Vaibhav Upadhyay, MD, PhD

Assistant Adjunct Professor

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.

Education
2021 - Pulmonary and Critical Care, UCSF
Chief Fellow, 2021 - Pulmonary and Critical Care, UCSF
2018 - Internal Medicine, UCSF
MD, 2015 - Medicine, University of Chicago
PhD, 2013 - Immunology, University of Chicago
BS, 2007 - Biochemistry, Duke University
Honors and Awards
  • ATS RCMB Abstract Scholarship, ATS, 2022
  • Jeffrey Golden Outstanding Clinical Fellow Award, UCSF Pulmonary and Critical Care Division, 2021
  • Pulmonary Division Clinical Fellow Award, UCSF Department of Medicine, 2020
  • UCSF Fellows Leadership Cohort, UCSF Department of Medicine, 2020
  • Pulmonary Division Clinical Fellow Award, UCSF Department of Medicine, 2019
  • Nominated for Clinical Fellow of the Year (one of a group of finalists), ZSFG Department of Medicine, 2019
  • Abstract selected for oral presentation, UCSF Resident Research Symposium, 2018
  • Jeffrey Weingarten Award, UCSF, Internal Medicine Residency, 2018
  • Graduation with Honors, University of Chicago, Pritzker School of Medicine, 2015
  • John Van Prohaska Award, University of Chicago, Pritzker School of Medicine, 2015
  • Best poster describing basic science investgiation, University of Chicago, Prtizker School of Medicine, 2015
  • Alpha omega alpha, University of Chicago, 2014
  • Travel scholarship, Keystone Symposia, 2013
  • Best Dissertation, University of Chicago, Committee on Immunology, 2013
  • Best Poster, ASCI/APSA Conference, 2012
  • Travel award, American Association of Immunologists, 2012
  • Summa cum laude, Duke University, 2007
  • American Chemistry Society Analytical Division Undergraduate Award, Duke University, 2006
  • Phi Beta Kappa, Duke University, 2006
Websites
Publications

  1. Trepka KR, Olson CA, Upadhyay V, Zhang C, Turnbaugh PJ. Pharma[e]cology: How the Gut Microbiome Contributes to Variations in Drug Response. Annual review of pharmacology and toxicology 2024. PMID: 39107044


  2. Upadhyay V, Yoon YM, Vazquez SE, Velez TE, Jones KD, Lee CT, Law CS, Wolters PJ, Lee S, Yang MM, Farrand E, Noth I, Strek ME, Anderson MS, DeRisi JL, Sperling AI, Shum AK. Phage Immunoprecipitation-Sequencing Reveals CDHR5 Autoantibodies in Select Patients With Interstitial Lung Disease. ACR Open Rheumatology 2024. PMID: 38952015


  3. Trepka KR, Kidder WA, Kyaw TS, Olson CA, Upadhyay V, Noecker C, Stanfield D, Steiding P, Spanogiannopoulos P, Dumlao D, Turnbaugh JA, Stachler MD, Van Blarigan EL, Venook AP, Atreya CE, Turnbaugh PJ. Expansion of a bacterial operon during cancer treatment ameliorates drug toxicity. bioRxiv : the preprint server for biology 2024. PMID: 38895199


  4. 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. Cell-Type Specificity of Mosaic Chromosome 1q Gain Resolved by snRNA-seq in a Case of Epilepsy With Hyaline Protoplasmic Astrocytopathy. Neurology. Genetics 2024. PMID: 38586598


  5. Leng K, Cadwell CR, Devine WP, Tihan T, Qi Z, Singhal N, Glenn O, Kamiya S, Wiita A, Berger A, Shieh JT, Titus EW, Paredes MF, Upadhyay V. Cell type specificity of mosaic chromosome 1q gain resolved by snRNA-seq in a case of epilepsy with hyaline protoplasmic astrocytopathy. bioRxiv : the preprint server for biology 2024. PMID: 38328093


  6. 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. 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 : the preprint server for health sciences 2023. PMID: 37961234


  7. 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. Variety of fruit and vegetables and alcohol intake are associated with gut microbial species and gene abundance in colorectal cancer survivors. The American journal of clinical nutrition 2023. PMID: 37474105


  8. 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. Mild SARS-CoV-2 infection results in long-lasting microbiota instability. mBio 2023. PMID: 37294090


