Vaibhav Upadhyay, MD, PhD

Assistant Professor

Medicine

+1 415 476-1528 ext. 2129

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.

Publications:

Expansion of a bacterial operon during cancer treatment ameliorates fluoropyrimidine toxicity.

Science translational medicine

Trepka KR, Kidder WA, Kyaw TS, Halsey T, Olson CA, Ortega EF, Noecker C, Upadhyay V, Stanfield D, Steiding P, Guthrie BGH, Spanogiannopoulos P, Dumlao D, Turnbaugh JA, Stachler MD, Van Blarigan EL, Venook AP, Atreya CE, Turnbaugh PJ

Gut bacterial lactate stimulates lung epithelial mitochondria and exacerbates acute lung injury.

bioRxiv : the preprint server for biology

Upadhyay V, Ortega EF, Ramirez Hernandez LA, Alexander M, Kaur G, Trepka K, Rock RR, Shima RT, Cheshire WC, Alipanah-Lechner N, Calfee CS, Matthay MA, Lee JV, Goga A, Jain IH, Turnbaugh PJ

Pharma[e]cology: How the Gut Microbiome Contributes to Variations in Drug Response.

Annual review of pharmacology and toxicology

Trepka KR, Olson CA, Upadhyay V, Zhang C, Turnbaugh PJ

A diet-dependent host metabolite shapes the gut microbiota to protect from autoimmunity.

Cell reports

Alexander M, Upadhyay V, Rock R, Ramirez L, Trepka K, Puchalska P, Orellana D, Ang QY, Whitty C, Turnbaugh JA, Tian Y, Dumlao D, Nayak R, Patterson A, Newman JC, Crawford PA, Turnbaugh PJ

Expansion of a bacterial operon during cancer treatment ameliorates drug toxicity.

bioRxiv : the preprint server for biology

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

Rationale and protocol for a safety, tolerability and feasibility randomized, parallel arm, double-blind, placebo-controlled, pilot study of a novel ketone ester targeting frailty via immunometabolic geroscience mechanisms.

PloS one

Stubbs BJ, Alvarez Azañedo G, Peralta S, Diaz SR, Gray W, Alexander L, Silverman-Martin W, Garcia TY, Blonquist TM, Upadhyay V, Turnbaugh PJ, Johnson JB, Newman JC

Phage Immunoprecipitation-Sequencing Reveals CDHR5 Autoantibodies in Select Patients With Interstitial Lung Disease.

ACR open rheumatology

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

A diet-dependent host metabolite shapes the gut microbiota to protect from autoimmunity.

bioRxiv : the preprint server for biology

Alexander M, Upadhyay V, Rock R, Ramirez L, Puchalska P, Orellana D, Ang QY, Turnbaugh JA, Tian Y, Dumlao D, Nayak R, Patterson A, Newman JC, Crawford PA, Turnbaugh PJ

Cell-Type Specificity of Mosaic Chromosome 1q Gain Resolved by snRNA-seq in a Case of Epilepsy With Hyaline Protoplasmic Astrocytopathy.

Neurology. Genetics

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.

bioRxiv : the preprint server for biology

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

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

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

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

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

Mild SARS-CoV-2 infection results in long-lasting microbiota instability.

mBio

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

PhIP-Seq uncovers novel autoantibodies and unique endotypes in interstitial lung disease.

bioRxiv : the preprint server for biology

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

Mild SARS-CoV-2 infection results in long-lasting microbiota instability.

bioRxiv : the preprint server for biology

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

nicX-ing bad habits with your microbial friends.

Nature metabolism

Upadhyay V, Turnbaugh PJ

Human gut bacterial metabolism drives Th17 activation and colitis.

Cell host & microbe

Alexander M, Ang QY, Nayak RR, Bustion AE, Sandy M, Zhang B, Upadhyay V, Pollard KS, Lynch SV, Turnbaugh PJ

Reporting guidelines for human microbiome research: the STORMS checklist.

