Paul Harrison
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.
70. Wang, Y., Yang, H.J. & Harrison, P.M. (2020) The relationship between protein domains and homopeptides in the Plasmodium falciparum proteome.听听
69. Harrison, P.M. (2020)听Variable absorption of mutational trends by prion-forming domains during听Saccharomycetes听evolution.听听听
68. Su, W.C. & Harrison, P.M. (2020)听Deep conservation of prion-like composition in the eukaryotic prion-former Pub1/Tia1 family and its relatives.听.听
67.听Su, T.Y. & Harrison, P.M. (2019)听Conservation of prion-like composition and sequence in prion-formers and prion-like proteins.听.
66.听Harrison, P.M. (2019)听Evolutionary behaviour of bacterial prion-like proteins.听.
65. Narasumani M &听Harrison PM听(2018) Discerning evolutionary trends in post-translational modification and the effect of intrinsic disorder: Analysis of methylation, acetylation and ubiquitination sites in human proteins.听听
64. Lee SJ, Kong M,听Harrison 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.听
63.听Harrison, P.M.听(2018) Compositionally biased dark matter in the protein universe (2018)听.
62.听Harrison, P.M.听(2017) fLPS: Fast discovery of compositional biases for the protein universe.听.
61. Hughes, B.G.,听Harrison, P.M.听& Hekimi, S. (2017) Estimating the occurrence of primary ubiquinone deficiency by analysis of large-scale sequencing data.听.
60.听Harrison, P.M.听(2017) Published fLPS compositional bias analysis software on Zenodo,听
59. An L. &听Harrison P.M.听(2016) The evolutionary scope and neurological disease linkage of yeast-prion-like proteins in humans.听
58. An L., Fitzpatrick D.A. &听Harrison P.M.听(2016) Emergence and evolution of prion and prion-like proteins in budding yeasts.听
57. Reimer J, Aloise M.N.,听Harrison P.M.听& Schmeing T.M. (2016) Synthetic cycle of the initiation module of a formylating nonribosomal peptide synthetase.听听
56. Narasumani M.,听Harrison P.M.听(2015) Bioinformatical parsing of folding-on-binding proteins reveals their compositional and evolutionary sequence design.听Scientific Reports听5: 18586.
55. Bouchard J., Oliver C.,听Harrison P.M.听(2015) The distribution and evolution of听Arabidopsis thaliana听cis natural antisense transcripts.听
54. Harbi D, Harrison P.M. (2014) Classifying prion and prion-like phenomena.听听.
53. Harbi D,听Harrison P.M. (2014) Interaction networks of prion, prionogenic and prion-like proteins in budding yeast, and their role in gene regulation.听听.
52.听Harrison P.M.听(2014) Computational methods for pseudogene annotation based on sequence homology.听听.
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, Mand谩kov谩 T, Lysak MA, van den Bergh E, Schranz ME,听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.听.
50. Gendoo DMA,听Harrison PM听(2012) The Landscape of the Prion Protein's Structural Response to Mutation Revealed by Principal Component Analysis of Multiple NMR Ensembles.听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听Paul M. Harrison听(2012) PrionHome: A database of prions and other sequences relevant to prion phenomena.听Epub 2012 Feb 20.
48. Gendoo DMA,听Harrison PM听(2011) Origins and Evolution of the HET-s Prion-Forming Protein: Searching for Other Amyloid-Forming Solenoids.听doi:10.1371/journal.pone.0027342
47. Ehsani S, Tao R, Pocanschi CL, Ren H,听Harrison PM, Schmitt-Ulms, GS (2011) Evidence for Retrogene Origins of the Prion Gene Family.听听doi:10.1371/journal.pone.0026800
46. Harbi, D, Parthiban, M, Gendoo, D, Ehsani, S, Kumar, M, Schmitt-Ulms, G, Sowdhamini, R, and听Harrison, PM听(2011) PrionOme: A database of prions and other sequences relevant to prion phenomena.听.
