Chris Ponting

Last updated

Chris Ponting
Chris Ponting.jpg
Born
Christopher Paul Ponting
NationalityBritish
Alma mater
Known forSMART [1]
Scientific career
Fields
Institutions University of Edinburgh
Thesis Structural Studies of Plasminogen and Related Proteins  (1992)
Website www.ed.ac.uk/mrc-human-genetics-unit/research/ponting-group

Christopher Paul Ponting is a British computational biologist, specializing in the evolution and function of genes and genomes. He is currently Chair of Medical Bioinformatics at the University of Edinburgh and group leader in the MRC Human Genetics Unit. He is also an Associate Faculty member of the Wellcome Trust Sanger Institute, a Fellow of the Academy of Medical Sciences, member of the European Molecular Biology Organisation and Fellow of the Royal Society of Edinburgh. [2] His research focuses on long noncoding RNA function and evolution, on single cell biology and on disease genomics. [3] [4] [5] [6] [7] [8] Outside of science, Chris is an amateur novelist and wrote an unpublished, science fiction novel about engineered viruses. [9]

Contents

Education

After receiving his Bachelor of Arts and Master of Science in physics from University of Oxford and the University of British Columbia, respectively, he returned to Oxford, completing his Doctor of Philosophy in biophysics in 1992 on structural studies of plasminogen. [10] [11]

Research

Ponting contributed to the Human Genome Project, [12] and participated in sequence comparison for the mouse, [13] rat, [14] chicken, [15] dog, [16] opossum, [17] and platypus [18] [19] [20] Genome Projects. He has also used comparative genomics to contribute directly to the understanding of chromatin structure [21] and the genetics of numerous conditions including asthma, [22] obesity, [23] Alzheimer's disease, [24] retinitis pigmentosa, [25] muscular dystrophies, [26] and Aicardi–Goutières syndrome. [27]

Additionally, his lab is part of DecodeME, a genetic study to determine the potential causes of myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). [28] [9]

Related Research Articles

<span class="mw-page-title-main">Identity by descent</span> Identical nucleotide sequence due to inheritance without recombination from a common ancestor

A DNA segment is identical by state (IBS) in two or more individuals if they have identical nucleotide sequences in this segment. An IBS segment is identical by descent (IBD) in two or more individuals if they have inherited it from a common ancestor without recombination, that is, the segment has the same ancestral origin in these individuals. DNA segments that are IBD are IBS per definition, but segments that are not IBD can still be IBS due to the same mutations in different individuals or recombinations that do not alter the segment.

<span class="mw-page-title-main">Michael Ashburner</span> English biologist (1942–2023)

Michael Ashburner was an English biologist and Professor in the Department of Genetics at University of Cambridge. He was also the former joint-head and co-founder of the European Bioinformatics Institute (EBI) of the European Molecular Biology Laboratory (EMBL) and a Fellow of Churchill College, Cambridge.

Christopher Francis Higgins is a British molecular biologist, geneticist, academic and scientific advisor. He was the Vice-Chancellor of Durham University from 2007 to 2014. He took early retirement on 30 September 2014, following a discussion at Senate on limiting the powers of the Vice Chancellor. He was previously the director of the MRC Clinical Sciences Centre and Head of Division in the Faculty of Medicine at Imperial College London.

Mark Bender Gerstein is an American scientist working in bioinformatics and Data Science. As of 2009, he is co-director of the Yale Computational Biology and Bioinformatics program.

Gerald Mayer Rubin is an American biologist, notable for pioneering the use of transposable P elements in genetics, and for leading the public project to sequence the Drosophila melanogaster genome. Related to his genomics work, Rubin's lab is notable for development of genetic and genomics tools and studies of signal transduction and gene regulation. Rubin also serves as a vice president of the Howard Hughes Medical Institute and executive director of the Janelia Research Campus.

<span class="mw-page-title-main">Synthetic genetic array</span>

Synthetic genetic array analysis (SGA) is a high-throughput technique for exploring synthetic lethal and synthetic sick genetic interactions (SSL). SGA allows for the systematic construction of double mutants using a combination of recombinant genetic techniques, mating and selection steps. Using SGA methodology a query gene deletion mutant can be crossed to an entire genome deletion set to identify any SSL interactions, yielding functional information of the query gene and the genes it interacts with. A large-scale application of SGA in which ~130 query genes were crossed to the set of ~5000 viable deletion mutants in yeast revealed a genetic network containing ~1000 genes and ~4000 SSL interactions. The results of this study showed that genes with similar function tend to interact with one another and genes with similar patterns of genetic interactions often encode products that tend to work in the same pathway or complex. Synthetic Genetic Array analysis was initially developed using the model organism S. cerevisiae. This method has since been extended to cover 30% of the S. cerevisiae genome. Methodology has since been developed to allow SGA analysis in S.pombe and E. coli.

