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

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, Harrison 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. Nature Genetics 45: 891-898.

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.



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