6502318 - DOI: 10.1371/journal.pgen.1008084
Bacteroides-Derived Sphingolipids Are Critical for Maintaining Intestinal Homeostasis and Symbiosis.
Cell Host Microbe. 2019;25(5):668-680.e7 - PMID: 31071294 - PMCID: PMC6544385 - DOI: 10.1016/j.chom.2019.04.002
Tetraspanin CD82 Organizes Dectin-1 into Signaling Domains to Mediate Cellular Responses to Candida albicans.
J Immunol. 2019;202(11):3256-3266 - PMID: 31010852 - PMCID: PMC6529278 - DOI: 10.4049/jimmunol.1801384
Adaptive Evolution within Gut Microbiomes of Healthy People.
Cell Host Microbe. 2019;25(5):656-667.e8 - PMID: 31028005 - PMCID: PMC6749991 - DOI: 10.1016/j.chom.2019.03.007
Gut Microbial Associations to Plasma Metabolites Linked to Cardiovascular Phenotypes and Risk: A Cross-Sectional Study.
Circ Res. 2019;124(12):1808-1820 - PMID: 30971183 - DOI: 10.1161/CIRCRESAHA.118.314642
Author Correction: Gut microbiome structure and metabolic activity in inflammatory bowel disease.
Nat Microbiol. 2019;4(5):898 - PMID: 30971771 - DOI: 10.1038/s41564-019-0442-5
Gut Microbiota Regulation of T Cells During Inflammation and Autoimmunity.
Annu Rev Immunol. 2019;37:599-624 - PMID: 31026411 - DOI: 10.1146/annurev-immunol-042718-041841
Clinical and biological predictors of response to standardised paediatric colitis therapy (PROTECT): a multicentre inception cohort study.
Lancet. 2019;393(10182):1708-1720 - PMID: 30935734 - PMCID: PMC6501846 - DOI: 10.1016/S0140-6736(18)32592-3
Salt-Inducible Kinases: Physiology, Regulation by cAMP, and Therapeutic Potential: (Trends Endocrinol. Metab. 29, 723-735, 2018).
Trends Endocrinol Metab. 2019;30(6):407 - PMID: 30837108 - DOI: 10.1016/j.tem.2019.01.009
Spatial and Temporal Mapping of Human Innate Lymphoid Cells Reveals Elements of Tissue Specificity.
Immunity. 2019;50(2):505-519.e4 - PMID: 30770247 - PMCID: PMC6594374 - DOI: 10.1016/j.immuni.2019.01.012
SLC39A8 missense variant is associated with Crohn's disease but does not have a major impact on gut microbiome composition in healthy subjects.
PLoS One. 2019;14(1):e0211328 - PMID: 30703110 - PMCID: PMC6354981 - DOI: 10.1371/journal.pone.0211328
A defined commensal consortium elicits CD8 T cells and anti-cancer immunity.
Nature. 2019;565(7741):600-605 - PMID: 30675064 - DOI: 10.1038/s41586-019-0878-z
The Crohn's disease polymorphism, ATG16L1 T300A, alters the gut microbiota and enhances the local Th1/Th17 response.
Ulcerative colitis mucosal transcriptomes reveal mitochondriopathy and personalized mechanisms underlying disease severity and treatment response.
Gut microbiota composition and functional changes in inflammatory bowel disease and irritable bowel syndrome.
Sci Transl Med. 2018;10(472):ePub - PMID: 30567928 - DOI: 10.1126/scitranslmed.aap8914
An ATG16L1-dependent pathway promotes plasma membrane repair and limits Listeria monocytogenes cell-to-cell spread.
Nat Microbiol. 2018;3(12):1472-1485 - PMID: 30478389 - DOI: 10.1038/s41564-018-0293-5
T Helper Cell Cytokines Modulate Intestinal Stem Cell Renewal and Differentiation.
Cell. 2018;175(5):1307-1320.e22 - PMID: 30392957 - PMCID: PMC6239889 - DOI: 10.1016/j.cell.2018.10.008
The human gut microbiome in early-onset type 1 diabetes from the TEDDY study.
Nature. 2018;562(7728):589-594 - PMID: 30356183 - PMCID: PMC6296767 - DOI: 10.1038/s41586-018-0620-2
Temporal development of the gut microbiome in early childhood from the TEDDY study.
Nature. 2018;562(7728):583-588 - PMID: 30356187 - PMCID: PMC6415775 - DOI: 10.1038/s41586-018-0617-x
Antigen discovery and specification of immunodominance hierarchies for MHCII-restricted epitopes.
Nat Med. 2018;24(11):1762-1772 - PMID: 30349087 - PMCID: PMC6312190 - DOI: 10.1038/s41591-018-0203-7
Compositional and Temporal Changes in the Gut Microbiome of Pediatric Ulcerative Colitis Patients Are Linked to Disease Course.
Cell Host Microbe. 2018;24(4):600-610.e4 - PMID: 30308161 - PMCID: PMC6277984 - DOI: 10.1016/j.chom.2018.09.009
Salt-Inducible Kinases: Physiology, Regulation by cAMP, and Therapeutic Potential.
Trends Endocrinol Metab. 2018;29(10):723-735 - PMID: 30150136 - PMCID: PMC6151151 - DOI: 10.1016/j.tem.2018.08.004
TMEM41B is a novel regulator of autophagy and lipid mobilization.
Impaired Aryl Hydrocarbon Receptor Ligand Production by the Gut Microbiota Is a Key Factor in Metabolic Syndrome.
Cell Metab. 2018;28(5):737-749.e4 - PMID: 30057068 - DOI: 10.1016/j.cmet.2018.07.001
Strain-Level Analysis of Mother-to-Child Bacterial Transmission during the First Few Months of Life.
Cell Host Microbe. 2018;24(1):146-154.e4 - PMID: 30001517 - PMCID: PMC6091882 - DOI: 10.1016/j.chom.2018.06.007
Nitric Oxide Engages an Anti-inflammatory Feedback Loop Mediated by Peroxiredoxin 5 in Phagocytes.
Cell Rep. 2018;24(4):838-850 - PMID: 30044981 - PMCID: PMC6156773 - DOI: 10.1016/j.celrep.2018.06.081
The causes and consequences of variation in human cytokine production in health.
Curr Opin Immunol. 2018;54:50-58 - PMID: 29913309 - DOI: 10.1016/j.coi.2018.05.012
Insights into the genetic epidemiology of Crohn's and rare diseases in the Ashkenazi Jewish population.