  9. Upadhyay V, Yoon YM, Vazquez SE, Velez TE, Jones KD, Lee CT, Law CS, Wolters PJ, Lee S, Yang MM, Farrand E, Noth I, Strek ME, Anderson M, DeRisi J, Sperling AI, Shum AK. PhIP-Seq uncovers novel autoantibodies and unique endotypes in interstitial lung disease. bioRxiv : the preprint server for biology 2023. PMID: 37163026


  10. 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. Mild SARS-CoV-2 infection results in long-lasting microbiota instability. bioRxiv : the preprint server for biology 2022. PMID: 36523400


  11. Upadhyay V, Turnbaugh PJ. nicX-ing bad habits with your microbial friends. Nature metabolism 2022. PMID: 36333489


  12. Alexander M, Ang QY, Nayak RR, Bustion AE, Sandy M, Zhang B, Upadhyay V, Pollard KS, Lynch SV, Turnbaugh PJ. Human gut bacterial metabolism drives Th17 activation and colitis. 2021. PMID: 34822777


  13. 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. Reporting guidelines for human microbiome research: the STORMS checklist. Volume 27 of Issue 11. Nature medicine 2021. PMID: 34789871


  14. Ang QY, Alba DL, Upadhyay V, Bisanz JE, Cai J, Lee HL, Barajas E, Wei G, Noecker C, Patterson AD, Koliwad SK, Turnbaugh PJ. The East Asian gut microbiome is distinct from colocalized white subjects and connected to metabolic health. 2021. PMID: 34617511


  15. Stubbs BJ, Koutnik AP, Goldberg EL, Upadhyay V, Turnbaugh PJ, Verdin E, Newman JC. Investigating Ketone Bodies as Immunometabolic Countermeasures against Respiratory Viral Infections. Med (New York, N.Y.) 2020. PMID: 32838361


  16. 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. Ketogenic Diets Alter the Gut Microbiome Resulting in Decreased Intestinal Th17 Cells. Cell 2020. PMID: 32437658


  17. Bisanz JE, Upadhyay V, Turnbaugh JA, Ly K, Turnbaugh PJ. Meta-Analysis Reveals Reproducible Gut Microbiome Alterations in Response to a High-Fat Diet. Volume 26 of Issue 2. Cell host & microbe 2019. PMID: 31324413


  18. Upadhyay V, Walker E, Govea A, Rife T, Jimenez I, Dulay M, Beaman J. Interprofessional primary care electronic intervention to reduce hypoglycaemic agent use in high-risk veterans with diabetes. BMJ open quality 2018. PMID: 30272031


  19. Zhang Y, Kim TJ, Wroblewska JA, Tesic V, Upadhyay V, Weichselbaum RR, Tumanov AV, Tang H, Guo X, Tang H, Fu YX. Type 3 innate lymphoid cell-derived lymphotoxin prevents microbiota-dependent inflammation. Volume 15 of Issue 7. Cellular & molecular immunology 2017. PMID: 28579615


  20. Kim TJ, Upadhyay V, Kumar V, Lee KM, Fu YX. Innate lymphoid cells facilitate NK cell development through a lymphotoxin-mediated stromal microenvironment. Volume 211 of Issue 7. The Journal of experimental medicine 2014. PMID: 24913234


  21. Upadhyay V, Fu YX. Lymphotoxin organizes contributions to host defense and metabolic illness from innate lymphoid cells. Volume 25 of Issue 2. Cytokine & growth factor reviews 2013. PMID: 24411493


  22. Upadhyay V, Fu YX. Linking the microbiota and metabolic disease with lymphotoxin. Volume 25 of Issue 7. International immunology 2013. PMID: 23657002


  23. Upadhyay V, Fu YX, Bromberg JS. From infection to colonization: the role of microbiota in transplantation. Volume 13 of Issue 4. American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons 2013. PMID: 23551627


  24. Upadhyay V, Fu YX. Lymphotoxin signalling in immune homeostasis and the control of microorganisms. Volume 13 of Issue 4. Nature reviews. Immunology 2013. PMID: 23524463


  25. 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. Lymphotoxin regulates commensal responses to enable diet-induced obesity. Volume 13 of Issue 10. Nature immunology 2012. PMID: 22922363