45. Westaway D, Daude N, Wohlgemuth S,听Harrison P听(2011) The PrP-like proteins Shadoo and Doppel.听.
44. Gendoo, D. &听Harrison, P.M.听(2011) Discordant and chameleon sequences: their distribution, and their implications for amyloidogenicity.听.
43. Harbi, D., Kumar, M. &听Harrison, P.M.听(2011) LPS-Annotate: complete annotation of compositionally-biased regions in the protein knowledgebase. Database (Oxford),听.
42. De Lima Morais, D. &听Harrison, P.M.听(2010) Large-scale evidence for conservation of NMD candidature across mammals.听. doi:10.1371/journal.pone.0011695.
41. Khachane, A. &听Harrison, P.M.听(2010) Mining mammalian transcript data for functional long non-coding RNAs.听doi:10.1371/journal.pone.0010316.
40. 听Harrison, P.M., Khachane, A & Kumar, M. (2010) Genomic assessment of the evolution of the prion protein gene family in vertebrates.听.
39. Khachane, AN &听Harrison, PM.听(2009) Strong association between pseudogenization mechanisms and gene sequence length.听.
38. Khachane, AN &听Harrison, PM.听(2009) Assessing the genomic evidence for conserved transcribed pseudogenes under selection.听听
37. De Lima Morais, D. &听Harrison, P.M. (2009) Genomic evidence for non-random endemic populations of decaying exons from mammalian genes.听.听
36. McEwen LA, Harris D, Schmid RF, Vogel J, Western T,听Harrison P.听(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,听P. Harrison, H. Bussey, C. Mandato, J. Vogel & G. Lesage. 听(2008) Genetic interaction network of the听Saccharomyces cerevisiae听type 1 phosphatase Glc7.听.
34. S.J. Marygold, A. Lambertsson, J. Roote, M. Ashburner, G. Millburn, N. Kenmochi,听P. M. Harrison, Z. Yu, T.C Kaufman, S.J Leevers & K.R Cook (2007) The Ribosomal Protein Genes and Minute Loci of听Drosophila melanogaster.听.
33.听P. M. Harrison听& Z. Yu (2007) Frame disruptions in human mRNA transcripts, and their relationship with splicing and protein structures.听听.听
32. Z. Yu, D. Morais, M. Ivanga &听P. M. Harrison. (2007) Analysis of the role of retrotransposition in vertebrate gene evolution.听.听
31. L. B. Harrison, Z. Yu, J. E Stajich, F. S Dietrich, &听P.M. Harrison.听(2007) Evolution of budding yeast prion-determinant sequences across diverse Fungi.听听
30. J. Karro, Y. Yan, D. Zheng, Z. Zhang, N. Carriero, P. Cayting,听P.M. Harrison, & M. Gerstein. (2007) Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation.听听.
29.听P.M. Harrison. (2006) Exhaustive assignment of compositional bias reveals universally prevalent biased regions: analysis of functional associations in human and听Drosophila.听BMC Bioinformatics听7: 441-441.听
28. Zhang Z., Carriero N., Zheng D., Karro J.,听Harrison P.M., Gerstein M. (2006) PseudoPipe: an automated pseudogene identification pipeline.听听.
27. Zheng D., Zhang Z.,听Harrison P.M., Karro J., Carriero N., Gerstein M. (2005) Integrated pseudogene annotation for human chromosome 22: evidence for transcription.听
26. Juretic N., Hoen D. R., Huynh M. L.,听Harrison P.M.听& Bureau T. E. (2005) The evolutionary fate of MULE-mediated duplications of host gene fragments in rice.听.
25.听P.M. Harrison听et al. (2005) Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability.听Nucleic Acids Res.听33听(8): 2374-83.听
24. Yang Liu,听P.M. Harrison听& M. Gerstein. (2004) Comprehensive analysis of pseudogenes in prokaryotes: widespread gene decay and failure of putative horizontally transferred genes.听.
