ArticleNature2024
Reverse metabolomics for the discovery of chemical structures from humans.
Open access · hybridAbstract read
In one paragraph
Article in Nature, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 112 papers, 1 of them a synthesis that pooled it.
0numbers the graph read from it
0cells of the map it votes in
112citing papers in PubMed, 1 pooled it
22.9field-weighted citation impact, top 1% of its field
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
112 citing papers in PubMed, 1 synthesis or guideline pooled it, 149 citations in OpenAlex.
- A priori sample size determination and power analysis in metabolic phenotyping and integrative metabolomics: an application framework based on a systematic review of literature.Metabolomics : Official journal of the Metabolomic Society · 2026Pooled it
- Untargeted and semi-targeted metabolomics approach for profiling small intestinal and fecal metabolome using high-resolution mass spectrometry.Metabolomics : Official journal of the Metabolomic Society · 2025Trial
- Expanding bile acid diversityNatural product reports · 2026Review
- X-Align: annotation-independent cross-platform alignment of untargeted metabolomics features.Chemical science · 2026Article
- Secreted filarial acetylcholine analogs modulate parasite reproduction and host physiology.Nature communications · 2026Article
- Column switching liquid chromatography dual mass spectrometry system for simultaneous untargeted metabolomics and targeted exposomics.Nature communications · 2026Article
- Evaluation of the substrate profile of microbial-host-isozyme reveals the role of BvDPP4 in inflammatory bowel disease.Science China. Life sciences · 2026Article
- Understanding and Reporting PFAS Exposure: Wide-Scope Retrospective Suspect Screening of High-Resolution Mass Spectrometry Data from Exposomics Studies.Environmental science & technology · 2026Article
- Purine-Metabolism Reprogramming Associated with Failed-Repair Proximal Tubule States in the AKI-to-CKD Transition.Metabolites · 2026Article
- Ordering molecular diversity in untargeted metabolomics via molecular community networking.Cell reports methods · 2026Article
- Glycocholic acid inhibits TRIB3-ID1 axis to acelerate colitis progression via suppressing intestinal stem cell renewal.Nature communications · 2026Article
- The microbiome regulates host metabolic health and diseases through microbial enzymes.Nature reviews. Gastroenterology & hepatology · 2026Review
- Mass spectrometry-based metabolomics approaches to interrogate host-microbiome interactions in mammalian systems.Natural product reports · 2026Review
- Exploring Acylcarnitine Metabolism Using Reverse Metabolomics.Analytical chemistry · 2026Article
- The Farnesoid X receptor-bile acid axis contributes to immune evasion in gastric cancer and its inhibition enhances efficacy of anti-PD-L1 therapy.Biochemistry and biophysics reports · 2026Article
- A lipidomics roadmap: from basic research to societal challenges.Nature communications · 2026Review
- Individual variability shapes ex vivo responses to resistant starch in inflammatory bowel disease derived microbiomes.NPJ biofilms and microbiomes · 2026Article
- Gut-to-bile transfer of microbially amidated minor bile acids in patients with hepatopancreatobiliary disorders.Hepatology (Baltimore, Md.) · 2026Article
- From Molecules to Metabolomes, Understanding Symbiosis through Small Molecules.Journal of natural products · 2026Review
- Systemic rhythmicity of host and bacterial bile acid amidates in the mouse.Cell systems · 2026Article
52 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
30 authors at 9 institutions in 1 country.
Emily C GentrySkaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.
Stephanie L CollinsDepartment of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.ORCID 0000-0002-2773-646X
Morgan PanitchpakdiSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.
Pedro Belda-FerreDepartment of Pediatrics, University of California, San Diego, La Jolla, CA, USA.ORCID 0000-0001-6532-1161
Allison K StewartDepartment of Chemistry, North Carolina State University, Raleigh, NC, USA.
Marvic Carrillo TerrazasDepartment of Pathology, University of California, San Diego, La Jolla, CA, USA.
Hsueh-Han LuDepartment of Pathology, University of California, San Diego, La Jolla, CA, USA.ORCID 0000-0002-0832-9607
Simone ZuffaSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.
Tingting YanLaboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
Julian Avila-PachecoBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0001-9388-3946
Damian R PlichtaBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0002-6555-2557
Allegra T AronSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.
Mingxun WangSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.ORCID 0000-0001-7647-6097
Alan K JarmuschSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.ORCID 0000-0002-2228-6308
Fuhua HaoCenter for Molecular Toxicology and Carcinogenesis, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, USA.ORCID 0000-0002-0865-5269
Mashette Syrkin-NikolauDivision of Gastroenterology, Department of Pediatrics, Rady Children's Hospital University of California San Diego, La Jolla, CA, USA.
Hera VlamakisBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0003-1086-9191
Ashwin N AnanthakrishnanDivision of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA.
Brigid S BolandDivision of Gastroenterology, University of California, San Diego, La Jolla, CA, USA.
Amy HemperlyDivision of Gastroenterology, Department of Pediatrics, Rady Children's Hospital University of California San Diego, La Jolla, CA, USA.
Niels Vande CasteeleDivision of Gastroenterology, University of California, San Diego, La Jolla, CA, USA.
