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Paul Harrison

Title: 
Associate Professor
Paul Harrison
Contact Information
Address: 

Stewart Biology Building, Room N7/16

Phone: 
514-398-6420
Email address: 
paul.harrison [at] mcgill.ca
Research areas: 
Molecular, Cellular and Developmental Biology
Areas of expertise: 

Bioinformatics and computational biology. Genome evolution and annotation; analysis and annotation of pseudogenes and long RNAs, and their implications; protein folding, amyloidogenesis and the prion phenomenon.

Selected publications: 

70. Wang, Y., Yang, H.J. & Harrison, P.M. (2020) The relationship between protein domains and homopeptides in the Plasmodium falciparum proteome.ÌýÌý

69. Harrison, P.M. (2020)ÌýVariable absorption of mutational trends by prion-forming domains duringÌýSaccharomycetesÌýevolution.ÌýÌýÌý

68. Su, W.C. & Harrison, P.M. (2020)ÌýDeep conservation of prion-like composition in the eukaryotic prion-former Pub1/Tia1 family and its relatives.Ìý.Ìý

67.ÌýSu, T.Y. & Harrison, P.M. (2019)ÌýConservation of prion-like composition and sequence in prion-formers and prion-like proteins.Ìý.

66.ÌýHarrison, P.M. (2019)ÌýEvolutionary behaviour of bacterial prion-like proteins.Ìý.

65. Narasumani M &ÌýHarrison PMÌý(2018) Discerning evolutionary trends in post-translational modification and the effect of intrinsic disorder: Analysis of methylation, acetylation and ubiquitination sites in human proteins.ÌýÌý

64. Lee SJ, Kong M,ÌýHarrison P, Hijri M. (2018) Conserved Proteins of the RNA Interference System in the Arbuscular Mycorrhizal Fungus Rhizoglomus irregulare Provide New Insight into the Evolutionary History of Glomeromycota.Ìý

63.ÌýHarrison, P.M.Ìý(2018) Compositionally biased dark matter in the protein universe (2018)Ìý.

62.ÌýHarrison, P.M.Ìý(2017) fLPS: Fast discovery of compositional biases for the protein universe.Ìý.

61. Hughes, B.G.,ÌýHarrison, P.M.Ìý& Hekimi, S. (2017) Estimating the occurrence of primary ubiquinone deficiency by analysis of large-scale sequencing data.Ìý.

60.ÌýHarrison, P.M.Ìý(2017) Published fLPS compositional bias analysis software on Zenodo,Ìý

59. An L. &ÌýHarrison P.M.Ìý(2016) The evolutionary scope and neurological disease linkage of yeast-prion-like proteins in humans.Ìý

58. An L., Fitzpatrick D.A. &ÌýHarrison P.M.Ìý(2016) Emergence and evolution of prion and prion-like proteins in budding yeasts.Ìý

57. Reimer J, Aloise M.N.,ÌýHarrison P.M.Ìý& Schmeing T.M. (2016) Synthetic cycle of the initiation module of a formylating nonribosomal peptide synthetase.ÌýÌý

56. Narasumani M.,ÌýHarrison P.M.Ìý(2015) Bioinformatical parsing of folding-on-binding proteins reveals their compositional and evolutionary sequence design.ÌýScientific ReportsÌý5: 18586.

55. Bouchard J., Oliver C.,ÌýHarrison P.M.Ìý(2015) The distribution and evolution ofÌýArabidopsis thalianaÌýcis natural antisense transcripts.Ìý

54. Harbi D, Harrison P.M. (2014) Classifying prion and prion-like phenomena.ÌýÌý.

53. Harbi D,ÌýHarrison P.M. (2014) Interaction networks of prion, prionogenic and prion-like proteins in budding yeast, and their role in gene regulation.ÌýÌý.

52.ÌýHarrison P.M.Ìý(2014) Computational methods for pseudogene annotation based on sequence homology.ÌýÌý.

51. Haudry A, Platts AE, Vello E, Hoen DR, Leclercq M, Williamson RJ, Forczek E, Joly-Lopez Z, Steffen JG, Hazzouri KM, Dewar K, Stinchcombe JR, Schoen DJ, Wang X, Schmutz J, Town CD, Edger PP, Pires JC, Schumaker KS, Jarvis DE, Mandáková T, Lysak MA, van den Bergh E, Schranz ME,ÌýHarrison PM, Moses AM, Bureau TE, Wright SI, Blanchette M. (2013) An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions.Ìý.

50. Gendoo DMA,ÌýHarrison PMÌý(2012) The Landscape of the Prion Protein's Structural Response to Mutation Revealed by Principal Component Analysis of Multiple NMR Ensembles.Ìýdoi:10.1371/journal.pcbi.1002646

49. Djamel Harbi, Marimuthu Parthiban, Deena M.A. Gendoo, Sepehr Ehsani, Manish Kumar, Gerold Schmitt-Ulms, Ramanathan Sowdhamini andÌýPaul M. HarrisonÌý(2012) PrionHome: A database of prions and other sequences relevant to prion phenomena.ÌýEpub 2012 Feb 20.

