Pardis Sabeti

Pardis Sabeti
Sabeti in 2011
Born
Pardis Christine Sabeti

(1975-12-25) 25 December 1975 (age 49)
Tehran, Iran
EducationMassachusetts Institute of Technology (BS)
New College, Oxford (MSc, DPhil)
Harvard University (MD)
AwardsTIME 100
National Academy of Medicine
Scientific career
FieldsEvolutionary genetics
Genetic epidemiology
Computational biology
InstitutionsHarvard University
Broad Institute
Howard Hughes Medical Institute
ThesisThe Effects of Natural Selection and Recombination on Genetic Diversity in Humans: An Investigation of Plasmodium Falciparum Malaria in African Populations (2002)
Doctoral advisorRyk Ward
Anthony Boyce[1]
WebsiteOfficial website

Pardis Christine Sabeti (Persian: پردیس ثابتی; born December 25, 1975) is an Iranian-American computational biologist, medical geneticist, and evolutionary geneticist.[2] She is a professor in the Center for Systems Biology and Department of Organismic and Evolutionary Biology at Harvard University, professor of Immunology and Infectious Disease at the Harvard T.H. Chan School of Public Health, core institute member at the Broad Institute, and an investigator of the Howard Hughes Medical Institute.[3][4]

Sabeti and her lab have pioneered technologies for detecting, tracking, and countering deadly pathogens, including Ebola,[5][6] Zika,[7] Lassa,[8][9] and SARS-CoV-2.[10][11]  They have also created some of the most powerful algorithms and molecular tools to characterize the human genome and transformative methods for gene delivery of new biomedicines to specific tissues.[12][13][14]

Sabeti was named one of Time Magazine's Persons of the Year in 2014 (Ebola Fighters), and one of the Time 100 most influential people in 2015.[15][16] Her continued efforts including during the COVID-19 pandemic led her to receive a Time 100 Impact Award and to be inducted into the National Academy of Medicine.[17][18] She is the current host of the educational series Against All Odds: Inside Statistics sponsored by Annenberg Learner and a Crash Course on Outbreak Science[19][20] and is the lead singer and a writer for the rock band Thousand Days.[21][22][23]

Early life and education

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Sabeti was born in 1975 in Tehran, Iran, to Nasrin and Parviz Sabeti. Her father came from a Baháʼí Faith family but never officially joined as a member[24][25] and was the deputy in SAVAK, Iran's intelligence agency, and a high ranking security official in Shah's regime.[26][27]

Her family fled Iran in October 1978, shortly before the Iranian Revolution, when Sabeti was two years old,[28] and found sanctuary in Florida.[26] As a child, Sabeti wanted to be a flower-shop owner, novelist, or doctor.[29][30] However, she was most passionate about math.[30] She had a sister, Parisa, who was 2 years older.[26] Growing up, Parisa taught Pardis the course material she had learned the year before in school, leading Pardis to be "almost two years ahead of her classmates" when the school year began.[26] Throughout her life, Sabeti played many sports including competitive tennis.[31]

Sabeti went to Trinity Preparatory School in Florida. In high school, she was a National Merit Scholar, class president, valedictorian, and member of the Varsity tennis team.[26] She additionally attributes part of her inspiration towards infectious disease research to the 1995 movie Outbreak.[32]

Sabeti attended the Massachusetts Institute of Technology (MIT), where she was a member of the varsity tennis team and class president, graduating in 1997 with a major in biology and a "perfect 5.0 average."[26] At MIT, she began her research career in David Bartel's laboratory[33] and was advised by Eric Lander,[34] and was a teaching assistant for undergraduate courses in genetics and biochemistry.[29] She created the MIT Freshman Leadership Program [35] and pioneered the school's larger pre-orientation programming.

