Wikipedia

David S. Wishart

[[

Canadian Researcher

|thumb|David S. Wishart]]

David Wishart
FRSC
BornDecember 7, 1961 (1961-12-07) (age 62)
Edmonton, Alberta, Canada
Alma materUniversity of Alberta
Yale University
OccupationProfessor
Known for
Awards
  • Canadian Research Chair Tier 1 (2023)
  • J. Gordin Kaplan Award for Excellence in Research (2023)
  • Distinguished University Professor (2018)
  • University of Alberta Alumni Award (2017)
  • ASTech Awards (1999, 2021)
  • Lifetime Fellowship, Metabolomics Society (2014)
Scientific career
Fields
InstitutionsUniversity of Alberta
Websitewww.wishartlab.com, www.tmicwishartnode.ca

David S. Wishart FRSC (born December 7, 1961) is a Canadian researcher in metabolomics and a Distinguished University Professor in the Department of Biological Sciences and the Department of Computing Science at the University of Alberta. Wishart also holds cross appointments in the Faculty of Pharmacy and Pharmaceutical Sciences and the Department of Laboratory Medicine and Pathology in the Faculty of Medicine and Dentistry. Additionally, Wishart holds a joint appointment in metabolomics at the Pacific Northwest National Laboratory in Richland, Washington. Wishart is well known for his pioneering contributions to the fields of protein NMR spectroscopy, bioinformatics, cheminformatics and metabolomics.[1][2][3] In 2011, Wishart founded the Metabolomics Innovation Centre (TMIC),[4] which is Canada's national metabolomics laboratory.

Wishart is also a biotech entrepreneur. Since 1995 he has launched eight start-up biotech companies, including Chenomx,[5] OMx Personal Health Analytics[6] and Molecular You Corp.[7] With more than 500 publications and >100,000 citations over his career,[8] he has been consistently ranked among the world's most cited scientists in any discipline[9][10] and among the world's most cited 200 life scientists.[11]

Early life and education

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Wishart was born and raised in Edmonton, Alberta, Canada and has one brother, Ian (a physician) and one sister, Sandy. His mother, Patricia worked as a naturalist and author; his father William was a wildlife biologist with the government of Alberta. Wishart identifies as Metis. He has both Cree and Assiniboine ancestry from his father's side and Scottish ancestry from his mother's side. As a youth, Wishart learned to hunt, fish and trap from his father, who also used to operate his own trapline.

Wishart received his B.Sc. (Honours, First Class) in physics from the University of Alberta in 1983 and his M.Phil. (1986) and Ph.D. degrees (1991) in molecular biophysics from Yale University. Wishart completed his Ph.D. under the supervision of Frederic M. Richards and his post-doctoral studies (1991–1995) under the supervision of Brian D. Sykes.[12]

Academic career

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Wishart started his academic career as an assistant professor in 1995 with the Faculty of Pharmacy and Pharmaceutical Sciences at the University of Alberta where he held the Bristol Myers Squibb Chair in Biotechnology for 10 years. He was promoted to associate professor in 2002 and full professor in 2003, joining the Departments of Computing Science and Biological Sciences in the Faculty of Science at the University of Alberta. Because of his growing involvement in clinical chemistry, Wishart was appointed as an adjunct professor in the Department of Laboratory Medicine and Pathology in 2012. Wishart was appointed as a Distinguished University Professor in 2018.[13] From 2004-2016, Wishart also served as a senior research officer and the director of nanobiology at the National Research Council of Canada with the National Institute of Nanotechnology, located on the University of Alberta campus.