<span class="mw-page-title-main">Gil McVean</span> British statistical geneticist (born 1973)

Gilean Alistair Tristram McVean is a professor of statistical genetics at the University of Oxford, fellow of Linacre College, Oxford and co-founder and director of Genomics plc. He also co-chaired the 1000 Genomes Project analysis group.

<span class="mw-page-title-main">Richard M. Durbin</span> British computational biologist

Richard Michael Durbin is a British computational biologist and Al-Kindi Professor of Genetics at the University of Cambridge. He also serves as an associate faculty member at the Wellcome Sanger Institute where he was previously a senior group leader.

Sir Michael Rudolf Stratton, is a British clinical scientist and the third director of the Wellcome Trust Sanger Institute. He currently heads the Cancer Genome Project and is a leader of the International Cancer Genome Consortium.

<span class="mw-page-title-main">PRDM9</span> Protein-coding gene in humans

PR domain zinc finger protein 9 is a protein that in humans is encoded by the PRDM9 gene. PRDM9 is responsible for positioning recombination hotspots during meiosis by binding a DNA sequence motif encoded in its zinc finger domain. PRDM9 is the only speciation gene found so far in mammals, and is one of the fastest evolving genes in the genome.

Stephen George Oliver is an Emeritus Professor in the Department of Biochemistry at the University of Cambridge, and a Fellow of Wolfson College, Cambridge.

Professor Nicholas Dixon Hastie CBE, FRS, FRSE is a British geneticist, and former Director of the MRC Human Genetics Unit at the University of Edinburgh.

<span class="mw-page-title-main">David Altshuler (physician)</span> American geneticist

David Matthew Altshuler is a clinical endocrinologist and human geneticist. He is Executive Vice President, Global Research and Chief Scientific Officer at Vertex Pharmaceuticals. Prior to joining Vertex in 2014, he was at the Broad Institute of Harvard and MIT, and was a Professor of Genetics and Medicine at Harvard Medical School, and in the Department of Biology at Massachusetts Institute of Technology. He was also a faculty member in the Department of Molecular Biology, Center for Human Genetic Research, and the Diabetes Unit, all at Massachusetts General Hospital. He was one of four Founding Core Members of the Broad Institute, and served as the Institute's Deputy Director, Chief Academic Officer, and Director of the Program in Medical and Population Genetics.

<span class="mw-page-title-main">Alfonso Valencia</span>

Alfonso Valencia is a Spanish biologist, ICREA Professor, current director of the Life Sciences department at Barcelona Supercomputing Center. and of Spanish National Bioinformatics Institute (INB-ISCIII). From 2015-2018, he was President of the International Society for Computational Biology. His research is focused on the study of biomedical systems with computational biology and bioinformatics approaches.

Sabera Nazneen Rahman is a geneticist who specialises in cancer research and is a non-executive director for Astra Zeneca. She was previously head of Genetics and Epidemiology at the Institute of Cancer Research.

<span class="mw-page-title-main">Julian Parkhill</span> Geneticist, working with pathogens

Julian Parkhill is Professor of Bacterial Evolution in the Department of Veterinary Medicine at the University of Cambridge. He previously served as head of pathogen genomics at the Wellcome Sanger Institute.

<span class="mw-page-title-main">Peter Keightley</span>

Peter D. Keightley FRS is Professor of Evolutionary Genetics at the Institute of Evolutionary Biology in School of Biological Sciences at the University of Edinburgh.

<span class="mw-page-title-main">Michael Goddard</span>

Michael Edward "Mike" Goddard is a professorial fellow in animal genetics at the University of Melbourne, Australia.