Sabeti was selected as Rhodes Scholar and completed a masters in human biology than doctorate work in evolutionary genetics in 2002,[1] at New College, Oxford, earning an M.Sc. and D.Phil. She went on to complete a Doctor of Medicine (M.D.) at Harvard Medical School in 2006 summa cum laude, being the third woman to receive this honor since the school had begun accepting female students.[34][36] The Paul & Daisy Soros Fellowships for New Americans supported her medical studies.[34] Initially, Sabeti planned to enter medicine and become a doctor, she decided to pursue research instead after completing medical school and discovering she preferred research to medicine.[30]

Career and research

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Human Genetics

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As a graduate student at Oxford and postdoctoral fellow with Eric Lander at the Broad Institute, Sabeti developed a family of statistical tests that identify regions of the genome under positive natural selection, by identifying common genetic variants found on unusually long haplotypes. Her tests, extended haplotype homozygosity (EHH), the long-range haplotype (LRH) test, and cross population extended haplotype homozygosity (XP-EHH), are designed to detect advantageous mutations whose frequency in human populations has risen rapidly over the last 10,000 years.[37][38][39][40][41][42][21] As a faculty member at Harvard, Sabeti and her group have developed a statistical test to pinpoint signals of selection, the Composite of Multiple Signals (CMS),[43]

Infectious Disease

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In 2014, having worked for a decade together in West Africa on Lassa fever and other infectious diseases, Sabeti and Christian Happi, a Cameroonian-Nigerian geneticist, and their teams launched the African Center of Excellence for Genomics of Infectious Disease (ACEGID) to enhance pathogen surveillance and education in Africa.[44] Their efforts in the Ebola outbreak in West Africa helped identify the first cases in Sierra Leone and Nigeria, and advanced genomic sequencing technology to identify a single point of infection from an animal reservoir to a human.[45] RNA changes further suggested that the first human infection was followed by exclusive human to human transmissions.[46] They also showed the virus was mutating to be able to infect human cells more easily.

Sabeti's team continued to support outbreak response, developing and deploying genomic and computational tools to elucidate the origins, evolution, and community transmission of viruses.  During the Zika epidemic in 2016, Sabeti's team assembled the largest sequencing study of the virus and showed the virus was circulating undetected for many months.[47] During the 2018 Lassa fever outbreak in Nigeria, her and Happi's team rapidly sequenced the virus on ground in the country, providing real-time feedback to the Nigeria CDC on the origins and spread of the outbreak. During COVID-19, her team led genomic investigations that elucidated the first superspreader events, variants of concern, and transmission from vaccinated individuals. In 2019, Sabeti and Happi's teams were awarded funding from the TED Audacious Project to build Sentinel, a pandemic pre-emption and response system."[48][49]

Other contributions

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Her lab developed a family of statistical tests to detect and characterize correlations in datasets of any kind, maximal information non-parametric exploration (MINE).[41] Sabeti has via her collaboration with Michael Mitzenmacher an Erdős number of 3.[50] In February 2021 Sabeti co-authored a paper on how a certain level of COVID-19 anti-bodies may provide lasting protection against the virus, studying 4300 employees of SpaceX with its CEO Elon Musk.[51][52]

Outreach and Teaching

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In May 2015, she delivered a TED Talk, called "How we'll fight the next deadly virus."[53] In September 2021, Sabeti joined the YouTube channel Crash Course to host its series on Outbreak Science. Sabeti hosted the Against All Odds video series with the goal of explaining statistics to high school and college students.[54] Sabeti is an annual participant in the Distinguished Lecture Series at the acclaimed Research Science Institute at MIT for high school students.

Awards and honors

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Sabeti was the 2012 recipient of Smithsonian magazine's American Ingenuity Award in the Natural Sciences category. In 2014, she received the Vilcek Prize for Creative Promise in Biomedical Science.[55] She is a World Economic Forum Young Global Leader and a National Geographic Emerging Explorer.

In addition to being named one of Time Magazine's Persons of the Year in 2014 (Ebola Fighters), Sabeti was listed as one of Time Magazine's 100 most influential people in 2015, and was awarded the Time 100 Impact Award in 2022.[56][17] Sabeti was on the list of the BBC's 100 Women announced on 23 November 2020.[57]

In 2015, Sabeti was selected for the prestigious Howard Hughes Medical Institute Investigator award.[58] She has also received a Burroughs Wellcome Fund Career Award in the Biomedical Sciences,[59] a Packard Foundation award in Science and Engineering,[39] and an NIH Director's New Innovator Award,[40] and a L'Oréal for Women in Science Fellowship.

