TY - JOUR AU - D'Errico, I. AU - Gadaleta, G. AU - Saccone, C. PY - 2004 DA - 2004// TI - Pseudogenes in metazoa: origin and features JO - Briefings in functional genomics & proteomics VL - 3 UR - https://doi.org/10.1093/bfgp/3.2.157 DO - 10.1093/bfgp/3.2.157 ID - D'Errico2004 ER - TY - JOUR AU - Zhang, Z. AU - Harrison, P. AU - Liu, Y. AU - Gerstein, M. PY - 2003 DA - 2003// TI - Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome JO - Genome Res VL - 13 UR - https://doi.org/10.1101/gr.1429003 DO - 10.1101/gr.1429003 ID - Zhang2003 ER - TY - JOUR AU - Zhang, Z. AU - Harrison, P. AU - Gerstein, M. PY - 2002 DA - 2002// TI - Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome JO - Genome Res VL - 12 UR - https://doi.org/10.1101/gr.331902 DO - 10.1101/gr.331902 ID - Zhang2002 ER - TY - JOUR AU - Zhang, Z. AU - Gerstein, M. PY - 2003 DA - 2003// TI - Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes JO - Nucleic acids research VL - 31 UR - https://doi.org/10.1093/nar/gkg745 DO - 10.1093/nar/gkg745 ID - Zhang2003 ER - TY - JOUR AU - Harrison, P. AU - Gerstein, M. PY - 2002 DA - 2002// TI - Studying genomes through the aeons: protein families, pseudogenes and proteome evolution JO - J Mol Biol VL - 318 UR - https://doi.org/10.1016/S0022-2836(02)00109-2 DO - 10.1016/S0022-2836(02)00109-2 ID - Harrison2002 ER - TY - JOUR AU - Betran, E. AU - Thornton, K. AU - Long, M. PY - 2002 DA - 2002// TI - Retroposed new genes out of the X in Drosophila JO - Genome research VL - 12 UR - https://doi.org/10.1101/gr.6049 DO - 10.1101/gr.6049 ID - Betran2002 ER - TY - JOUR AU - Esnault, C. AU - Maestre, J. AU - Heidmann, T. PY - 2000 DA - 2000// TI - Human LINE retrotransposons generate processed pseudogenes JO - Nature genetics VL - 24 UR - https://doi.org/10.1038/74184 DO - 10.1038/74184 ID - Esnault2000 ER - TY - JOUR AU - Pavlicek, A. AU - Paces, J. AU - Elleder, D. AU - Hejnar, J. PY - 2002 DA - 2002// TI - Processed pseudogenes of human endogenous retroviruses generated by LINEs: their integration, stability, and distribution JO - Genome research VL - 12 UR - https://doi.org/10.1101/gr.216902. Article published online before print in February 2002 DO - 10.1101/gr.216902. Article published online before print in February 2002 ID - Pavlicek2002 ER - TY - JOUR AU - Torrents, D. AU - Suyama, M. AU - Zdobnov, E. AU - Bork, P. PY - 2003 DA - 2003// TI - A genome-wide survey of human pseudogenes JO - Genome research VL - 13 UR - https://doi.org/10.1101/gr.1455503 DO - 10.1101/gr.1455503 ID - Torrents2003 ER - TY - JOUR AU - Brosius, J. PY - 1999 DA - 1999// TI - RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements JO - Gene VL - 238 UR - https://doi.org/10.1016/S0378-1119(99)00227-9 DO - 10.1016/S0378-1119(99)00227-9 ID - Brosius1999 ER - TY - JOUR AU - Harrison, P. M. AU - Zheng, D. AU - Zhang, Z. AU - Carriero, N. AU - Gerstein, M. PY - 2005 DA - 2005// TI - Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability JO - Nucleic acids research VL - 33 UR - https://doi.org/10.1093/nar/gki531 DO - 10.1093/nar/gki531 ID - Harrison2005 ER - TY - JOUR AU - Marques, A. C. AU - Dupanloup, I. AU - Vinckenbosch, N. AU - Reymond, A. AU - Kaessmann, H. PY - 2005 DA - 2005// TI - Emergence of young human genes after a burst of retroposition in primates JO - PLoS biology VL - 3 UR - https://doi.org/10.1371/journal.pbio.0030357 DO - 10.1371/journal.pbio.0030357 ID - Marques2005 ER - TY - JOUR AU - Emerson, J. J. AU - Kaessmann, H. AU - Betran, E. AU - Long, M. PY - 2004 DA - 2004// TI - Extensive gene traffic on the mammalian X chromosom JO - Science VL - 303 UR - https://doi.org/10.1126/science.1090042 DO - 10.1126/science.1090042 ID - Emerson2004 ER - TY - JOUR AU - Harrison, P. M. AU - Hegyi, H. AU - Balasubramanian, S. AU - Luscombe, N. M. AU - Bertone, P. AU - Echols, N. AU - Johnson, T. AU - Gerstein, M. PY - 2002 DA - 2002// TI - Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22 JO - Genome Res VL - 12 UR - https://doi.org/10.1101/gr.207102 DO - 10.1101/gr.207102 ID - Harrison2002 ER - TY - STD TI - Ensembl database [ http://www.ensembl.org ] . ID - ref15 ER - TY - JOUR AU - Altschul, S. F. AU - Madden, T. L. AU - Schaffer, A. A. AU - Zhang, J. AU - Zhang, Z. AU - Miller, W. AU - Lipman, D. J. PY - 1997 DA - 1997// TI - Gapped BLAST and PSI-BLAST: a new generation of protein database search programs JO - Nucleic acids research VL - 25 UR - https://doi.org/10.1093/nar/25.17.3389 DO - 10.1093/nar/25.17.3389 ID - Altschul1997 ER - TY - JOUR AU - Ophir, R. AU - Graur, D. PY - 1997 DA - 1997// TI - Patterns and rates of indel evolution in processed pseudogenes from humans and murids JO - Gene VL - 205 UR - https://doi.org/10.1016/S0378-1119(97)00398-3 DO - 10.1016/S0378-1119(97)00398-3 ID - Ophir1997 ER - TY - STD TI - ORDB [ http://senselab.med.yale.edu/senselab/ORDB ]. ID - ref18 ER - TY - STD TI - Repeatmasker [ http://www.repeatmasker.org ] . ID - ref19 ER - TY - JOUR AU - Yang, Z. PY - 1997 DA - 1997// TI - PAML: a program package for phylogenetic analysis by maximum likelihood JO - Comput Appl Biosci VL - 13 ID - Yang1997 ER - TY - JOUR AU - Cooper, G. M. AU - Brudno, M. AU - Stone, E. A. AU - Dubchak, I. AU - Batzoglou, S. AU - Sidow, A. PY - 2004 DA - 2004// TI - Characterization of evolutionary rates and constraints in three mammalian genomes JO - Genome Res VL - 14 UR - https://doi.org/10.1101/gr.2034704 DO - 10.1101/gr.2034704 ID - Cooper2004 ER - TY - JOUR AU - Britten, R. J. AU - Rowen, L. AU - Williams, J. AU - Cameron, R. A. PY - 2003 DA - 2003// TI - Majority of divergence between closely-related DNA samples is due to indels JO - PNAS VL - 100 UR - https://doi.org/10.1073/pnas.0330964100 DO - 10.1073/pnas.0330964100 ID - Britten2003 ER - TY - JOUR AU - Felsenstein, J. PY - 1989 DA - 1989// TI - PHYLIP - Phylogeny Inference Package (Version 3.2) JO - Cladistics VL - 5 ID - Felsenstein1989 ER - TY - JOUR AU - Consortium, G. O. PY - 2004 DA - 2004// TI - The Gene Ontology (GO) database and informatics resource JO - Nucleic acids research VL - 32 UR - https://doi.org/10.1093/nar/gkh036 DO - 10.1093/nar/gkh036 ID - Consortium2004 ER - TY - STD TI - Gene Ontology [ http://www.geneontology.org ] . ID - ref25 ER - TY - JOUR AU - Chandonia, J. M. AU - Hon, G. AU - Walker, N. S. AU - Lo Conte, L. AU - Koehl, P. AU - Levitt, M. AU - Brenner, S. E. PY - 2004 DA - 2004// TI - The ASTRAL Compendium in 2004 JO - Nucleic acids research VL - 32 UR - https://doi.org/10.1093/nar/gkh034 DO - 10.1093/nar/gkh034 ID - Chandonia2004 ER - TY - STD TI - NCBI [ http://www.ncbi.nih.gov ] . ID - ref27 ER - TY - JOUR AU - Consortium, I. C. G. S. PY - 2004 DA - 2004// TI - Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution JO - Nature VL - 432 UR - https://doi.org/10.1038/nature03154 DO - 10.1038/nature03154 ID - Consortium2004 