23.听P.M. Harrison, N. Carriero, Yang Liu, & M. Gerstein. (2003) A 鈥榩olyORFomic鈥� analysis using disabled-homology filtering reveals a small population of undiscovered but conserved short ORFs in prokaryotes.听.
22. Z. Zhang,听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.听. 听听
21.听P.M. Harrison听& M. Gerstein. (2003) A method to assess compositionally biased regions in biological sequences and its application to glutamine/asparagine-rich domains in eukaryotic proteomes.听.
20. J. L. Rinn *, G. Euskirchen *, P. Bertone *, R. Goetsch, N. M. Luscombe, S. Hartman,听P.M. Harrison, P. Miller, M. Gerstein, S. Weissman & M. Snyder. (2003)听The Transcriptional Activity of Human Chromosome 22.听听. 听(*co- primary authors.)
19.听P.M. Harrison, D. Milburn, Z. Zhang, P. Bertone & M. Gerstein. (2003)听Identification of pseudogenes in the听Drosophila melanogaster听genome.听
18. Z. Zhang,听P.M. Harrison听& M. Gerstein. (2002)听Digging deep for ancient relics: 听A survey of protein motifs in the intergenic sequences of four eukaryotic genomes.听. 听
17. Z. Zhang,听P.M. Harrison听& M. Gerstein. (2002) Identification and analysis of over 2000 ribosomal-protein pseudogenes in the human genome.听. 听
16. S. Balasubramanian ,听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 --- 听Analysis in terms of protein features and pseudogenes.听. 听
15.听P.M. Harrison & M. Gerstein. (2002) Studying genomes through the aeons: 听Protein families, pseudogenes and proteome evolution.听. 听
14. N. Echols,听P.M. Harrison, S. Balasubramanian, N. Luscombe, P. Bertone, Z. Zhang & M. Gerstein.听(2002) Comprehensive analysis of amino acid 听and nucleotide composition in eukaryotic genomes, comparing genes and pseudogenes.听. 听
13. 听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.听. 听听听
12.听P.M. Harrison, A. Kumar, N. Lan, N. Echols, M. Snyder & M. Gerstein. (2002)听A small reservoir of disabled ORFs in the Saccharomyces cerevisia e genome and its implications for the dynamics of proteome evolution.听. 听
11.听P.M. Harrison, H. Hegyi, S. Balasubramanian, N. Luscombe, P. Bertone, T. Johnson, N. Echols & M. Gerstein. (2002)听Molecular fossils in the human genome: Identification and analysis of the pseudogenes in chromosomes 21 and 22.听. 听听听
10. A. Kumar,听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.听. 听听听
9.听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.听听.
8.听P.M. Harrison, N. Echols & M. Gerstein. (2001) Digging for dead genes: an analysis of the characteristics of the pseudogene population in the听Caenorhabditis elegans听genome.听. 听
7. R.C.Moore*, I.Y.Lee*, G.L.Silverman,听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.听. 听(*joint primary authors.)
6.听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.听听. 听
5.听P.M. Harrison, P.Bamborough, V.Daggett, S.B.Prusiner & F.E.Cohen. (1997) The prion folding problem.听听. 听
4. M.Lohmeyer,听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听Cripto.听听.
3.听P.M. Harrison听"Analysis and prediction of protein structure: Disulphide bridges", Ph.D. Thesis, 1996 (University College, London).
2.听P.M. Harrison听and M.J.E. Sternberg. (1996) The disulphide beta-cross: From cystine geometry and clustering to the classification of small, disulphide-rich protein folds.听J. Mol. Biol.听264:听603-623.
1.听P.M. Harrison听and M.J.E. Sternberg. (1994) Analysis and classification of disulphide connectivity in proteins.听J. Mol. Biol.听244:听448-463.