Richard Hughey
Richard Hughey
Professor of Computer Engineering and Biomolecular Engineering, University of California Santa Cruz
Verified email at soe.ucsc.edu - Homepage
Title
Cited by
Cited by
Year
Hidden Markov models for detecting remote protein homologies.
K Karplus, C Barrett, R Hughey
Bioinformatics (Oxford, England) 14 (10), 846-856, 1998
13801998
Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure
J Gough, K Karplus, R Hughey, C Chothia
Journal of molecular biology 313 (4), 903-919, 2001
12432001
Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods
J Park, K Karplus, C Barrett, R Hughey, D Haussler, T Hubbard, C Chothia
Journal of molecular biology 284 (4), 1201-1210, 1998
6471998
Hidden Markov models for sequence analysis: extension and analysis of the basic method
R Hughey, A Krogh
Bioinformatics 12 (2), 95-107, 1996
6411996
Stochastic context-free grammers for tRNA modeling
Y Sakakibara, M Brown, R Hughey, IS Mian, K Sjölander, RC Underwood, ...
Nucleic acids research 22 (23), 5112-5120, 1994
5091994
Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology
K Sjölander, K Karplus, M Brown, R Hughey, A Krogh, IS Mian, ...
Bioinformatics 12 (4), 327-345, 1996
4331996
Combining local‐structure, fold‐recognition, and new fold methods for protein structure prediction
K Karplus, R Karchin, J Draper, J Casper, Y Mandel‐Gutfreund, ...
Proteins: Structure, Function, and Bioinformatics 53 (S6), 491-496, 2003
3522003
Using Dirichlet mixture priors to derive hidden Markov models for protein families.
M Brown, R Hughey, A Krogh, IS Mian, K Sjölander, D Haussler
Ismb 1, 47-55, 1993
2451993
Predicting protein structure using hidden Markov models
K Karplus, K Sjölander, C Barrett, M Cline, D Haussler, R Hughey, L Holm, ...
Proteins: Structure, Function, and Bioinformatics 29 (S1), 134-139, 1997
2111997
Predicting protein structure using only sequence information
K Karplus, C Barrett, M Cline, M Diekhans, L Grate, R Hughey
Proteins: Structure, Function, and Bioinformatics 37 (S3), 121-125, 1999
1791999
What is the value added by human intervention in protein structure prediction?
K Karplus, R Karchin, C Barrett, S Tu, M Cline, M Diekhans, L Grate, ...
Proteins: Structure, Function, and Bioinformatics 45 (S5), 86-91, 2001
1692001
Scoring hidden Markov models
C Barrett, R Hughey, K Karplus
Bioinformatics 13 (2), 191-199, 1997
1361997
SAM: Sequence alignment and modeling software system
R Hughey, A Krogh
University of California at Santa Cruz, 1995
1351995
SAM‐T04: What is new in protein–structure prediction for CASP6
K Karplus, S Katzman, G Shackleford, M Koeva, J Draper, B Barnes, ...
Proteins: Structure, Function, and Bioinformatics 61 (S7), 135-142, 2005
1332005
Parallel hardware for sequence comparison and alignment
R Hughey
Bioinformatics 12 (6), 473-479, 1996
1281996
Predicting reliable regions in protein sequence alignments
M Cline, R Hughey, K Karplus
Bioinformatics 18 (2), 306-314, 2002
1122002
Statistical modeling, phylogenetic analysis and structure prediction of a protein splicing domain common to inteins and hedgehog proteins
JZ DALGAARD, MJ MOSER, R Hughey, IS Mian
Journal of Computational Biology 4 (2), 193-214, 1997
941997
The UCSC Kestrel parallel processor
A Di Bias, DM Dahle, M Diekhans, L Grate, J Hirschberg, K Karplus, ...
IEEE Transactions on Parallel and Distributed Systems 16 (1), 80-92, 2005
792005
Reduced space sequence alignment
JA Grice, R Hughey, D Speck
Bioinformatics 13 (1), 45-53, 1997
661997
Weighting hidden Markov models for maximum discrimination.
R Karchin, R Hughey
Bioinformatics (Oxford, England) 14 (9), 772-782, 1998
571998
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