Research

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Wishart's research interests span a number of areas including structural biology, computational biology, bioinformatics, nanobiology, metabolomics, nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry. A common theme to his research career has been the development of techniques, technology cores, protocols, data resources or computer programs that make science simpler, faster, cheaper or easier.[1][2][3]

Biomolecular NMR

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Wishart began his research career in the field of protein NMR in the early 1990s, focusing on using NMR spectroscopy to characterize protein structure and protein denaturation. At the time, protein structural analysis by NMR required hundreds of hours of manual data analysis and data tabulation. In an effort to accelerate the process, Wishart discovered a trend with regard to how the NMR chemical shifts of amino acid residues changed systematically with regard to their secondary structure. He proceeded to develop a technique, called the chemical shift index, also known as CSI, that used a set of simple rules and simple chemical shift tables that allowed scientists to directly use protein chemical shift assignments to rapidly determine the type and location of protein secondary structures in proteins in just seconds.[14][15] Subsequently, Wishart showed how NMR chemical shifts could be used to easily and rapidly measure protein flexibility via the random coil index or RCI.[16][17] Later, he showed how it was possible to use chemical shifts to determine protein backbone torsion angles with a program called PREDITOR.[18] Wishart also determined how chemical shifts could be used to measure residue accessible surface area,[19] and to identify super secondary structure elements.[19][20] To further extend this work, Wishart developed innovative methods to determine the 3D structure of proteins using a technique called chemical shift threading with programs such as GeNMR, CS23D and E-Thrifty.[21][22][23] To help compare and assess existing protein NMR structures, Wishart also developed methods to accurately predict protein chemical shifts from 3D coordinates using programs such as ShiftX and ShiftX2.[24][25] At the same time he also developed methods to re-reference incorrectly assigned protein chemical shifts using programs such as SHIFTCOR and PANAV.[26] These programs were used to help create protein NMR databases such as RefDB that contain 1000s of re-referenced chemical shifts.[27] Wishart's papers describing these NMR methods have been cited more than 15,000 times and are now considered[by whom?] to be foundational techniques for much of modern protein NMR.

Metabolomics

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In the early 2000s, Wishart turned his attention from looking at big molecules such as proteins to looking at small molecules (metabolites). In 2001 he developed and then patented NMR-based techniques (leading to the spin-off company Chenomx[5]) that permitted the rapid identification and quantification of metabolites by NMR in biofluids.[28] In 2005, he conceived of the Human Metabolome Project (HMP) [29] – the metabolomic equivalent of the Human Genome Project. Wishart raised over $10 million in funding from Genome Canada and launched a multi-institutional, pan-Canadian program to systematically identify all metabolites, drugs and xenobiotics in clinically important human biofluids. The goal of HMP is to provide the scientific community with easily accessible reference data about human metabolites, thereby making metabolomic data analysis more comprehensive and much simpler. As of 2022, the HMP is still ongoing and has led to the identification of more than 240,000 human metabolites, 6000 drugs and drug metabolites, 70,000 food constituents and 3000 toxins and contaminants.[30][31][32] This information, along with many tools to facilitate metabolite identification and interpretation, have been archived in several publicly available databases created by the Wishart lab. These include the Human Metabolome Database (HMDB), which contains data on human metabolites and their structures, along with descriptions, NMR spectra and MS spectra.[33] Another resource developed from the project is DrugBank,[31] a database of all known, approved drugs and their target molecules. Other databases developed by the Wishart lab include FooDB,[32] a database of food constituents and food additives; and T3DB,[34] a database of toxic compounds and contaminants as well as their toxicological effects.

In 2011, Wishart founded The Metabolomics Innovation Centre (TMIC) and served as its first director (2011-2019).[35] Wishart's laboratory within TMIC houses over $8 million in modern LC-MS, GC-MS and NMR equipment. His lab routinely processes more than 20,000 samples each year. Using this wide array of equipment, Wishart helped develop a number of quantitative metabolomics techniques for NMR [36][37] and liquid chromatography mass spectrometry.[38][39]  Using these methods, Wishart and his team have conducted comprehensive, quantitative metabolome analyses of human serum,[40] urine,[41] saliva,[42] cerebrospinal fluid [43] and feces.[44]

Computational biology and open science

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Wishart has made all his lab's data resources, computer programs, algorithms and techniques publicly accessible. This open science/open access initiative has been aimed at providing tools and techniques to make biomolecular NMR, metabolomics, structural biology and a number of related techniques more accessible for all scientists. So far, this initiative has led Wishart's lab to develop and release more than 100 publicly accessible web servers and web-based databases,[45] including NP-MRD[46] and CFM-ID.[47] To further his open-science efforts, Wishart co-founded several educational bioinformatics programs such as the Canadian Bioinformatics Workshops and has been actively involved in other international standardization and open-source initiatives to make computational biology resources more widely available and accessible.

