Research

I research Bioinformatics & Computational biology. A publications list is below.

Current major areas of interest are:

Publications

39. Khachane, AN & Harrison, PM. (2009) "Strong association between pseudogenization mechanisms and gene sequence length", Biology Direct, 4: 38

38. Khachane, AN & Harrison, PM. (2009) "Assessing the genomic evidence for conserved transcribed pseudogenes under selection", BMC Genomics, 10: 435 [DATA HERE]

37. De Lima Morais, D. & Harrison, P.M. (2009). "Genomic evidence for non-random endemic populations of decaying exons from mammalian genes". BMC Genomics, 10: 309. [DATA HERE]

36. McEwen LA, Harris D, Schmid RF, Vogel J, Western T, Harrison P. (2009) "Evaluation of the redesign of an undergraduate cell biology course." CBE Life Sci. Educ. 8(1): 72-8.

35. M. Logan, T. Nguyen, N. Szapiel, J. Knockleby, H. Por, M. Zadworny, M. Neszt, P. Harrison, H. Bussey, C. Mandato, J. Vogel & G. Lesage.  (2008). “Genetic interaction network of the Saccharomyces cerevisiae type 1 phosphatase Glc7”, BMC Genomics, 9, 336.

34. S.J. Marygold, A. Lambertsson, J. Roote, M. Ashburner, G. Millburn, N. Kenmochi, P. M. Harrison, Z. Yu, T.C Kaufman, S.J Leevers & K.R Cook. (2007) “The Ribosomal Protein Genes and Minute Loci of Drosophila melanogaster”, Genome Biology 8: R216.

33. P. M. Harrison & Z. Yu . (2007) “Frame disruptions in human mRNA transcripts, and their relationship with splicing and protein structures”, BMC Genomics 8: 371. [DATA HERE]

32. Z. Yu, D. Morais, M. Ivanga & P. M. Harrison. (2007). “Analysis of the role of retrotransposition in vertebrate gene evolution”, BMC Bioinformatics  8: 308. [DATA HERE]

31. L. B. Harrison, Z. Yu, J. E Stajich, F. S Dietrich, & P.M. Harrison. (2007) "Evolution of budding yeast prion-determinant sequences across diverse Fungi" J. Mol. Biol. 368: 273-282. [DATA HERE]

30. J. Karro, Y. Yan, D. Zheng, Z. Zhang, N. Carriero, P. Cayting, P.M. Harrison, & M. Gerstein. (2007) "Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation" Nucleic Acids Res. 35: D55-D60.

29. P.M. Harrison. (2006) "Exhaustive assignment of compositional bias reveals universally prevalent biased regions: analysis of functional associations in human and Drosophila" BMC Bioinformatics 7: 441-441. [DATA HERE]

28. Zhang Z., Carriero N., Zheng D., Karro J., Harrison P.M., Gerstein M. (2006)  “PseudoPipe: an automated pseudogene identification pipeline” Bioinformatics 15: 1437-1439.

27. Zheng D., Zhang Z., Harrison P.M., Karro J., Carriero N., Gerstein M. (2005) “Integrated pseudogene annotation for human chromosome 22: evidence for transcription” Journal of Molecular Biology 349: 27-45.

26. Juretic N., Hoen D. R., Huynh M. L., Harrison P.M. & Bureau T. E. (2005) "The evolutionary fate of MULE-mediated duplications of host gene fragments in rice" Genome Res. 15: 1292-7.

25. P.M. Harrison et al. (2005) "Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability"  Nucleic Acids Res. 33(8): 2374-83. [DATA HERE]

24. Yang Liu, P.M. Harrison & M. Gerstein. (2004). “Comprehensive analysis of pseudogenes in prokaryotes: widespread gene decay and failure of putative horizontally transferred genes ”, Genome Biol. 5: R64.

23. P.M. Harrison, N. Carriero, Yang Liu, & M. Gerstein. (2003). “A ‘polyORFomic’ analysis using disabled-homology filtering reveals a small population of undiscovered but conserved short ORFs in prokaryotes”, J. Mol. Biol. 333(5): 885-892.

22. Z. Zhang, P.M. Harrison, Yin Liu, & M. Gerstein. (2003). “ Millions of years of evolution preserved: A comprehensive catalogue of the processed pseudogenes in the human genome”. Genome Res. 13(12): 2541-2558.   

21. P.M. Harrison & M. Gerstein. (2003). “A method to assess compositionally biased regions in biological sequences and its application to glutamine/asparagine-rich domains in eukaryotic proteomes” Genome Biol. 4(6): R40.1-14 [Epub].  [DATA HERE]

20. J. L. Rinn *, G. Euskirchen *, P. Bertone *, R. Goetsch, N. M. Luscombe, S. Hartman, P.M. Harrison, P. Miller, M. Gerstein, S. Weissman & M. Snyder. (2003).  “The Transcriptional Activity of Human Chromosome 22” Genes Dev. 17: 529-540.  (*co- primary authors.)

