P M Harrison

Summary

Affiliation: Yale University
Country: USA

Publications

  1. ncbi request reprint A "polyORFomic" analysis of prokaryote genomes using disabled-homology filtering reveals conserved but undiscovered short ORFs
    Paul M Harrison
    Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, P O Box 208114, New Haven, CT 06520 8114, USA
    J Mol Biol 333:885-92. 2003
  2. pmc Conformational propagation with prion-like characteristics in a simple model of protein folding
    P M Harrison
    Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94143, USA
    Protein Sci 10:819-35. 2001
  3. pmc A method to assess compositional bias in biological sequences and its application to prion-like glutamine/asparagine-rich domains in eukaryotic proteomes
    Paul M Harrison
    Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520 8114, USA
    Genome Biol 4:R40. 2003
  4. pmc Identification of pseudogenes in the Drosophila melanogaster genome
    Paul M Harrison
    Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, PO Box 208114, New Haven, CT 06520 8114, USA
    Nucleic Acids Res 31:1033-7. 2003
  5. pmc Digging for dead genes: an analysis of the characteristics of the pseudogene population in the Caenorhabditis elegans genome
    P M Harrison
    Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, PO Box 208114, New Haven, CT 06511-8114, USA
    Nucleic Acids Res 29:818-30. 2001
  6. ncbi request reprint Studying genomes through the aeons: protein families, pseudogenes and proteome evolution
    Paul M Harrison
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520 8114, USA
    J Mol Biol 318:1155-74. 2002
  7. ncbi request reprint Evolution of budding yeast prion-determinant sequences across diverse fungi
    Luke B Harrison
    Department of Biology, McGill University, Stewart Biology Building, 1205 Docteur Penfield Ave, Montreal, QC, Canada H3A 1B1
    J Mol Biol 368:273-82. 2007
  8. pmc Exhaustive assignment of compositional bias reveals universally prevalent biased regions: analysis of functional associations in human and Drosophila
    Paul M Harrison
    Dept of Biology, McGill University, Stewart Biology Building, 1205 Dr, Penfield Ave, Montreal, QC, H3A 1B1, Canada
    BMC Bioinformatics 7:441. 2006
  9. ncbi request reprint PseudoPipe: an automated pseudogene identification pipeline
    Zhaolei Zhang
    Banting and Best Department of Medical Research, Donnelly CCBR, University of Toronto 160 College Street, Toronto, ON M5S 3E1, Canada
    Bioinformatics 22:1437-9. 2006
  10. pmc Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability
    Paul M Harrison
    Department of Biology, McGill University Stewart Biology Building, 1205 Dr Penfield Avenue, Montreal, Quebec, Canada H3A 1B1
    Nucleic Acids Res 33:2374-83. 2005

