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Keywords

High Performance Computing, Scientific Computing, Research Computing, Molecular Biophysics

Biography

Multiple decades supporting and building increasingly complicated scientific computing organizations. Held various leadership roles in academia and industry, simultaneously supporting teams as a player, coach and manager. Constantly works to try and blend aliquots of executive, with a smattering of engineering. Plays well with others, especially at scale.

Activities

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Education and qualifications (2)

University of Oxford: Oxford, GB

1996 to 2000 | D. Phil (Molecular Biophysics)
Education
Source: Self-asserted source
James Cuff

University of Manchester: Manchester, GB

1993 to 1996 | B.Sc. (Hons) (Chemistry)
Education
Source: Self-asserted source
James Cuff

Funding (5)

CIF21 DIBBs: EI: North East Storage Exchange

2017-07-01 to 2022-09-30 | Grant
Directorate for Computer & Information Science & Engineering (Alexandria, US)
URL: https://app.dimensions.ai/details/grant/grant.7070442
GRANT_NUMBER: 1753840
Source: Self-asserted source
James Cuff via DimensionsWizard

CIF21 DIBBs: EI: North East Storage Exchange

2016-11-01 to 2017-10-31 | Grant
Directorate for Computer & Information Science & Engineering (Alexandria, US)
URL: https://app.dimensions.ai/details/grant/grant.5541546
GRANT_NUMBER: 1640831
Source: Self-asserted source
James Cuff via DimensionsWizard

Advanced Cyberinfrastructre - Research and Educational Facilitation: Campus-Based Computational Research Support

2014-03-01 to 2018-08-31 | Grant
Directorate for Computer & Information Science & Engineering (Alexandria, US)
URL: https://app.dimensions.ai/details/grant/grant.3492251
GRANT_NUMBER: 1341935
Source: Self-asserted source
James Cuff via DimensionsWizard

Developmental Mechanisms of Beak Shape Evolution in Galapagos Finches

2013-03-01 to 2016-06-30 | Grant
Directorate for Biological Sciences (Alexandria, US)
URL: https://app.dimensions.ai/details/grant/grant.3481854
GRANT_NUMBER: 1257122
Source: Self-asserted source
James Cuff via DimensionsWizard

Developmental origins of mental illness: evolution and reversibility

2011-09-05 to 2023-03-31 | Grant
National Institute of Mental Health (Bethesda, US)
URL: https://app.dimensions.ai/details/grant/grant.2440991
GRANT_NUMBER: P50MH094271
Source: Self-asserted source
James Cuff via DimensionsWizard

Works (21)

Welcome to the first issue of <scp> <i>Applied AI Letters</i> </scp>

Applied AI Letters
2020-08-04 | Journal article
DOI: 10.1002/ail2.8
Part of ISSN: 2689-5595
Contributors: Edward O. Pyzer‐Knapp; James Cuff; Jack Patterson; Olexandr Isayev; Simon Maskell
Source: Self-asserted source
James Cuff via Crossref Metadata Search

A High-Availability Cloud for Research Computing

Computer
2017 | Journal article
DOI: 10.1109/mc.2017.182
Part of ISSN: 0018-9162
Contributors: Justin Riley; John Noss; Wes Dillingham; James Cuff; Ignacio M. Llorente
Source: Self-asserted source
James Cuff via Crossref Metadata Search

The Medical Science DMZ.

Journal of the American Medical Informatics Association : JAMIA
2016-05 | Journal article
DOI: 10.1093/jamia/ocw032
PMID: 27136944
PMC: PMC5070525
Contributors: Peisert S; Barnett W; Dart E; Cuff J; Grossman RL; Balas E; Berman A; Shankar A; Tierney B
Source: Self-asserted source
James Cuff via Europe PubMed Central

A high-resolution map of human evolutionary constraint using 29 mammals.

Nature
2011-10 | Journal article
DOI: 10.1038/nature10530
PMID: 21993624
PMC: PMC3207357
Contributors: Lindblad-Toh K; Garber M; Zuk O; Lin MF; Parker BJ; Washietl S; Kheradpour P; Ernst J; Jordan G; Mauceli E et al.
Source: Self-asserted source
James Cuff via Europe PubMed Central

Distinguishing protein-coding and noncoding genes in the human genome.

Proceedings of the National Academy of Sciences of the United States of America
2007-11 | Journal article
DOI: 10.1073/pnas.0709013104
PMID: 18040051
PMC: PMC2148306
Contributors: Clamp M; Fry B; Kamal M; Xie X; Cuff J; Lin MF; Kellis M; Lindblad-Toh K; Lander ES
Source: Self-asserted source
James Cuff via Europe PubMed Central

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.

Genome research
2007-06 | Journal article
DOI: 10.1101/gr.6034307
PMID: 17567995
PMC: PMC1891336
Contributors: Margulies EH; Cooper GM; Asimenos G; Thomas DJ; Dewey CN; Siepel A; Birney E; Keefe D; Schwartz AS; Hou M et al.
Source: Self-asserted source
James Cuff via Europe PubMed Central

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Nature
2007-06 | Journal article
DOI: 10.1038/nature05874
PMID: 17571346
PMC: PMC2212820
Contributors: ENCODE Project Consortium; Birney E; Stamatoyannopoulos JA; Dutta A; Guigó R; Gingeras TR; Margulies EH; Weng Z; Snyder M; Dermitzakis ET et al.
Source: Self-asserted source
James Cuff via Europe PubMed Central

Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences.