48. Gendoo DMA,ÌýHarrison PMÌý(2011) Origins and Evolution of the HET-s Prion-Forming Protein: Searching for Other Amyloid-Forming Solenoids.Ìýdoi:10.1371/journal.pone.0027342

47. Ehsani S, Tao R, Pocanschi CL, Ren H,ÌýHarrison PM, Schmitt-Ulms, GS (2011) Evidence for Retrogene Origins of the Prion Gene Family.ÌýÌýdoi:10.1371/journal.pone.0026800

46. Harbi, D, Parthiban, M, Gendoo, D, Ehsani, S, Kumar, M, Schmitt-Ulms, G, Sowdhamini, R, andÌýHarrison, PMÌý(2011) PrionOme: A database of prions and other sequences relevant to prion phenomena.Ìý.

45. Westaway D, Daude N, Wohlgemuth S,ÌýHarrison PÌý(2011) The PrP-like proteins Shadoo and Doppel.Ìý.

44. Gendoo, D. &ÌýHarrison, P.M.Ìý(2011) Discordant and chameleon sequences: their distribution, and their implications for amyloidogenicity.Ìý.

43. Harbi, D., Kumar, M. &ÌýHarrison, P.M.Ìý(2011) LPS-Annotate: complete annotation of compositionally-biased regions in the protein knowledgebase. Database (Oxford),Ìý.

42. De Lima Morais, D. &ÌýHarrison, P.M.Ìý(2010) Large-scale evidence for conservation of NMD candidature across mammals.Ìý. doi:10.1371/journal.pone.0011695.

41. Khachane, A. &ÌýHarrison, P.M.Ìý(2010) Mining mammalian transcript data for functional long non-coding RNAs.Ìýdoi:10.1371/journal.pone.0010316.

40. ÌýHarrison, P.M., Khachane, A & Kumar, M. (2010) Genomic assessment of the evolution of the prion protein gene family in vertebrates.Ìý.

39. Khachane, AN &ÌýHarrison, PM.Ìý(2009) Strong association between pseudogenization mechanisms and gene sequence length.Ìý.

38. Khachane, AN &ÌýHarrison, PM.Ìý(2009) Assessing the genomic evidence for conserved transcribed pseudogenes under selection.ÌýÌý

37. De Lima Morais, D. &ÌýHarrison, P.M. (2009) Genomic evidence for non-random endemic populations of decaying exons from mammalian genes.Ìý.Ìý

36. McEwen LA, Harris D, Schmid RF, Vogel J, Western T,ÌýHarrison P.Ìý(2009) Evaluation of the redesign of an undergraduate cell biology course.

35. M. Logan, T. Nguyen, N. Szapiel, J. Knockleby, H. Por, M. Zadworny, M. Neszt,ÌýP. Harrison, H. Bussey, C. Mandato, J. Vogel & G. Lesage. Ìý(2008) Genetic interaction network of theÌýSaccharomyces cerevisiaeÌýtype 1 phosphatase Glc7.Ìý.

34. S.J. Marygold, A. Lambertsson, J. Roote, M. Ashburner, G. Millburn, N. Kenmochi,ÌýP. M. Harrison, Z. Yu, T.C Kaufman, S.J Leevers & K.R Cook (2007) The Ribosomal Protein Genes and Minute Loci ofÌýDrosophila melanogaster.Ìý.

33.ÌýP. M. HarrisonÌý& Z. Yu (2007) Frame disruptions in human mRNA transcripts, and their relationship with splicing and protein structures.ÌýÌý.Ìý

32. Z. Yu, D. Morais, M. Ivanga &ÌýP. M. Harrison. (2007) Analysis of the role of retrotransposition in vertebrate gene evolution.Ìý.Ìý

31. L. B. Harrison, Z. Yu, J. E Stajich, F. S Dietrich, &ÌýP.M. Harrison.Ìý(2007) Evolution of budding yeast prion-determinant sequences across diverse Fungi.ÌýÌý

30. J. Karro, Y. Yan, D. Zheng, Z. Zhang, N. Carriero, P. Cayting,ÌýP.M. Harrison, & M. Gerstein. (2007) Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation.ÌýÌý.

29.ÌýP.M. Harrison. (2006) Exhaustive assignment of compositional bias reveals universally prevalent biased regions: analysis of functional associations in human andÌýDrosophila.ÌýBMC BioinformaticsÌý7: 441-441.Ìý

28. Zhang Z., Carriero N., Zheng D., Karro J.,ÌýHarrison P.M., Gerstein M. (2006) PseudoPipe: an automated pseudogene identification pipeline.ÌýÌý.

27. Zheng D., Zhang Z.,ÌýHarrison P.M., Karro J., Carriero N., Gerstein M. (2005) Integrated pseudogene annotation for human chromosome 22: evidence for transcription.Ìý

26. Juretic N., Hoen D. R., Huynh M. L.,ÌýHarrison P.M.Ìý& Bureau T. E. (2005) The evolutionary fate of MULE-mediated duplications of host gene fragments in rice.Ìý.

