Michael Snyder

Michael P. Snyder, PhD, Stanford Ascherman Professor, Department of Genetics; Director, Stanford Center of Genomics and Personalized Medicine, Stanford University School of Medicine 

Research Description: Dr. Snyder is a leader in the field of functional genomics and proteomics, and a leader in the ENCODE project. His laboratory study was the first to perform a large-scale functional genomics project in any organism, and has developed many technologies in genomics and proteomics. These technologies have been used for characterizing genomes, proteomes and regulatory networks. He has also combined different state-of–the-art “omics” technologies to perform the first longitudinal detailed integrative personal omics profile (iPOP) of person and used this to assess disease risk and monitor disease states for personalized medicine. He has published studies of diabetes development with these approaches, and collaborates extensively with SDRC investigators, including Drs. Chang, Greenleaf, Haddad and McLaughlin in diabetes-related research. Based on this experience, Dr. Snyder also serves as an advisor to the Genomics & Analysis Core in SDRC, and is a member of the SDRC Executive Committee. 

Selected relevant publications (Stanford DRC members in BOLD):

  1. Sailani MR, Metwally AA, Zhou W, Rose SMS, Ahadi S, Contrepois K, Mishra T, Zhang MJ, Kidziński Ł, Chu TJ, Snyder MP. Deep longitudinal multiomics profiling reveals two biological seasonal patterns in California. Nat Commun. 2020 Oct 1;11(1):4933. doi: 10.1038/s41467-020-18758-1. PMID: 33004787; PMCID: PMC7529769. [cites P30] 

  2. Zhou W, Sailani MR, Contrepois K, Zhou Y, Ahadi S, Leopold SR, Zhang MJ, Rao V, Avina M, Mishra T, Johnson J, Lee-McMullen B, Chen S, Metwally AA, Tran TDB, Nguyen H, Zhou X, Albright B, Hong BY, Petersen L, Bautista E, Hanson B, Chen L, Spakowicz D, Bahmani A, Salins D, Leopold B, Ashland M, Dagan-Rosenfeld O, Rego S, Limcaoco P, Colbert E, Allister C, Perelman D, Craig C, Wei E, Chaib H, Hornburg D, Dunn J, Liang L, Rose SMS, Kukurba K, Piening B, Rost H, Tse D, McLaughlin T, Sodergren E, Weinstock GM, Snyder M. Longitudinal multi-omics of host-microbe dynamics in prediabetes. Nature. 2019 May;569(7758):663-671. PMID: 31142858 [cites P30] 

  3. Schüssler-Fiorenza Rose SM, Contrepois K, Moneghetti KJ, Zhou W, Mishra T, Mataraso S, Dagan-Rosenfeld O, Ganz AB, Dunn J, Hornburg D, Rego S, Perelman D, Ahadi S, Sailani MR, Zhou Y, Leopold SR, Chen J, Ashland M, Christle JW, Avina M, Limcaoco P, Ruiz C, Tan M, Butte AJ, Weinstock GM, Slavich GM, Sodergren E, McLaughlin TL, Haddad F, Snyder MP. A longitudinal big data approach for precision health. Nat Med. 2019 May;25(5):792-804. doi: 10.1038/s41591-019-0414-6. Epub 2019 May 8. PMID: 31068711; PMCID: PMC6713274. [cites P30] 

  4. Piening BD, Zhou W, Contrepois K, Röst H, Gu Urban GJ, Mishra T, Hanson BM, Bautista EJ, Leopold S, Yeh CY, Spakowicz D, Banerjee I, Chen C, Kukurba K, Perelman D, Craig C, Colbert E, Salins D, Rego S, Lee S, Zhang C, Wheeler J, Sailani MR,Liang L, Abbott C, Gerstein M, Mardinoglu A, Smith U, Rubin DL, Pitteri S, Sodergren E, McLaughlin TL, Weinstock GM, Snyder MP. Integrative Personal Omics Profiles during Periods of Weight Gain and Loss. Cell Syst. 6(2): 157-170, 2018. [cites P30] 

  5. Harper RL, Zhou X, Marciano DP, Cao A, Wang L, Chen G, Adil MS, Zhou W, Maguire P, Deivanayagam S, Yu Q, Viswanathan V, Yang D, Martin M, Isobe S, Otsuki S, Burgess J, Inglis A, Kelley D, Del Rosario PA, Hsi A, Haddad F, Zamanian RT, Boehm M, Snyder MP, Rabinovitch M. Altered maturation and activation state of circulating monocytes is associated with their enhanced recruitment in pulmonary arterial hypertension. Respir Res. 2025 Apr 15;26(1):148. doi: 10.1186/s12931-025-03182-0. PMID: 40234964; PMCID: PMC11998417. 