References

  1. ↑ Schultz, J.; Milpetz, F.; Bork, P.; Ponting, C. (1998). "SMART, a simple modular architecture research tool: Identification of signaling domains". Proceedings of the National Academy of Sciences of the United States of America. 95 (11): 5857–5864. Bibcode:1998PNAS...95.5857S. doi: 10.1073/pnas.95.11.5857 . PMC   34487 . PMID   9600884.
  2. ↑ "Professor Christopher Paul Ponting FMedSci FRSE - The Royal Society of Edinburgh". The Royal Society of Edinburgh. Retrieved 14 March 2018.
  3. ↑ Chris Ponting's publications indexed by the Scopus bibliographic database. (subscription required)
  4. ↑ Sims, David (2014). "Sequencing depth and coverage: key considerations in genomic analyses". Nature Reviews Genetics. 15 (2): 121–132. doi:10.1038/nrg3642. PMID   24434847. S2CID   13325739.
  5. ↑ Rands, Chris M. (2014). "8.2% of the Human Genome Is Constrained: Variation in Rates of Turnover across Functional Element Classes in the Human Lineage". PLOS Genetics. 10 (7): e1004525. doi: 10.1371/journal.pgen.1004525 . PMC   4109858 . PMID   25057982.
  6. ↑ Gibbs, R. A.; Weinstock, G. M.; Metzker, M. L.; Muzny, D. M.; Sodergren, E. J.; Scherer, S; Scott, G; Steffen, D; Worley, K. C.; Burch, P. E.; Okwuonu, G; Hines, S; Lewis, L; Deramo, C; Delgado, O; Dugan-Rocha, S; Miner, G; Morgan, M; Hawes, A; Gill, R; Celera; Holt, R. A.; Adams, M. D.; Amanatides, P. G.; Baden-Tillson, H; Barnstead, M; Chin, S; Evans, C. A.; Ferriera, S; et al. (2004). "Genome sequence of the Brown Norway rat yields insights into mammalian evolution". Nature. 428 (6982): 493–521. Bibcode:2004Natur.428..493G. doi: 10.1038/nature02426 . PMID   15057822.
  7. ↑ Drosophila 12 Genomes, Consortium; Clark, A. G.; Eisen, M. B.; Smith, D. R.; Bergman, C. M.; Oliver, B; Markow, T. A.; Kaufman, T. C.; Kellis, M; Gelbart, W; Iyer, V. N.; Pollard, D. A.; Sackton, T. B.; Larracuente, A. M.; Singh, N. D.; Abad, J. P.; Abt, D. N.; Adryan, B; Aguade, M; Akashi, H; Anderson, W. W.; Aquadro, C. F.; Ardell, D. H.; Arguello, R; Artieri, C. G.; Barbash, D. A.; Barker, D; Barsanti, P; Batterham, P; et al. (2007). "Evolution of genes and genomes on the Drosophila phylogeny". Nature. 450 (7167): 203–18. Bibcode:2007Natur.450..203C. doi: 10.1038/nature06341 . PMID   17994087.{{cite journal}}: CS1 maint: numeric names: authors list (link)
  8. ↑ Mulder, N. J.; Apweiler, R; Attwood, T. K.; Bairoch, A; Barrell, D; Bateman, A; Binns, D; Biswas, M; Bradley, P; Bork, P; Bucher, P; Copley, R. R.; Courcelle, E; Das, U; Durbin, R; Falquet, L; Fleischmann, W; Griffiths-Jones, S; Haft, D; Harte, N; Hulo, N; Kahn, D; Kanapin, A; Krestyaninova, M; Lopez, R; Letunic, I; Lonsdale, D; Silventoinen, V.; Orchard, S. E.; Pagni, M.; Pagni, Marco; Peyruc, D.; Ponting, C.P.; Selengut, J.D.; Servant, F.; Sigrist, C.J.A.; Vaughan, R.; Zdobnov, E.M. (2003). "The InterPro Database, 2003 brings increased coverage and new features". Nucleic Acids Research. 31 (1): 315–8. doi:10.1093/nar/gkg046. PMC   165493 . PMID   12520011.
  9. 1 2 The Bioinformatics CRO Podcast . Episode 2, 2020.
  10. ↑ Ponting, Christopher Paul (1992). Structural Studies of Plasminogen and Related Proteins (DPhil thesis). University of Oxford. OCLC   556763136.
  11. ↑ "Prof. Chris P Ponting BA MSc DPhil". University of Oxford. Archived from the original on 7 April 2014.