Sabeti was inducted in the National Academy of Medicine in 2020.[18]

Personal life

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Sabeti is the lead singer and songwriter for the rock band Thousand Days.[21][22][23] In her spare time, Sabeti enjoys playing volleyball and participates in Harvard's summer volleyball league.[60]

On July 17, 2015, Sabeti suffered a near-fatal accident at a conference in Montana.[31] She was a passenger in an ATV that went over a cliff, and catapulted onto boulders. She shattered her pelvis and knees, and sustained a brain injury.[31] She completed rehab to return to teaching.[31]

Filmography

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  • Against All Odds ... Host (32 episodes)[61]
  • Crash Course - Outbreak Science Host (15 episodes)[20]

References

[edit]
  1. ^ a b Sabeti, Pardis Christine (2002). The effects of natural selection and recombination on genetic diversity in humans : an investigation of Plasmodium falciparum malaria in African populations. jisc.ac.uk (DPhil thesis). University of Oxford. OCLC 64594684. EThOS uk.bl.ethos.410671. Archived from the original on 7 March 2019. Retrieved 6 March 2019.
  2. ^ Pardis Sabeti publications from Europe PubMed Central
  3. ^ "FAS Center for Systems Biology, Harvard University". Archived from the original on 17 May 2008.
  4. ^ "Pardis Sabeti". @broadinstitute. 6 July 2015. Retrieved 11 August 2024.
  5. ^ Gire, Stephen K.; Goba, Augustine; Andersen, Kristian G.; Sealfon, Rachel S. G.; Park, Daniel J.; Kanneh, Lansana; Jalloh, Simbirie; Momoh, Mambu; Fullah, Mohamed; Dudas, Gytis; Wohl, Shirlee; Moses, Lina M.; Yozwiak, Nathan L.; Winnicki, Sarah; Matranga, Christian B. (12 September 2014). "Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak". Science. 345 (6202): 1369–1372. Bibcode:2014Sci...345.1369G. doi:10.1126/science.1259657. ISSN 0036-8075. PMC 4431643. PMID 25214632.
  6. ^ Park, Daniel J.; Dudas, Gytis; Wohl, Shirlee; Goba, Augustine; Whitmer, Shannon L.M.; Andersen, Kristian G.; Sealfon, Rachel S.; Ladner, Jason T.; Kugelman, Jeffrey R.; Matranga, Christian B.; Winnicki, Sarah M.; Qu, James; Gire, Stephen K.; Gladden-Young, Adrianne; Jalloh, Simbirie (June 2015). "Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone". Cell. 161 (7): 1516–1526. doi:10.1016/j.cell.2015.06.007. PMC 4503805. PMID 26091036.
  7. ^ Metsky, Hayden C.; Matranga, Christian B.; Wohl, Shirlee; Schaffner, Stephen F.; Freije, Catherine A.; Winnicki, Sarah M.; West, Kendra; Qu, James; Baniecki, Mary Lynn; Gladden-Young, Adrianne; Lin, Aaron E.; Tomkins-Tinch, Christopher H.; Ye, Simon H.; Park, Daniel J.; Luo, Cynthia Y. (15 June 2017). "Zika virus evolution and spread in the Americas". Nature. 546 (7658): 411–415. Bibcode:2017Natur.546..411M. doi:10.1038/nature22402. ISSN 0028-0836. PMC 5563848. PMID 28538734.
  8. ^ Andersen, Kristian G.; Shapiro, B. Jesse; Matranga, Christian B.; Sealfon, Rachel; Lin, Aaron E.; Moses, Lina M.; Folarin, Onikepe A.; Goba, Augustine; Odia, Ikponwonsa; Ehiane, Philomena E.; Momoh, Mambu; England, Eleina M.; Winnicki, Sarah; Branco, Luis M.; Gire, Stephen K. (August 2015). "Clinical Sequencing Uncovers Origins and Evolution of Lassa Virus". Cell. 162 (4): 738–750. doi:10.1016/j.cell.2015.07.020. PMC 4537774. PMID 26276630.
