James Cuff

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. 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.; Jordan, G.; Mauceli, E.; Ward, L. D.; Lowe, C. B.; Holloway, A. K.; Clamp, M.; Gnerre, S.; Alföldi, J.; Beal, K.; Chang, J.; Clawson, H.; Cuff, J.; Di Palma, F.; Fitzgerald, S.; Flicek, P.; Guttman, M.; Hubisz, M. J.; Jaffe, D. B.; Jungreis, I.; Kent, W. J.; Kostka, D.; Lara, M. (2011). "A high-resolution map of human evolutionary constraint using 29 mammals". Nature. 478 (7370): 476–482. Bibcode:2011Natur.478..476.. doi:10.1038/nature10530. PMC 3207357. PMID 21993624.
  5. Clamp, M.; Fry, B.; Kamal, M.; Xie, X.; Cuff, J.; Lin, M. F.; Kellis, M.; Lindblad-Toh, K.; Lander, E. S. (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. PMC 2148306. PMID 18040051.
  6. Bernstein, B. E.; Mikkelsen, T. S.; Xie, X.; Kamal, M.; Huebert, D. J.; Cuff, J.; Fry, B.; Meissner, A.; Wernig, M.; Plath, K.; Jaenisch, R.; Wagschal, A.; Feil, R.; Schreiber, S. L.; Lander, E. S. (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.; Curwen, V.; Down, T.; Durbin, R.; Eyras, E.; Gilbert, J.; Hammond, M.; Huminiecki, L.; Kasprzyk, A.; Lehvaslaiho, H.; Lijnzaad, P.; Melsopp, C.; Mongin, E.; Pettett, R.; Pocock, M.; Potter, S.; Rust, A.; Schmidt, E.; Searle, S.; Slater, G.; Smith, J.; Spooner, W.; Stabenau, A. (2002). "The Ensembl genome database project". Nucleic Acids Research. 30 (1): 38–41. doi:10.1093/nar/30.1.38. PMC 99161. 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.
  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.; 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.
  12. 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.
  13. 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. 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; et al. (2007). "Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project". Nature. 447 (7146): 799–816. Bibcode:2007Natur.447..799B. doi:10.1038/nature05874. PMC 2212820. PMID 17571346.
  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. PMC 479128. PMID 15123594.
  16. Department of Commerce press release, 24 August 2011
  17. https://github.com/mclamp/jauth/
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