Frank J GonzalezLaboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.ORCID 0000-0002-7990-2140
Clary B ClishBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0001-8259-9245
Ramnik J XavierBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0002-5630-5167
Hiutung ChuDepartment of Pathology, University of California, San Diego, La Jolla, CA, USA.
Erin S BakerDepartment of Chemistry, North Carolina State University, Raleigh, NC, USA.ORCID 0000-0001-5246-2213
Andrew D PattersonCenter for Molecular Toxicology and Carcinogenesis, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, USA.ORCID 0000-0003-2073-0070
Rob KnightDepartment of Pediatrics, University of California, San Diego, La Jolla, CA, USA.ORCID 0000-0002-0975-9019
Dionicio SiegelSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.
Pieter C DorresteinSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA. pdorrestein@health.ucsd.edu.ORCID 0000-0002-3003-1030
University of California San Diego · USBroad Institute · USNational Institutes of Health · USPennsylvania State University · USUniversity of San Diego · USLa Jolla Institute for Immunology · USMassachusetts General Hospital · USNorth Carolina State University · USUniversity of North Carolina at Chapel Hill · US
Funding
Pilot & Feasibility ProgramP30DK043351 · NIDDK · MASSACHUSETTS GENERAL HOSPITAL · PI Ramnik J Xavier · 1991 to 2026
$35.3MROLE OF DIETARY CONSTITUENTS ON GENE EXPRESSION IN INTESTINAL EPITHELIUMP30DK040561 · NIDDK · MASSACHUSETTS GENERAL HOSPITAL · PI Elizabeth Austen Lawson, Takara Leah Stanley · 1994 to 2026
$31.6MSingle cell, multi-parametric high throughput platform to classify endocrine disruptor potential of mixturesP42ES027704 · NIEHS · TEXAS A&M UNIVERSITY · PI Efstratios Pistikopoulos · 2017 to 2026
$21.2MTranslational Research Support CoreP30ES025128 · NIEHS · NORTH CAROLINA STATE UNIVERSITY RALEIGH · PI Sue Fenton · 2015 to 2026
$18.3MXenobiotic ReceptorsZIABC005708 · NCI · DIVISION OF BASIC SCIENCES - NCI · PI GONZALEZ, FRANK J · 2009 to 2025
$16.4MUncovering the Mechanisms of PFAS-induced ImmunotoxicityP42ES031009 · NIEHS · NORTH CAROLINA STATE UNIVERSITY RALEIGH · PI PLANCHART, ANTONIO J. · 2020 to 2024
$9.3MTrainingP41GM103484 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI BAFNA, VINEET, BANDEIRA, NUNO · 2012 to 2018
$8.7MUnified Computation Tools for Natural Products ResearchR01GM107550 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI COTTRELL, GARRISON W, GERWICK, WILLIAM HENRY · 2013 to 2025
$8.2MTraining Grant in GastroenterologyT32DK007202 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI GHOSH, PRADIPTA · 1985 to 2022
$7.7MUnderstanding the role of lipids in structure and function of membrane proteinsRM1GM145416 · NIGMS · TEXAS A&M UNIVERSITY · PI Erin S Baker, Arthur D Laganowsky · 2022 to 2026
$7.4MMass Spectrometry-based Untargeted MetabolomicsZICES103363 · NIEHS · NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES · PI JARMUSCH, ALAN · 2021 to 2025
$6.5MCollaborative Microbial Metabolite CenterU24DK133658 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI PIETER C DORRESTEIN · 2022 to 2026
$2.9MNCI NIH HHS R03 CA211211NIAID NIH HHS R01 AI167860NIDDK NIH HHS K23 DK123406NIDDK NIH HHS P30 DK040561NIDDK NIH HHS P30 DK043351NIDDK NIH HHS R00 DK110534NIDDK NIH HHS R01 DK136117NIDDK NIH HHS T32 DK007202NIDDK NIH HHS U01 DK119702NIDDK NIH HHS U24 DK133658NIEHS NIH HHS P30 ES025128NIEHS NIH HHS P42 ES027704NIEHS NIH HHS P42 ES031009NIGMS NIH HHS P41 GM103484NIGMS NIH HHS R01 GM107550NIGMS NIH HHS R01 GM141277NIGMS NIH HHS RM1 GM145416
Abstract
Determining the structure and phenotypic context of molecules detected in untargeted metabolomics experiments remains challenging. Here we present reverse metabolomics as a discovery strategy, whereby tandem mass spectrometry spectra acquired from newly synthesized compounds are searched for in public metabolomics datasets to uncover phenotypic associations. To demonstrate the concept, we broadly synthesized and explored multiple classes of metabolites in humans, including N-acyl amides, fatty acid esters of hydroxy fatty acids, bile acid esters and conjugated bile acids. Using repository-scale analysis
Indexed as
AmidesBile Acids and SaltsEstersFatty AcidsMetabolomicsAnimalsBifidobacteriumCD4-Positive T-LymphocytesClostridiumCohort StudiesCrohn DiseaseEnterococcusHumansInflammatory Bowel DiseasesInterferon-gammaPhenotypeAmidesBile Acids and SaltsEstersFatty AcidsIFNG protein, humanInterferon-gammaPregnane X Receptor
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.