ArticleNature genetics2017
A functional genomics predictive network model identifies regulators of inflammatory bowel disease.
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Article in Nature genetics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 159 papers, 1 of them a synthesis that pooled it.
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159citing papers in PubMed, 1 pooled it
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Who cites it
159 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Guidelines for bioinformatics of single-cell sequencing data analysis in Alzheimer's disease: review, recommendation, implementation and application.Molecular neurodegeneration · 2022Pooled it
- Multiomic characterisation of the clinical efficacy of guselkumab induction therapy in ulcerative colitis.BMJ open gastroenterology · 2026Trial
- From signals to systems: the epigenetic-microbiome-mitochondrial axis in IBD pathogenesis.Gut microbes · 2026Review
- Food-Based Therapies in Pediatric Inflammatory Bowel Diseases.Nutrients · 2026Review
- Meflin confers antifibrotic properties to intestinal fibroblasts in inflammatory bowel disease.The Journal of clinical investigation · 2026Article
- BIRC3 (Encoding cIAP2) Variants Result in Dysregulated RIPK1 Signaling Leading to Increased Epithelial Cell Death and Are Associated With Monogenic Crohn's Disease.Gastroenterology · 2026Article
- TIPE2 gene knockdown in mice attenuates experimental colitis by diminishing inflammatory cell infiltration.Molecular therapy. Nucleic acids · 2026Article
- Inflammation rewires the enteric nervous system through neurogenic monocyte recruitment.The Journal of experimental medicine · 2026Article
- Viral mimicry acts as a tumor suppressor in colitis.Nature communications · 2026Article
- Integrative eQTL and Mendelian Randomization Analyses with Experimental Validation Prioritize Genetic Candidate Biomarkers for Crohn's Disease.Endocrine, metabolic & immune disorders drug targets · 2026Article
- Aimed at Subtype Discrimination but Yielding a Shared Marker: Integrative Analysis of Blood Transcriptomes Reveals UpregulatedClinical and experimental gastroenterology · 2026Article
- Generative AI-augmented transcriptomic and microbiome analysis across inflammatory and fibrotic disease states in Crohn's disease.Frontiers in artificial intelligence · 2026Article
- The plasticity and metabolic reprogramming of macrophage in ulcerative colitis.Frontiers in immunology · 2026Review
- Integrative Analysis of Intestinal Transcriptomes UnderscoresBioinformatics and biology insights · 2026Article
- Airway transcriptome networks for ozone and PMGenome medicine · 2025Article
- Distinct colitis-associated macrophages drive NOD2-dependent bacterial sensing and gut homeostasis.The Journal of clinical investigation · 2025Article
- Dysregulation of cellular metabolism within the gut-brain axis is associated with behavioural changes in chronic intestinal inflammation.Journal of neuroinflammation · 2025Article
- Hem1 controls T cell activation, memory, and the regulated release of immunosuppressive and proinflammatory cytokines.JCI insight · 2025Article
- Phenome-wide association study of monogenic inflammatory bowel disease genes in diverse biobanks identifies population-specific and shared Goldilocks alleles: implications for Precision Medicine.Journal of Crohn's & colitis · 2025Article
- A Multiomic Network Approach to Uncover Disease Modifying Mechanisms of Inborn Errors of Metabolism.Journal of inherited metabolic disease · 2025Article
99 more citing papers are in PubMed but not listed here.
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Authors and funding
38 authors.
Lauren A PetersDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
Jacqueline PerrigoueJanssen Research and Development, LLC., Spring House, Pennsylvania, USA.
Arthur MorthaDepartment of Immunology, University of Toronto, Toronto, Ontario, Canada.
Alina IugaDepartment of Pathology and Cell Biology, Columbia University Medical Center, New York, New York, USA.
Won-Min SongDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.ORCID http://orcid.org/0000-0003-0948-119X
Eric M NeimanJanssen Research and Development, LLC., Spring House, Pennsylvania, USA.
Sean R LlewellynDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
Antonio Di NarzoDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
Brian A KiddDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.ORCID http://orcid.org/0000-0003-2110-1145
Shannon E TelescoJanssen Research and Development, LLC., Spring House, Pennsylvania, USA.
Yongzhong ZhaoDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
Aleksandar StojmirovicJanssen Research and Development, LLC., Spring House, Pennsylvania, USA.
Jocelyn SendeckiJanssen Research and Development, LLC., Spring House, Pennsylvania, USA.
Khader ShameerDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
Riccardo MiottoDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
Bojan LosicDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
Hardik ShahIcahn Institute of Genomics and Multi-scale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
Eunjee LeeDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
Minghui WangDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.ORCID http://orcid.org/0000-0001-9171-4962
Jeremiah J FaithDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
Andrew KasarskisDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
Carrie BrodmerkelJanssen Research and Development, LLC., Spring House, Pennsylvania, USA.
Mark CurranJanssen Research and Development, LLC., Spring House, Pennsylvania, USA.
