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Michael P Snyder

From EverybodyWiki Bios & Wiki












Michael P Snyder
Born1955
Pottstown, Pennsylvania
🏳️ NationalityAmerican
🎓 Alma materUniversity of Rochester California Institute of Technology
💼 Occupation
Known forRNA sequencing, ChIP-chip and ChIP-seq(11), Genomics, Pioneering multi-omic longitudinal health tracking, Wearable technology, Systems Biology, Systems medicine

Michael P. Snyder is an American genomicist, systems biologist, inventor and entrepreneur. He is the Stanford B. Ascherman Professor[2][3] and as of 2009, Chair of Genetics and Director of Genomics and Personalized Medicine at Stanford University School of Medicine[2], and the former Director of the Yale Center for Genomics and Proteomics.[1] He was elected to The American Academy of Arts and Sciences in 2015.[4] During his tenure as chair of the department at Stanford, the U.S. News & World Report has ranked Stanford University first or tied for first in Genetics, Genomics and Bioinformatics under his leadership.[5]

Snyder has co-founded companies in genetics, genomics, and personalized medicine, including Personalis[6], a company that develops software to interpret genomes after sequencing; January AI[7], a health startup; Protometrix[8]; Affomix;[9] and Q Bio.[10]

Snyder has been a principal investigator of the ENCODE project since its inception in 2003,[11] and co-director of the CIRM Center for Stem Cell Genomics[12] and Director of the Center for Genome of Gene Regulation[13].

Snyder pioneered the use of multi-omic longitudinal profiling to track health.[14][15]

Early life and education

Snyder was born in 1955 and grew up outside of Pottstown, Pennsylvania[16][17]. His father, Kermit Snyder, was an accountant and his mother, Phyllis Snyder, was an elementary school teacher. Snyder attended Owen J Roberts High school in Pottstown. He received a BA in chemistry and biology from the University of Rochester, NY on a scholarship [18]. He went on to receive a PhD in biology from the California Institute of Technology, where he trained in the laboratory of Norman Davidson.[19] Snyder completed his postdoctoral training at Stanford University School of Medicine in the laboratory of Ronald W. Davis.[19] There he was involved in several projects including establishment of successful cloning of genes using antibodies (lambagt11;) (4).

Career

Snyder was hired by Yale University in 1986 as an Assistant Professor in the Department of Biology[20], and was granted tenure in 1994. In 1998, the Department of Biology split into two departments, one focused on ecology and one on molecular biology. Snyder served as chair of the new Molecular, Cellular and Developmental Biology (MCDB) department from 1998 to 2004.[19]. His laboratory worked on chromosome segregation and cell polarity, for which he discovered a number of important genes involved in these processes.[21][22]

His laboratory proposed the first models by which eucaryotes select sites of cell growth.[23][24]

Snyder was also the Director for the Center for Genomics and Proteomics at Yale University (2002–2009), elected to the Genetics Society of America Board of Directors (2006–2009), elected President of US Human Proteome Organization (2006–2008), PI, Center of Excellence in the Genome Sciences (CEGS) (2001–2011), President, Human Proteome Organization (HUPO) (2017–2018)[25][26], PI, NIH Training Grant in Genomics and Proteomics (2004–2022).

In 2009, Snyder moved to Stanford University to Chair the Genetics Department and to direct the Center for Genomics and Personalized Medicine.[27],[19] Snyder has been Principal Investigator of Center of Excellence in the Genome Sciences (CEGS) (2001–2011), NIH Training Grants in Genomics and Proteomics (first at Yale, now at Stanford) (2004–present), and is co-director of the CIRM Center for Stem Cell Genomics[28] and Director for the Center for Genome of Gene Regulation[29]. Snyder was elected and has served as President of US Human Proteome Organization (2006–2008) and the international Human Proteome Organization (2017–2018). He currently leads the National Institutes of Health's Encyclopedia of DNA Elements (Encode)'s Production Center for Mapping Regulatory Regions of the Human Genome.[30]

Snyder has co-founded biotechnology companies, including Personalis[31], SensOmics[32], Qbio[33][34][35], January AI[36], Filtricine, Mirvie, Protos, Protometrix[37] (now part of Thermo Fisher Scientific), and Affomix[38] (now part of Illumina).[39]