  12. ↑ Lander, E. S.; Linton, M.; Birren, B.; Nusbaum, C.; Zody, C.; Baldwin, J.; Devon, K.; Dewar, K.; Doyle, M.; Fitzhugh, W.; Funke, R.; Gage, D.; Harris, K.; Heaford, A.; Howland, J.; Kann, L.; Lehoczky, J.; Levine, R.; McEwan, P.; McKernan, K.; Meldrim, J.; Mesirov, J. P.; Miranda, C.; Morris, W.; Naylor, J.; Raymond, C.; Rosetti, M.; Santos, R.; Sheridan, A.; et al. (February 2001). "Initial sequencing and analysis of the human genome". Nature. 409 (6822): 860–921. Bibcode:2001Natur.409..860L. doi: 10.1038/35057062 . hdl: 2027.42/62798 . ISSN   0028-0836. PMID   11237011.
  13. ↑ Chinwalla, A. T.; Waterston, L. L.; Lindblad-Toh, K. D.; Birney, G. A.; Rogers, L. A.; Abril, R. S.; Agarwal, T. A.; Agarwala, L. W.; Ainscough, E. R.; Alexandersson, J. D.; An, T. L.; Antonarakis, W. E.; Attwood, J. O.; Baertsch, M. N.; Bailey, K. H.; Barlow, C. S.; Beck, T. C.; Berry, B.; Birren, J.; Bloom, E.; Bork, R. H.; Botcherby, M. C.; Bray, R. K.; Brent, S. P.; Brown, P.; Brown, E.; Bult, B.; Burton, T.; Butler, D. G.; et al. (2002). "Initial sequencing and comparative analysis of the mouse genome". Nature. 420 (6915): 520–562. Bibcode:2002Natur.420..520W. doi: 10.1038/nature01262 . PMID   12466850.
  14. ↑ Amos, Jonathan (31 March 2004). "Rat's 'life code' read by science". BBC News . Retrieved 19 December 2008.
  15. ↑ "Chicken gives up genetic secrets". BBC News . 9 December 2004. Retrieved 19 December 2008.
  16. ↑ Lindblad-Toh, K.; Wade, C. M.; Mikkelsen, T. S.; Karlsson, E. K.; Jaffe, D. B.; Kamal, M.; Clamp, M.; Chang, J. L.; Kulbokas, E. J.; Zody, M. C.; Mauceli, E.; Xie, X.; Breen, M.; Wayne, R. K.; Ostrander, E. A.; Ponting, C. P.; Galibert, F.; Smith, D. R.; Dejong, P. J.; Kirkness, E.; Alvarez, P.; Biagi, T.; Brockman, W.; Butler, J.; Chin, C. W.; Cook, A.; Cuff, J.; Daly, M. J.; Decaprio, D.; et al. (2005). "Genome sequence, comparative analysis and haplotype structure of the domestic dog". Nature. 438 (7069): 803–819. Bibcode:2005Natur.438..803L. doi: 10.1038/nature04338 . PMID   16341006.
  17. ↑ Mikkelsen, T. S.; Wakefield, M. J.; Aken, B.; Amemiya, C. T.; Chang, J. L.; Duke, S.; Garber, M.; Gentles, A. J.; Goodstadt, L.; Heger, A.; Jurka, J.; Kamal, M.; Mauceli, E.; Searle, S. M. J.; Sharpe, T.; Baker, M. L.; Batzer, M. A.; Benos, P. V.; Belov, K.; Clamp, M.; Cook, A.; Cuff, J.; Das, R.; Davidow, L.; Deakin, J. E.; Fazzari, M. J.; Glass, J. L.; Grabherr, M.; Greally, J. M.; et al. (2007). "Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences". Nature. 447 (7141): 167–177. Bibcode:2007Natur.447..167M. doi: 10.1038/nature05805 . PMID   17495919.
  18. ↑ Warren, W. C.; Hillier, L. W.; Marshall Graves, J. A.; Birney, E.; Ponting, C. P.; Grützner, F.; Belov, K.; Miller, W.; Clarke, L.; Chinwalla, A. T.; Yang, S. P.; Heger, A.; Locke, D. P.; Miethke, P.; Waters, P. D.; Veyrunes, F. D. R.; Fulton, L.; Fulton, B.; Graves, T.; Wallis, J.; Puente, X. S.; López-Otín, C.; Ordóñez, G. R.; Eichler, E. E.; Chen, L.; Cheng, Z.; Deakin, J. E.; Alsop, A.; Thompson, K.; et al. (2008). "Genome analysis of the platypus reveals unique signatures of evolution". Nature. 453 (7192): 175–183. Bibcode:2008Natur.453..175W. doi:10.1038/nature06936. PMC   2803040 . PMID   18464734.
  19. ↑ http://www.nature.com/nature/videoarchive/platypusgenome/ Discussing the platypus genome
  20. ↑ Briggs, Helen (7 May 2008). "Platypus genetic code unravelled". BBC News . Retrieved 19 December 2008.
