James Cuff
James Cuff
Independent Consultant
Verified email at jcuff.net - Homepage
Title
Cited by
Cited by
Year
Initial sequencing and comparative analysis of the mouse genome
RH Waterston, K Lindblad-Toh, E Birney, J Rogers, JF Abril, P Agarwal, ...
Nature 420 (6915), 520-562, 2002
71432002
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
ENCODE Project Consortium
nature 447 (7146), 799, 2007
51712007
A bivalent chromatin structure marks key developmental genes in embryonic stem cells
BE Bernstein, TS Mikkelsen, X Xie, M Kamal, DJ Huebert, J Cuff, B Fry, ...
Cell 125 (2), 315-326, 2006
50012006
Finishing the euchromatic sequence of the human genome
International Human Genome Sequencing Consortium
Nature 431 (7011), 931, 2004
39872004
Genome sequence, comparative analysis and haplotype structure of the domestic dog
K Lindblad-Toh, CM Wade, TS Mikkelsen, EK Karlsson, DB Jaffe, ...
Nature 438 (7069), 803-819, 2005
24522005
The jalview java alignment editor
M Clamp, J Cuff, SM Searle, GJ Barton
Bioinformatics 20 (3), 426-427, 2004
16402004
The Ensembl genome database project
T Hubbard, D Barker, E Birney, G Cameron, Y Chen, L Clark, T Cox, J Cuff, ...
Nucleic acids research 30 (1), 38-41, 2002
16002002
JPred: a consensus secondary structure prediction server.
JA Cuff, ME Clamp, AS Siddiqui, M Finlay, GJ Barton
Bioinformatics (Oxford, England) 14 (10), 892-893, 1998
12021998
A high-resolution map of human evolutionary constraint using 29 mammals
K Lindblad-Toh, M Garber, O Zuk, MF Lin, BJ Parker, S Washietl, ...
Nature 478 (7370), 476-482, 2011
9542011
Application of multiple sequence alignment profiles to improve protein secondary structure prediction
JA Cuff, GJ Barton
Proteins: Structure, Function, and Bioinformatics 40 (3), 502-511, 2000
9532000
Evaluation and improvement of multiple sequence methods for protein secondary structure prediction
JA Cuff, GJ Barton
Proteins: Structure, Function, and Bioinformatics 34 (4), 508-519, 1999
7531999
Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences
TS Mikkelsen, MJ Wakefield, B Aken, CT Amemiya, JL Chang, S Duke, ...
Nature 447 (7141), 167-177, 2007
6812007
Distinguishing protein-coding and noncoding genes in the human genome
M Clamp, B Fry, M Kamal, X Xie, J Cuff, MF Lin, M Kellis, K Lindblad-Toh, ...
Proceedings of the National Academy of Sciences 104 (49), 19428-19433, 2007
6552007
An overview of Ensembl
E Birney, TD Andrews, P Bevan, M Caccamo, Y Chen, L Clarke, G Coates, ...
Genome research 14 (5), 925-928, 2004
5012004
Ensembl 2002: accommodating comparative genomics
M Clamp, D Andrews, D Barker, P Bevan, G Cameron, Y Chen, L Clark, ...
Nucleic Acids Research 31 (1), 38-42, 2003
2752003
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
EH Margulies, GM Cooper, G Asimenos, DJ Thomas, CN Dewey, A Siepel, ...
Genome research 17 (6), 760-774, 2007
2372007
Ensembl 2004
E Birney, D Andrews, P Bevan, M Caccamo, G Cameron, Y Chen, ...
Nucleic acids research 32 (suppl_1), D468-D470, 2004
2262004
Broad Institute Sequencing Platform and Whole Genome Assembly Team; Baylor College of Medicine Human Genome Sequencing Center Sequencing Team; Genome Institute at Washington …
K Lindblad-Toh, M Garber, O Zuk, MF Lin, BJ Parker, S Washietl, ...
Nature 478 (7370), 476-482, 0
63
The Ensembl computing architecture
JA Cuff, GMP Coates, TJR Cutts, M Rae
Genome research 14 (5), 971-975, 2004
402004
ProtEST: protein multiple sequence alignments from expressed sequence tags
JA Cuff, E Birney, ME Clamp, GJ Barton
Bioinformatics 16 (2), 111-116, 2000
302000
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