Biography:James Cuff

From HandWiki
Dr. James Andrew Cuff
Born1974 (age 49–50)[citation needed]
Alma materChrist Church, Oxford
Scientific career
InstitutionsHarvard University
Broad Institute

European Bioinformatics Institute
University of Oxford
University of Manchester
ThesisProtein Structure Prediction (1999)
Doctoral advisorGeoffrey J. Barton[1]
Websiteblog.jcuff.net
about.me/jcuff
twitter.com/jamesdotcuff
scholar.harvard.edu/jcuff

James Andrew Cuff, (born Preston, Lancashire) is a British biophysicist. Cuff has held leadership positions at Harvard University, the Broad Institute, The Wellcome Trust Sanger Institute and the European Bioinformatics Institute.

Education

Cuff holds a PhD in Protein structure prediction[1] from the University of Oxford, and holds a Bachelor of Science in Chemistry from The University of Manchester.

Research

Cuff's research investigates genomics, protein structure prediction, bioinformatics and High Performance Computing (HPC).[2][3] Cuff worked as a part of teams that completed the first simultaneous genome analysis of twenty nine mammals,[4] the refinement of the human gene count,[5] and the first bivalent chromatin structures to be found in embryonic stem cells.[6] In addition, Cuff has contributed to several large-scale bioinformatics and computational biology projects including Ensembl,[7] Jalview,[8] and the first online consensus secondary structure prediction algorithm JPred.[9][10] He supported the resolution of the mouse, dog and monodelphis genomes[11][12][13] and the early ENCODE project.[14]

Based on early work with computer clusters,[15] Cuff has aided with the design and architecture of the Massachusetts Green High Performance Computing Center, a multimillion-dollar[16] data centre project between Harvard University, MIT, Boston University, Northeastern University, and University of Massachusetts. Cuff is also a co-developer on a popular open source authentication method called JAuth.[17] Cuff is also a Principal Investigator.

References

  1. ↑ 1.0 1.1 Cuff, James (1999). Protein Structure Prediction (PhD thesis). University of Oxford.
  2. ↑ James Cuff publications indexed by Google Scholar
  3. ↑ List of publications from Microsoft Academic
  4. ↑ Lindblad-Toh, K.; Garber, M.; Zuk, O.; Lin, M. F.; Parker, B. J.; Washietl, S.; Kheradpour, P.; Ernst, J. et al. (2011). "A high-resolution map of human evolutionary constraint using 29 mammals". Nature 478 (7370): 476–482. doi:10.1038/nature10530. PMID 21993624. 
  5. ↑ Clamp, M.; Fry, B.; Kamal, M.; Xie, X.; Cuff, J.; Lin, M. F.; Kellis, M.; Lindblad-Toh, K. et al. (2007). "Distinguishing protein-coding and noncoding genes in the human genome". Proceedings of the National Academy of Sciences 104 (49): 19428–19433. doi:10.1073/pnas.0709013104. PMID 18040051. 
  6. ↑ Bernstein, B. E.; Mikkelsen, T. S.; Xie, X.; Kamal, M.; Huebert, D. J.; Cuff, J.; Fry, B.; Meissner, A. et al. (2006). "A Bivalent Chromatin Structure Marks Key Developmental Genes in Embryonic Stem Cells". Cell 125 (2): 315–326. doi:10.1016/j.cell.2006.02.041. PMID 16630819. 
  7. ↑ Hubbard, T.; Barker, D.; Birney, E.; Cameron, G.; Chen, Y.; Clark, L.; Cox, T.; Cuff, J. et al. (2002). "The Ensembl genome database project". Nucleic Acids Research 30 (1): 38–41. doi:10.1093/nar/30.1.38. PMID 11752248. 
  8. ↑ Clamp, M.; Cuff, J.; Searle, S. M.; Barton, G. J. (2004). "The Jalview Java alignment editor". Bioinformatics 20 (3): 426–427. doi:10.1093/bioinformatics/btg430. PMID 14960472. 
  9. ↑ Cuff, J. A.; Barton, G. J. (2000). "Application of multiple sequence alignment profiles to improve protein secondary structure prediction". Proteins: Structure, Function, and Genetics 40 (3): 502–511. doi:10.1002/1097-0134(20000815)40:3<502::AID-PROT170>3.0.CO;2-Q. PMID 10861942. 
  10. ↑ Cuff, J. A.; Barton, G. J. (1999). "Evaluation and improvement of multiple sequence methods for protein secondary structure prediction". Proteins: Structure, Function, and Genetics 34 (4): 508–519. doi:10.1002/(SICI)1097-0134(19990301)34:4<508::AID-PROT10>3.0.CO;2-4. PMID 10081963. https://discovery.dundee.ac.uk/en/publications/f12e4e25-689e-4d50-80e7-5d206ac0546f. 
  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. et al. (2002). "Initial sequencing and comparative analysis of the mouse genome". Nature 420 (6915): 520–562. doi:10.1038/nature01262. PMID 12466850. 
  12. ↑ Lindblad-Toh, K.; Wade, C. M.; Mikkelsen, T. S.; Karlsson, E. K.; Jaffe, D. B.; Kamal, M.; Clamp, M.; Chang, J. L. et al. (2005). "Genome sequence, comparative analysis and haplotype structure of the domestic dog". Nature 438 (7069): 803–819. doi:10.1038/nature04338. PMID 16341006. Bibcode: 2005Natur.438..803L. 
  13. ↑ Mikkelsen, T. S.; Wakefield, M. J.; Aken, B.; Amemiya, C. T.; Chang, J. L.; Duke, S.; Garber, M.; Gentles, A. J. et al. (2007). "Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences". Nature 447 (7141): 167–177. doi:10.1038/nature05805. PMID 17495919. 
  14. ↑ ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET (2007). "Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project". Nature 447 (7146): 799–816. doi:10.1038/nature05874. PMID 17571346. Bibcode: 2007Natur.447..799B. 
  15. ↑ Cuff, J. A.; Coates, G. M.; Cutts, T. J.; Rae, M. (2004). "The Ensembl Computing Architecture". Genome Research 14 (5): 971–975. doi:10.1101/gr.1866304. PMID 15123594. 
  16. ↑ Department of Commerce press release, 24 August 2011
  17. ↑ https://github.com/mclamp/jauth/




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