  6. Metwally AA, Perelman D, Park H, Wu Y, Jha A, Sharp S, Celli A, Ayhan E, Abbasi F, Gloyn AL, McLaughlin T, Snyder M. Predicting Type 2 Diabetes Metabolic Phenotypes Using Continuous Glucose Monitoring and a Machine Learning Framework. medRxiv [Preprint]. 2024 Sep 9:2024.07.20.24310737. doi: 10.1101/2024.07.20.24310737. PMID: 39108516; PMCID: PMC11302614. 

  7. Park H, Metwally AA, Delfarah A, Wu Y, Perelman D, Rodgar M, Mayer C, Celli A, McLaughlin T, Mignot E, Snyder M. Lifestyle Profiling Using Wearables and Prediction of Glucose Metabolism in Individuals with Normoglycemia or Prediabetes. medRxiv [Preprint]. 2024 Sep 6:2024.09.05.24312545. doi: 10.1101/2024.09.05.24312545. PMID: 39281757; PMCID: PMC11398605. 

  8. Zahedani AD, McLaughlin T, Veluvali A, Aghaeepour N, Hosseinian A, Agarwal S, Ruan J, Tripathi S, Woodward M, Hashemi N, Snyder M. Digital health application integrating wearable data and behavioral patterns improves metabolic health. NPJ Digit Med. 2023 Nov 25;6(1):216. doi: 10.1038/s41746-023-00956-y. Erratum in: NPJ Digit Med. 2024 Jan 12;7(1):9. doi: 10.1038/s41746-024-00996-y. PMID: 38001287; PMCID: PMC10673832. 

  9. Taylor S, Isobe S, Cao A, Contrepois K, Benayoun BA, Jiang L, Wang L, Melemenidis S, Ozen MO, Otsuki S, Shinohara T, Sweatt AJ, Kaplan J, Moonen JR, Marciano DP, Gu M, Miyagawa K, Hayes B, Sierra RG, Kupitz CJ, Del Rosario PA, Hsi A, Thompson AAR, Ariza ME, Demirci U, Zamanian RT, Haddad F, Nicolls MR, Snyder MP, Rabinovitch M. Endogenous Retroviral Elements Generate Pathologic Neutrophils in Pulmonary Arterial Hypertension. Am J Respir Crit Care Med. 2022 Oct 15;206(8):1019-1034. doi: 10.1164/rccm.202102-0446OC. PMID: 35696338; PMCID: PMC9801997. 

  10. Lancaster SM, Lee-McMullen B, Abbott CW, Quijada JV, Hornburg D, Park H, Perelman D, Peterson DJ, Tang M, Robinson A, Ahadi S, Contrepois K, Hung CJ, Ashland M, McLaughlin T, Boonyanit A, Horning A, Sonnenburg JL, Snyder MP. Global, distinctive, and personal changes in molecular and microbial profiles by specific fibers in humans. Cell Host Microbe. 2022 Jun 8;30(6):848-862.e7. doi: 10.1016/j.chom.2022.03.036. Epub 2022 Apr 27. PMID: 35483363; PMCID: PMC9187607. 

  11. Wang YJ, Zhang X, Lam CK, Guo H, Wang C, Zhang S, Wu JC, Snyder M, Li J. Systems analysis of de novo mutations in congenital heart diseases identified a protein network in the hypoplastic left heart syndrome. Cell Syst. 2022 Nov 16;13(11):895-910.e4. doi: 10.1016/j.cels.2022.09.001. Epub 2022 Sep 26. PMID: 36167075; PMCID: PMC9671831. 

  12. Abbasi F, Lamendola C, Harris CS, Harris V, Tsai MS, Tripathi P, Abbas F, Reaven GM, Reaven PD, Snyder MP, Kim SH, Knowles JW. Statins Are Associated With Increased Insulin Resistance and Secretion. Arterioscler Thromb Vasc Biol. 2021 Nov;41(11):2786-2797. doi: 10.1161/ATVBAHA.121.316159. Epub 2021 Aug 26. PMID: 34433298; PMCID: PMC8551023. 

