Research Topics
| P M HarrisonSummaryAffiliation: Yale University Country: USA Publications
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Publications
A "polyORFomic" analysis of prokaryote genomes using disabled-homology filtering reveals conserved but undiscovered short ORFsPaul 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..- Conformational propagation with prion-like characteristics in a simple model of protein foldingP M Harrison
Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94143, USA
Protein Sci 10:819-35. 2001.... - A method to assess compositional bias in biological sequences and its application to prion-like glutamine/asparagine-rich domains in eukaryotic proteomesPaul 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... - Identification of pseudogenes in the Drosophila melanogaster genomePaul 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... - Digging for dead genes: an analysis of the characteristics of the pseudogene population in the Caenorhabditis elegans genomeP 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... - Studying genomes through the aeons: protein families, pseudogenes and proteome evolutionPaul 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.. - Evolution of budding yeast prion-determinant sequences across diverse fungiLuke 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... - Exhaustive assignment of compositional bias reveals universally prevalent biased regions: analysis of functional associations in human and DrosophilaPaul 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... - PseudoPipe: an automated pseudogene identification pipelineZhaolei 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..Finally, pseudogenes are classified based on a combination of criteria including homology, intron-exon structure, and existence of stop codons and frameshifts... - Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding abilityPaul 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... - Comprehensive analysis of pseudogenes in prokaryotes: widespread gene decay and failure of putative horizontally transferred genesYang 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... - Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genomeZhaolei 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... - An integrated approach for finding overlooked genes in yeastAnuj 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... - Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22Paul 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... - A question of size: the eukaryotic proteome and the problems in defining itPaul 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).. - Digging deep for ancient relics: a survey of protein motifs in the intergenic sequences of four eukaryotic genomesZhao 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.. - Integrated pseudogene annotation for human chromosome 22: evidence for transcriptionDeyou 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)... - The evolutionary fate of MULE-mediated duplications of host gene fragments in riceNikoleta Juretic
Department of Biology, McGill University, Montreal, Quebec H3A 1B1, Canada
Genome Res 15:1292-7. 2005.... - The transcriptional activity of human Chromosome 22John 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... - Analysis of the role of retrotransposition in gene evolution in vertebratesZhan 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... - The ribosomal protein genes and Minute loci of Drosophila melanogasterSteven 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...