Dr. Paul M. Harrison
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Research and Publications

Research

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

Current major areas of interest are:

  • Analysis of genome & proteome evolution
  • Annotation of genomes & proteomes
  • Analysis & simulation of protein folding, amyloidogenesis & prions.

Publications

50. Gendoo DMA, Harrison PM (2012) The Landscape of the Prion Protein's Structural Response to Mutation Revealed by Principal Component Analysis of Multiple NMR Ensembles. PLoS Comput Biol 8 (8): e1002646. doi:10.1371/journal.pcbi.1002646

49. Djamel Harbi, Marimuthu Parthiban, Deena M.A. Gendoo, Sepehr Ehsani, Manish Kumar, Gerold Schmitt-Ulms, Ramanathan Sowdhamini and Paul M. Harrison (2012) PrionHome: A database of prions and other sequences relevant to prion phenomena. PLoS One. 2012;7 (2):e31785. Epub 2012 Feb 20.

48. Gendoo DMA, Harrison PM (2011) Origins and Evolution of the HET-s Prion-Forming Protein: Searching for Other Amyloid-Forming Solenoids. PLoS ONE 6 (11): e27342. doi:10.1371/journal.pone.0027342

47. Ehsani S, Tao R, Pocanschi CL, Ren H, Harrison PM, Schmitt-Ulms, GS (2011) Evidence for Retrogene Origins of the Prion Gene Family. PLoS ONE 6 (10): e26800. doi:10.1371/journal.pone.0026800

46. Harbi, D, Parthiban, M, Gendoo, D, Ehsani, S, Kumar, M, Schmitt-Ulms, G, Sowdhamini, R, and Harrison, PM (2011) PrionOme: A database of prions and other sequences relevant to prion phenomena. Nature Precedings, npre.2011.6430.1.

45. Westaway D, Daude N, Wohlgemuth S, Harrison P (2011) The PrP-like proteins Shadoo and Doppel. Top Curr Chem. 2011;305: 225-56.

44. Gendoo, D. & Harrison, P.M. (2011) Discordant and chameleon sequences: their distribution, and their implications for amyloidogenicity. Protein Science, DOI 10.1002/pro.590.

43. Harbi, D., Kumar, M. & Harrison, P.M. (2011) LPS-Annotate: complete annotation of compositionally-biased regions in the protein knowledgebase. Database (Oxford), doi: 10.1093/database/baq031.

42. De Lima Morais, D. & Harrison, P.M. (2010) Large-scale evidence for conservation of NMD candidature across mammals. PLoS ONE 5 (7): e11695. doi:10.1371/journal.pone.0011695.

41. Khachane, A. & Harrison, P.M. (2010) Mining mammalian transcript data for functional long non-coding RNAs. PLoS ONE 5 (4): e10316. doi:10.1371/journal.pone.0010316.

40.  Harrison, P.M., Khachane, A & Kumar, M. (2010) Genomic assessment of the evolution of the prion protein gene family in vertebrates. Genomics 95 (5): 268-77.

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].

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: 15/08/2012 McGill Centre for Bioinformatics DBRIBiology Home McGill Home