Research

Snyder has made contributions to medicine, genomics and biotechnology. To support their research, Snyder’s laboratory has invented a number of novel systems-wide and genomics technologies. Snyder's laboratory at Yale initially focused on studying the genome of the yeast Saccharomyces cerevisiae, a eukaryote model organism commonly used in genetics and molecular biology.[40] Later, the lab began to use the same techniques to look at the human genome.[40]

In 2003, the Encyclopedia of DNA Elements (ENCODE) project was launched by the US National Human Genome Research Institute (NHGRI), with the goal of identifying all functional elements in the human genome. He has been a Principal Investigator in the ENCODE project since its inception in 2003 and his lab has contributed a large number of data sets.[19] These data contributed to the discovery that there are many more transcription factor binding sites than originally thought(13), and that twice as much of the human genome is transcribed into mature RNA(16).

The Snyder laboratory then showed that transcription factor binding sites vary greatly among people (25) and closely related species, showing that much of the diversity between individuals and closely related species happens at the level of gene regulation (27,28), rather than changes in the genes themselves.

Snyder broadened his lab's genomics research to include the fields of proteomics, transcriptomics, and metabolomics. After his 2009 move to Stanford, Snyder also began to focus on using these omics technologies to monitor human health. In 2012, the lab published the first deep longitudinal profiling of a single person using multi-omics technologies, producing a data set colloquially known as the Snyderome. This research approach later expanded to over 100 people and included data generated by wearable biosensors.

Libraries and arrays

Snyder’s laboratory set up the first large-scale systems project to study all yeast genes and proteins simultaneously using a transposon tagging strategy to analyze gene expression, protein localization, and gene disruption (9,10). This was the first large-scale systems analysis of genes and proteins in any organism. The libraries and approaches were released publicly and now in use by laboratories worldwide.

Beyond the genome, the Snyder lab was also the first to set up protein and proteome microarrays for the large-scale characterization of protein function and antibody reactivity (21,22). They demonstrated many novel biological activities of protein kinases and other yeast proteins and showed they can be useful for autoantibody profiling (23).

Their laboratory constructed the first human chromosome array (15) and later the first whole genome array (16) to map transcription factor binding sites and novel transcribed regions of the genome.

In collaboration with Dr. Patrick Brown’s laboratory, the Snyder laboratory developed ChIP-on-chip (11) to carry out the first genome wide mapping of transcription factor binding sites. Initially established for yeast(11), they later applied the methods to humans (13).

Next-generation sequencing

The ChIP-chip technique for mapping of transcription factor binding sites was ultimately morphed into ChIP-seq, in order to take advantage of DNA sequencing rather than using DNA microarrays.(12) The ChIP-seq method was foundational for multiple multicenter consortia projects including the ENCODE project ((14)). They later invented RNA-seq to better map transcriptomes, both protein coding and noncoding (17,18).

With the advent of high-throughput DNA sequencing technologies, Snyder's laboratory was the first to sequence an organism using such technology. Snyder's laboratory sequenced the human pathogen Acinetobacter baumannii and invented paired end sequencing using new high-throughput sequencing technologies (20), using this to demonstrate that there were ten times as much structural variation (SV) in the human genome than previously realized and that most SV deletions and insertions were due to nonhomologous recombination, an unexpected discovery at the time, since most SVs were proposed to be due to homologous recombination events.[41],[42]

Beyond the genome, the Snyder laboratory was also the first to set up protein and proteome microarrays for the large-scale characterization of protein function and antibody reactivity.[43][44]) They demonstrated many novel biological activities of protein kinases and other yeast proteins and showed they can be useful for autoantibody profiling.[45]