  21. ↑ Jenuwein, T.; Eisenhaber, S.; O'Carroll, F.; Strahl, D. N.; Sun, B. D.; Schmid, Z. W.; Opravil, M.; Mechtler, S.; Ponting, K.; Allis, C. P.; Jenuwein, C. D. (2000). "Regulation of chromatin structure by site-specific histone H3 methyltransferases". Nature. 406 (6796): 593–599. Bibcode:2000Natur.406..593R. doi:10.1038/35020506. PMID   10949293. S2CID   205008015.
  22. ↑ Zhang, Y.; Leaves, N. I.; Anderson, G. G.; Ponting, C. P.; Broxholme, J.; Holt, R.; Edser, P.; Bhattacharyya, S.; Dunham, A.; Adcock, I. M.; Pulleyn, L.; Barnes, P. J.; Harper, J. I.; Abecasis, G. A.; Cardon, L.; White, M.; Burton, J.; Matthews, L.; Mott, R.; Ross, M.; Cox, R.; Moffatt, M. F.; Cookson, W. O. C. M. (2003). "Positional cloning of a quantitative trait locus on chromosome 13q14 that influences immunoglobulin E levels and asthma". Nature Genetics. 34 (2): 181–186. doi:10.1038/ng1166. hdl: 10044/1/57392 . PMID   12754510. S2CID   20807679.
  23. ↑ Gerken, T.; Girard, C. A.; Tung, Y. -C. L.; Webby, C. J.; Saudek, V.; Hewitson, K. S.; Yeo, G. S. H.; McDonough, M. A.; Cunliffe, S.; McNeill, L. A.; Galvanovskis, J.; Rorsman, P.; Robins, P.; Prieur, X.; Coll, A. P.; Ma, M.; Jovanovic, Z.; Farooqi, I. S.; Sedgwick, B.; Barroso, I.; Lindahl, T.; Ponting, C. P.; Ashcroft, F. M.; O'Rahilly, S.; Schofield, C. J. (2007). "The Obesity-Associated FTO Gene Encodes a 2-Oxoglutarate-Dependent Nucleic Acid Demethylase". Science. 318 (5855): 1469–1472. Bibcode:2007Sci...318.1469G. doi:10.1126/science.1151710. PMC   2668859 . PMID   17991826.
  24. ↑ Ponting, C. P.; Hutton, M.; Nyborg, A.; Baker, M.; Jansen, K.; Golde, T. E. (2002). "Identification of a novel family of presenilin homologues". Human Molecular Genetics. 11 (9): 1037–1044. doi: 10.1093/hmg/11.9.1037 . PMID   11978763.
  25. ↑ Abd El-Aziz, M. M.; Barragan, I.; O'Driscoll, C. A.; Goodstadt, L.; Prigmore, E.; Borrego, S.; Mena, M.; Pieras, J. I.; El-Ashry, M. F.; Safieh, L. A.; Shah, A.; Cheetham, M. E.; Carter, N. P.; Chakarova, C.; Ponting, C. P.; Bhattacharya, S. S.; Antinolo, G. (2008). "EYS, encoding an ortholog of Drosophila spacemaker, is mutated in autosomal recessive retinitis pigmentosa". Nature Genetics. 40 (11): 1285–1287. doi:10.1038/ng.241. PMC   2719291 . PMID   18836446.
  26. ↑ Dickens, N. J.; Beatson, S.; Ponting, C. P. (2002). "Cadherin-like domains in α-dystroglycan, α/ε-sarcoglycan and yeast and bacterial proteins". Current Biology. 12 (6): R197–R199. doi: 10.1016/S0960-9822(02)00748-0 . PMID   11909544. S2CID   15872294.
  27. ↑ Crow, Y. J.; Leitch, A.; Hayward, B. E.; Garner, A.; Parmar, R.; Griffith, E.; Ali, M.; Semple, C.; Aicardi, J.; Babul-Hirji, R.; Baumann, C.; Baxter, P.; Bertini, E.; Chandler, K. E.; Chitayat, D.; Cau, D.; Déry, C.; Fazzi, E.; Goizet, C.; King, M. D.; Klepper, J.; Lacombe, D.; Lanzi, G.; Lyall, H.; Martínez-Frías, M. A. L.; Mathieu, M. L.; McKeown, C.; Monier, A.; Oade, Y.; Quarrell, O. W. (2006). "Mutations in genes encoding ribonuclease H2 subunits cause Aicardi-Goutières syndrome and mimic congenital viral brain infection". Nature Genetics. 38 (8): 910–916. doi:10.1038/ng1842. PMID   16845400. S2CID   8076225.
  28. ↑ Chris Ponting Research Group MRC Human Genetics Research Unit. July 2021.
This page is based on this Wikipedia article
Text is available under the CC BY-SA 4.0 license; additional terms may apply.
Images, videos and audio are available under their respective licenses.