Detail Information

Publications21

  1. ncbi request reprint A "polyORFomic" analysis of prokaryote genomes using disabled-homology filtering reveals conserved but undiscovered short ORFs
    Paul M Harrison
    Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, P O Box 208114, New Haven, CT 06520 8114, USA
    J Mol Biol 333:885-92. 2003
    ..Data on uhORFs are available from http://pseudogene.org/polyo..
  2. pmc Conformational propagation with prion-like characteristics in a simple model of protein folding
    P M Harrison
    Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94143, USA
    Protein Sci 10:819-35. 2001
    ....
  3. pmc A method to assess compositional bias in biological sequences and its application to prion-like glutamine/asparagine-rich domains in eukaryotic proteomes
    Paul M Harrison
    Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520 8114, USA
    Genome Biol 4:R40. 2003
    ..We find more than 170 prion-like (Q+N)-rich regions in budding yeast, and, strikingly, many fewer in fission yeast. Also, some residues, such as tryptophan or isoleucine, are unlikely to form biased regions in any eukaryotic proteome...
  4. pmc Identification of pseudogenes in the Drosophila melanogaster genome
    Paul M Harrison
    Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, PO Box 208114, New Haven, CT 06520 8114, USA
    Nucleic Acids Res 31:1033-7. 2003
    ..The data are useful for molecular evolution study in Drosophila...
  5. pmc Digging for dead genes: an analysis of the characteristics of the pseudogene population in the Caenorhabditis elegans genome
    P M Harrison
    Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, PO Box 208114, New Haven, CT 06511-8114, USA
    Nucleic Acids Res 29:818-30. 2001
    ..1) is approximately two-thirds pseudogenic. Furthermore, over a hundred apparent pseudogenic fragments do not have any obvious homologs in the worm...
  6. ncbi request reprint Studying genomes through the aeons: protein families, pseudogenes and proteome evolution
    Paul M Harrison
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520 8114, USA
    J Mol Biol 318:1155-74. 2002
    ..Further information about pseudogenes is available at http://genecensus.org/pseudogene..
  7. ncbi request reprint Evolution of budding yeast prion-determinant sequences across diverse fungi
    Luke B Harrison
    Department of Biology, McGill University, Stewart Biology Building, 1205 Docteur Penfield Ave, Montreal, QC, Canada H3A 1B1
    J Mol Biol 368:273-82. 2007
    ..Our findings on yeast prion evolution provide further support for the functional significance of these molecules...
  8. pmc Exhaustive assignment of compositional bias reveals universally prevalent biased regions: analysis of functional associations in human and Drosophila
    Paul M Harrison
    Dept of Biology, McGill University, Stewart Biology Building, 1205 Dr, Penfield Ave, Montreal, QC, H3A 1B1, Canada
    BMC Bioinformatics 7:441. 2006
    ..Compositionally biased (CB) regions are stretches in protein sequences made from mainly a distinct subset of amino acid residues; such regions are frequently associated with a structural role in the cell, or with protein disorder...
  9. ncbi request reprint PseudoPipe: an automated pseudogene identification pipeline
    Zhaolei Zhang
    Banting and Best Department of Medical Research, Donnelly CCBR, University of Toronto 160 College Street, Toronto, ON M5S 3E1, Canada
    Bioinformatics 22:1437-9. 2006
    ..These are disabled copies of functional genes that have been retained in the genome by gene duplication or retrotransposition events. Pseudogenes are important resources in understanding the evolutionary history of genes and genomes...
  10. pmc Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability
    Paul M Harrison
    Department of Biology, McGill University Stewart Biology Building, 1205 Dr Penfield Avenue, Montreal, Quebec, Canada H3A 1B1
    Nucleic Acids Res 33:2374-83. 2005
    ..This is likely linked to well-documented extensive lineage-specific SINE/LINE activity. The list of TPPsigs is available at: http://www.biology.mcgill.ca/faculty/harrison/tppg/bppg.tov (or) http:pseudogene.org...
  11. pmc Comprehensive analysis of pseudogenes in prokaryotes: widespread gene decay and failure of putative horizontally transferred genes
    Yang Liu
    Department of Molecular Biophysics and Biochemistry, Yale University, PO Box 208114, New Haven, CT 06520 8114, USA
    Genome Biol 5:R64. 2004
    ..Pseudogenes often manifest themselves as disabled copies of known genes. In prokaryotes, it was generally believed (with a few well-known exceptions) that they were rare...
  12. pmc Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome
    Zhaolei Zhang
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520 8114, USA
    Genome Res 13:2541-58. 2003
    ..The prevalence of processed pseudogenes agrees well with germ-line gene expression. Highly expressed ribosomal proteins account for approximately 20% of the total. Other notables include cyclophilin-A, keratin, GAPDH, and cytochrome c...
  13. ncbi request reprint An integrated approach for finding overlooked genes in yeast
    Anuj Kumar
    Department of Molecular, Cellular, and Developmental Biology, Yale University, P O Box 208103, New Haven, CT 06520 8103, USA
    Nat Biotechnol 20:58-63. 2002
    ..In total, the genes discovered using this approach constitute 2% of the yeast genome and represent a wealth of overlooked biology...
  14. pmc Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22
    Paul M Harrison
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520 8114, USA
    Genome Res 12:272-80. 2002
    ..Finally, we find that chromosome 22 pseudogene population is dominated by immunoglobulin segments, which have a greater rate of disablement per amino acid than the other pseudogene populations and are also substantially more diverged...
  15. pmc A question of size: the eukaryotic proteome and the problems in defining it
    Paul M Harrison
    Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, PO Box 208114, New Haven, CT 06520 8114, USA
    Nucleic Acids Res 30:1083-90. 2002
    ..Further information relating to yeast is available at http://genecensus.org/yeast/orfome)..
  16. ncbi request reprint Digging deep for ancient relics: a survey of protein motifs in the intergenic sequences of four eukaryotic genomes
    Zhao Lei Zhang
    Department of Molecular Biophysics and Biochemistry, Yale University, Bass Center 432A, 266 Whitney Avenue, P O Box 208114, New Haven, CT 06520 8114, USA
    J Mol Biol 323:811-22. 2002
    ..Moreover, we find that in aggregate the over-represented pseudomotif patterns occupy a substantial fraction of the intergenic regions. Further information is available at http://pseudogene.org..
  17. ncbi request reprint Integrated pseudogene annotation for human chromosome 22: evidence for transcription
    Deyou Zheng
    Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA
    J Mol Biol 349:27-45. 2005
    ..pseudogene.org)...
  18. pmc The evolutionary fate of MULE-mediated duplications of host gene fragments in rice
    Nikoleta Juretic
    Department of Biology, McGill University, Montreal, Quebec H3A 1B1, Canada
    Genome Res 15:1292-7. 2005
    ....
  19. pmc The transcriptional activity of human Chromosome 22
    John L Rinn
    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520 8103, USA
    Genes Dev 17:529-40. 2003
    ..mbb.yale.edu/chr22...
  20. pmc Analysis of the role of retrotransposition in gene evolution in vertebrates
    Zhan Yu
    Department of Biology, McGill University, Stewart Biology Building, 1205 Docteur Penfield Ave, Montreal, QC, H3A 1B1 Canada
    BMC Bioinformatics 8:308. 2007
    ..The dynamics of gene evolution are influenced by several genomic processes. One such process is retrotransposition, where an mRNA transcript is reverse-transcribed and reintegrated into the genomic DNA...
  21. pmc The ribosomal protein genes and Minute loci of Drosophila melanogaster
    Steven J Marygold
    Growth Regulation Laboratory, Cancer Research UK London Research Institute, Lincoln s Inn Fields, London WC2A 3PX, UK
    Genome Biol 8:R216. 2007
    ..While more than 50 Minute loci have been defined genetically, only 15 have so far been characterized molecularly and shown to correspond to RP genes...