PLoS Genet. 2018;14(5):e1007329 - PMID: 29795570 - PMCID: PMC5967709 - DOI: 10.1371/journal.pgen.1007329
Integration of multi-omics data and deep phenotyping enables prediction of cytokine responses.
Nat Immunol. 2018;19(7):776-786 - PMID: 29784908 - PMCID: PMC6022810 - DOI: 10.1038/s41590-018-0121-3
Genetic Markers Predict Primary Nonresponse and Durable Response to Anti-Tumor Necrosis Factor Therapy in Ulcerative Colitis.
Inflamm Bowel Dis. 2018;24(8):1840-1848 - PMID: 29718226 - PMCID: PMC6128143 - DOI: 10.1093/ibd/izy083
Without Adaptive Immunity, There's a Cost to Responding STAT.
Cell Metab. 2018;27(4):705-707 - PMID: 29617636 - DOI: 10.1016/j.cmet.2018.03.011
A common mechanism links activities of butyrate in the colon.
ACS Chem Biol. 2018;13(5):1291-1298 - PMID: 29584955 - DOI: 10.1021/acschembio.8b00073
C1orf106 is a colitis risk gene that regulates stability of epithelial adherens junctions.
Science. 2018;359(6380):1161-1166 - PMID: 29420262 - PMCID: PMC6008784 - DOI: 10.1126/science.aan0814
Strain Tracking Reveals the Determinants of Bacterial Engraftment in the Human Gut Following Fecal Microbiota Transplantation.
Cell Host Microbe. 2018;23(2):229-240.e5 - PMID: 29447696 - DOI: 10.1016/j.chom.2018.01.003
Host genetic variation and its microbiome interactions within the Human Microbiome Project.
Loss of Response to Anti-Tumor Necrosis Factor Alpha Therapy in Crohn's Disease Is Not Associated with Emergence of Novel Inflammatory Pathways.
Dig Dis Sci. 2018;63(3):738-745 - PMID: 29372477 - PMCID: PMC6152907 - DOI: 10.1007/s10620-018-4932-8
Genomic and expression analyses identify a disease modifying variant for fibrostenotic Crohn's disease.
J Crohns Colitis. 2018;12(5):582-588 - PMID: 29361163 - DOI: 10.1093/ecco-jcc/jjy001
Dynamics of metatranscription in the inflammatory bowel disease gut microbiome.
Nat Microbiol. 2018;3(3):337-346 - PMID: 29311644 - PMCID: PMC6131705 - DOI: 10.1038/s41564-017-0089-z
A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients.
A single-cell survey of the small intestinal epithelium.
A role for bacterial urease in gut dysbiosis and Crohn's disease.
Sci Transl Med. 2017;9(416):ePub - PMID: 29141885 - PMCID: PMC5808452 - DOI: 10.1126/scitranslmed.aah6888
Transcription factor TFEB cell-autonomously modulates susceptibility to intestinal epithelial cell injury in vivo.
p40 (phox) -Deficient Mice Exhibit Impaired Bacterial Clearance and Enhanced Pro-inflammatory Responses during Salmonella enterica serovar Typhimurium Infection.
Small-molecule inhibitors directly target CARD9 and mimic its protective variant in inflammatory bowel disease.
Proc Natl Acad Sci U S A. 2017;114(43):11392-11397 - PMID: 29073062 - PMCID: PMC5664502 - DOI: 10.1073/pnas.1705748114
SHANK3 Regulates Intestinal Barrier Function Through Modulating ZO-1 Expression Through the PKCε-dependent Pathway.
Inflamm Bowel Dis. 2017;23(10):1730-1740 - PMID: 28906292 - DOI: 10.1097/MIB.0000000000001250
Ectopic colonization of oral bacteria in the intestine drives TH1 cell induction and inflammation.
Autophagy-Independent Lysosomal Targeting Regulated by ULK1/2-FIP200 and ATG9.
Cell Rep. 2017;20(10):2341-2356 - PMID: 28877469 - PMCID: PMC5699710 - DOI: 10.1016/j.celrep.2017.08.034
The Ubiquitin Ligase Smurf1 Functions in Selective Autophagy of Mycobacterium tuberculosis and Anti-tuberculous Host Defense.
Cell Host Microbe. 2017;22(3):421-423 - PMID: 28910640 - PMCID: PMC5818210 - DOI: 10.1016/j.chom.2017.08.005
SHANK3 Regulates Intestinal Barrier Function Through Modulating ZO-1 Expression Through the PKCε-dependent Pathway.
Inflamm Bowel Dis. 2017;:ePub - PMID: 28922251
Human genetic variation and the gut microbiome in disease.
Nat Rev Genet. 2017;18(11):690-699 - PMID: 28824167 - DOI: 10.1038/nrg.2017.63
Small-molecule studies identify CDK8 as a regulator of IL-10 in myeloid cells.
Nat Chem Biol. 2017;13(10):1102-1108 - PMID: 28805801 - PMCID: PMC5693369 - DOI: 10.1038/nchembio.2458
Paneth cells secrete lysozyme via secretory autophagy during bacterial infection of the intestine.
Science. 2017;357(6355):1047-1052 - PMID: 28751470 - PMCID: PMC5702267 - DOI: 10.1126/science.aal4677
Intestinal virome changes precede autoimmunity in type I diabetes-susceptible children.
Proc Natl Acad Sci U S A. 2017;114(30):E6166-E6175 - PMID: 28696303 - PMCID: PMC5544325 - DOI: 10.1073/pnas.1706359114
Indoleacrylic Acid Produced by Commensal Peptostreptococcus Species Suppresses Inflammation.
Cell Host Microbe. 2017;22(1):25-37.e6 - PMID: 28704649 - PMCID: PMC5672633 - DOI: 10.1016/j.chom.2017.06.007
Fine-mapping inflammatory bowel disease loci to single-variant resolution.
E3 Ubiquitin ligase ZNRF4 negatively regulates NOD2 signalling and induces tolerance to MDP.
Dissecting the human microbiome with single-cell genomics.
Selective Induction of Homeostatic Th17 Cells in the Murine Intestine by Cholera Toxin Interacting with the Microbiota.
Epitope-specific immunotherapy targeting CD4-positive T cells in coeliac disease: two randomised, double-blind, placebo-controlled phase 1 studies.
Lancet Gastroenterol Hepatol. 2017;2(7):479-493 - PMID: 28506538 - PMCID: PMC5676538 - DOI: 10.1016/S2468-1253(17)30110-3
Gut Microbiome Function Predicts Response to Anti-integrin Biologic Therapy in Inflammatory Bowel Diseases.