  13. Stevenson DK, Wong RJ, Aghaeepour N, Maric I, Angst MS, Contrepois K, Darmstadt GL, Druzin ML, Eisenberg ML, Gaudilliere B, Gibbs RS, Gotlib IH, Gould JB, Lee HC, Ling XB, Mayo JA, Moufarrej MN, Quaintance CC, Quake SR, Relman DA, Sirota M, Snyder MP, Sylvester KG, Hao S, Wise PH, Shaw GM, Katz M. Towards personalized medicine in maternal and child health: integrating biologic and social determinants. Pediatr Res. 2021 Jan;89(2):252-258. doi: 10.1038/s41390-020-0981-8. Epub 2020 May 26. PMID: 32454518; PMCID: PMC8061757. 

  14. Julian TH, Glascow N, Barry ADF, Moll T, Harvey C, Klimentidis YC, Newell M, Zhang S, Snyder MP, Cooper-Knock J, Shaw PJ. Physical exercise is a risk factor for amyotrophic lateral sclerosis: Convergent evidence from Mendelian randomisation, transcriptomics and risk genotypes. EBioMedicine. 2021 Jun;68:103397. doi: 10.1016/j.ebiom.2021.103397. Epub 2021 May 26. PMID: 34051439; PMCID: PMC8170114. 

  15. Roodgar M, Babveyh A, Nguyen LH, Zhou W, Sinha R, Lee H, Hanks JB, Avula M, Jiang L, Jian R, Lee H, Song G, Chaib H, Weissman IL, Batzoglou S, Holmes S, Smith DG, Mankowski JL, Prost S, Snyder MP. Chromosome-level de novo assembly of the pig-tailed macaque genome using linked-read sequencing and HiC proximity scaffolding. Gigascience. 2020 Jul 1;9(7):giaa069. doi: 10.1093/gigascience/giaa069. PMID: 32649757; PMCID: PMC7350979. 

  16. Zhou X, Johnson JS, Spakowicz D, Zhou W, Zhou Y, Sodergren E, Snyder M, Weinstock GM. Longitudinal Analysis of Serum Cytokine Levels and Gut Microbial Abundance Links IL-17/IL-22 With Clostridia and Insulin Sensitivity in Humans. Diabetes. 2020 Aug;69(8):1833-1842. doi: 10.2337/db19-0592. Epub 2020 May 4. PMID: 32366680; PMCID: PMC7372073. 

  17. Contrepois K, Wu S, Moneghetti KJ, Hornburg D, Ahadi S, Tsai MS, Metwally AA, Wei E, Lee-McMullen B, Quijada JV, Chen S, Christle JW, Ellenberger M, Balliu B, Taylor S, Durrant MG, Knowles DA, Choudhry H, Ashland M, Bahmani A, Enslen B, Amsallem M, Kobayashi Y, Avina M, Perelman D, Schüssler-Fiorenza Rose SM, Zhou W, Ashley EA, Montgomery SB, Chaib H, Haddad F, Snyder MP. Molecular Choreography of Acute Exercise. Cell. 2020 May 28;181(5):1112-1130.e16. doi: 10.1016/j.cell.2020.04.043. PMID: 32470399; PMCID: PMC7299174. 

  18. Roodgar M, Good BH, Garud NR, Martis S, Avula M, Zhou W, Lancaster SM, Lee H, Babveyh A, Nesamoney S, Pollard KS, Snyder MP. Longitudinal linked-read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment. Genome Res. 2021 Aug;31(8):1433-1446. doi: 10.1101/gr.265058.120. Epub 2021 Jul 22. PMID: 34301627; PMCID: PMC8327913. 

  19. Metwally AA, Mehta P, Johnson BS, Nagarjuna A, Snyder MP. COVID-19-Induced New-Onset Diabetes: Trends and Technologies. Diabetes. 2021 Oct 22:dbi210029. PMID: 34686519. 

  20. Metwally AA, Zhang T, Wu S, Kellogg R, Zhou W, Contrepois K, Tang H, Snyder M. Robust Identification of Temporal Biomarkers in Longitudinal Omics Studies. Bioinformatics. 2022 Jun 28;38(15):3802–11. PMID: 35762936; PMCID: PMC9344853. 

  21. Zhang S, Cooper-Knock J, Weimer AK, Shi M, Moll T, Marshall JNG, Harvey C, Nezhad HG, Franklin J, Souza CDS, Ning K, Wang C, Li J, Dilliott AA, Farhan S, Elhaik E, Pasniceanu I, Livesey MR, Eitan C, Hornstein E, Kenna KP; Project MinE ALS Sequencing Consortium, Veldink JH, Ferraiuolo L, Shaw PJ, Snyder MP. Genome-wide identification of the genetic basis of amyotrophic lateral sclerosis. Neuron. 2022 Mar 16;110(6):992-1008.e11.PMID: 35045337; PMCID: PMC9017397. 