  9. ^ Siddle, Katherine J.; Eromon, Philomena; Barnes, Kayla G.; Mehta, Samar; Oguzie, Judith U.; Odia, Ikponmwosa; Schaffner, Stephen F.; Winnicki, Sarah M.; Shah, Rickey R.; Qu, James; Wohl, Shirlee; Brehio, Patrick; Iruolagbe, Christopher; Aiyepada, John; Uyigue, Eghosa (November 2018). "Genomic Analysis of Lassa Virus during an Increase in Cases in Nigeria in 2018". New England Journal of Medicine. 379 (18): 1745–1753. doi:10.1056/NEJMoa1804498. ISSN 0028-4793. PMC 6181183. PMID 30332564.
  10. ^ Lemieux, Jacob E.; Siddle, Katherine J.; Shaw, Bennett M.; Loreth, Christine; Schaffner, Stephen F.; Gladden-Young, Adrianne; Adams, Gordon; Fink, Timelia; Tomkins-Tinch, Christopher H.; Krasilnikova, Lydia A.; DeRuff, Katherine C.; Rudy, Melissa; Bauer, Matthew R.; Lagerborg, Kim A.; Normandin, Erica (5 February 2021). "Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events". Science. 371 (6529). doi:10.1126/science.abe3261. ISSN 0036-8075. PMC 7857412. PMID 33303686.
  11. ^ Siddle, Katherine J.; Krasilnikova, Lydia A.; Moreno, Gage K.; Schaffner, Stephen F.; Vostok, Johanna; Fitzgerald, Nicholas A.; Lemieux, Jacob E.; Barkas, Nikolaos; Loreth, Christine; Specht, Ivan; Tomkins-Tinch, Christopher H.; Paull, Jillian S.; Schaeffer, Beau; Taylor, Bradford P.; Loftness, Bryn (February 2022). "Transmission from vaccinated individuals in a large SARS-CoV-2 Delta variant outbreak". Cell. 185 (3): 485–492.e10. doi:10.1016/j.cell.2021.12.027. PMC 8695126. PMID 35051367.
  12. ^ Sabeti, Pardis C.; Reich, David E.; Higgins, John M.; Levine, Haninah Z. P.; Richter, Daniel J.; Schaffner, Stephen F.; Gabriel, Stacey B.; Platko, Jill V.; Patterson, Nick J.; McDonald, Gavin J.; Ackerman, Hans C.; Campbell, Sarah J.; Altshuler, David; Cooper, Richard; Kwiatkowski, Dominic (October 2002). "Detecting recent positive selection in the human genome from haplotype structure". Nature. 419 (6909): 832–837. Bibcode:2002Natur.419..832S. doi:10.1038/nature01140. ISSN 0028-0836. PMID 12397357.
  13. ^ The International HapMap Consortium; Sabeti, Pardis C.; Varilly, Patrick; Fry, Ben; Lohmueller, Jason; Hostetter, Elizabeth; Cotsapas, Chris; Xie, Xiaohui; Byrne, Elizabeth H.; McCarroll, Steven A.; Gaudet, Rachelle; Schaffner, Stephen F.; Lander, Eric S. (October 2007). "Genome-wide detection and characterization of positive selection in human populations". Nature. 449 (7164): 913–918. Bibcode:2007Natur.449..913S. doi:10.1038/nature06250. ISSN 0028-0836. PMC 2687721. PMID 17943131.
  14. ^ Tewhey, Ryan; Kotliar, Dylan; Park, Daniel S.; Liu, Brandon; Winnicki, Sarah; Reilly, Steven K.; Andersen, Kristian G.; Mikkelsen, Tarjei S.; Lander, Eric S.; Schaffner, Stephen F.; Sabeti, Pardis C. (June 2016). "Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay". Cell. 165 (6): 1519–1529. doi:10.1016/j.cell.2016.04.027. PMC 4957403. PMID 27259153.
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  18. ^ a b "Dr. Pardis Sabeti is elected to the National Academy of Medicine". africa.harvard.edu. Retrieved 2 February 2024.
  19. ^ "Against All Odds, Inside Statistics". Annenberg Learner. Annenberg Foundation. Archived from the original on 30 November 2015. Retrieved 18 November 2018.