Cell Host Microbe. 2017;21(5):603-610.e3 - PMID: 28494241 - PMCID: PMC5705050 - DOI: 10.1016/j.chom.2017.04.010
Reovirus infection triggers inflammatory responses to dietary antigens and development of celiac disease.
Maintenance of macrophage transcriptional programs and intestinal homeostasis by epigenetic reader SP140.
A Microbiome Foundation for the Study of Crohn's Disease.
Cell Host Microbe. 2017;21(3):301-304 - PMID: 28279336 - PMCID: PMC5684696 - DOI: 10.1016/j.chom.2017.02.012
Prediction of complicated disease course for children newly diagnosed with Crohn's disease: a multicentre inception cohort study.
Lancet. 2017;389(10080):1710-1718 - PMID: 28259484 - PMCID: PMC5719489 - DOI: 10.1016/S0140-6736(17)30317-3
The Ubiquitin Ligase Smurf1 Functions in Selective Autophagy of Mycobacterium tuberculosis and Anti-tuberculous Host Defense.
Cell Host Microbe. 2017;21(1):59-72 - PMID: 28017659 - PMCID: PMC5699477 - DOI: 10.1016/j.chom.2016.11.002
The Role of the Histone Methyltransferase Enhancer of Zeste Homolog 2 (EZH2) in the Pathobiological Mechanisms Underlying Inflammatory Bowel Disease (IBD).
J Biol Chem. 2017;292(2):706-722 - PMID: 27909059 - PMCID: PMC5241744 - DOI: 10.1074/jbc.M116.749663
The Csk-Associated Adaptor PAG Inhibits Effector T Cell Activation in Cooperation with Phosphatase PTPN22 and Dok Adaptors.
Cell Rep. 2016;17(10):2776-2788 - PMID: 27926878 - PMCID: PMC5656005 - DOI: 10.1016/j.celrep.2016.11.035
Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity.
Cell. 2016;167(7):1897 - PMID: 27984736 - DOI: 10.1016/j.cell.2016.11.046
TMEM258 Is a Component of the Oligosaccharyltransferase Complex Controlling ER Stress and Intestinal Inflammation.
Cell Rep. 2016;17(11):2955-2965 - PMID: 27974209 - PMCID: PMC5661940 - DOI: 10.1016/j.celrep.2016.11.042
Visceral Adiposity, Genetic Susceptibility, and Risk of Complications Among Individuals with Crohn's Disease.
Inflamm Bowel Dis. 2017;23(1):82-88 - PMID: 27893544 - PMCID: PMC5177457 - DOI: 10.1097/MIB.0000000000000978
Glutaminolysis and Fumarate Accumulation Integrate Immunometabolic and Epigenetic Programs in Trained Immunity.
Cell Metab. 2016;24(6):807-819 - PMID: 27866838 - PMCID: PMC5742541 - DOI: 10.1016/j.cmet.2016.10.008
Differential Effects of Environmental and Genetic Factors on T and B Cell Immune Traits.
Cell Rep. 2016;17(9):2474-2487 - PMID: 27818087 - PMCID: PMC5130901 - DOI: 10.1016/j.celrep.2016.10.053
A Functional Genomics Approach to Understand Variation in Cytokine Production in Humans.
Cell. 2016;167(4):1099-1110.e14 - PMID: 27814507 - DOI: 10.1016/j.cell.2016.10.017
Host and Environmental Factors Influencing Individual Human Cytokine Responses.
Cell. 2016;167(4):1111-1124.e13 - PMID: 27814508 - PMCID: PMC5787854 - DOI: 10.1016/j.cell.2016.10.018
Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity.
Cell. 2016;167(4):1125-1136.e8 - PMID: 27814509 - PMCID: PMC5131922 - DOI: 10.1016/j.cell.2016.10.020
RNF166 Determines Recruitment of Adaptor Proteins during Antibacterial Autophagy.
Cell Rep. 2016;17(9):2183-2194 - PMID: 27880896 - PMCID: PMC5192565 - DOI: 10.1016/j.celrep.2016.11.005
Vedolizumab Therapy Is Associated with an Improvement in Sleep Quality and Mood in Inflammatory Bowel Diseases.
Dig Dis Sci. 2017;62(1):197-206 - PMID: 27796768 - PMCID: PMC5218976 - DOI: 10.1007/s10620-016-4356-2
SIKs control osteocyte responses to parathyroid hormone.
Interplay of host genetics and gut microbiota underlying the onset and clinical presentation of inflammatory bowel disease.
Succinate Dehydrogenase Supports Metabolic Repurposing of Mitochondria to Drive Inflammatory Macrophages.
Cell. 2016;167(2):457-470.e13 - PMID: 27667687 - PMCID: PMC5863951 - DOI: 10.1016/j.cell.2016.08.064
Increased Intestinal Microbial Diversity Following Fecal Microbiota Transplant for Active Crohn's Disease.
Inflamm Bowel Dis. 2016;22(9):2182-90 - PMID: 27542133 - PMCID: PMC4995064 - DOI: 10.1097/MIB.0000000000000893
Characterization of candidate genes in inflammatory bowel disease-associated risk loci.
JCI Insight. 2016;1(13):e87899 - PMID: 27668286 - PMCID: PMC5033062 - DOI: 10.1172/jci.insight.87899
A protein-truncating R179X variant in RNF186 confers protection against ulcerative colitis.
Understanding human immune function using the resources from the Human Functional Genomics Project.
Nat Med. 2016;22(8):831-3 - PMID: 27490433 - DOI: 10.1038/nm.4140
A pleiotropic missense variant in SLC39A8 is associated with Crohn's disease and human gut microbiome composition.
Gastroenterology. 2016;151(4):724-32 - PMID: 27492617 - PMCID: PMC5037008 - DOI: 10.1053/j.gastro.2016.06.051
Dysbiosis, inflammation, and response to treatment: a longitudinal study of pediatric subjects with newly diagnosed inflammatory bowel disease.
Inter-individual variability and genetic influences on cytokine responses to bacteria and fungi.
Functional CRISPR screening identifies the ufmylation pathway as a regulator of SQSTM1/p62.
Microbiota as Therapeutic Targets.
Dig Dis. 2016;34(5):558-65 - PMID: 27331403 - DOI: 10.1159/000445263
Profiling DNA damage-induced phosphorylation in budding yeast reveals diverse signaling networks.
