Vaibhav Upadhyay, MD, PhD

Title(s)Assistant Professor, Medicine
SchoolSchool of Medicine
Address513 Parnassus Avenue, HSW, #1526
San Francisco CA 94143
Phone415-476-1528 ext. 2129
ORCID ORCID Icon0000-0002-7652-1043 Additional info
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    Collapse Biography 
    Collapse Education and Training
    University of Chicago, ChicagoMD2015Medicine
    University of Chicago, ChicagoPhD2013Immunology
    Duke University, DurhamBS2007Biochemistry
    UCSF, San Francisco2018Internal Medicine
    UCSF, San Francisco2021Pulmonary and Critical Care
    UCSF, San FranciscoChief Fellow2021Pulmonary and Critical Care
    Collapse Awards and Honors
    Duke University2006Phi Beta Kappa
    Duke University2006American Chemistry Society Analytical Division Undergraduate Award
    Duke University2007Summa cum laude
    ASCI/APSA Conference2012Best Poster
    American Association of Immunologists2012Travel award
    Keystone Symposia2013Travel scholarship
    University of Chicago, Committee on Immunology2013Best Dissertation
    University of Chicago2014Alpha omega alpha
    University of Chicago, Pritzker School of Medicine2015Graduation with Honors
    University of Chicago, Pritzker School of Medicine2015John Van Prohaska Award
    University of Chicago, Prtizker School of Medicine2015Best poster describing basic science investgiation
    UCSF, Internal Medicine Residency2018Jeffrey Weingarten Award
    UCSF Resident Research Symposium2018Abstract selected for oral presentation
    ZSFG Department of Medicine2019Nominated for Clinical Fellow of the Year (one of a group of finalists)
    UCSF Department of Medicine2019Pulmonary Division Clinical Fellow Award
    UCSF Department of Medicine2020Pulmonary Division Clinical Fellow Award
    UCSF Department of Medicine2020UCSF Fellows Leadership Cohort
    UCSF Pulmonary and Critical Care Division2021Jeffrey Golden Outstanding Clinical Fellow Award
    ATS2022ATS RCMB Abstract Scholarship

    Collapse Overview 
    Collapse Overview
    I'm a K08 funded physician scientist studying impact of gut microorganisms on human health and applying multi-omic technologies to the study of chronic diseases with clinical focus in pulmonary medicine.

    Collapse Research 
    Collapse Research Activities and Funding
    Impact of gut bacterial metabolites on lung function and disease
    NIH/NHLBI 1K08HL165106-01A1Apr 1, 2023 - Mar 31, 2028
    Role: Principal Investigator
    Description: Acute Lung Injury is a devastating and prevalent condition with poorly understood links to the gut microbiome. I propose to study how host control of a key gut bacterium changes pulmonary metabolite exposure from the gut microbiome and downstream inflammation during Acute Lung Injury. This project will lay the foundation for future studies defining how gut bacteria change lung function in alignment with NHLBI strategic vision 1.CQ.07.
    The Gut Microbiome in Predisposition to and as a Marker of Sars-CoV-2 Infection
    Benioff Center for Microbiome Medicine 2013260Jul 1, 2020 - Jul 1, 2021
    Role: PI, Investigator
    Description: Trainee pilot grant to identify changes in the microbiome of humans and ABSL3 infected mice secondary to SARS-CoV-2.
    Exploration of Novel Autoantigens in Patients with Idiopathic Pneumonia with Autoimmune Features
    UCSF CTSI Jun 1, 2017 - Jun 1, 2018
    Role: PI, investigator
    Description: Project to identify novel autoantigens in patients with interstitial lung disease.