Personal life

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Wishart is married to Debby Waldman, a freelance writer and editor from Utica, New York. He has two children: Elizabeth, an epidemiologist; and Noah, a civil engineer. They all live and work in Edmonton, Alberta.[citation needed]

References

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  1. ^ a b "Wishart, Dr. David – ASTech Foundation". Retrieved 2022-04-08.
  2. ^ a b "David Wishart - Directory@UAlberta". apps.ualberta.ca. Retrieved 2022-04-08.
  3. ^ a b "Honorary Fellowships – Metabolomics Society". Retrieved 2022-04-08.
  4. ^ "People". The Metabolomics Innovation Center. Retrieved 2022-04-08.
  5. ^ a b "Chenomx Inc | Metabolite Discovery and Measurement". Retrieved 2022-04-08.
  6. ^ "DrugBank | About DrugBank". www.drugbank.com. Retrieved 2022-04-08.
  7. ^ "Our Team – Molecular You". molecularyou.com. Retrieved 2022-04-08.
  8. ^ "David Wishart". scholar.google.com. Retrieved 2022-04-08.
  9. ^ Ioannidis, John P. A.; Baas, Jeroen; Klavans, Richard; Boyack, Kevin W. (2019-08-12). "A standardized citation metrics author database annotated for scientific field". PLOS Biology. 17 (8): e3000384. doi:10.1371/journal.pbio.3000384. ISSN 1545-7885. PMC 6699798. PMID 31404057.
  10. ^ Baas, Jeroen; Boyack, Kevin; Ioannidis, John P. A. (19 October 2021). "August 2021 data-update for "Updated science-wide author databases of standardized citation indicators"". 3. Elsevier BV. doi:10.17632/btchxktzyw.3. Retrieved 17 December 2022. {{cite journal}}: Cite journal requires |journal= (help)
  11. ^ "Highly Cited Researchers". publons.com. Retrieved 2022-04-08.
  12. ^ "Brian Sykes | Biochemistry". www.ualberta.ca. Retrieved 2022-04-08.
  13. ^ "University of Alberta Distinguished Professor | Office of the Provost and Vice-President (Academic)". www.ualberta.ca. Retrieved 2022-04-08.
  14. ^ Wishart, D. S.; Sykes, B. D.; Richards, F. M. (1992-02-18). "The chemical shift index: a fast and simple method for the assignment of protein secondary structure through NMR spectroscopy". Biochemistry. 31 (6): 1647–1651. doi:10.1021/bi00121a010. ISSN 0006-2960. PMID 1737021.
  15. ^ Wishart, DavidS.; Sykes, BrianD. (March 1994). "The 13C Chemical-Shift Index: A simple method for the identification of protein secondary structure using 13C chemical-shift data". Journal of Biomolecular NMR. 4 (2): 171–180. doi:10.1007/BF00175245. ISSN 0925-2738. PMID 8019132. S2CID 42323147.
  16. ^ Berjanskii, Mark V.; Wishart, David S. (2005-11-01). "A Simple Method To Predict Protein Flexibility Using Secondary Chemical Shifts". Journal of the American Chemical Society. 127 (43): 14970–14971. doi:10.1021/ja054842f. ISSN 0002-7863. PMID 16248604.
  17. ^ Berjanskii, Mark V.; Wishart, David S. (January 2008). "Application of the random coil index to studying protein flexibility". Journal of Biomolecular NMR. 40 (1): 31–48. doi:10.1007/s10858-007-9208-0. ISSN 0925-2738. PMID 17985196. S2CID 40798448.