Proc Natl Acad Sci U S A. 2016;113(26):E3667-75 - PMID: 27298372 - PMCID: PMC4932963 - DOI: 10.1073/pnas.1602827113
The T300A Crohn's disease risk polymorphism impairs function of the WD40 domain of ATG16L1.
Genetic Coding Variant in GPR65 Alters Lysosomal pH and Links Lysosomal Dysfunction with Colitis Risk.
Immunity. 2016;44(6):1392-1405 - PMID: 27287411 - PMCID: PMC4936415 - DOI: 10.1016/j.immuni.2016.05.007
Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans.
Cell. 2016;165(6):1551 - PMID: 27259157 - DOI: 10.1016/j.cell.2016.05.056
Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability.
Sci Transl Med. 2016;8(343):343ra81 - PMID: 27306663 - PMCID: PMC5032909 - DOI: 10.1126/scitranslmed.aad0917
Metagenomic Characterization of Microbial Communities In Situ Within the Deeper Layers of the Ileum in Crohn's Disease.
Cell Mol Gastroenterol Hepatol. 2016;2(5):563-566.e5 - PMID: 28174737 - PMCID: PMC5042890 - DOI: 10.1016/j.jcmgh.2016.05.011
Development of Chemical Probes for Investigation of Salt-Inducible Kinase Function In Vivo.
ACS Chem Biol. 2016;11(8):2105-11 - PMID: 27224444 - PMCID: PMC4992440 - DOI: 10.1021/acschembio.6b00217
Simultaneous Pathway Activity Inference and Gene Expression Analysis Using RNA Sequencing.
CARD9 impacts colitis by altering gut microbiota metabolism of tryptophan into aryl hydrocarbon receptor ligands.
Gene-microbiota interactions contribute to the pathogenesis of inflammatory bowel disease.
Clinical Activity and Quality of Life Indices Are Valid Across Ulcerative Colitis But Not Crohn's Disease Phenotypes.
Dig Dis Sci. 2016;61(9):2627-35 - PMID: 27142671 - PMCID: PMC4982770 - DOI: 10.1007/s10620-016-4180-8
Mechanisms of Pediatric Inflammatory Bowel Disease.
Annu Rev Immunol. 2016;34:31-64 - PMID: 27168239 - DOI: 10.1146/annurev-immunol-032414-112151
Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity.
Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans.
Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans.
Trained immunity: A program of innate immune memory in health and disease.
Timothy C. Wang, MD: Our next AGA President.
Gastroenterology. 2016;150(5):1231-1236 - PMID: 27018487 - DOI: 10.1053/j.gastro.2016.03.021
?v Integrins combine with LC3 and atg5 to regulate Toll-like receptor signalling in B cells.
Impaired antibacterial autophagy links granulomatous intestinal inflammation in Niemann-Pick disease type C1 and XIAP deficiency with NOD2 variants in Crohn's disease.
New Regulatory Roles of Galectin-3 in the High-affinity IgE Receptor Signaling.
Sub-clinical detection of gut microbial biomarkers of obesity and type 2 diabetes.
Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition).
Autophagy. 2016;12(1):1-222 - PMID: 26799652 - PMCID: PMC4835977 - DOI: 10.1080/15548627.2015.1100356
Proton pump inhibitors affect the gut microbiome.
Flow Cytometric Analysis of Mononuclear Phagocytes in Non-diseased Human Lung and Lung-draining Lymph Nodes.
Am J Respir Crit Care Med. 2016;193(6):614-626 - PMID: 26551758 - PMCID: PMC4824940 - DOI: 10.1164/rccm.201507-1376OC
Ubiquitin Ligase TRIM62 Regulates CARD9-Mediated Anti-fungal Immunity and Intestinal Inflammation.
Immunity. 2015;43(4):715-726 - PMID: 26488816 - PMCID: PMC4672733 - DOI: 10.1016/j.immuni.2015.10.005
Ubiquitin Ligase TRIM62 Regulates CARD9-Mediated Anti-fungal Immunity and Intestinal Inflammation.
Immunity. 2015;43(4):715-26 - PMID: 26488816 - PMCID: PMC4672733 - DOI: 10.1016/j.immuni.2015.10.005
The Gut Microbiome Contributes to a Substantial Proportion of the Variation in Blood Lipids.
Circ Res. 2015;117(9):817-24 - PMID: 26358192 - PMCID: PMC4596485 - DOI: 10.1161/CIRCRESAHA.115.306807
A Noncanonical Autophagy Pathway Restricts Toxoplasma gondii Growth in a Strain-Specific Manner in IFN-?-Activated Human Cells.
A Noncanonical Autophagy Pathway Restricts Toxoplasma gondii Growth in a Strain-Specific Manner in IFN-?-Activated Human Cells.
ConStrains identifies microbial strains in metagenomic datasets.
Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses.
Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses.
Common Genetic Variants Influence Circulating Vitamin D Levels in Inflammatory Bowel Diseases.
Inflamm Bowel Dis. 2015;21(11):2507-2514 - PMID: 26241000 - PMCID: PMC4615315 - DOI: 10.1097/MIB.0000000000000524
Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples.
Functional genomics identifies negative regulatory nodes controlling phagocyte oxidative burst.
Small-molecule enhancers of autophagy modulate cellular disease phenotypes suggested by human genetics.
Proc Natl Acad Sci U S A. 2015;112(31):E4281-7 - PMID: 26195741 - PMCID: PMC4534235 - DOI: 10.1073/pnas.1512289112
Body Mass Index, Genetic Susceptibility, and Risk of Complications Among Individuals with Crohn's Disease.
Inflamm Bowel Dis. 2015;21(10):2304-2310 - PMID: 26181430 - PMCID: PMC4567407 - DOI: 10.1097/MIB.0000000000000498
Role of Autophagy in the Maintenance of Intestinal Homeostasis.
Gastroenterology. 2015;149(3):553-62 - PMID: 26170139 - PMCID: PMC4550567 - DOI: 10.1053/j.gastro.2015.06.046
Integrated Genomics of Crohn's Disease Risk Variant Identifies a Role for CLEC12A in Antibacterial Autophagy.
Cell Rep. 2015;11(12):1905-1918 - PMID: 26095365 - PMCID: PMC4507440 - DOI: 10.1016/j.celrep.2015.05.045
Identification of an anti-inflammatory protein from Faecalibacterium prausnitzii, a commensal bacterium deficient in Crohn's disease.
CARMA3 Is Critical for the Initiation of Allergic Airway Inflammation.