19. P.M. Harrison, D. Milburn, Z. Zhang, P. Bertone & M. Gerstein. (2003).  “Identification of pseudogenes in the Drosophila melanogaster genome” Nucleic Acids Res. 31: 1033-1037.  

18. Z. Zhang, P.M. Harrison & M. Gerstein. (2002).  “Digging deep for ancient relics:  A survey of protein motifs in the intergenic sequences of four eukaryotic genomes” J. Mol. Biol. 323: 811-822.  

17. Z. Zhang, P.M. Harrison & M. Gerstein. (2002). “Identification and analysis of over 2000 ribosomal-protein pseudogenes in the human genome” Genome Res. 12: 1466-1482.  

16. S. Balasubramanian , P.M. Harrison, H. Hegyi, P. Bertone, N. Luscombe, N. Echols, P. McGarvey, Z. Zhang & M. Gerstein.  (2002).  “SNPs on human chromosomes 21 and 22 ---  Analysis in terms of protein features and pseudogenes” Pharmacogenomics 3: 393-402.  

15. P.M. Harrison & M. Gerstein.  (2002). “Studying genomes through the aeons:  Protein families, pseudogenes and proteome evolution ” J. Mol. Biol. 318: 1155-1174.  

14. N. Echols, P.M. Harrison, S. Balasubramanian, N. Luscombe, P. Bertone, Z. Zhang & M. Gerstein.  (2002). “Comprehensive analysis of amino acid  and nucleotide composition in eukaryotic genomes, comparing genes and pseudogenes” Nucleic Acids Res. 30: 2515-2523.  

13.  P.M. Harrison, A. Kumar, N. Lan, M. Snyder & M. Gerstein.  (2002) “A question of size: The eukaryotic proteome and the problems in defining it” Nucleic Acids Res. 30: 1083-1090.    

12. P.M. Harrison, A. Kumar, N. Lan, N. Echols, M. Snyder & M. Gerstein. (2002).  “A small reservoir of disabled ORFs in the Saccharomyces cerevisia e genome and its implications for the dynamics of proteome evolution” J. Mol. Biol. 316: 409-419.  

11. P.M. Harrison, H. Hegyi, S. Balasubramanian, N. Luscombe, P. Bertone, T. Johnson, N. Echols & M. Gerstein.  (2002).  “Molecular fossils in the human genome: Identification and analysis of the pseudogenes in chromosomes 21 and 22” Genome Res. 12: 272-280.    

10. A. Kumar, P.M. Harrison, K.-H. Cheung, N. Lan, N. Echols, P. Bertone, P. Miller, M. B. Gerstein & M. Snyder. (2002). “An integrated approach for finding overlooked genes in yeast” Nat. Biotechnol. 20: 58-63.    

9. P.M. Harrison, H.S.Chan, S.B.Prusiner & F.E.Cohen. (2001) "Conformational propagation with prion-like characteristics in a simple model of protein folding" Protein Sci. 10: 819-835.

8. P.M. Harrison, N. Echols & M. Gerstein. (2001) "Digging for dead genes:  an analysis of the characteristics of the pseudogene population in the Caenorhabditis elegans genome" Nucl. Acids Res. 29: 818-830.  

7. R.C.Moore*, I.Y.Lee*, G.L.Silverman, P.M. Harrison, R.Strome, C.Heinrich, A.Karunaratne, S.H.Pasternak, M.A.Chishti, Y.Liang, P.Mastrangelo, K.Wang, A.F.Smit, S.Katamine, G.A.Carlson, F.E.Cohen, S.B.Prusiner, D.W.Melton, P.Tremblay, L.E.Hood & D.Westaway. (1999) "Ataxia in prion protein deficient mice is associated with upregulation of the novel PrP-like protein doppel" J. Mol. Biol. 292: 797-817.  (*joint primary authors.)

6. P. M. Harrison, H.S.Chan, S.B.Prusiner & F.E.Cohen. (1999) "Thermodynamics of model prions and its implications for the problem of prion protein folding" J. Mol. Biol. 286: 593-606.  

5. P.M. Harrison, P.Bamborough, V.Daggett, S.B.Prusiner & F.E.Cohen. (1997) “The prion folding problem" Curr. Opin. Struct. Biol. 7: 53-59.  

4. M.Lohmeyer, P.M. Harrison, S. Kannan, M. DeSantis, N.J.O'Reilly, M.J.E.Sternberg, D.S.Salomon & W.J.Gullick. (1997) "Chemical synthesis, structural modelling and biological activity of the epidermal growth factor-like domain of human cripto" Biochemistry 36: 3837-3845.

3. P.M. Harrison "Analysis and prediction of protein structure: Disulphide bridges", Ph.D. Thesis, 1996 (University College, London).

2. P.M. Harrison and M.J.E. Sternberg. (1996) "The disulphide beta-cross: From cystine geometry and clustering to the classification of small, disulphide-rich protein folds" J. Mol. Biol. 264: 603-623.

1. P.M. Harrison and M.J.E. Sternberg. (1994) "Analysis and classification of disulphide connectivity in proteins" J. Mol. Biol. 244: 448-463.

Last update: Oct. 7, 2009