Omics profiling and data-driven medicine

Using the same in-depth omics approaches he applied to yeast, upon his move to Stanford in 2009, Snyder began to apply systems-wide analysis to human health (29). The Snyder laboratory carried out the first deep longitudinal profiling of one person using multi-omics technologies (genomics, transcriptomics, proteomics, metabolomics, etc.). This deep profiling used genomics for the first time to predict disease risk and follow disease onset at a level not previously achieved.[46] Highlighted in Cell journal's 40th anniversary issue [47], Snyder presents "how personalized medicine may be applied to individuals over long time frames, analyzing transcription, metabolite, and cytokine fluctuations through periods of health and disease alongside fully sequenced genomes".[48]. This approach of collecting longitudinal deep data on humans is now being applied by many groups worldwide. The Snyder lab has demonstrated that self-tracking using wearable biosensors can be used for monitoring health and illness. Together these studies demonstrate the power of using longitudinal tracking and big data to manage human health.[49]

Selected publications

  1. Alavi, Arash, et al. "Real-time alerting system for COVID-19 and other stress events using wearable data | Nature Medicine".. Nature medicine 2021 Nov 29:1-0.
  2. Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A, Thiessen N, …, Snyder M and Jones S. "Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing - PubMed".. Nat Methods. 2007;4:651-7.
  3. Horak, Christine E., et al. "GATA-1 binding sites mapped in the beta-globin locus by using mammalian chIp-chip analysis - PubMed".. Proceedings of the National Academy of Sciences 99.5 (2002): 2924-2929.
  4. The ENCODE Project Consortium. "An integrated encyclopedia of DNA elements in the human genome - PubMed".. Nature. 2012. 489(7414): 57-74.
  5. Wang Z, Gerstein M, Snyder M. "RNA-Seq: a revolutionary tool for transcriptomics - PubMed".. Nat Rev Genet. 2009 Jan;10(1):57-63. PMID 19015660.
  6. Hudson ME, Pozdnyakova I, Haines K, Mor G, Snyder M. "Identification of differentially expressed proteins in ovarian cancer using high-density protein microarrays - PubMed".. Proc Natl Acad Sci USA. 2007;104: 17494-9.
  7. Kasowski M, Grubert F, Heffelfinger C, Hariharan M, Asabere A, Waszak SM, Habegger L, Rozowsky J, Shi M, Urban AE, … Weissman SM, Gerstein MB, Korbel JO, Snyder M. "Variation in transcription factor binding among humans - PubMed".. Science. 2010. 328(5975): 232-5. Epub 2010. PMID 20299548.
  8. Borneman AR, Gianoulis TA, Zhang ZD, Yu H, Rozowsky J, Seringhaus MR, Wang LY, Gerstein M, Snyder M. "Divergence of transcription factor binding sites across related yeast species - PubMed".. Science. 2007;317: 815-19.
  9. Chen R, Mias GI, Li-Pook-Than J, Jiang L, … Snyder M. "Personal omics profiling reveals dynamic molecular and medical phenotypes - PubMed".. Cell. 2012;148:1293-307.
  10. Li X, Dunn J, Salins D, Zhou G, Zhou W, Schüssler-Fiorenza Rose SM, Perelman D, Colbert E, Runge R, Rego S, Sonecha R, Datta S, McLaughlin T, Snyder M. "Digital Health: Tracking Physiomes and Activity Using Wearable Biosensors Reveals Useful Health-Related Information - PubMed".. 2017 Jan 12;15(1):e2001402. doi: 10.1371/journal.pbio.2001402. PMID 28081144

Book

Snyder authored a book for a general audience: Genomics and Personalized Medicine: What Everyone Needs to Know Oxford University Press (2016) ISBN 978-0-19023-476-8 Search this book on ..

Awards and honors

  • Pew Scholars (1987)[50]
  • Lewis B Cullman named chair, Yale (1996)[51]
  • Burroughs Wellcome Scholar Award (2000)[1]
  • Connecticut Medal of Science (2007)[51]
  • Stanford B. Ascherman named chair, Stanford (2011)[19]
  • Member of the American Academy of Sciences (elected 2015)[4]
  • George W. Beadle Award, Genetics Society of America (2019) [19]