The kinase DYRK1A reciprocally regulates the differentiation of Th17 and regulatory T cells.
An Integrative View of Microbiome-Host Interactions in Inflammatory Bowel Diseases.
Cell Host Microbe. 2015;17(5):577-591 - PMID: 25974300 - PMCID: PMC4498258 - DOI: 10.1016/j.chom.2015.04.008
Discovery of a Small-Molecule Probe for V-ATPase Function.
Associations between host gene expression, the mucosal microbiome, and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease.
Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature.
A novel role for KLF14 in T regulatory cell differentiation.
Cell Mol Gastroenterol Hepatol. 2015;1(2):188-202.e4 - PMID: 25750932 - PMCID: PMC4349492 - DOI: 10.1016/j.jcmgh.2014.12.007
The Dynamics of the Human Infant Gut Microbiome in Development and in Progression toward Type 1 Diabetes.
Cell Host Microbe. 2015;17(2):260-273 - PMID: 25662751 - PMCID: PMC4689191 - DOI: 10.1016/j.chom.2015.01.001
Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease.
Pyruvate Kinase M2 Regulates Hif-1? Activity and IL-1? Induction and Is a Critical Determinant of the Warburg Effect in LPS-Activated Macrophages.
Early life environment and natural history of inflammatory bowel diseases.
BMC Gastroenterol. 2014;14(1):216 - PMID: 25510175 - PMCID: PMC4300207 - DOI: 10.1186/s12876-014-0216-8
Complex host genetics influence the microbiome in inflammatory bowel disease.
Autophagy and checkpoints for intracellular pathogen defense.
Curr Opin Gastroenterol. 2015;31(1):14-23 - PMID: 25394238 - PMCID: PMC4330559 - DOI: 10.1097/MOG.0000000000000134
Autophagy Controls BCG-Induced Trained Immunity and the Response to Intravesical BCG Therapy for Bladder Cancer.
PLoS Pathog. 2014;10(10):e1004485 - PMID: 25356988 - PMCID: PMC4214925 - DOI: 10.1371/journal.ppat.1004485
BCG-induced trained immunity in NK cells: Role for non-specific protection to infection.
Clin Immunol. 2014;155(2):213-219 - PMID: 25451159 - PMCID: PMC5084088 - DOI: 10.1016/j.clim.2014.10.005
Genetics of immune-mediated disorders: from genome-wide association to molecular mechanism.
Curr Opin Immunol. 2014;31C:51-57 - PMID: 25458995 - PMCID: PMC5080657 - DOI: 10.1016/j.coi.2014.09.007
An Image-Based Genetic Assay Identifies Genes in T1D Susceptibility Loci Controlling Cellular Antiviral Immunity in Mouse.
PLoS One. 2014;9(9):e108777 - PMID: 25268627 - PMCID: PMC4182575 - DOI: 10.1371/journal.pone.0108777
CRISPR-Cas9 Knockin Mice for Genome Editing and Cancer Modeling.
Transmembrane adaptor protein PAG/CBP is involved in both positive and negative regulation of mast cell signaling.
Mol Cell Biol. 2014;34(23):4285-300 - PMID: 25246632 - PMCID: PMC4248753 - DOI: 10.1128/MCB.00983-14
Small-molecule control of cytokine function: new opportunities for treating immune disorders.
Curr Opin Chem Biol. 2014;23C:23-30 - PMID: 25222143 - PMCID: PMC5087273 - DOI: 10.1016/j.cbpa.2014.08.013
Immunochip SNP array identifies novel genetic variants conferring susceptibility to candidaemia.
Rational design of highly active sgRNAs for CRISPR-Cas9-mediated gene inactivation.
Epigenetic programming of monocyte-to-macrophage differentiation and trained innate immunity.
mTOR- and HIF-1?-mediated aerobic glycolysis as metabolic basis for trained immunity.
Multivariate inference of pathway activity in host immunity and response to therapeutics.
Nucleic Acids Res. 2014;42(16):10288-306 - PMID: 25147207 - PMCID: PMC4176341 - DOI: 10.1093/nar/gku722
An alteration in ATG16L1 stability in Crohn disease.
Small-molecule screening identifies inhibition of salt-inducible kinases as a therapeutic strategy to enhance immunoregulatory functions of dendritic cells.
Proc Natl Acad Sci U S A. 2014;111(34):12468-12473 - PMID: 25114223 - PMCID: PMC4151730 - DOI: 10.1073/pnas.1412308111
Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature.
SLCO3A1, a Novel Crohn's Disease-Associated Gene, Regulates NF-?B Activity and Associates with Intestinal Perforation.
PLoS One. 2014;9(6):e100515 - PMID: 24945726 - PMCID: PMC4063938 - DOI: 10.1371/journal.pone.0100515
Inflammatory Bowel Disease as a Model for Translating the Microbiome.
Immunity. 2014;40(6):843-854 - PMID: 24950204 - PMCID: PMC4135443 - DOI: 10.1016/j.immuni.2014.05.013
Dectin-1 dependent LC3 recruitment to phagosomes enhances fungicidal activity in macrophages.
J Infect Dis. 2014;210(11):1844-54 - PMID: 24842831 - PMCID: PMC4271056 - DOI: 10.1093/infdis/jiu290
Atg16L1 T300A variant decreases selective autophagy resulting in altered cytokine signaling and decreased antibacterial defense.
Proc Natl Acad Sci U S A. 2014;111(21):7741-7746 - PMID: 24821797 - PMCID: PMC4040621 - DOI: 10.1073/pnas.1407001111
Genetic Polymorphisms in Metabolizing Enzymes Modifying the Association Between Smoking and Inflammatory Bowel Diseases.
Inflamm Bowel Dis. 2014;20(5):783-9 - PMID: 24651583 - PMCID: PMC4113010 - DOI: 10.1097/MIB.0000000000000014
The treatment-naive microbiome in new-onset Crohn's disease.
Cell Host Microbe. 2014;15(3):382-92 - PMID: 24629344 - PMCID: PMC4059512 - DOI: 10.1016/j.chom.2014.02.005
Human Genome-Wide RNAi Screen Identifies an Essential Role for Inositol Pyrophosphates in Type-I Interferon Response.
PLoS Pathog. 2014;10(2):e1003981 - PMID: 24586175 - PMCID: PMC3937324 - DOI: 10.1371/journal.ppat.1003981
IL-1 receptor blockade restores autophagy and reduces inflammation in chronic granulomatous disease in mice and in humans.