Anuk DasJanssen Research and Development, LLC., Spring House, Pennsylvania, USA.
Joshua R FriedmanJanssen Research and Development, LLC., Spring House, Pennsylvania, USA.ORCID http://orcid.org/0000-0001-9382-8429
Yoshinori FukuiDivision of Immunogenetics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.
Mary Beth HumphreyUniversity of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA.
Brian M IritaniDepartment of Comparative Medicine, University of Washington, Seattle, Washington, USA.
Nicholas SibingaDepartment of Medicine (Cardiovascular Division), Albert Einstein College of Medicine, Bronx, New York, USA.ORCID http://orcid.org/0000-0003-4838-910X
Teresa K TarrantThurston Arthritis Research Center and Department of Medicine, Division of Rheumatology, Allergy, and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
Carmen ArgmannDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
Ke HaoDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
Panos RoussosDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
Jun ZhuDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.ORCID http://orcid.org/0000-0003-0834-8178
Bin ZhangDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
Radu DobrinJanssen Research and Development, LLC., Spring House, Pennsylvania, USA.
Lloyd F MayerThe Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
Eric E SchadtDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.ORCID http://orcid.org/0000-0002-7892-8808
Funding
Translational Research CoreP30DK020541 · NIDDK · ALBERT EINSTEIN COLLEGE OF MEDICINE, INC · PI STREAMSON C CHUA · 2015 to 2026
$27.7MIntegrative Network Biology Approaches to Identify, Characterize and Validate Molecular Subtypes in Alzheimer's DiseaseU01AG046170 · NIA · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI EHRLICH, MICHELLE E, GANDY, SAMUEL E. · 2013 to 2022
$26.0MHigher Order Chromatin and Genetic Risk for Alzheimer's DiseaseR01AG050986 · NIA · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI ROUSSOS, PANAGIOTIS · 2015 to 2025
$11.2MIntegrated Multiscale Networks in SchizophreniaR01MH109897 · NIMH · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI BRENNAND, KRISTEN JENNIFER, ROUSSOS, PANAGIOTIS · 2016 to 2020
$3.0MAllograft inflammatory factor-1 in atherosclerosisR01HL128066 · NHLBI · ALBERT EINSTEIN COLLEGE OF MEDICINE, INC · PI SIBINGA, NICHOLAS E · 2015 to 2018
$2.1MTargeting Fnip1 to disrupt B cell development, metabolism, and transformationR01AI114556 · NIAID · UNIVERSITY OF WASHINGTON · PI IRITANI, BRIAN M · 2015 to 2019
$2.0MTransforming Genomics with 5 PB Big Omics Data Engine Cray CS300-AC SupercomputerS10OD018522 · OD · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI KOVATCH, PATRICIA · 2014 to 2014
$1.9MDeveloping methods for curating multi-omics dataU01HG008451 · NHGRI · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI ZHU, JUN · 2015 to 2017
$1.5MFolliculin Interacting Proteins in Lymphocyte Development and AutoimmunityR21AI109020 · NIAID · UNIVERSITY OF WASHINGTON · PI IRITANI, BRIAN M · 2014 to 2015
$425kFnip1 Function in Lymphocyte Development, Activation and MetabolismR56AI092093 · NIAID · UNIVERSITY OF WASHINGTON · PI IRITANI, BRIAN M · 2013 to 2013
$353kNHGRI NIH HHS U01 HG008451NHLBI NIH HHS R01 HL128066NIAID NIH HHS R01 AI114556NIAID NIH HHS R21 AI109020NIAID NIH HHS R56 AI092093NIA NIH HHS R01 AG050986NIA NIH HHS U01 AG046170NIDDK NIH HHS P30 DK020541NIH HHS S10 OD018522NIMH NIH HHS R01 MH109897
Abstract
A major challenge in inflammatory bowel disease (IBD) is the integration of diverse IBD data sets to construct predictive models of IBD. We present a predictive model of the immune component of IBD that informs causal relationships among loci previously linked to IBD through genome-wide association studies (GWAS) using functional and regulatory annotations that relate to the cells, tissues, and pathophysiology of IBD. Our model consists of individual networks constructed using molecular data generated from intestinal samples isolated from three populations of patients with IBD at different stages of disease. We performed key driver analysis to identify genes predicted to modulate network regulatory states associated with IBD, prioritizing and prospectively validating 12 of the top key drivers experimentally. This validated key driver set not only introduces new regulators of processes central to IBD but also provides the integrated circuits of genetic, molecular, and clinical traits that can be directly queried to interrogate and refine the regulatory framework defining IBD.
Indexed as
Gene Regulatory NetworksGenes, RegulatorModels, GeneticAdoptive TransferAnimalsCausalityCells, CulturedColitisDatasets as TopicDisease Models, AnimalFemaleGene Knockdown TechniquesGenetic Predisposition to DiseaseGenome-Wide Association StudyGenomicsHumansRNA, Small Interfering
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