Chris Ponting

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Chris Ponting
Chris Ponting.jpg
Born Christopher Paul Ponting
Residence Scotland
Nationality British
Fields
Institutions University of Edinburgh
Alma mater
Thesis Structural Studies of Plasminogen and Related Proteins (1992)
Doctoral students
Known for SMART[1]
Website
www.hgu.mrc.ac.uk/people/chris.ponting.html

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 and member of the European Molecular Biology Organisation. His research focuses on long noncoding RNA function and evolution, on single cell biology and on disease genomics.[2][3][4][5][6][7]

Education[edit]

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.[8][9]

Research[edit]

Ponting contributed to the Human Genome Project,[10] and participated in sequence comparison for the mouse,[11] rat,[12] chicken,[13] dog,[14] opossum,[15] and platypus[16][17][18] Genome Projects. He has also used comparative genomics to contribute directly to the understanding of chromatin structure[19] and the genetics of numerous conditions including asthma,[20] obesity,[21] Alzheimer's disease,[22] retinitis pigmentosa,[23] muscular dystrophies,[24] and Aicardi–Goutières syndrome.[25]

References[edit]

  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. PMC 34487Freely accessible. PMID 9600884. doi:10.1073/pnas.95.11.5857. 
  2. ^ Chris Ponting's publications indexed by the Scopus bibliographic database, a service provided by Elsevier. (subscription required)
  3. ^ Sims, David (2014). "Sequencing depth and coverage: key considerations in genomic analyses". Nature Reviews Genetics. 15 (2): 121–132. PMID 24434847. doi:10.1038/nrg3642. 
  4. ^ 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. PMC 4109858Freely accessible. PMID 25057982. doi:10.1371/journal.pgen.1004525. 
  5. ^ 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. PMID 15057822. doi:10.1038/nature02426. 
  6. ^ 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. PMID 17994087. doi:10.1038/nature06341. 
  7. ^ 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. PMC 165493Freely accessible. PMID 12520011. doi:10.1093/nar/gkg046. 
  8. ^ Ponting, Christopher Paul (1992). Structural Studies of Plasminogen and Related Proteins (DPhil thesis). University of Oxford. OCLC 556763136. 
  9. ^ "Prof. Chris P Ponting BA MSc DPhil". University of Oxford. Archived from the original on 2014-04-07. 
  10. ^ 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. (Feb 2001). "Initial sequencing and analysis of the human genome". Nature. 409 (6822): 860–921. Bibcode:2001Natur.409..860L. ISSN 0028-0836. PMID 11237011. doi:10.1038/35057062. 
  11. ^ 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.; Campbell, J. (2002). "Initial sequencing and comparative analysis of the mouse genome". Nature. 420 (6915): 520–562. Bibcode:2002Natur.420..520W. PMID 12466850. doi:10.1038/nature01262. 
  12. ^ Amos, Jonathan (31 March 2004). "Rat's 'life code' read by science". BBC News. Retrieved 19 December 2008. 
  13. ^ "Chicken gives up genetic secrets". BBC News. 9 December 2004. Retrieved 19 December 2008. 
  14. ^ 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. PMID 16341006. doi:10.1038/nature04338. 
  15. ^ 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.; Gu, W. (2007). "Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences". Nature. 447 (7141): 167–177. Bibcode:2007Natur.447..167M. PMID 17495919. doi:10.1038/nature05805. 
  16. ^ 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.; Kirby, P. (2008). "Genome analysis of the platypus reveals unique signatures of evolution". Nature. 453 (7192): 175–183. Bibcode:2008Natur.453..175W. PMC 2803040Freely accessible. PMID 18464734. doi:10.1038/nature06936. 
  17. ^ http://www.nature.com/nature/videoarchive/platypusgenome/ Discussing the platypus genome
  18. ^ Briggs, Helen (7 May 2008). "Platypus genetic code unravelled". BBC News. Retrieved 19 December 2008. 
  19. ^ 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. PMID 10949293. doi:10.1038/35020506. 
  20. ^ 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. PMID 12754510. doi:10.1038/ng1166. 
  21. ^ 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. PMC 2668859Freely accessible. PMID 17991826. doi:10.1126/science.1151710. 
  22. ^ 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. PMID 11978763. doi:10.1093/hmg/11.9.1037. 
  23. ^ 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. PMC 2719291Freely accessible. PMID 18836446. doi:10.1038/ng.241. 
  24. ^ 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. PMID 11909544. doi:10.1016/S0960-9822(02)00748-0. 
  25. ^ 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. PMID 16845400. doi:10.1038/ng1842.