Proc Natl Acad Sci U S A. 2014;111(9):3526-31 - PMID: 24550444 - PMCID: PMC3948220 - DOI: 10.1073/pnas.1322831111
The Microbiome in Inflammatory Bowel Diseases: Current Status and the Future Ahead.
Gastroenterology. 2014;146(6):1489-99 - PMID: 24560869 - PMCID: PMC4034132 - DOI: 10.1053/j.gastro.2014.02.009
SMAD3 gene variant is a risk factor for recurrent surgery in patients with Crohn's disease.
J Crohns Colitis. 2014;8(8):845-51 - PMID: 24461721 - PMCID: PMC4237062 - DOI: 10.1016/j.crohns.2014.01.003
Differential Effect of Genetic Burden on Disease Phenotypes in Crohn's Disease and Ulcerative Colitis: Analysis of a North American Cohort.
Am J Gastroenterol. 2014;109(3):395-400 - PMID: 24419484 - PMCID: PMC4225079 - DOI: 10.1038/ajg.2013.464
Autophagy is essential for cardiac morphogenesis during vertebrate development.
Autosis is a Na+,K+-ATPase-regulated form of cell death triggered by autophagy-inducing peptides, starvation, and hypoxia-ischemia.
Proc Natl Acad Sci U S A. 2013;110(51):20364-71 - PMID: 24277826 - PMCID: PMC3870705 - DOI: 10.1073/pnas.1319661110
Autophagy is redundant for the host defense against systemic Candida albicans infections.
Eur J Clin Microbiol Infect Dis. 2014;33(5):711-22 - PMID: 24202731 - DOI: 10.1007/s10096-013-2002-x
Autophagy at the crossroads of metabolism and cellular defense.
Curr Opin Gastroenterol. 2013;29(6):588-96 - PMID: 24100719 - DOI: 10.1097/MOG.0b013e328365d34d
Long-Lasting Effects of BCG Vaccination on Both Heterologous Th1/Th17 Responses and Innate Trained Immunity.
Selective Modulation of Autophagy, Innate Immunity, and Adaptive Immunity by Small Molecules.
Novel Mechanism of Tumor Suppression by Polarity Gene Discs Large 1 (DLG1) Revealed in a Murine Model of Pediatric B-ALL.
Cancer Immunol Res. 2013;1(6):426-37 - PMID: 24778134 - PMCID: PMC4006353 - DOI: 10.1158/2326-6066.CIR-13-0065
Advances in inflammatory bowel disease pathogenesis: linking host genetics and the microbiome.
Deep Resequencing of GWAS Loci Identifies Rare Variants in CARD9, IL23R and RNF186 That Are Associated with Ulcerative Colitis.
PLoS Genet. 2013;9(9):e1003723 - PMID: 24068945 - PMCID: PMC3772057 - DOI: 10.1371/journal.pgen.1003723
Atg16l1 is Required for Autophagy in Intestinal Epithelial Cells and Protection of Mice from Salmonella Infection.
Gastroenterology. 2013;145(6):1347-57 - PMID: 23973919 - PMCID: PMC3840157 - DOI: 10.1053/j.gastro.2013.08.035
Beclin 2 Functions in Autophagy, Degradation of G Protein-Coupled Receptors, and Metabolism.
Functional profiling of the gut microbiome in disease-associated inflammation.
Genetic risk factors for Clostridium difficile infection in ulcerative colitis.
Aliment Pharmacol Ther. 2013;38(5):522-30 - PMID: 23848254 - PMCID: PMC3755009 - DOI: 10.1111/apt.12425
Skin Microbiome Imbalance in Patients with STAT1/STAT3 Defects Impairs Innate Host Defense Responses.
Card9 Mediates Intestinal Epithelial Cell Restitution, T-helper 17 Responses, and Control of Bacterial Infection in Mice.
Gastroenterology. 2013;145(3):591-601.e3 - PMID: 23732773 - PMCID: PMC3781941 - DOI: 10.1053/j.gastro.2013.05.047
Conformational stability, vibrational spectra, HOMO-LUMO and NBO analysis of 1,3,4-thiadiazolidine-2,5-dithione with experimental (FT-IR and FT-Raman) techniques and scaled quantum mechanical calculations.
Spectrochim Acta A Mol Biomol Spectrosc. 2013;113:171-81 - PMID: 23727670 - DOI: 10.1016/j.saa.2013.04.108
How Does Genotype Influence Disease Phenotype in Inflammatory Bowel Disease?
Inflamm Bowel Dis. 2013;19(9):2021-30 - PMID: 23644824 - PMCID: PMC3720704 - DOI: 10.1097/MIB.0b013e318281f5c5
Concomitant BRAF and PI3K/mTOR Blockade Is Required for Effective Treatment of BRAFV600E Colorectal Cancer.
Clin Cancer Res. 2013;19(10):2688-98 - PMID: 23549875 - PMCID: PMC3815598 - DOI: 10.1158/1078-0432.CCR-12-2556
From genetics of inflammatory bowel disease towards mechanistic insights.
Trends Immunol. 2013;34(8):371-8 - PMID: 23639549 - PMCID: PMC3735683 - DOI: 10.1016/j.it.2013.04.001
Genome-wide Analysis of Immune System Genes by Expressed Sequence Tag Profiling.
J Immunol. 2013;190(11):5578-5587 - PMID: 23616578 - PMCID: PMC3703829 - DOI: 10.4049/jimmunol.1203471
Succinate is an inflammatory signal that induces IL-1? through HIF-1?.
Receptor interacting protein kinase 2-mediated mitophagy regulates inflammasome activation during virus infection.
Polarity gene discs large homolog 1 regulates the generation of memory T cells.
Cutting Edge: cell-autonomous control of IL-7 response revealed in a novel stage of precursor B cells.
Development of a Colon Cancer GEMM-Derived Orthotopic Transplant Model for Drug Discovery and Validation.
Clin Cancer Res. 2013;19(11):2929-40 - PMID: 23403635 - PMCID: PMC3951107 - DOI: 10.1158/1078-0432.CCR-12-2307
Mutations causing medullary cystic kidney disease type 1 lie in a large VNTR in MUC1 missed by massively parallel sequencing.
?-6 Polyunsaturated fatty acids extend life span through the activation of autophagy.
Autophagy modulates Borrelia burgdorferi-induced production of interleukin-1? (IL-1?).
J Biol Chem. 2013;288(12):8658-66 - PMID: 23386602 - PMCID: PMC3605684 - DOI: 10.1074/jbc.M112.412841
Identification of a candidate therapeutic autophagy-inducing peptide.
