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Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure.
Gough J, Karplus K, Hughey R, Chothia C. Gough J, et al. Among authors: hughey r. J Mol Biol. 2001 Nov 2;313(4):903-19. doi: 10.1006/jmbi.2001.5080. J Mol Biol. 2001. PMID: 11697912
Calibrating E-values for hidden Markov models using reverse-sequence null models.
Karplus K, Karchin R, Shackelford G, Hughey R. Karplus K, et al. Among authors: hughey r. Bioinformatics. 2005 Nov 15;21(22):4107-15. doi: 10.1093/bioinformatics/bti629. Epub 2005 Aug 25. Bioinformatics. 2005. PMID: 16123115
Predicting protein structure using only sequence information.
Karplus K, Barrett C, Cline M, Diekhans M, Grate L, Hughey R. Karplus K, et al. Among authors: hughey r. Proteins. 1999;Suppl 3:121-5. doi: 10.1002/(sici)1097-0134(1999)37:3+<121::aid-prot16>3.3.co;2-h. Proteins. 1999. PMID: 10526360
Hidden Markov models for detecting remote protein homologies.
Karplus K, Barrett C, Hughey R. Karplus K, et al. Among authors: hughey r. Bioinformatics. 1998;14(10):846-56. doi: 10.1093/bioinformatics/14.10.846. Bioinformatics. 1998. PMID: 9927713
Weighting hidden Markov models for maximum discrimination.
Karchin R, Hughey R. Karchin R, et al. Among authors: hughey r. Bioinformatics. 1998;14(9):772-82. doi: 10.1093/bioinformatics/14.9.772. Bioinformatics. 1998. PMID: 9918947
Reduced space hidden Markov model training.
Tarnas C, Hughey R. Tarnas C, et al. Among authors: hughey r. Bioinformatics. 1998 Jun;14(5):401-6. doi: 10.1093/bioinformatics/14.5.401. Bioinformatics. 1998. PMID: 9682053
Scoring hidden Markov models.
Barrett C, Hughey R, Karplus K. Barrett C, et al. Among authors: hughey r. Comput Appl Biosci. 1997 Apr;13(2):191-9. doi: 10.1093/bioinformatics/13.2.191. Comput Appl Biosci. 1997. PMID: 9146967
Hidden Markov models for sequence analysis: extension and analysis of the basic method.
Hughey R, Krogh A. Hughey R, et al. Comput Appl Biosci. 1996 Apr;12(2):95-107. doi: 10.1093/bioinformatics/12.2.95. Comput Appl Biosci. 1996. PMID: 8744772
Using Dirichlet mixture priors to derive hidden Markov models for protein families.
Brown M, Hughey R, Krogh A, Mian IS, Sjölander K, Haussler D. Brown M, et al. Among authors: hughey r. Proc Int Conf Intell Syst Mol Biol. 1993;1:47-55. Proc Int Conf Intell Syst Mol Biol. 1993. PMID: 7584370
Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods.
Park J, Karplus K, Barrett C, Hughey R, Haussler D, Hubbard T, Chothia C. Park J, et al. Among authors: hughey r. J Mol Biol. 1998 Dec 11;284(4):1201-10. doi: 10.1006/jmbi.1998.2221. J Mol Biol. 1998. PMID: 9837738
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