ER - TY - JOUR AU - Haas, N. B. AU - Grabowski, J. M. AU - Sivitz, A. B. AU - Burch, J. B. PY - 1997 DA - 1997// TI - Chicken repeat 1 (CR1) elements, which define an ancient family of vertebrate non-LTR retrotransposons, contain two closely spaced open reading frames. JO - Gene VL - 197 UR - https://doi.org/10.1016/S0378-1119(97)00276-X DO - 10.1016/S0378-1119(97)00276-X ID - Haas1997 ER - TY - JOUR AU - Roest Crollius, H. AU - Jaillon, O. AU - Dasilva, C. AU - Ozouf-Costaz, C. AU - Fizames, C. AU - Fischer, C. AU - Bouneau, L. AU - Billault, A. AU - Quetier, F. AU - Saurin, W. AU - Bernot, A. AU - J., W. PY - 2000 DA - 2000// TI - Characterization and repeat analysis of the compact genome of the freshwater pufferfish Tetraodon nigroviridis JO - Genome Res VL - 10 UR - https://doi.org/10.1101/gr.10.7.939 DO - 10.1101/gr.10.7.939 ID - Roest Crollius2000 ER - TY - JOUR AU - Consortium, R. G. S. P. PY - 2004 DA - 2004// TI - Genome sequence of the Brown Norway rat yields insights into mammalian evolution JO - Nature VL - 428 UR - https://doi.org/10.1038/nature02426 DO - 10.1038/nature02426 ID - Consortium2004 ER - TY - JOUR AU - Consortium, M. G. S. PY - 2002 DA - 2002// TI - Initial sequencing and comparative analysis of the mouse genome JO - Nature VL - 420 UR - https://doi.org/10.1038/nature01262 DO - 10.1038/nature01262 ID - Consortium2002 ER - TY - JOUR AU - Genomics, C. PY - 2001 DA - 2001// TI - The sequence of the human genome JO - Science VL - 291 UR - https://doi.org/10.1126/science.1058040 DO - 10.1126/science.1058040 ID - Genomics2001 ER - TY - JOUR AU - Consortium, E. N. C. O. D. E. P. PY - 2004 DA - 2004// TI - The ENCODE (ENCyclopedia Of DNA Elements) Project JO - Science VL - 306 UR - https://doi.org/10.1126/science.1105136 DO - 10.1126/science.1105136 ID - Consortium2004 ER - TY - JOUR AU - Harrison, P. M. AU - Carriero, N. AU - Liu, Y. AU - Gerstein, M. PY - 2003 DA - 2003// TI - A "polyORFomic" analysis of prokaryote genomes using disabled-homology filtering reveals conserved but undiscovered short ORFs JO - J Mol Biol VL - 333 UR - https://doi.org/10.1016/j.jmb.2003.09.016 DO - 10.1016/j.jmb.2003.09.016 ID - Harrison2003 ER - TY - JOUR AU - Kellis, M. AU - Patterson, N. AU - Endrizzi, M. AU - Birren, B. AU - Lander, E. S. PY - 2003 DA - 2003// TI - Sequencing and comparison of yeast species to identify genes and regulatory elements JO - Nature VL - 423 UR - https://doi.org/10.1038/nature01644 DO - 10.1038/nature01644 ID - Kellis2003 ER - TY - JOUR AU - Harrison, P. M. PY - 2006 DA - 2006// TI - Exhaustive assignment of compositional bias reveals universally prevalent biased regions: analysis of functional associations in human and Drosophila. JO - BMC Bioinformatics VL - 7 UR - https://doi.org/10.1186/1471-2105-7-441 DO - 10.1186/1471-2105-7-441 ID - Harrison2006 ER - TY - JOUR AU - Modrek, B. AU - Lee, C. J. PY - 2003 DA - 2003// TI - Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/or loss JO - Nat Genet VL - 34 UR - https://doi.org/10.1038/ng1159 DO - 10.1038/ng1159 ID - Modrek2003 ER - TY - JOUR AU - Wang, W. AU - J, W. PY - 2005 DA - 2005// TI - Origin and evolution of new exons in rodents JO - Genome Res VL - 15 UR - https://doi.org/10.1101/gr.3929705 DO - 10.1101/gr.3929705 ID - Wang2005 ER - TY - STD TI - http://biology.mcgill.ca/faculty/harrison/retro [ http://biology.mcgill.ca/faculty/harrison/retro ] . ID - ref40 ER -