James Cuff

Last updated

Dr. James Andrew Cuff
Born1974 (age 47–48)[ citation needed ]
Nationality United Kingdom
Citizenship United States of America
Alma mater Christ Church, Oxford
Spouse Michele Clamp
Scientific career
Fields Molecular Biophysics
High Performance Computing
Institutions MIT
Harvard University
Broad Institute
European Bioinformatics Institute
University of Oxford
University of Manchester
Thesis Protein Structure Prediction  (1999)
Doctoral advisor Geoffrey J. Barton [1]
Website Mastodon
LinkedIn

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.

Contents

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

Based on early work with computer clusters, [14] Cuff has aided with the design and architecture of the Massachusetts Green High Performance Computing Center, a multimillion-dollar [15] 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. [16] Cuff was a Principal Investigator for the National Institute of Mental Health funded Conte Center at Harvard, the National Science Foundation funded North East Storage Exchange, and their Advanced Cyberinfrastructre, Research and Educational Facilitation projects.

In 2017, Cuff retired early as the Assistant Dean and Distinguished Engineer for FAS Research Computing at Harvard University jointly with his spouse Michele Clamp, who was the then Director of Informatics in June 2017.

In 2022, Cuff returned from early retirement as the inaugural Executive Director of the new Office of Research Computing and Data [17] at MIT, continuing his earlier work [18] with the Massachusetts Green High Performance Computing Center.

Most cited papers

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References

  1. 1 2 Cuff, James (1999). Protein Structure Prediction (PhD thesis). University of Oxford.
  2. ↑ James Cuff publications indexed by Microsoft Academic
  3. ↑ 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.
  4. ↑ 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.
  5. ↑ 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.
  6. ↑ 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.
  7. ↑ 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.
  8. ↑ 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.
  9. ↑ 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.
  10. ↑ 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.
  11. ↑ 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.
  12. ↑ 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.
  13. ↑ 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.
  14. ↑ 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.
  15. ↑ Department of Commerce press release, 24 August 2011
  16. ↑ "GitHub - harvardinformatics/JAuth: Java GUI client to generate Google authentication codes". 13 September 2021.
  17. ↑ "MIT to launch new Office of Research Computing and Data". MIT News.
  18. ↑ "UMass, Harvard, MIT and others investing $5M in high-performance computer center in Holyoke that's key to academic research". Daily Hampshire Gazette.
  19. 1 2 3 4 5 Google Scholar author page. Accessed March 8, 2021
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