  18. ^ Berjanskii, M. V.; Neal, S.; Wishart, D. S. (2006-07-01). "PREDITOR: a web server for predicting protein torsion angle restraints". Nucleic Acids Research. 34 (Web Server): W63–W69. doi:10.1093/nar/gkl341. ISSN 0305-1048. PMC 1538894. PMID 16845087.
  19. ^ a b Hafsa, Noor E.; Wishart, David S. (November 2014). "CSI 2.0: a significantly improved version of the Chemical Shift Index". Journal of Biomolecular NMR. 60 (2–3): 131–146. doi:10.1007/s10858-014-9863-x. ISSN 0925-2738. PMID 25273503. S2CID 24871947.
  20. ^ Hafsa, Noor E.; Arndt, David; Wishart, David S. (2015-07-01). "CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts". Nucleic Acids Research. 43 (W1): W370–W377. doi:10.1093/nar/gkv494. ISSN 0305-1048. PMC 4489240. PMID 25979265.
  21. ^ Berjanskii, M.; Tang, P.; Liang, J.; Cruz, J. A.; Zhou, J.; Zhou, Y.; Bassett, E.; MacDonell, C.; Lu, P.; Lin, G.; Wishart, D. S. (2009-07-01). "GeNMR: a web server for rapid NMR-based protein structure determination". Nucleic Acids Research. 37 (Web Server): W670–W677. doi:10.1093/nar/gkp280. ISSN 0305-1048. PMC 2703936. PMID 19406927.
  22. ^ Wishart, D. S.; Arndt, D.; Berjanskii, M.; Tang, P.; Zhou, J.; Lin, G. (2008-05-19). "CS23D: a web server for rapid protein structure generation using NMR chemical shifts and sequence data". Nucleic Acids Research. 36 (Web Server): W496–W502. doi:10.1093/nar/gkn305. ISSN 0305-1048. PMC 2447725. PMID 18515350.
  23. ^ Hafsa, Noor E.; Berjanskii, Mark V.; Arndt, David; Wishart, David S. (January 2018). "Rapid and reliable protein structure determination via chemical shift threading". Journal of Biomolecular NMR. 70 (1): 33–51. doi:10.1007/s10858-017-0154-1. ISSN 0925-2738. PMID 29196969. S2CID 3495790.
  24. ^ Neal, Stephen (2003). "Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts". Journal of Biomolecular NMR. 26 (3): 215–240. doi:10.1023/A:1023812930288. PMID 12766419. S2CID 29425090.
  25. ^ Han, Beomsoo; Liu, Yifeng; Ginzinger, Simon W.; Wishart, David S. (May 2011). "SHIFTX2: significantly improved protein chemical shift prediction". Journal of Biomolecular NMR. 50 (1): 43–57. doi:10.1007/s10858-011-9478-4. ISSN 0925-2738. PMC 3085061. PMID 21448735.
  26. ^ Wang, Bowei; Wang, Yunjun; Wishart, David S. (June 2010). "A probabilistic approach for validating protein NMR chemical shift assignments". Journal of Biomolecular NMR. 47 (2): 85–99. doi:10.1007/s10858-010-9407-y. ISSN 0925-2738. PMID 20446018. S2CID 22564072.
  27. ^ Zhang, Haiyan; Neal, Stephen; Wishart, David S. (2003). "RefDB: A database of uniformly referenced protein chemical shifts". Journal of Biomolecular NMR. 25 (3): 173–195. doi:10.1023/A:1022836027055. PMID 12652131. S2CID 12786364.
  28. ^ "Compound Identification and Quantitation in Liquid Mixtures -- Method and Process Using an Automated Nuclear Magnetic Resonance Measurement System". Canadian Patent Database.
  29. ^ Wishart, David S (June 2007). "Proteomics and the Human Metabolome Project". Expert Review of Proteomics. 4 (3): 333–335. doi:10.1586/14789450.4.3.333. ISSN 1478-9450. PMID 17552914. S2CID 9501798.