  20. ^ a b What Is Outbreak Science? Crash Course Outbreak Science #1, 7 September 2021, retrieved 2 February 2024
  21. ^ a b c Furman, Eric (16 July 2007). "Geniuses who will change your life". CNN.com. Retrieved 27 July 2007.
  22. ^ a b Kahn, Joseph (14 June 2008). "Infectious melodies". Boston.com. Retrieved 14 June 2012.
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  24. ^ Minority Rights Group Report, Volumes 2-51, The group 1982, page 114.
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  28. ^ "Medical & Musical Journeys: An Interview with One of Time's Persons of the Year, Pardis Sabeti". The Huffington Post. 10 February 2016. Retrieved 1 May 2016.
  29. ^ a b "Three from MIT Named Rhodes, Marshall Scholars - The Tech". tech.mit.edu. Archived from the original on 11 May 2016. Retrieved 28 May 2016.
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  31. ^ a b c d "Fifteen Professors to Meet | Magazine | The Harvard Crimson". www.thecrimson.com. Retrieved 1 May 2016.
  32. ^ Medina, Kai (December 2020). "Surrounding yourself with the best people". KaiMedinaE.
  33. ^ Sabeti PC, Unrau PJ, Bartel DP (1997). "Accessing rare activities from random RNA sequences: the importance of the length of molecules in the starting pool". Chem Biol. 4 (10): 767–74. doi:10.1016/s1074-5521(97)90315-x. PMID 9375255.
  34. ^ a b c Oskin, Becky (14 June 2006). "Burroughs Wellcome Fund Awardee Profile of Pardis Sabeti". Archived from the original on 14 December 2019. Retrieved 12 October 2007.
  35. ^ "New freshman program encourages unity and diversity". MIT News | Massachusetts Institute of Technology. 23 October 1996. Retrieved 11 August 2024.
  36. ^ "Broad scientist Pardis Sabeti receives prestigious research awards | Broad Institute of MIT and Harvard". www.broadinstitute.org. 14 June 2006. Retrieved 28 May 2016.
  37. ^ Sabeti, P. C.; Reich, D. E.; Higgins, J. M.; Levine, H. Z. P.; Richter, D. J.; Schaffner, S. F.; Gabriel, S. B.; Platko, J. V.; Patterson, N. J.; McDonald, G. J.; Ackerman, H. C.; Campbell, S. J.; Altshuler, D.; Cooper, R.; Kwiatkowski, D.; Ward, R.; Lander, E. S. (2002). "Detecting recent positive selection in the human genome from haplotype structure". Nature. 419 (6909): 832–837. Bibcode:2002Natur.419..832S. doi:10.1038/nature01140. PMID 12397357. S2CID 4404534.
  38. ^ Sabeti, Pardis C.; Varilly, Patrick; Fry, Ben; Lohmueller, Jason; Hostetter, Elizabeth; Cotsapas, Chris; Xie, Xiaohui; Byrne, Elizabeth H.; McCarroll, Steven A.; Gaudet, Rachelle; Schaffner, Stephen F.; Lander, Eric S.; The International HapMap Consortium; Frazer, Kelly A.; Ballinger, Dennis G.; Cox, David R.; Hinds, David A.; Stuve, Laura L.; Gibbs, Richard A.; Belmont, John W.; Boudreau, Andrew; Hardenbol, Paul; Leal, Suzanne M.; Pasternak, Shiran; Wheeler, David A.; Willis, Thomas D.; Yu, Fuli; Yang, Huanming; Zeng, Changqing Zeng; et al. (2007). "Genome-wide detection and characterization of positive selection in human populations". Nature. 449 (7164): 913–918. Bibcode:2007Natur.449..913S. doi:10.1038/nature06250. PMC 2687721. PMID 17943131.
  39. ^ a b "Packard Foundation Fellowship Directory: Pardis Sabeti". Archived from the original on 13 April 2020. Retrieved 14 June 2012.
