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Richard Hughey

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TOP 3
Kevin Karplus; Rachel Karchin; George Shackelford; Richard Hughey
Calibrating E-values for hidden Markov models using reverse-sequence null models.
Cristian Ionescu-Zanetti; Lee-Ping Wang; Dino Di Carlo; Paul Hung; Andrea Di Blas; Richard Hughey; Luke P Lee
Alkaline hemolysis fragility is dependent on cell shape: results from a morphology tracker.
Kevin Karplus; Sol Katzman; George Shackleford; Martina Koeva; Jenny Draper; Bret Barnes; Marcia Soriano; Richard Hughey
SAM-T04: what is new in protein-structure prediction for CASP6.

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All Publications

2005: Kevin Karplus; Rachel Karchin; George Shackelford; Richard Hughey
Calibrating E-values for hidden Markov models using reverse-sequence null models.
Bioinformatics (Oxford, England) 2005;21(22):4107-15.
2005: Cristian Ionescu-Zanetti; Lee-Ping Wang; Dino Di Carlo; Paul Hung; Andrea Di Blas; Richard Hughey; Luke P Lee
Alkaline hemolysis fragility is dependent on cell shape: results from a morphology tracker.
Cytometry. Part A : the journal of the International Society for Analytical Cytology 2005;65(2):116-23.
2005: Kevin Karplus; Sol Katzman; George Shackleford; Martina Koeva; Jenny Draper; Bret Barnes; Marcia Soriano; Richard Hughey
SAM-T04: what is new in protein-structure prediction for CASP6.
Proteins 2005;61 Suppl 7():135-42.
2003: Kevin Karplus; Rachel Karchin; Jenny Draper; Jonathan Casper; Yael Mandel-Gutfreund; Mark Diekhans; Richard Hughey
Combining local-structure, fold-recognition, and new fold methods for protein structure prediction.
Proteins 2003;53 Suppl 6():491-6.
2002: Melissa Cline; Richard Hughey; Kevin Karplus
Predicting reliable regions in protein sequence alignments.
Bioinformatics (Oxford, England) 2002;18(2):306-14.
2002: A Di Blas; A Jagota; Richard Hughey
Energy function-based approaches to graph coloring.
IEEE transactions on neural networks / a publication of the IEEE Neural Networks Council 2002;13(1):81-91.
2001: Julian Gough; Kevin Karplus; Richard Hughey; Cyrus Chothia
Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure.
Journal of molecular biology 2001;313(4):903-19.
2001: Kevin Karplus; Rachel Karchin; C Barrett; S Tu; Melissa Cline; Mark Diekhans; Leslie Grate; J Casper; Richard Hughey
What is the value added by human intervention in protein structure prediction?
Proteins 2001;Suppl 5():86-91.
2001: E Rice; Richard Hughey
Molecular fingerprinting on the SIMD parallel processor Kestrel.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2001;():323-34.
2001: Leslie Grate; Mark Diekhans; D Dahle; Richard Hughey
Sequence analysis with the Kestrel SIMD parallel processor.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2001;():263-74.
2000: R Wheeler; Richard Hughey
Optimizing reduced-space sequence analysis.
Bioinformatics (Oxford, England) 2000;16(12):1082-90.
1999: Kevin Karplus; C Barrett; Melissa Cline; Mark Diekhans; Leslie Grate; Richard Hughey
Predicting protein structure using only sequence information.
Proteins 1999;Suppl 3():121-5.
1998: J Park; Kevin Karplus; C Barrett; Richard Hughey; David Haussler; Tim Hubbard; Cyrus Chothia
Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods.
Journal of molecular biology 1998;284(4):1201-10.
1998: C Tarnas; Richard Hughey
Reduced space hidden Markov model training.
Bioinformatics (Oxford, England) 1998;14(5):401-6.
1998: Kevin Karplus; C Barrett; Richard Hughey
Hidden Markov models for detecting remote protein homologies.
Bioinformatics (Oxford, England) 1998;14(10):846-56.
1998: Rachel Karchin; Richard Hughey
Weighting hidden Markov models for maximum discrimination.
Bioinformatics (Oxford, England) 1998;14(9):772-82.
1997: C Barrett; Richard Hughey; Kevin Karplus
Scoring hidden Markov models.
Computer applications in the biosciences : CABIOS 1997;13(2):191-9.
1997: J A Grice; Richard Hughey; D Speck
Reduced space sequence alignment.
Computer applications in the biosciences : CABIOS 1997;13(1):45-53.
1997: Kevin Karplus; Kimmen Sjölander; C Barrett; Melissa Cline; David Haussler; Richard Hughey; L Holm; Chris Sander
Predicting protein structure using hidden Markov models.
Proteins 1997;Suppl 1():134-9.
1997: jacob dalgaard; MJ Moser; Richard Hughey; I Saira Mian
Statistical modeling, phylogenetic analysis and structure prediction of a protein splicing domain common to inteins and hedgehog proteins.
Journal of computational biology : a journal of computational molecular cell biology 1997;4(2):193-214.
1996: Richard Hughey
Parallel hardware for sequence comparison and alignment.
Computer applications in the biosciences : CABIOS 1996;12(6):473-9.
1996: Kimmen Sjölander; Kevin Karplus; M Brown; Richard Hughey; A Krogh; I Saira Mian; David Haussler
Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology.
Computer applications in the biosciences : CABIOS 1996;12(4):327-45.
1996: Richard Hughey; A Krogh
Hidden Markov models for sequence analysis: extension and analysis of the basic method.
Computer applications in the biosciences : CABIOS 1996;12(2):95-107.
1995: J A Grice; Richard Hughey; D Speck
Parallel sequence alignment in limited space.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 1995;3():145-53.
1994: Y Sakakibara; M Brown; Richard Hughey; I Saira Mian; Kimmen Sjölander; R C Underwood; David Haussler
Stochastic context-free grammars for tRNA modeling.
Nucleic acids research 1994;22(23):5112-20.
1994: Leslie Grate; M Herbster; Richard Hughey; David Haussler; I Saira Mian; Harry F Noller
RNA modeling using Gibbs sampling and stochastic context free grammars.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 1994;2():138-46.
1993: M Brown; Richard Hughey; A Krogh; I Saira Mian; Kimmen Sjölander; David Haussler
Using Dirichlet mixture priors to derive hidden Markov models for protein families.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 1993;1():47-55.