25.ÌýP.M. HarrisonÌýet al. (2005) Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability.ÌýNucleic Acids Res.Ìý33Ìý(8): 2374-83.Ìý

24. Yang Liu,ÌýP.M. HarrisonÌý& M. Gerstein. (2004) Comprehensive analysis of pseudogenes in prokaryotes: widespread gene decay and failure of putative horizontally transferred genes.Ìý.

23.ÌýP.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.Ìý.

22. Z. Zhang,ÌýP.M. Harrison, Yin Liu, & M. Gerstein. (2003) Millions of years of evolution preserved: A comprehensive catalogue of the processed pseudogenes in the human genome.Ìý. ÌýÌý

21.ÌýP.M. HarrisonÌý& M. Gerstein. (2003) A method to assess compositionally biased regions in biological sequences and its application to glutamine/asparagine-rich domains in eukaryotic proteomes.Ìý.

20. J. L. Rinn *, G. Euskirchen *, P. Bertone *, R. Goetsch, N. M. Luscombe, S. Hartman,ÌýP.M. Harrison, P. Miller, M. Gerstein, S. Weissman & M. Snyder. (2003)ÌýThe Transcriptional Activity of Human Chromosome 22.ÌýÌý. Ìý(*co- primary authors.)

19.ÌýP.M. Harrison, D. Milburn, Z. Zhang, P. Bertone & M. Gerstein. (2003)ÌýIdentification of pseudogenes in theÌýDrosophila melanogasterÌýgenome.Ìý

18. Z. Zhang,ÌýP.M. HarrisonÌý& M. Gerstein. (2002)ÌýDigging deep for ancient relics: ÌýA survey of protein motifs in the intergenic sequences of four eukaryotic genomes.Ìý. Ìý

17. Z. Zhang,ÌýP.M. HarrisonÌý& M. Gerstein. (2002) Identification and analysis of over 2000 ribosomal-protein pseudogenes in the human genome.Ìý. Ìý

16. S. Balasubramanian ,ÌýP.M. Harrison, H. Hegyi, P. Bertone, N. Luscombe, N. Echols, P. McGarvey, Z. Zhang & M. Gerstein. (2002) SNPs on human chromosomes 21 and 22 --- ÌýAnalysis in terms of protein features and pseudogenes.Ìý. Ìý

15.ÌýP.M. Harrison & M. Gerstein. (2002) Studying genomes through the aeons: ÌýProtein families, pseudogenes and proteome evolution.Ìý. Ìý

14. N. Echols,ÌýP.M. Harrison, S. Balasubramanian, N. Luscombe, P. Bertone, Z. Zhang & M. Gerstein.Ìý(2002) Comprehensive analysis of amino acid Ìýand nucleotide composition in eukaryotic genomes, comparing genes and pseudogenes.Ìý. Ìý

13. ÌýP.M. Harrison, A. Kumar, N. Lan, M. Snyder & M. Gerstein. (2002) A question of size: The eukaryotic proteome and the problems in defining it.Ìý. ÌýÌýÌý

12.ÌýP.M. Harrison, A. Kumar, N. Lan, N. Echols, M. Snyder & M. Gerstein. (2002)ÌýA small reservoir of disabled ORFs in the Saccharomyces cerevisia e genome and its implications for the dynamics of proteome evolution.Ìý. Ìý

11.ÌýP.M. Harrison, H. Hegyi, S. Balasubramanian, N. Luscombe, P. Bertone, T. Johnson, N. Echols & M. Gerstein. (2002)ÌýMolecular fossils in the human genome: Identification and analysis of the pseudogenes in chromosomes 21 and 22.Ìý. ÌýÌýÌý

10. A. Kumar,ÌýP.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.Ìý. ÌýÌýÌý

9.ÌýP.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.ÌýÌý.

8.ÌýP.M. Harrison, N. Echols & M. Gerstein. (2001) Digging for dead genes: an analysis of the characteristics of the pseudogene population in theÌýCaenorhabditis elegansÌýgenome.Ìý. Ìý

7. R.C.Moore*, I.Y.Lee*, G.L.Silverman,ÌýP.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.Ìý. Ìý(*joint primary authors.)

6.ÌýP. 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.ÌýÌý. Ìý

5.ÌýP.M. Harrison, P.Bamborough, V.Daggett, S.B.Prusiner & F.E.Cohen. (1997) The prion folding problem.ÌýÌý. Ìý

4. M.Lohmeyer,ÌýP.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 humanÌýCripto.ÌýÌý.

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

2.ÌýP.M. HarrisonÌýand M.J.E. Sternberg. (1996) The disulphide beta-cross: From cystine geometry and clustering to the classification of small, disulphide-rich protein folds.ÌýJ. Mol. Biol.Ìý264:Ìý603-623.

1.ÌýP.M. HarrisonÌýand M.J.E. Sternberg. (1994) Analysis and classification of disulphide connectivity in proteins.ÌýJ. Mol. Biol.Ìý244:Ìý448-463.

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