  40. ^ a b "Iranian Scientist Wins NIH 2009 Innovator Award". 24 October 2009. Retrieved 14 June 2012.
  41. ^ a b Reshef, D. N.; Reshef, Y. A.; Finucane, H. K.; Grossman, S. R.; McVean, G.; Turnbaugh, P. J.; Lander, E. S.; Mitzenmacher, M.; Sabeti, P. C. (2011). "Detecting Novel Associations in Large Data Sets". Science. 334 (6062): 1518–1524. Bibcode:2011Sci...334.1518R. doi:10.1126/science.1205438. PMC 3325791. PMID 22174245.
  42. ^ Deen, Lango (25 July 2005). "One-on-One with Pardis Sabeti". Science Spectrum Online. Archived from the original on 28 September 2007. Retrieved 27 July 2007.
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  44. ^ "About ACEGID – ACEGID". Retrieved 2 February 2024.
  45. ^ Kolata, Gina (1 December 2014). "Sifting Through Genes in Search of Answers on Ebola". The New York Times. ISSN 0362-4331. Retrieved 28 May 2016.
  46. ^ Single animal to human transmission event responsible for 2014 Ebola outbreak NIH press release, August 29, 2014
  47. ^ Metsky, Hayden C.; Matranga, Christian B.; Wohl, Shirlee; Schaffner, Stephen F.; Freije, Catherine A.; Winnicki, Sarah M.; West, Kendra; Qu, James; Baniecki, Mary Lynn; Gladden-Young, Adrianne; Lin, Aaron E.; Tomkins-Tinch, Christopher H.; Ye, Simon H.; Park, Daniel J.; Luo, Cynthia Y. (15 June 2017). "Zika virus evolution and spread in the Americas". Nature. 546 (7658): 411–415. Bibcode:2017Natur.546..411M. doi:10.1038/nature22402. ISSN 0028-0836. PMC 5563848. PMID 28538734.
  48. ^ Bazelon, Emily (3 June 2020). "What Will College Be Like in the Fall?". The New York Times. Retrieved 3 June 2020.
  49. ^ Siliezar, Juan (13 May 2020). "Responding to this pandemic, preparing for the next". www.harvard.edu. Retrieved 3 June 2020.
  50. ^ Reshef, Yakir A.; Reshef, David N.; Finucane, Hilary K.; Sabeti, Pardis C.; Mitzenmacher, Michael (2016). "Measuring dependence powerfully and equitably". J. Mach. Learn. Res. 17 (212): 63. arXiv:1505.02213.
  51. ^ Krouse, Sarah (21 February 2021). "Elon Musk got 4,000 SpaceX workers to join a COVID-19 study. Here's what he learned". Wall Street Journal. Retrieved 21 February 2021 – via foxbusiness.com.
  52. ^ Bartsch, Yannic C.; Fischinger, Stephanie; Siddiqui, Sameed M.; Chen, Zhilin; Yu, Jingyou; Gebre, Makda; Atyeo, Caroline; Gorman, Matthew J.; Zhu, Alex Lee; Kang, Jaewon; Burke, John S.; Slein, Matthew; Gluck, Matthew J.; Beger, Samuel; Hu, Yiyuan; Rhee, Justin; Petersen, Eric; Mormann, Benjamin; de St Aubin, Michael; Hasdianda, Mohammad A.; Jambaulikar, Guruprasad; Boyer, Edward W.; Sabeti, Pardis C.; Barouch, Dan H.; Julg, Boris D.; Musk, Elon R.; Menon, Anil S.; Lauffenburger, Douglas A.; Nilles, Eric J.; Alter, Galit (15 February 2021). "Discrete SARS-CoV-2 antibody titers track with functional humoral stability". Nature Communications. 12 (1): 1018. Bibcode:2021NatCo..12.1018B. doi:10.1038/s41467-021-21336-8. PMC 7884400. PMID 33589636.
  53. ^ Sabeti, Pardis (4 February 2016). "How we'll fight the next deadly virus". www.ted.com. Retrieved 19 May 2016.
  54. ^ "Against all odds".
  55. ^ "The Vilcek Foundation -". www.vilcek.org. Archived from the original on 25 June 2016. Retrieved 9 December 2015.
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