M. W. Gonzalez and W. R. Pearson (2010) Bioinformatics "RefProtDom: A protein database with improved domain boundaries and homology relationships" Advance access published on Aug 6, 2010 doi:10.1093/bioinformatics/btq426 [PDF]
M. L. Sierk, M. E. Smoot, E. J. Bass, and W. R. Pearson (2010) "Improving pairwise sequence alignment accuracy using near-optimal alignments" BMC Bioinformatics 11:146 doi:10.1186/1471-2105-11-146 [Entrez] [PDF]
M. W. Gonzalez and W. R. Pearson (2010) "Homologous over-extension: a challenge for iterative similarity searches" Nuc. Acids Research 38:2177-2189 [Entrez] [PDF]
D. T. Lavelle and W. R. Pearson (2010) "Globally, unrelated protein sequences appear random" Bioinformatics 26:310-318 [Entrez] [PDF]
W. R. Pearson and M. L. Sierk (2005) "The limits of protein sequence comparison?" Curr Opin Struct Biol. 15:254-260. [Entrez] [PDF]
M. L. Sierk and W. R. Pearson (2004) "Sensitivity and selectivity in protein structure comparison." Protein Sci. 13:773-85.
[Entrez][PDF] Data sets
M. E. Smoot, S. A. Guerlain, and W. R. Pearson (2004) "Visualization
of near-optimal alignments" Bioinformatics 20:953-958
[Entrez] [PDF]
Mackey, A. J., Haystead, T. A., and Pearson, W. R. (2003)
CRP: Cleavage of Radiolabeled Phosphoproteins. Nuc. Acids
Res. 31:3859-3861.
[Entrez]
[PDF]
Ivarsson, Y., Mackey, A. J., Edalat, M., Pearson, W. R., and
Mannervik, B. (2003) Identification of residues in
glutathione transferase capable of driving functional
diversification in evolution - a novel approach to protein
redesign. J Biol Chem 278:8733-8738.
[Entrez]
[PDF]
MacDonald, J. A., Mackey, A. J., Pearson, W. R., and
Haystead, T. A. J. (2002) A Strategy for the Rapid
Identification of Phosphorylation Sites in the
Phosphoproteome. Mol. Cell. Proteomics 1:314-322.
[Entrez]
[PDF]
Coggan, M., Flanagan, J. U., Parker, M. W., Pearson, W. R.,
Vichai, V., and Board, P. G. (2002) Identification and
characterization of GSTT3, a third murine theta class
glutathione transferase. Biochem. J. 366:323-332.
[Entrez]
[PDF]
Reese, J. T. and Pearson, W. R. (2002) Empirical
determination of effective gap penalties for sequence
comparison. Bioinformatics 18:1500-1507.
[Entrez]
[PDF]
Mackey, A. J., Haystead, T. A. J., and Pearson, W. R. (2002)
Getting more from less - Algorithms for rapid protein
identification with multiple short peptide sequences. Mol.
Cell. Proteomics 1:139-147.
[Entrez]
[PDF]
Pearson, W. R. (2001) Training for bioinformatics and computational biology. Bioinformatics 17:761-762. [Entrez] [PDF]
Whittington, A. T., Vichai, V., Webb, G. C., Baker, R. T.,
Pearson, W. R., and Board, P. G. (1999) Gene structure,
expression, and chromosomal localization of murine theta
class glutathione transferase mGSTT1-1. Biochem. J.
337:141-151 .
[Entrez]
[PDF]
Wood, T. C. and Pearson, W. R. (1999) Evolution of Protein
Sequences and Structures. J. Mol. Biol. 291:977-995.
[Entrez]
[PDF]
Retief, J. D., Lynch, K. R., and Pearson, W. R. (1999)
Panning for genes - a visual strategy for identifying novel
gene orthologs and paralogs. Genome Res. 9:373-382.
[Entrez]
[PDF]
Pearson, W. R., Robins, G., and Zhang, T. (1999)
Generalized neighbor-joining: more reliable phylogenetic
tree reconstruction. Mol. Biol. Evol. 16:806-816.
[Entrez]
[PDF]
Patskovsky, Y. V., Huang, M., Takayama, T., Listowsky, I.,
and Pearson, W. R. (1999) Distinctive structure of the
human GSTM3 gene - Inverted orientation relative to the Mu
class glutatione transferase gene cluster. Arch. Biochem.
Biophys. 361:85-93.
[Entrez]
[PDF]
Damer, C. K., Partridge, J., Pearson, W. R., and Haystead,
T. A. J. (1998) Rapid identification of protein
phosphatase 1-binding proteins by mixed peptide sequencing
and data base searching. Characterization of a novel
holoenzymic form of protein phosphatase 1. J. Biol. Chem.
273:24396-24405.
[Entrez]
[PDF]
Pearson, W. R. (1998) Empirical statistical estimates for
sequence similarity searches. J. Mol. Biol. 276:71-84.
[Entrez]
[PDF]
Xu, S., Wang, Y., Roe, B., and Pearson, W. R. (1998)
Characterization of the human class-mu glutathione
transferase gene cluster and the GSTM1 deletion. J. Biol.
Chem. 273:3517-3527.
[Entrez]
[PDF]
Pearson, W. R. (1998) Empirical statistical estimates for
sequence similarity searches. J. Mol. Biol. 276:71-84.
[Entrez]
[PDF]
Pearson W. R., Wood T., Zhang Z., Miller W. (1997)
Comparison of DNA sequences with protein sequences.
Genomics. 46:24-36.
[Entrez]
[PDF]
Pearson, W. R. (1995) Comparison of methods for searching protein sequence databases. Protein Sci. 1995 4:1145-60.
[Entrez]
Pearson, W. R. and Lipman, D. J. (1988) Improved tools for biological sequence comparison Proc. Natl. Acad. Sci. US 85:2444-2448
[Entrez]
[PDF]
Lipman, D. J. and Pearson, W. R. (1985) Rapid and Sensitive Protein Similarity Searches Science 227:1435-1441
[Entrez]
[PDF]
Macke, A. J. and Pearson, W. R. (2004) "Using relational databases for improved sequence similarity searching and large-scale genomic analyses." Curr Protoc Bioinformatics. Chapter 9:Unit 9.4. [Entrez] [PDF]
Mackey, A. J. and Pearson, W. R., "Relational Databases for
Biologists," ISMB02 - Tutorial, Edmunton, Alberta (2002) .
[PDF]
Pearson, W. R. and Wood, T. C. (2001) Statistical
significance in biological sequence comparison. In Handbook
of Statistical Genetics, D. J. Balding, M. Bishop, and C.
Cannings, ed. (London, UK: Wiley), pp. 39-65.
[PDF]
Pearson, W. R., "Protein sequence comparison and protein
evolution," ISMB95 - Tutorial, Cambridge, UK (1995). (presented
in revised form at ISMB2000, San Diego.
[PDF]
wrp@virginia.edu