  22. Wei W, Riley NM, Lyu X, Shen X, Guo J, Raun SH, Zhao M, Moya-Garzon MD, Basu H, Sheng-Hwa Tung A, Li VL, Huang W, Wiggenhorn AL, Svensson KJ, Snyder MP, Bertozzi CR, Long JZ. Organism-wide, cell-type-specific secretome mapping of exercise training in mice. Cell Metab. 2023 Jul. PMID: 37141889; PMCID: PMC10524249. 

  23. Zhou X, Shen X, Johnson JS, Spakowicz DJ, Agnello M, Zhou W, Avina M, Honkala A, Chleilat F, Chen SJ, Cha K, Leopold S, Zhu C, Chen L, Lyu L, Hornburg D, Wu S, Zhang X, Jiang C, Jiang L, Jiang L, Jian R, Brooks AW, Wang M, Contrepois K, Gao P, Rose SMS, Tran TDB, Nguyen H, Celli A, Hong BY, Bautista EJ, Dorsett Y, Kavathas PB, Zhou Y, Sodergren E, Weinstock GM, Snyder MP. Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease. Cell Host Microbe. 2024 Apr 10;32(4):506-526.e9. doi: 10.1016/j.chom.2024.02.012. Epub 2024 Mar 12. PMID: 38479397; PMCID: PMC11022754. 

  24. Shen X, Wang C, Zhou X, Zhou W, Hornburg D, Wu S, Snyder MP. Nonlinear dynamics of multi-omics profiles during human aging. Nat Aging. 2024 Nov;4(11):1619-1634. doi: 10.1038/s43587-024-00692-2. Epub 2024 Aug 14. PMID: 39143318; PMCID: PMC11564093. 

  25. Balvert M, Cooper-Knock J, Stamp J, Byrne RP, Mourragui S, van Gils J, Benonisdottir S, Schlüter J, Kenna K, Abeln S, Iacoangeli A, Daub JT, Browning BL, Taş G, Hu J, Wang Y, Alhathli E, Harvey C, Pianesi L, Schulte SC, González-Domínguez J, Garrisson E; Lorentz workshop on epistasis; Snyder MP, Schönhuth A, Sng LMF, Twine NA. Considerations in the search for epistasis. Genome Biol. 2024 Nov 19;25(1):296. doi: 10.1186/s13059-024-03427-z. Erratum in: Genome Biol. 2025 Jan 20;26(1):12. doi: 10.1186/s13059-025-03477-x. PMID: 39563431; PMCID: PMC11574992. 

  26. Metwally AA, Perelman D, Park H, Wu Y, Jha A, Sharp S, Celli A, Ayhan E, Abbasi F, Gloyn AL, McLaughlin T, Snyder MP. Prediction of metabolic subphenotypes of type 2 diabetes via continuous glucose monitoring and machine learning. Nat Biomed Eng. 2024 Dec 23:10.1038/s41551-024-01311-6. doi: 10.1038/s41551-024-01311-6. Epub ahead of print. PMID: 39715896; PMCID: PMC12183321. 

  27. Park H, Metwally AA, Delfarah A, Wu Y, Perelman D, Mayer C, McGinity C, Rodgar M, Celli A, McLaughlin T, Mignot E, Snyder M. High-resolution lifestyle profiling and metabolic subphenotypes of type 2 diabetes. NPJ Digit Med. 2025 Jun 11;8(1):352. doi: 10.1038/s41746-025-01728-6. PMID: 40500312; PMCID: PMC12159136. 

  28. Wu Y, Ehlert B, Metwally AA, Perelman D, Park H, Brooks AW, Abbasi F, Michael B, Celli A, Bejikian C, Ayhan E, Lu Y, Lancaster SM, Hornburg D, Ramirez L, Bogumil D, Pollock S, Wong F, Bradley D, Gutjahr G, Rangan ES, Wang T, McGuire L, Venkat Rangan P, Ræder H, Shipony Z, Lipson D, McLaughlin T, Snyder MP. Individual variations in glycemic responses to carbohydrates and underlying metabolic physiology. Nat Med. 2025 Jul;31(7):2232-2243. doi: 10.1038/s41591-025-03719-2. Epub 2025 Jun 4. PMID: 40467897; PMCID: PMC12283382.