    Collapse ORNG Applications 
    Collapse Collaboration Interests

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Cell-Type Specificity of Mosaic Chromosome 1q Gain Resolved by snRNA-seq in a Case of Epilepsy With Hyaline Protoplasmic Astrocytopathy. Neurol Genet. 2024 Apr; 10(2):e200142. Leng K, Cadwell CR, Devine WP, Tihan T, Qi Z, Singhal NS, Glenn OA, Kamiya S, Wiita AP, Berger AC, Shieh JT, Titus EW, Paredes MF, Upadhyay V. PMID: 38586598; PMCID: PMC10997208.
      View in: PubMed   Mentions:
    2. Cell type specificity of mosaic chromosome 1q gain resolved by snRNA-seq in a case of epilepsy with hyaline protoplasmic astrocytopathy. bioRxiv. 2024 Jan 25. Leng K, Cadwell CR, Patrick Devine W, Tihan T, Qi Z, Singhal N, Glenn O, Kamiya S, Wiita A, Berger A, Shieh JT, Titus EW, Paredes MF, Upadhyay V. PMID: 38328093; PMCID: PMC10849466.
      View in: PubMed   Mentions:
    3. Rationale and protocol for a safety, tolerability and feasibility randomized, parallel group, double-blind, placebo-controlled, pilot study of a novel ketone ester targeting frailty via immunometabolic geroscience mechanisms. medRxiv. 2023 Oct 26. Stubbs BJ, Alvarez-Azanedo G, Peralta S, Roa-Diaz S, Gray W, Alexander L, Silverman-Martin W, Garcia T, Blonquist TM, Upadhyay V, Turnbaugh PJ, Johnson JB, Newman JC. PMID: 37961234; PMCID: PMC10635199.
      View in: PubMed   Mentions:
    4. Variety of Fruit and Vegetables and Alcohol Intake are Associated with Gut Microbial Species and Gene Abundance in Colorectal Cancer Survivors. Am J Clin Nutr. 2023 09; 118(3):518-529. Kyaw TS, Upadhyay V, Tolstykh I, Van Loon K, Laffan A, Stanfield D, Gempis D, Kenfield SA, Chan JM, Piawah S, Atreya CE, Ng K, Venook A, Kidder W, Turnbaugh PJ, Van Blarigan EL. PMID: 37474105; PMCID: PMC10550847.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimals
    5. Mild SARS-CoV-2 infection results in long-lasting microbiota instability. mBio. 2023 08 31; 14(4):e0088923. Upadhyay V, Suryawanshi RK, Tasoff P, McCavitt-Malvido M, Kumar RG, Murray VW, Noecker C, Bisanz JE, Hswen Y, Ha CWY, Sreekumar B, Chen IP, Lynch SV, Ott M, Lee S, Turnbaugh PJ. PMID: 37294090; PMCID: PMC10470529.
      View in: PubMed   Mentions: 3     Fields:    Translation:AnimalsCells
    6. Mild SARS-CoV-2 infection results in long-lasting microbiota instability. bioRxiv. 2022 Dec 08. Upadhyay V, Suryawanshi R, Tasoff P, McCavitt-Malvido M, Kumar GR, Murray VW, Noecker C, Bisanz JE, Hswen Y, Ha C, Sreekumar B, Chen IP, Lynch SV, Ott M, Lee S, Turnbaugh PJ. PMID: 36523400; PMCID: PMC9753784.
      View in: PubMed   Mentions: 2  
    7. nicX-ing bad habits with your microbial friends. Nat Metab. 2022 Nov; 4(11):1442-1443. Upadhyay V, Turnbaugh PJ. PMID: 36333489.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    8. Human gut bacterial metabolism drives Th17 activation and colitis. Cell Host Microbe. 2022 01 12; 30(1):17-30.e9. Alexander M, Ang QY, Nayak RR, Bustion AE, Sandy M, Zhang B, Upadhyay V, Pollard KS, Lynch SV, Turnbaugh PJ. PMID: 34822777; PMCID: PMC8785648.
      View in: PubMed   Mentions: 58     Fields:    Translation:HumansAnimalsCells
    9. Reporting guidelines for human microbiome research: the STORMS checklist. Nat Med. 2021 11; 27(11):1885-1892. Mirzayi C, Renson A, Genomic Standards Consortium, Massive Analysis and Quality Control Society, Zohra F, Elsafoury S, Geistlinger L, Kasselman LJ, Eckenrode K, van de Wijgert J, Loughman A, Marques FZ, MacIntyre DA, Arumugam M, Azhar R, Beghini F, Bergstrom K, Bhatt A, Bisanz JE, Braun J, Bravo HC, Buck GA, Bushman F, Casero D, Clarke G, Collado MC, Cotter PD, Cryan JF, Demmer RT, Devkota S, Elinav E, Escobar JS, Fettweis J, Finn RD, Fodor AA, Forslund S, Franke A, Furlanello C, Gilbert J, Grice E, Haibe-Kains B, Handley S, Herd P, Holmes S, Jacobs JP, Karstens L, Knight R, Knights D, Koren O, Kwon DS, Langille M, Lindsay B, McGovern D, McHardy AC, McWeeney S, Mueller NT, Nezi L, Olm M, Palm N, Pasolli E, Raes J, Redinbo MR, Rühlemann M, Balfour Sartor R, Schloss PD, Schriml L, Segal E, Shardell M, Sharpton T, Smirnova E, Sokol H, Sonnenburg JL, Srinivasan S, Thingholm LB, Turnbaugh PJ, Upadhyay V, Walls RL, Wilmes P, Yamada T, Zeller G, Zhang M, Zhao N, Zhao L, Bao W, Culhane A, Devanarayan V, Dopazo J, Fan X, Fischer M, Jones W, Kusko R, Mason CE, Mercer TR, Sansone SA, Scherer A, Shi L, Thakkar S, Tong W, Wolfinger R, Hunter C, Segata N, Huttenhower C, Dowd JB, Jones HE, Waldron L. PMID: 34789871; PMCID: PMC9105086.