References

  1. ↑ 1.0 1.1 1.2 "Michael P. Snyder".
  2. ↑ 2.0 2.1 "Michael Snyder, Ph.D., STANFORD W. ASCHERMAN PROFESSOR OF GENETICS". Stanford profiles. 20 August 2015. Retrieved 19 April 2022.
  3. ↑ https://genestogenomes.org/snyder-beadle/
  4. ↑ 4.0 4.1 "Michael Snyder". American Academy of Arts and Sciences.
  5. ↑ https://www.usnews.com/best-graduate-schools/top-science-schools/genetics-rankings
  6. ↑ https://www.nytimes.com/2012/06/03/business/geneticists-research-finds-his-own-diabetes.html
  7. ↑ https://www.nytimes.com/2022/03/14/well/eat/ai-diet-personalized.html
  8. ↑ https://www.genomeweb.com/archive/invitrogen-buys-protein-chip-maker-protometrix#.YlO0w8hBzIU
  9. ↑ https://online.stanford.edu/instructors/michael-snyder
  10. ↑ https://www.thetimes.co.uk/article/whats-your-ageing-type-the-four-ways-we-grow-old-bhd2lrscp
  11. ↑ Abascal, Federico; Acosta, Reyes; Addleman, Nicholas J.; Adrian, Jessika; Afzal, Veena; Aken, Bronwen; et al. (2020). "Perspectives on ENCODE". Nature. 583 (7818): 693–98. Bibcode:2020Natur.583..693E. doi:10.1038/s41586-020-2449-8. PMC 7410827 Check |pmc= value (help). PMID 32728248 Check |pmid= value (help).
  12. ↑ "The CIRM Center of Excellence in Stem Cell Genomics (CESCG)". 26 February 2015.
  13. ↑ http://www.genomacrg.cl/
  14. ↑ Zhou W, Sailani MR, Contrepois K, Zhou Y, Ahadi S, Leopold SR, et al. (May 2019). "Longitudinal multi-omics of host-microbe dynamics in prediabetes". Nature. 569 (7758): 663–71. doi:10.1038/s41586-019-1236-x. PMC 6666404 Check |pmc= value (help). PMID 31142858.
  15. ↑ "How Multi-Omics Profiling Can Redefine Precision Health and Medicine - US". ThermoFisher Scientific.
  16. ↑ https://ctcase.org/member/michael-p-snyder/
  17. ↑ https://www.wsj.com/articles/BL-HEB-49289
  18. ↑ https://psmag.com/social-justice/making-it-personal-geneticist-michael-snyder-puts-a-face-to-personalized-medicine-57554
  19. ↑ 19.0 19.1 19.2 19.3 19.4 19.5 19.6 Schmidt, Silke (9 April 2019). "Congratulations to Michael Snyder for receiving the 2019 George W. Beadle Award!". Genetics Society of America. Retrieved 8 February 2021.
  20. ↑ https://psmag.com/social-justice/making-it-personal-geneticist-michael-snyder-puts-a-face-to-personalized-medicine-57554
  21. ↑ Page BD, Snyder M (August 1992). "CIK1: a developmentally regulated spindle pole body-associated protein important for microtubule functions in Saccharomyces cerevisiae". Genes Dev. 6 (8): 1414–29. doi:10.1101/gad.6.8.1414. PMID 1644287.
  22. ↑ Roemer T, Madden K, Chang J, Snyder M (April 1996). "Selection of axial growth sites in yeast requires Axl2p, a novel plasma membrane glycoprotein". Genes Dev. 10 (7): 777–93. doi:10.1101/gad.10.7.777. PMID 8846915.
  23. ↑ Snyder M, Gehrung S, Page BD (August 1991). "Studies concerning the temporal and genetic control of cell polarity in Saccharomyces cerevisiae". J Cell Biol. 114 (3): 515–32. doi:10.1083/jcb.114.3.515. PMC 2289092. PMID 1860883.
  24. ↑ Roemer T, Madden K, Chang J, Snyder M (April 1996). "Selection of axial growth sites in yeast requires Axl2p, a novel plasma membrane glycoprotein". Genes Dev. 10 (7): 777–93. doi:10.1101/gad.10.7.777. PMID 8846915.
  25. ↑ https://ctcase.org/member/michael-p-snyder/
  26. ↑ https://news.yale.edu/2008/06/12/yale-s-snyder-awarded-2007-connecticut-medal-science
  27. ↑ https://genestogenomes.org/snyder-beadle/
