| Hidden Markov models for detecting remote protein homologies. K Karplus, C Barrett, R Hughey Bioinformatics (Oxford, England) 14 (10), 846-856, 1998 | 1488 | 1998 |
| 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 | 1457 | 2001 |
| 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 | 701 | 1998 |
| Hidden Markov models for sequence analysis: extension and analysis of the basic method R Hughey, A Krogh Bioinformatics 12 (2), 95-107, 1996 | 700 | 1996 |
| 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 | 563 | 1994 |
| 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 | 482 | 1996 |
| 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 | 364 | 2003 |
| 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 | 272 | 1993 |
| 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 | 230 | 1997 |
| 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 | 187 | 1999 |
| 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 | 179 | 2001 |
| Scoring hidden Markov models C Barrett, R Hughey, K Karplus Bioinformatics 13 (2), 191-199, 1997 | 151 | 1997 |
| SAM: Sequence alignment and modeling software system R Hughey, A Krogh University of California at Santa Cruz, 1995 | 151 | 1995 |
| Parallel hardware for sequence comparison and alignment R Hughey Bioinformatics 12 (6), 473-479, 1996 | 143 | 1996 |
| 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 | 137 | 2005 |
| Predicting reliable regions in protein sequence alignments M Cline, R Hughey, K Karplus Bioinformatics 18 (2), 306-314, 2002 | 123 | 2002 |
| 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 | 106 | 1997 |
| 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 | 85 | 2005 |
| Reduced space sequence alignment JA Grice, R Hughey, D Speck Bioinformatics 13 (1), 45-53, 1997 | 74 | 1997 |
| Weighting hidden Markov models for maximum discrimination. R Karchin, R Hughey Bioinformatics (Oxford, England) 14 (9), 772-782, 1998 | 62 | 1998 |