  30. ^ Wishart, David S; Guo, AnChi; Oler, Eponine; Wang, Fei; Anjum, Afia; Peters, Harrison; Dizon, Raynard; Sayeeda, Zinat; Tian, Siyang; Lee, Brian L; Berjanskii, Mark (2022-01-07). "HMDB 5.0: the Human Metabolome Database for 2022". Nucleic Acids Research. 50 (D1): D622–D631. doi:10.1093/nar/gkab1062. ISSN 0305-1048. PMC 8728138. PMID 34986597.
  31. ^ a b Law, Vivian; Knox, Craig; Djoumbou, Yannick; Jewison, Tim; Guo, An Chi; Liu, Yifeng; Maciejewski, Adam; Arndt, David; Wilson, Michael; Neveu, Vanessa; Tang, Alexandra (January 2014). "DrugBank 4.0: shedding new light on drug metabolism". Nucleic Acids Research. 42 (D1): D1091–D1097. doi:10.1093/nar/gkt1068. ISSN 0305-1048. PMC 3965102. PMID 24203711.
  32. ^ a b Scalbert, Augustin; Andres-Lacueva, Cristina; Arita, Masanori; Kroon, Paul; Manach, Claudine; Urpi-Sarda, Mireia; Wishart, David (2011-05-11). "Databases on Food Phytochemicals and Their Health-Promoting Effects". Journal of Agricultural and Food Chemistry. 59 (9): 4331–4348. doi:10.1021/jf200591d. ISSN 0021-8561. PMID 21438636.
  33. ^ Wishart, David S; Guo, AnChi; Oler, Eponine; Wang, Fei; Anjum, Afia; Peters, Harrison; Dizon, Raynard; Sayeeda, Zinat; Tian, Siyang; Lee, Brian L; Berjanskii, Mark (2022-01-07). "HMDB 5.0: the Human Metabolome Database for 2022". Nucleic Acids Research. 50 (D1): D622–D631. doi:10.1093/nar/gkab1062. ISSN 0305-1048. PMC 8728138. PMID 34986597.
  34. ^ Wishart, David; Arndt, David; Pon, Allison; Sajed, Tanvir; Guo, An Chi; Djoumbou, Yannick; Knox, Craig; Wilson, Michael; Liang, Yongjie; Grant, Jason; Liu, Yifeng (2015-01-28). "T3DB: the toxic exposome database". Nucleic Acids Research. 43 (D1): D928–D934. doi:10.1093/nar/gku1004. ISSN 1362-4962. PMC 4383875. PMID 25378312.
  35. ^ "Home". The Metabolomics Innovation Centre.
  36. ^ Lipfert, Matthias; Rout, Manoj Kumar; Berjanskii, Mark; Wishart, David S. (2019), Gowda, G. A. Nagana; Raftery, Daniel (eds.), "Automated Tools for the Analysis of 1D-NMR and 2D-NMR Spectra", NMR-Based Metabolomics, Methods in Molecular Biology, vol. 2037, New York, NY: Springer New York, pp. 429–449, doi:10.1007/978-1-4939-9690-2_24, ISBN 978-1-4939-9689-6, PMID 31463859, S2CID 201665386, retrieved 2022-04-08
  37. ^ Ravanbakhsh, Siamak; Liu, Philip; Bjordahl, Trent C.; Mandal, Rupasri; Grant, Jason R.; Wilson, Michael; Eisner, Roman; Sinelnikov, Igor; Hu, Xiaoyu; Luchinat, Claudio; Greiner, Russell (2015-05-27). Monleon, Daniel (ed.). "Accurate, Fully-Automated NMR Spectral Profiling for Metabolomics". PLOS ONE. 10 (5): e0124219. arXiv:1409.1456. Bibcode:2015PLoSO..1024219R. doi:10.1371/journal.pone.0124219. ISSN 1932-6203. PMC 4446368. PMID 26017271.
  38. ^ Zheng, Jiamin; Zhang, Lun; Johnson, Mathew; Mandal, Rupasri; Wishart, David S. (2020-08-04). "Comprehensive Targeted Metabolomic Assay for Urine Analysis". Analytical Chemistry. 92 (15): 10627–10634. doi:10.1021/acs.analchem.0c01682. ISSN 0003-2700. PMID 32634308. S2CID 220405141.
