Pearson, W. R., Li, W., and Lopez, R. (2016) "Query-seeded iterative similarity searching improves selectivity 5—20-fold" Nuc. Acids Res. 10.1093/nar/gkw1207 [PDF].
Triant, D. A. and Pearson, W. R. (2015) "Most partial domains in proteins are alignment and annotation artifacts" Genome Biology 16:99 [Entrez] [Journal] [PDF]
Furnham N, Holliday GL, de Beer TA, Jacobsen JO, Pearson WR, Thornton JM. (2013) "The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes." Nucleic Acids Res. 42:D485-489 [Entrez] [PDF]"
Mills, L. J. and Pearson, W. R. (2013) "Adjusting Scoring Matrices to Correct Overextended Alignments" Bioinformatics. 29:3007-2013 doi: 10.1093/bioinformatics/btt517. [Entrez] [PDF]
Li W, McWilliam H, Goujon M, Cowley A, Lopez R, Pearson WR. (2012) "PSI-Search: iterative HOE-reduced profile SSEARCH searching." Bioinformatics. [Entrez] [PDF]
Holliday GL, Andreini C, Fischer JD, Rahman SA, Almonacid DE, Williams ST, Pearson WR. (2012) "MACiE: exploring the diversity of biochemical reactions." Nucleic Acids Res. 2012 Jan;40(Database issue):D783-9. [Entrez] [PDF]
M. W. Gonzalez and W. R. Pearson (2010) "RefProtDom: A protein database with improved domain boundaries and homology relationships" Bioinformatics 26:2361-2362 [Entrez] [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]
B. M. Cantarel, H. G. Morrison, and W. Pearson (2006) "Exploring the Relationship between Sequence Similarity and Accurate Phylogenetic Trees" Mol. Biol. Evol. [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]
Pearson, W. R. (2016) Curr. Prot. Bioinformatics Chapter 3: Unit 3.9 "Finding protein and nucleotide similarities with FASTA" doi: 10.1002/0471250953.bi0309s53. [Entrez]
Pearson, W. R. (2015) Curr. Prot. Bioinformatics Chapter 3: Unit 4.12 "Protein function prediction: Problems and pitfalls" doi: 10.1002/0471250953.bi0412s51 [Entrez]
Pearson, W. R. (2013) Curr. Prot. Bioinformatics Chapter 3: Unit 3.5 "Selecting the Right Similarity-Scoring Matrix" doi: 10.1002/0471250953.bi0305s43. [Entrez] [PDF]
Pearson, W. R. (2013) "An Introduction to Similarity ("Homology") Searching" Curr. Prot. Bioinformatics Chapter 3: Unit 3.1 doi: 10.1002/0471250953.bi0301s42. [Entrez] [PDF]
Mackey, 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., (2002) "Relational Databases for Biologists," ISMB02 - Tutorial, Edmunton, Alberta [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]