  28. ↑ https://www.cirm.ca.gov/researchers/genomics-initiative/about
  29. ↑ https://med.stanford.edu/news/all-news/2015/02/snyder-awarded-7-million-from-genome-institute.html
  30. ↑ https://reporter.nih.gov/project-details/9247694
  31. ↑ https://www.nytimes.com/2012/06/03/business/geneticists-research-finds-his-own-diabetes.html
  32. ↑ "SensOmics, See the Unseen". SensOmics, See the Unseen.
  33. ↑ https://www.thetimes.co.uk/article/whats-your-ageing-type-the-four-ways-we-grow-old-bhd2lrscp
  34. ↑ https://q.bio/about/
  35. ↑ https://stanfordmag.org/contents/body-count
  36. ↑ https://www.nytimes.com/2022/03/14/well/eat/ai-diet-personalized.html
  37. ↑ https://www.genomeweb.com/archive/invitrogen-buys-protein-chip-maker-protometrix#.YlO0w8hBzIU
  38. ↑ https://online.stanford.edu/instructors/michael-snyder
  39. ↑ "Snyder Lab". Stanford.edu. Retrieved 2 December 2021.
  40. ↑ 40.0 40.1 Bechard, Deni Ellis (December 2021). "Body Count: How Michael Snyder's self-monitoring project could transform human health". Stanford Magazine. Retrieved 2 December 2021.
  41. ↑ https://www.science.org/doi/abs/10.1126/science.1149504
  42. ↑ Korbel JO, Urban AE, Affourtit JP, Godwin B, Grubert F, et al. (October 2007). "Paired-end mapping reveals extensive structural variation in the human genome". Science. 318 (5849): 420–26. doi:10.1126/science.1149504. PMC 2674581. PMID 17901297.
  43. ↑ Zhu H, Bilgin M, Bangham R, Hall D, Casamayor A, et al. (September 2001). "Global analysis of protein activities using proteome chips". Science. 293 (5537): 2101–05. doi:10.1126/science.1062191. PMID 11474067.
  44. ↑ Zhu H, Klemic JF, Chang S, Bertone P, Casamayor A, et al. (November 2000). "Analysis of yeast protein kinases using protein chips". Nat Genet. 26 (3): 283–89. doi:10.1038/81576. PMID 11062466.
  45. ↑ Hudson ME, Pozdnyakova I, Haines K, Mor G, Snyder M (October 2007). "Identification of differentially expressed proteins in ovarian cancer using high-density protein microarrays". Proc Natl Acad Sci U S A. 104 (44): 17494–9. doi:10.1073/pnas.0708572104. PMC 2077284. PMID 17954908.
  46. ↑ Chen R, Mias GI, Li-Pook-Than J, Jiang L, Lam HY, et al. (March 2012). "Personal omics profiling reveals dynamic molecular and medical phenotypes". Cell. 148 (6): 1293–307. doi:10.1016/j.cell.2012.02.009. PMC 3341616. PMID 22424236.
  47. ↑ https://www.cell.com/cell/issue?pii=S0092-8674(12)X0006-0
  48. ↑ https://www.cell.com/cell/fulltext/S0092-8674(12)00281-4
  49. ↑ Li X, Dunn J, Salins D, Zhou G, Zhou W, et al. (January 2017). "Digital Health: Tracking Physiomes and Activity Using Wearable Biosensors Reveals Useful Health-Related Information". PLoS Biol. 15 (1): e2001402. doi:10.1371/journal.pbio.2001402. PMC 5230763. PMID 28081144.
  50. ↑ "Directory of Scholars". pewtrusts.org.
  51. ↑ 51.0 51.1 "Yale's Snyder Awarded 2007 Connecticut Medal of Science". 12 June 2008.



Category:American geneticists Category:1955 births Category:Stanford University School of Medicine faculty Category:California Institute of Technology alumni Category:20th-century American inventors Category:21st-century American inventors Category:Jewish American scientists Category:Members of the United States National Academy of Sciences Category:Biotechnologists Category:21st-century American Jews Category:Living people



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