      View in: PubMed   Mentions: 99     Fields:    Translation:Humans
    10. The East Asian gut microbiome is distinct from colocalized White subjects and connected to metabolic health. Elife. 2021 10 07; 10. Ang QY, Alba DL, Upadhyay V, Bisanz JE, Cai J, Lee HL, Barajas E, Wei G, Noecker C, Patterson AD, Koliwad SK, Turnbaugh PJ. PMID: 34617511; PMCID: PMC8612731.
      View in: PubMed   Mentions: 20     Fields:    Translation:Cells
    11. Investigating Ketone Bodies as Immunometabolic Countermeasures against Respiratory Viral Infections. Med. 2020 12 18; 1(1):43-65. Stubbs BJ, Koutnik AP, Goldberg EL, Upadhyay V, Turnbaugh PJ, Verdin E, Newman JC. PMID: 32838361; PMCID: PMC7362813.
      View in: PubMed   Mentions: 28  Translation:HumansCellsPHPublic Health
    12. Ketogenic Diets Alter the Gut Microbiome Resulting in Decreased Intestinal Th17 Cells. Cell. 2020 06 11; 181(6):1263-1275.e16. Ang QY, Alexander M, Newman JC, Tian Y, Cai J, Upadhyay V, Turnbaugh JA, Verdin E, Hall KD, Leibel RL, Ravussin E, Rosenbaum M, Patterson AD, Turnbaugh PJ. PMID: 32437658; PMCID: PMC7293577.
      View in: PubMed   Mentions: 187     Fields:    Translation:HumansAnimalsCells
    13. Meta-Analysis Reveals Reproducible Gut Microbiome Alterations in Response to a High-Fat Diet. Cell Host Microbe. 2019 08 14; 26(2):265-272.e4. Bisanz JE, Upadhyay V, Turnbaugh JA, Ly K, Turnbaugh PJ. PMID: 31324413; PMCID: PMC6708278.
      View in: PubMed   Mentions: 123     Fields:    Translation:HumansAnimalsCells
    14. Interprofessional primary care electronic intervention to reduce hypoglycaemic agent use in high-risk veterans with diabetes. BMJ Open Qual. 2018; 7(3):e000221. Upadhyay V, Walker E, Govea A, Rife T, Jimenez I, Dulay M, Beaman J. PMID: 30272031; PMCID: PMC6157516.
      View in: PubMed   Mentions: 1     Fields:    
    15. Type 3 innate lymphoid cell-derived lymphotoxin prevents microbiota-dependent inflammation. Cell Mol Immunol. 2018 07; 15(7):697-709. Zhang Y, Kim TJ, Wroblewska JA, Tesic V, Upadhyay V, Weichselbaum RR, Tumanov AV, Tang H, Guo X, Tang H, Fu YX. PMID: 28579615; PMCID: PMC6123485.
      View in: PubMed   Mentions: 8     Fields:    Translation:AnimalsCells
    16. Innate lymphoid cells facilitate NK cell development through a lymphotoxin-mediated stromal microenvironment. J Exp Med. 2014 Jun 30; 211(7):1421-31. Kim TJ, Upadhyay V, Kumar V, Lee KM, Fu YX. PMID: 24913234; PMCID: PMC4076579.
      View in: PubMed   Mentions: 9     Fields:    Translation:AnimalsCells
    17. Lymphotoxin organizes contributions to host defense and metabolic illness from innate lymphoid cells. Cytokine Growth Factor Rev. 2014 Apr; 25(2):227-33. Upadhyay V, Fu YX. PMID: 24411493; PMCID: PMC3999173.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansAnimalsCells
    18. Linking the microbiota and metabolic disease with lymphotoxin. Int Immunol. 2013 Jul; 25(7):397-403. Upadhyay V, Fu YX. PMID: 23657002; PMCID: PMC4719164.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansAnimalsCells
    19. From infection to colonization: the role of microbiota in transplantation. Am J Transplant. 2013 Apr; 13(4):829. Upadhyay V, Fu YX, Bromberg JS. PMID: 23551627; PMCID: PMC3914761.
      View in: PubMed   Mentions: 3     Fields:    
    20. Lymphotoxin signalling in immune homeostasis and the control of microorganisms. Nat Rev Immunol. 2013 Apr; 13(4):270-9. Upadhyay V, Fu YX. PMID: 23524463; PMCID: PMC3900493.
      View in: PubMed   Mentions: 58     Fields:    Translation:HumansAnimalsCells
    21. Lymphotoxin regulates commensal responses to enable diet-induced obesity. Nat Immunol. 2012 Oct; 13(10):947-53. Upadhyay V, Poroyko V, Kim TJ, Devkota S, Fu S, Liu D, Tumanov AV, Koroleva EP, Deng L, Nagler C, Chang EB, Tang H, Fu YX. PMID: 22922363; PMCID: PMC3718316.
      View in: PubMed   Mentions: 69     Fields:    Translation:AnimalsCells
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