Research Topics
Species | Paul M HarrisonSummaryAffiliation: McGill University Country: Canada Publications
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Detail Information
Publications
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...- Genetic interaction network of the Saccharomyces cerevisiae type 1 phosphatase Glc7Michael R Logan
Department of Biology, McGill University, Montreal QC, Canada
BMC Genomics 9:336. 2008..We apply this approach to the conserved type 1 protein phosphatase Glc7, which regulates numerous cellular processes in budding yeast... - 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... - Frame disruptions in human mRNA transcripts, and their relationship with splicing and protein structuresPaul Harrison
Department of Biology, McGill University, Stewart Biology Building, 1205 Docteur Penfield Ave, Montreal, QC, H3A 1B1 Canada
BMC Genomics 8:371. 2007..Such annotation is complicated by the occurrence of disrupted mRNAs (dmRNAs), harbouring frameshifts and premature stop codons, which can be considered indicators of decay into pseudogenes... - 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... - Genomic assessment of the evolution of the prion protein gene family in vertebratesPaul M Harrison
Department of Biology, McGill University, Montreal, QC, Canada
Genomics 95:268-77. 2010..These annotations and evolutionary analyses will be of further use for functional characterisation of the PrP-GF, and will be updatable in a semi-automated fashion as more genomes accumulate... - 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... - Assessing the genomic evidence for conserved transcribed pseudogenes under selectionAmit N Khachane
Department of Biology, McGill University, Stewart Biology Building, 1205 Docteur Penfield Ave, Montreal, QC, H3A 1B1 Canada
BMC Genomics 10:435. 2009..The most obvious indicators of such functional importance are significant evidence of conservation and selection pressure... - Genomic evidence for non-random endemic populations of decaying exons from mammalian genesDavid Delima Morais
Department of Biology, McGill University, Stewart Biology Building, 1205 Docteur Penfield Ave, Montreal, QC, H3A 1B1, Canada
BMC Genomics 10:309. 2009..Gene duplication is classically discussed as leading to neofunctionalization (generation of new functions), subfunctionalization (generation of a varied function), or pseudogenization (loss of the gene and its function)... - Large-scale evidence for conservation of NMD candidature across mammalsDavid A de Lima Morais
Department of Biology, McGill University, Montreal, Quebec, Canada
PLoS ONE 5:e11695. 2010..AS coupled with mRNA nonsense-mediated decay (NMD) can also control the transcript abundance. Here, we have investigated the genome-scale conservation of alternatively-spliced NMD candidates (AS-NMD candidates), in mammals... - 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... - Origins and evolution of the HET-s prion-forming protein: searching for other amyloid-forming solenoidsDeena M A Gendoo
Department of Biology, McGill University, Montreal, Quebec, Canada
PLoS ONE 6:e27342. 2011..We discuss the implications of our findings on future identification of amyloid-forming proteins sharing the solenoid fold... - PrionHome: a database of prions and other sequences relevant to prion phenomenaDjamel Harbi
Department of Biology, McGill University, Montreal, Quebec, Canada
PLoS ONE 7:e31785. 2012..We anticipate that this database will be a useful experimental aid and reference resource. It is freely available at: http://libaio.biol.mcgill.ca/prion... - Mining mammalian transcript data for functional long non-coding RNAsAmit N Khachane
Department of Biology, McGill University, Montreal, Quebec, Canada
PLoS ONE 5:e10316. 2010..It is therefore essential to use bioinformatic approaches to identify the likely functional candidates in a high throughput manner... - Strong association between pseudogenization mechanisms and gene sequence lengthAmit N Khachane
Department of Biology, McGill University, Stewart Biology Building, Montreal, QC, H3A 1B1, Canada
Biol Direct 4:38. 2009..Protein-coding genes longer than 3000 bp are 6 times more likely to produce nonprocessed pseudogenes than processed ones. REVIEWERS: This article was reviewed by Dr. Dan Graur and Dr. Craig Nelson (nominated by Dr. J Peter Gogarten)... - LPS-annotate: complete annotation of compositionally biased regions in the protein knowledgebaseDjamel Harbi
Department of Biology, McGill University, Stewart Biology Building, 1205 Dr Penfield Ave, Montreal, QC, H3A 1B1, Canada
Database (Oxford) 2011:baq031. 2011..It can be accessed at http://libaio.biol.mcgill.ca/lps-annotate.html. Database URL: http://libaio.biol.mcgill.ca/lps-annotate.html... - Discordant and chameleon sequences: their distribution and implications for amyloidogenicityDeena M A Gendoo
Department of Biology, McGill University, Montreal, Quebec, Canada H3A 1B1
Protein Sci 20:567-79. 2011..We present a detailed analysis of discordant and chameleons segments in the family of one of the amyloidogenic proteins, the Prion Protein... - 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.... - 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... - 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.. - 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.. - 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... - 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... - 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... - 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... - 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.. - 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).. - 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... - 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)... - 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... - 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...