  39. ^ Zheng, Jiamin; Mandal, Rupasri; Wishart, David S. (December 2018). "A sensitive, high-throughput LC-MS/MS method for measuring catecholamines in low volume serum". Analytica Chimica Acta. 1037: 159–167. Bibcode:2018AcAC.1037..159Z. doi:10.1016/j.aca.2018.01.021. PMID 30292290. S2CID 52931501.
  40. ^ Psychogios, Nikolaos; Hau, David D.; Peng, Jun; Guo, An Chi; Mandal, Rupasri; Bouatra, Souhaila; Sinelnikov, Igor; Krishnamurthy, Ramanarayan; Eisner, Roman; Gautam, Bijaya; Young, Nelson (2011-02-16). Flower, Darren (ed.). "The Human Serum Metabolome". PLOS ONE. 6 (2): e16957. Bibcode:2011PLoSO...616957P. doi:10.1371/journal.pone.0016957. ISSN 1932-6203. PMC 3040193. PMID 21359215.
  41. ^ Bouatra, Souhaila; Aziat, Farid; Mandal, Rupasri; Guo, An Chi; Wilson, Michael R.; Knox, Craig; Bjorndahl, Trent C.; Krishnamurthy, Ramanarayan; Saleem, Fozia; Liu, Philip; Dame, Zerihun T. (2013-09-04). Dzeja, Petras (ed.). "The Human Urine Metabolome". PLOS ONE. 8 (9): e73076. Bibcode:2013PLoSO...873076B. doi:10.1371/journal.pone.0073076. ISSN 1932-6203. PMC 3762851. PMID 24023812.
  42. ^ Dame, Zerihun T.; Aziat, Farid; Mandal, Rupasri; Krishnamurthy, Ram; Bouatra, Souhaila; Borzouie, Shima; Guo, An Chi; Sajed, Tanvir; Deng, Lu; Lin, Hong; Liu, Philip (December 2015). "The human saliva metabolome". Metabolomics. 11 (6): 1864–1883. doi:10.1007/s11306-015-0840-5. ISSN 1573-3882. S2CID 18794642.
  43. ^ Mandal, Rupasri; Guo, An Chi; Chaudhary, Kruti K; Liu, Philip; Yallou, Faizath S; Dong, Edison; Aziat, Farid; Wishart, David S (2012). "Multi-platform characterization of the human cerebrospinal fluid metabolome: a comprehensive and quantitative update". Genome Medicine. 4 (4): 38. doi:10.1186/gm337. ISSN 1756-994X. PMC 3446266. PMID 22546835.
  44. ^ Karu, Naama; Deng, Lu; Slae, Mordechai; Guo, An Chi; Sajed, Tanvir; Huynh, Hien; Wine, Eytan; Wishart, David S. (November 2018). "A review on human fecal metabolomics: Methods, applications and the human fecal metabolome database". Analytica Chimica Acta. 1030: 1–24. Bibcode:2018AcAC.1030....1K. doi:10.1016/j.aca.2018.05.031. PMID 30032758. S2CID 51710218.
  45. ^ "Web Servers - Wishart Research Group". www.wishartlab.com. Retrieved 2022-04-08.
  46. ^ Wishart, David S; Sayeeda, Zinat; Budinski, Zachary; Guo, AnChi; Lee, Brian L; Berjanskii, Mark; Rout, Manoj; Peters, Harrison; Dizon, Raynard; Mah, Robert; Torres-Calzada, Claudia (2022-01-07). "NP-MRD: the Natural Products Magnetic Resonance Database". Nucleic Acids Research. 50 (D1): D665–D677. doi:10.1093/nar/gkab1052. ISSN 0305-1048. PMC 8728158. PMID 34791429.
  47. ^ Wang, Fei; Liigand, Jaanus; Tian, Siyang; Arndt, David; Greiner, Russell; Wishart, David S. (2021-08-31). "CFM-ID 4.0: More Accurate ESI-MS/MS Spectral Prediction and Compound Identification". Analytical Chemistry. 93 (34): 11692–11700. doi:10.1021/acs.analchem.1c01465. ISSN 0003-2700. PMC 9064193. PMID 34403256. S2CID 237197237.
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