ATG5 regulates plasma cell differentiation.
Angiotensin II Drives the Production of Tumor-Promoting Macrophages.
Immunity. 2013;38(2):296-308 - PMID: 23333075 - PMCID: PMC3582771 - DOI: 10.1016/j.immuni.2012.10.015
Functional genomics identifies type I interferon pathway as central for host defense against Candida albicans.
The LRR and RING Domain Protein LRSAM1 Is an E3 Ligase Crucial for Ubiquitin-Dependent Autophagy of Intracellular Salmonella Typhimurium.
Cell Host Microbe. 2012;12(6):778-90 - PMID: 23245322 - PMCID: PMC3785244 - DOI: 10.1016/j.chom.2012.10.019
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
Common alleles that influence autophagy and the risk for inflammatory bowel disease.
Curr Opin Immunol. 2012;24(5):522-9 - PMID: 23041451 - DOI: 10.1016/j.coi.2012.08.001
Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment.
Bacille Calmette-Guerin induces NOD2-dependent nonspecific protection from reinfection via epigenetic reprogramming of monocytes.
Proc Natl Acad Sci U S A. 2012;109(43):17537-42 - PMID: 22988082 - PMCID: PMC3491454 - DOI: 10.1073/pnas.1202870109
Essential cell autonomous role for interferon regulatory factor 1 in interferon-?-mediated inhibition of norovirus replication in macrophages.
p40phox Expression Regulates Neutrophil Recruitment and Function during the Resolution Phase of Intestinal Inflammation.
Enhanced Tim3 Activity Improves Survival after Influenza Infection.
Enhanced Tim3 activity improves survival after influenza infection.
Candida albicans Infection Affords Protection against Reinfection via Functional Reprogramming of Monocytes.
Cell Host Microbe. 2012;12(2):223-32 - PMID: 22901542 - PMCID: PMC3864037 - DOI: 10.1016/j.chom.2012.06.006
Case 23-2012.
N Engl J Med. 2012;367(4):363-73 - PMID: 22830467 - DOI: 10.1056/NEJMcpc1109275
Non-invasive mapping of the gastrointestinal microbiota identifies children with inflammatory bowel disease.
Helminth Infection Impairs Autophagy-Mediated Killing of Bacterial Enteropathogens by Macrophages.
Establishment and characterization of a novel chordoma cell line: CH22.
J Orthop Res. 2012;30(10):1666-73 - PMID: 22504929 - DOI: 10.1002/jor.22113
Regulation of monocyte functional heterogeneity by miR-146a and Relb.
Cell Rep. 2012;1(4):317-324 - PMID: 22545247 - PMCID: PMC3334310 - DOI: 10.1016/j.celrep.2012.02.009
Autophagy and the immune system.
Annu Rev Immunol. 2012;30:611-46 - PMID: 22449030 - DOI: 10.1146/annurev-immunol-020711-074948
Nondegradative Role of Atg5-Atg12/ Atg16L1 Autophagy Protein Complex in Antiviral Activity of Interferon Gamma.
Cell Host Microbe. 2012;11(4):397-409 - PMID: 22520467 - PMCID: PMC3348177 - DOI: 10.1016/j.chom.2012.03.002
Guidelines for the use and interpretation of assays for monitoring autophagy.
ONCOGENIC KRAS REGULATES BMP4 EXPRESSION IN COLON CANCER CELL LINES.
Am J Physiol Gastrointest Liver Physiol. 2012;302(10):G1223-30 - PMID: 22383492 - PMCID: PMC3362092 - DOI: 10.1152/ajpgi.00047.2011
Tribbles 2 (Trib2) is a novel regulator of toll-like receptor 5 signaling.
Genome-wide siRNA screen for mediators of NF-?B activation.
Proc Natl Acad Sci U S A. 2012;109(7):2467-72 - PMID: 22308454 - PMCID: PMC3289371 - DOI: 10.1073/pnas.1120542109
Image-based genome-wide siRNA screen identifies selective autophagy factors.
CARMA1 is necessary for optimal T cell responses in a murine model of allergic asthma.
J Immunol. 2011;187(12):6197-207 - PMID: 22075698 - PMCID: PMC3237896 - DOI: 10.4049/jimmunol.1101348
Caspase 8 inhibits programmed necrosis by processing CYLD.
Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease.
HCV causes chronic endoplasmic reticulum stress leading to adaptation and interference with the unfolded protein response.
Phosphoprotein associated with glycosphingolipid-enriched microdomains differentially modulates SRC kinase activity in brain maturation.
Leucine-rich repeat (LRR) proteins: integrators of pattern recognition and signaling in immunity.
Use of an optical trap for study of host-pathogen interactions for dynamic live cell imaging.
Genetics and pathogenesis of inflammatory bowel disease.
A Francisella tularensis locus required for spermine responsiveness is necessary for virulence.
MyD88-dependent TLR1/2 signals educate dendritic cells with gut-specific imprinting properties.
Recurrent chromosomal copy number alterations in sporadic chordomas.
Bacterial and host determinants of MAL activation upon EPEC infection: the roles of Tir, ABRA, and FLRT3.
PLoS Pathog. 2011;7(4):e1001332 - PMID: 21490959 - PMCID: PMC3072376 - DOI: 10.1371/journal.ppat.1001332
Crohn disease: a current perspective on genetics, autophagy and immunity.
Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47.
Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology.
PLoS Genet. 2011;7(1):e1001273 - PMID: 21249183 - PMCID: PMC3020935 - DOI: 10.1371/journal.pgen.1001273
Control and manipulation of pathogens with an optical trap for live cell imaging of intercellular interactions.
PLoS One. 2010;5(12):e15215 - PMID: 21217821 - PMCID: PMC3013098 - DOI: 10.1371/journal.pone.0015215
Failure and exploitation of autophagy in human pathologies-cellular integrity between inflammation, infection, and cell survival.
Semin Immunopathol. 2010;32(4):319-22 - PMID: 21107575 - DOI: 10.1007/s00281-010-0229-5
Ubiquitin accumulation in autophagy-deficient mice is dependent on the Nrf2-mediated stress response pathway: a potential role for protein aggregation in autophagic substrate selection.
LRRK2 is involved in the IFN-gamma response and host response to pathogens.
Human IRGM gene "to be or not to be".
Semin Immunopathol. 2010;32(4):437-44 - PMID: 20737271 - DOI: 10.1007/s00281-010-0224-x
Genome-wide analysis reveals mechanisms modulating autophagy in normal brain aging and in Alzheimer's disease.
