James Cuff

Dr. James Andrew Cuff
CitizenshipUnited States of America
EducationChrist Church, Oxford
SpouseMichele Clamp
Scientific career
FieldsMolecular Biophysics
High Performance Computing
WorkplacesMIT
Harvard University
Broad Institute
European Bioinformatics Institute
University of Oxford
University of Manchester
ThesisProtein Structure Prediction (1999)
Geoff Barton

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

Education

Cuff holds a PhD in protein structure prediction 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).[citation needed] Cuff worked as a part of teams that completed the first simultaneous genome analysis of twenty nine mammals, the refinement of the human gene count, and the first bivalent chromatin structures to be found in embryonic stem cells. In addition, Cuff has contributed to several large-scale bioinformatics and computational biology projects including Ensembl, Jalview, and the first online consensus secondary structure prediction algorithm JPred. He supported the resolution of the mouse, dog and monodelphis genomes and the early ENCODE project.

Based on early work with computer clusters, Cuff has aided with the design and architecture of the Massachusetts Green High Performance Computing Center, a multimillion-dollar 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.

In 2022, MIT created a new Office of Research Computing and Data and Cuff returned from early retirement as its inaugural Executive Director, continuing his earlier work with the Massachusetts Green High Performance Computing Center.

Most cited papers

Publications

  1. 1 2 Cuff, James (1999). Protein Structure Prediction (PhD thesis). University of Oxford.
  2. ↑ 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.
  3. ↑ 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.
  4. ↑ 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. S2CID 9993008.
  5. ↑ 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.
  6. ↑ 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.
  7. ↑ 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.
  8. ↑ 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.
  9. ↑ 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.
  10. ↑ 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.
  11. ↑ 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.
  12. ↑ 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.
  13. ↑ 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.

References

  1. ↑ Atwood, John (24 August 2011). "U.S. Commerce Department Awards $2.1 Million to Advance Business Development in Holyoke, Massachusetts Innovation District". Department of Commerce press release. Archived from the original on 15 November 2011.
  2. ↑ Cuff, James; Clamp, Michele; Neugeboren, Jonah; Kitzmkller, Aaron (13 September 2021). "harvardinformatics/JAuth: Java GUI client to generate Google authentication codes". GitHub.
  3. ↑ Office of the Vice President for Research (5 May 2022). "MIT to launch new Office of Research Computing and Data". MIT News. See also "MIT Office of Research Computing and Data (ORCD)". MIT. Retrieved 3 September 2026.
  4. ↑ "MIT Office of Research Computing and Data (ORCD)". MIT. Retrieved 3 September 2026.
  5. ↑ Mtchedlishvili, Nino (10 November 2022). "UMass, Harvard, MIT and others investing $5M in high-performance computer center in Holyoke that's key to academic research". Daily Hampshire Gazette.
  6. 1 2 3 4 5 "James Cuff". Google Scholar author page. Retrieved 8 March 2021.