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James Cuff
James Cuff
Office of Research Computing and Data @ MIT
Verified email at mit.edu - Homepage
Title
Cited by
Cited by
Year
Initial sequencing and comparative analysis of the mouse genome
European Bioinformatics Institute: Birney Ewan 3 Goldman Nick 3 Kasprzyk ...
Nature 420 (6915), 520-562, 2002
85142002
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
61232006
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
Management Group Liefer Laura A. 51 Wetterstrand Kris A. 51 Good Peter J. 51 ...
nature 447 (7146), 799-816, 2007
59152007
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
30922005
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
19562002
The jalview java alignment editor
M Clamp, J Cuff, SM Searle, GJ Barton
Bioinformatics 20 (3), 426-427, 2004
18312004
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
12891998
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
12352011
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
10422000
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
8761999
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
8072007
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
7712007
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
5572004
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
2892003
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
2482007
Ensembl 2004
E Birney, D Andrews, P Bevan, M Caccamo, G Cameron, Y Chen, ...
Nucleic acids research 32 (suppl_1), D468-D470, 2004
2332004
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, 2011
822011
Initial sequencing and comparative analysis of the mouse genome
C Asif T, C Lisa L, D Kimberly D, F Ginger A, F Lucinda A, F Robert S, ...
Nature 420 (6915), 2002
792002
Broad Institute Genome Sequencing Platform. Broad Institute Whole Genome Assembly Team 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, 167-177, 2007
72*2007
The Ensembl computing architecture
JA Cuff, GMP Coates, TJR Cutts, M Rae
Genome research 14 (5), 971-975, 2004
412004
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