Proc Natl Acad Sci U S A. 2010;107(32):14164-9 - PMID: 20660724 - PMCID: PMC2922576 - DOI: 10.1073/pnas.1009485107
Wnt signaling regulates mitochondrial physiology and insulin sensitivity.
A systems biology viewpoint on autophagy in health and disease.
Curr Opin Gastroenterol. 2010;26(4):302-9 - PMID: 20571384 - DOI: 10.1097/MOG.0b013e32833ae2ed
A genome-wide siRNA screen reveals multiple mTORC1 independent signaling pathways regulating autophagy under normal nutritional conditions.
Dev Cell. 2010;18(6):1041-52 - PMID: 20627085 - PMCID: PMC2935848 - DOI: 10.1016/j.devcel.2010.05.005
Characterization and analysis of human chordoma cell lines.
Spine (Phila Pa 1976). 2010;35(13):1257-64 - PMID: 20461036 - PMCID: PMC3769690 - DOI: 10.1097/BRS.0b013e3181c2a8b0
Virus-plus-susceptibility gene interaction determines Crohn's disease gene Atg16L1 phenotypes in intestine.
Differential expression of microRNA (miRNA) in chordoma reveals a role for miRNA-1 in Met expression.
J Orthop Res. 2010;28(6):746-52 - PMID: 20041488 - DOI: 10.1002/jor.21055
Gene enrichment profiles reveal T-cell development, differentiation, and lineage-specific transcription factors including ZBTB25 as a novel NF-AT repressor.
Blood. 2010;115(26):5376-84 - PMID: 20410506 - PMCID: PMC2902135 - DOI: 10.1182/blood-2010-01-263855
Exploring the interplay of barrier function and leukocyte recruitment in intestinal inflammation by targeting fucosyltransferase VII and trefoil factor 3.
Am J Physiol Gastrointest Liver Physiol. 2010;299(1):G43-53 - PMID: 20299601 - PMCID: PMC2904110 - DOI: 10.1152/ajpgi.00228.2009
Genome-wide association identifies multiple ulcerative colitis susceptibility loci.
Autophagy at the gut interface: mucosal responses to stress and the consequences for inflammatory bowel diseases.
The IFITM proteins mediate cellular resistance to influenza A H1N1 virus, West Nile virus, and dengue virus.
Common variants at five new loci associated with early-onset inflammatory bowel disease.
Autophagy, immunity and human disease.
Curr Opin Gastroenterol. 2009;25(6):512-20 - PMID: 19826372 - PMCID: PMC2849745 - DOI: 10.1097/MOG.0b013e32833104f1
Regulation of inflammatory responses by gut microbiota and chemoattractant receptor GPR43.
A genome-wide genetic screen for host factors required for hepatitis C virus propagation.
Proc Natl Acad Sci U S A. 2009;106(38):16410-5 - PMID: 19717417 - PMCID: PMC2752535 - DOI: 10.1073/pnas.0907439106
Building complex biological networks based upon model organisms: mapping the human autophagy interactome via a hybrid yeast-human protein interaction network.
Autophagy. 2009;5(6):884-6 - PMID: 19535904 - DOI: 10.4161/auto.9094
Identification of Atg5-dependent transcriptional changes and increases in mitochondrial mass in Atg5-deficient T lymphocytes.
Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions.
PLoS Genet. 2009;5(6):e1000534 - PMID: 19557189 - PMCID: PMC2694358 - DOI: 10.1371/journal.pgen.1000534
An integrative genomics approach identifies Hypoxia Inducible Factor-1 (HIF-1)-target genes that form the core response to hypoxia.
Nucleic Acids Res. 2009;37(14):4587-602 - PMID: 19491311 - PMCID: PMC2724271 - DOI: 10.1093/nar/gkp425
The cytoskeletal scaffold Shank3 is recruited to pathogen-induced actin rearrangements.
Exp Cell Res. 2009;315(12):2001-11 - PMID: 19371741 - PMCID: PMC2693461 - DOI: 10.1016/j.yexcr.2009.04.003
A novel hybrid yeast-human network analysis reveals an essential role for FNBP1L in antibacterial autophagy.
Selective activation of nuclear factor kappa B in the cochlea by sensory and inflammatory stress.
Neuroscience. 2009;160(2):530-9 - PMID: 19285117 - PMCID: PMC2673023 - DOI: 10.1016/j.neuroscience.2009.02.073
Selective activation of nuclear factor kappa B in the cochlea by sensory and inflammatory stress.
Neuroscience. 2009;160(2):530-9 - PMID: 19285117 - PMCID: PMC2673023 - DOI: 10.1016/j.neuroscience.2009.02.073
A functional genomic screen identifies cellular cofactors of hepatitis C virus replication.
Cell Host Microbe. 2009;5(3):298-307 - PMID: 19286138 - PMCID: PMC2756022 - DOI: 10.1016/j.chom.2009.02.001
Genetic variants in the region harbouring IL2/IL21 associated with ulcerative colitis.
HIF-1alpha and HIF-2alpha have divergent roles in colon cancer.
On the level: IRGM gene function is all about expression.
Differential requirement for CARMA1 in agonist-selected T-cell development.
The Nore1B/Mst1 complex restrains antigen receptor-induced proliferation of naïve T cells.
Proc Natl Acad Sci U S A. 2008;105(51):20321-6 - PMID: 19073936 - PMCID: PMC2600581 - DOI: 10.1073/pnas.0810773105
Identification of a molecular signaling network that regulates a cellular necrotic cell death pathway.
Role for beta-catenin and HOX transcription factors in Caenorhabditis elegans and mammalian host epithelial-pathogen interactions.
Proc Natl Acad Sci U S A. 2008;105(45):17469-74 - PMID: 18981407 - PMCID: PMC2582251 - DOI: 10.1073/pnas.0809527105
Impaired autophagy of an intracellular pathogen induced by a Crohn's disease associated ATG16L1 variant.
A key role for autophagy and the autophagy gene Atg16l1 in mouse and human intestinal Paneth cells.
Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn's disease.
RNA interference screen for human genes associated with West Nile virus infection.
Genome-wide association studies: a new window into immune-mediated diseases.
Genome-wide association studies: a new window into immune-mediated diseases.
MAST3: a novel IBD risk factor that modulates TLR4 signaling.
Hoxc6 is overexpressed in gastrointestinal carcinoids and interacts with JunD to regulate tumor growth.
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