Nature medicine

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

The East Asian gut microbiome is distinct from colocalized white subjects and connected to metabolic health.

eLife

Ang QY, Alba DL, Upadhyay V, Bisanz JE, Cai J, Lee HL, Barajas E, Wei G, Noecker C, Patterson AD, Koliwad SK, Turnbaugh PJ

Investigating Ketone Bodies as Immunometabolic Countermeasures against Respiratory Viral Infections.

Med (New York, N.Y.)

Stubbs BJ, Koutnik AP, Goldberg EL, Upadhyay V, Turnbaugh PJ, Verdin E, Newman JC

Ketogenic Diets Alter the Gut Microbiome Resulting in Decreased Intestinal Th17 Cells.

Cell

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

Meta-Analysis Reveals Reproducible Gut Microbiome Alterations in Response to a High-Fat Diet.

Cell host & microbe

Bisanz JE, Upadhyay V, Turnbaugh JA, Ly K, Turnbaugh PJ

Interprofessional primary care electronic intervention to reduce hypoglycaemic agent use in high-risk veterans with diabetes.

BMJ open quality

Upadhyay V, Walker E, Govea A, Rife T, Jimenez I, Dulay M, Beaman J

Custom People Group:

UCSF Microbiome Researchers

The Benioff Center for Microbiome Medicine

Vaibhav Upadhyay, MD, PhD

Expansion of a bacterial operon during cancer treatment ameliorates fluoropyrimidine toxicity.

Gut bacterial lactate stimulates lung epithelial mitochondria and exacerbates acute lung injury.

Pharma[e]cology: How the Gut Microbiome Contributes to Variations in Drug Response.

A diet-dependent host metabolite shapes the gut microbiota to protect from autoimmunity.

Expansion of a bacterial operon during cancer treatment ameliorates drug toxicity.

Rationale and protocol for a safety, tolerability and feasibility randomized, parallel arm, double-blind, placebo-controlled, pilot study of a novel ketone ester targeting frailty via immunometabolic geroscience mechanisms.

Phage Immunoprecipitation-Sequencing Reveals CDHR5 Autoantibodies in Select Patients With Interstitial Lung Disease.

A diet-dependent host metabolite shapes the gut microbiota to protect from autoimmunity.

Cell-Type Specificity of Mosaic Chromosome 1q Gain Resolved by snRNA-seq in a Case of Epilepsy With Hyaline Protoplasmic Astrocytopathy.

Cell type specificity of mosaic chromosome 1q gain resolved by snRNA-seq in a case of epilepsy with hyaline protoplasmic astrocytopathy.

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.

Variety of fruit and vegetables and alcohol intake are associated with gut microbial species and gene abundance in colorectal cancer survivors.

Mild SARS-CoV-2 infection results in long-lasting microbiota instability.

PhIP-Seq uncovers novel autoantibodies and unique endotypes in interstitial lung disease.

Mild SARS-CoV-2 infection results in long-lasting microbiota instability.

nicX-ing bad habits with your microbial friends.

Human gut bacterial metabolism drives Th17 activation and colitis.

Reporting guidelines for human microbiome research: the STORMS checklist.

The East Asian gut microbiome is distinct from colocalized white subjects and connected to metabolic health.

Investigating Ketone Bodies as Immunometabolic Countermeasures against Respiratory Viral Infections.

Ketogenic Diets Alter the Gut Microbiome Resulting in Decreased Intestinal Th17 Cells.

Meta-Analysis Reveals Reproducible Gut Microbiome Alterations in Response to a High-Fat Diet.

Interprofessional primary care electronic intervention to reduce hypoglycaemic agent use in high-risk veterans with diabetes.

Type 3 innate lymphoid cell-derived lymphotoxin prevents microbiota-dependent inflammation.

Innate lymphoid cells facilitate NK cell development through a lymphotoxin-mediated stromal microenvironment.

Lymphotoxin organizes contributions to host defense and metabolic illness from innate lymphoid cells.

Linking the microbiota and metabolic disease with lymphotoxin.

From infection to colonization: the role of microbiota in transplantation.

Lymphotoxin signalling in immune homeostasis and the control of microorganisms.

Lymphotoxin regulates commensal responses to enable diet-induced obesity.

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Vaibhav Upadhyay, MD, PhD