Nature
2007-05 | Journal article
DOI: 10.1038/nature05805
PMID: 17495919
Contributors: Mikkelsen TS; Wakefield MJ; Aken B; Amemiya CT; Chang JL; Duke S; Garber M; Gentles AJ; Goodstadt L; Heger A et al.
Source: Self-asserted source
James Cuff via Europe PubMed Central

A bivalent chromatin structure marks key developmental genes in embryonic stem cells.

Cell
2006-04 | Journal article
DOI: 10.1016/j.cell.2006.02.041
PMID: 16630819
Contributors: Bernstein BE; Mikkelsen TS; Xie X; Kamal M; Huebert DJ; Cuff J; Fry B; Meissner A; Wernig M; Plath K et al.
Source: Self-asserted source
James Cuff via Europe PubMed Central

Genome sequence, comparative analysis and haplotype structure of the domestic dog.

Nature
2005-12 | Journal article
DOI: 10.1038/nature04338
PMID: 16341006
Contributors: Lindblad-Toh K; Wade CM; Mikkelsen TS; Karlsson EK; Jaffe DB; Kamal M; Clamp M; Chang JL; Kulbokas EJ; Zody MC et al.
Source: Self-asserted source
James Cuff via Europe PubMed Central

The Ensembl computing architecture.

Genome research
2004-05 | Journal article
DOI: 10.1101/gr.1866304
PMID: 15123594
PMC: PMC479128
Contributors: Cuff JA; Coates GM; Cutts TJ; Rae M
Source: Self-asserted source
James Cuff via Europe PubMed Central

An overview of Ensembl.

Genome research
2004-04 | Journal article
DOI: 10.1101/gr.1860604
PMID: 15078858
PMC: PMC479121
Contributors: Birney E; Andrews TD; Bevan P; Caccamo M; Chen Y; Clarke L; Coates G; Cuff J; Curwen V; Cutts T et al.
Source: Self-asserted source
James Cuff via Europe PubMed Central

Ensembl 2004.

Nucleic acids research
2004-01 | Journal article
DOI: 10.1093/nar/gkh038
PMID: 14681459
PMC: PMC308772
Contributors: Birney E; Andrews D; Bevan P; Caccamo M; Cameron G; Chen Y; Clarke L; Coates G; Cox T; Cuff J et al.
Source: Self-asserted source
James Cuff via Europe PubMed Central

The Jalview Java alignment editor.

Bioinformatics (Oxford, England)
2004-01 | Journal article
DOI: 10.1093/bioinformatics/btg430
PMID: 14960472
Contributors: Clamp M; Cuff J; Searle SM; Barton GJ
Source: Self-asserted source
James Cuff via Europe PubMed Central

Ensembl 2002: accommodating comparative genomics.

Nucleic acids research
2003-01 | Journal article
DOI: 10.1093/nar/gkg083
PMID: 12519943
PMC: PMC165530
Contributors: Clamp M; Andrews D; Barker D; Bevan P; Cameron G; Chen Y; Clark L; Cox T; Cuff J; Curwen V et al.
Source: Self-asserted source
James Cuff via Europe PubMed Central

Initial sequencing and comparative analysis of the mouse genome.

Nature
2002-12 | Journal article
DOI: 10.1038/nature01262
PMID: 12466850
Contributors: Mouse Genome Sequencing Consortium; Waterston RH; Lindblad-Toh K; Birney E; Rogers J; Abril JF; Agarwal P; Agarwala R; Ainscough R; Alexandersson M et al.
Source: Self-asserted source
James Cuff via Europe PubMed Central

The Ensembl genome database project.

Nucleic acids research
2002-01 | Journal article
DOI: 10.1093/nar/30.1.38
PMID: 11752248
PMC: PMC99161
Contributors: Hubbard T; Barker D; Birney E; Cameron G; Chen Y; Clark L; Cox T; Cuff J; Curwen V; Down T et al.
Source: Self-asserted source
James Cuff via Europe PubMed Central

Application of multiple sequence alignment profiles to improve protein secondary structure prediction.

Proteins
2000-08 | Journal article
DOI: 10.1002/1097-0134(20000815)40:3<502::aid-prot170>3.0.co;2-q
PMID: 10861942
Contributors: Cuff JA; Barton GJ
Source: Self-asserted source
James Cuff via Europe PubMed Central

ProtEST: protein multiple sequence alignments from expressed sequence tags.

Bioinformatics (Oxford, England)
2000-02 | Journal article
DOI: 10.1093/bioinformatics/16.2.111
PMID: 10842731
Contributors: Cuff JA; Birney E; Clamp ME; Barton GJ
Source: Self-asserted source
James Cuff via Europe PubMed Central

Evaluation and improvement of multiple sequence methods for protein secondary structure prediction.

Proteins
1999-03 | Journal article
DOI: 10.1002/(sici)1097-0134(19990301)34:4<508::aid-prot10>3.0.co;2-4
PMID: 10081963
Contributors: Cuff JA; Barton GJ
Source: Self-asserted source
James Cuff via Europe PubMed Central

JPred: a consensus secondary structure prediction server.

Bioinformatics (Oxford, England)
1998-01 | Journal article
DOI: 10.1093/bioinformatics/14.10.892
PMID: 9927721
Contributors: Cuff JA; Clamp ME; Siddiqui AS; Finlay M; Barton GJ
Source: Self-asserted source
James Cuff via Europe PubMed Central
How many people are using ORCID?