Searching journal content for articles similar to Gonçalves et al. 10 (5): 672.

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  1. LETTER: A Novel Class of Mammalian-Specific Tailless Retropseudogenes
    • Jürgen Schmitz,
    • Gennady Churakov,
    • Hans Zischler,
    • and Jürgen Brosius
    Genome Res. October 2004 14: 1911-1915; Published in Advance September 13, 2004, doi:10.1101/gr.2720104
    ...to document the likely events from processing to RT priming and genomic integration, and allowed us to propose a potential mechanism of tailless retropseudogene generation. RESULTS AND DISCUSSION Search Results and Species Distribution Using a computational, -wide search strategy for extracting preferentially...
  2. Method: The multicomparative 2-n-way genome suite
    • Gennady Churakov,
    • Fengjun Zhang,
    • Norbert Grundmann,
    • Wojciech Makalowski,
    • Angela Noll,
    • Liliya Doronina,
    • and Jürgen Schmitz
    Genome Res. October 2020 30: 1508-1516; Published in Advance July 29, 2020, doi:10.1101/gr.262261.120
    ...and comparing inserted elements among various s. The suite comprises two user-friendly web-based modules. The 2-way module generates pairwise whole- alignments of target and query species. The resulting coordinates of blocks (matching sequences) and gaps (missing sequences) from multiple 2-ways...
  3. Research: Speciation network in Laurasiatheria: retrophylogenomic signals
    • Liliya Doronina,
    • Gennady Churakov,
    • Andrej Kuritzin,
    • Jingjing Shi,
    • Robert Baertsch,
    • Hiram Clawson,
    • and Jürgen Schmitz
    Genome Res. June 2017 27: 997-1003; Published in Advance March 15, 2017, doi:10.1101/gr.210948.116
    ...L1 elements, 47 long terminal repeats (LTRs), and 20 retropseudogenes. However, the short interspersed elements (SINEs) frequently used as phylogenetic markers within mammalian orders did not cross order boundaries in laurasiatherians and were therefore not suitable for the superorder Laurasiatheria...
  4. Research: Haploid selection drives new gene male germline expression
    • Julia B. Raices,
    • Paulo A. Otto,
    • and Maria D. Vibranovski
    Genome Res. July 2019 29: 1115-1122; Published in Advance June 20, 2019, doi:10.1101/gr.238824.118
    ...by explaining the general prevalence of their testis expression, and a parsimonious solution for new alleles to avoid being lost by genetic drift or pseudogenization.New gene origination is thought to play a major role in phenotypic evolution (Kaessmann 2010; Chen et al. 2013). New genes may originate from...
  5. Research: The life history of retrocopies illuminates the evolution of new mammalian genes
    • Francesco Nicola Carelli,
    • Takashi Hayakawa,
    • Yasuhiro Go,
    • Hiroo Imai,
    • Maria Warnefors,
    • and Henrik Kaessmann
    Genome Res. March 2016 26: 301-314; Published in Advance January 4, 2016, doi:10.1101/gr.198473.115
    ...reconstruction of the “life history” of mammalian retrogenes highlights retroposition as a general model for understanding new gene birth and functional evolution. [Supplemental material is available for this article.] In addition tomutations that alter sequences or activities of preexisting genes (Necsulea...
  6. Platypus Special/Letter: Retroposed SNOfall—A mammalian-wide comparison of platypus snoRNAs
    • Jürgen Schmitz,
    • Anja Zemann,
    • Gennady Churakov,
    • Heiner Kuhl,
    • Frank Grützner,
    • Richard Reinhardt,
    • and Jürgen Brosius
    Genome Res. June 2008 18: 1005-1010; Published in Advance May 7, 2008, doi:10.1101/gr.7177908
    ...housekeeping function implies high genomic conservation. However, in nematodes, we recently found an extraordinary degree of plasticity in the generation of snoRNA paralogs as well as in the selection of their modified targets ( Zemann et al. 2006 ). In a process termed cis -duplication, we found that some sno...
  7. Review: Origins, evolution, and phenotypic impact of new genes
    • Henrik Kaessmann
    Genome Res. October 2010 20: 1313-1326; Published in Advance July 22, 2010, doi:10.1101/gr.101386.109
    ...). Thus, these RNASE1 duplications represent striking cases of convergent molecular evolution. They were likely facilitated by the frequent occurrence of segmental duplication, which allows similar duplication events that are highly beneficial to be repeatedly fixed during evolution. More generally...
  8. Research: Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division
    • Alexej Abyzov,
    • Rebecca Iskow,
    • Omer Gokcumen,
    • David W. Radke,
    • Suganthi Balasubramanian,
    • Baikang Pei,
    • Lukas Habegger,
    • The 1000 Genomes Project Consortium,
    • Charles Lee,
    • and Mark Gerstein
    Genome Res. December 2013 23: 2042-2052; Published in Advance September 11, 2013, doi:10.1101/gr.154625.113
    ...; Wen et al. 2011; Pei et al. 2012). For instance, some transcribed processed pseudogenes express antisense transcripts which pair to the mRNA of their parent genes, generating a natural endogenous small interfering RNA and, consequently, reducing the expression of the parent gene (Tam et al. 2008...
    OPEN ACCESS ARTICLE
  9. LETTER: Retroposed Copies of the HMG Genes: A Window to Genome Dynamics
    • Liora Z. Strichman-Almashanu,
    • Michael Bustin,
    • and David Landsman
    Genome Res. May 1, 2003 13: 800-812; doi:10.1101/gr.893803
    .... ↵ Goncalves I. , Duret L. , Mouchiroud D. ( 2000 ) Nature and structure of human genes that generate retropseudogenes. Genome Res. 10 : 672 – 678 . ↵ Harrison P.M. , Hegyi H. , Balasubramanian S. , Luscombe N.M. , Bertone P. , Echols N. , Johnson T. , Gerstein M. ( 2002 ) Molecular fossils in the human...
  10. LETTER: Systematic genome-wide annotation of spliceosomal proteins reveals differential gene family expansion
    • Nuno L. Barbosa-Morais,
    • Maria Carmo-Fonseca,
    • and Samuel Aparício
    Genome Res. January 2006 16: 66-77; Published in Advance December 12, 2005, doi:10.1101/gr.3936206
    ...2EST: A BLAST2 server for searching expressed sequence tag (EST) databases with eukaryotic gene-sized queries. Nucleic Acids Res. 29 : 1272 -1277. ↵ Goncalves, I., Duret, L., and Mouchiroud, D. 2000 . Nature and structure of human genes that generate retropseudogenes. Genome Res. 10 : 672 -678...
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