Searching journal content for articles similar to Albà and Guigó 14 (4): 549.

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  1. Method: Greater strength of selection and higher proportion of beneficial amino acid changing mutations in humans compared with mice and Drosophila melanogaster
    • Ying Zhen,
    • Christian D. Huber,
    • Robert W. Davies,
    • and Kirk E. Lohmueller
    Genome Res. January 2021 31: 110-120; Published in Advance November 18, 2020, doi:10.1101/gr.256636.119
    ...methodWe first estimated α from coding regions of primates, rodents, and Drosophila. We analyzed published genomic data sets to obtain counts of synonymous and nonsynonymous polymorphisms (PS and PN) and divergent sites between species (DS and DN). For computation of α in humans, we used chimpanzee...
  2. Research: Long terminal repeats power evolution of genes and gene expression programs in mammalian oocytes and zygotes
    • Vedran Franke,
    • Sravya Ganesh,
    • Rosa Karlic,
    • Radek Malik,
    • Josef Pasulka,
    • Filip Horvat,
    • Maja Kuzman,
    • Helena Fulka,
    • Marketa Cernohorska,
    • Jana Urbanova,
    • Eliska Svobodova,
    • Jun Ma,
    • Yutaka Suzuki,
    • Fugaku Aoki,
    • Richard M. Schultz,
    • Kristian Vlahovicek,
    • and Petr Svoboda
    Genome Res. August 2017 27: 1384-1394; Published in Advance May 18, 2017, doi:10.1101/gr.216150.116
    ...sequence is conserved across mammals. Remarkably, the syntenic human locus carries anMLT1-derived 5′ exon of an oocyte-specific unannotated lncRNA (Supplemental Fig. S6B). The human and rodent lncRNAs are unrelated; the conserved D6Ertd527e 3′ exon region resides in the first intron of the human lnc...
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  3. Research: Degrees of convergent evolution in rodent adaptations to arid environments
    • Domitille Chalopin,
    • Carine Rey,
    • Jeremy Ganofsky,
    • Juliana Blin,
    • Pascale Chevret,
    • Marion Mouginot,
    • Laurent Guéguen,
    • Bastien Boussau,
    • Sophie Pantalacci,
    • and Marie Sémon
    Genome Res. March 2026 36: 472-486; Published in Advance January 21, 2026, doi:10.1101/gr.280089.124
    .... The subfamily Murinae originated about 11.2 MY ago and today represents ∼20% of all rodents (Aghová et al. 2018). In these two nested radiations, repeated transitions to arid environments have occurred, with examples of ancient adaptations as well as more recent ones. This provides a unique opportunity...
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  4. Research: Experimental and pan-cancer genome analyses reveal widespread contribution of acrylamide exposure to carcinogenesis in humans
    • Maria Zhivagui,
    • Alvin W.T. Ng,
    • Maude Ardin,
    • Mona I. Churchwell,
    • Manuraj Pandey,
    • Claire Renard,
    • Stephanie Villar,
    • Vincent Cahais,
    • Alexis Robitaille,
    • Liacine Bouaoun,
    • Adriana Heguy,
    • Kathryn Z. Guyton,
    • Martha R. Stampfer,
    • James McKay,
    • Monica Hollstein,
    • Magali Olivier,
    • Steven G. Rozen,
    • Frederick A. Beland,
    • Michael Korenjak,
    • and Jiri Zavadil
    Genome Res. April 2019 29: 521-531; Published in Advance March 7, 2019, doi:10.1101/gr.242453.118
    ...that acrylamide causes cancer in rodents, yet epidemiological studies conducted to date are limited and, thus far, have yielded inconclusive data on association of human cancers with acrylamide exposure. In this study, we experimentally identify a novel and unique mutational signature imprinted by acrylamide...
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  5. Research: Natural selection drives the accumulation of amino acid tandem repeats in human proteins
    • Loris Mularoni,
    • Alice Ledda,
    • Macarena Toll-Riera,
    • and M. Mar Albà
    Genome Res. June 2010 20: 745-754; Published in Advance March 24, 2010, doi:10.1101/gr.101261.109
    ...Natural selection drives the accumulation of amino acid tandem repeats in human proteins Loris Mularoni 1 , 2 , 5 , Alice Ledda 1 , 5 , Macarena Toll-Riera 1 , 3 and M. Mar Albà 1 , 3 , 4 , 6 1 Biomedical Informatics...
  6. Research: Genome-wide evidence for selection acting on single amino acid repeats
    • Wilfried Haerty and
    • G. Brian Golding
    Genome Res. June 2010 20: 755-760; Published in Advance January 7, 2010, doi:10.1101/gr.101246.109
    ...Acids Res 34:W472–W476. Alba MM, Guigo R. 2004. Comparative analysis of amino acid repeats in rodents and humans. Genome Res 14: 549–554. Alba MM, Santibanez-Koref MF, Hancock JM. 1999a. Amino acid reiterations in yeast are overrepresented in particular classes of proteins and show evidence...
  7. LETTER: Origin and evolution of new exons in rodents
    • Wen Wang,
    • Hongkun Zheng,
    • Shuang Yang,
    • Haijing Yu,
    • Jun Li,
    • Huifeng Jiang,
    • Jianning Su,
    • Lei Yang,
    • Jianguo Zhang,
    • Jason McDermott,
    • Ram Samudrala,
    • Jian Wang,
    • Huanming Yang,
    • Jun Yu,
    • Karsten Kristiansen,
    • Gane Ka-Shu Wong,
    • and Jun Wang
    Genome Res. September 2005 15: 1258-1264; Published in Advance August 18, 2005, doi:10.1101/gr.3929705
    ...), to identify newly evolved exons in mouse and rat (rodents) by using double outgroups (first human and then pig). Results and Discussion Identification of newly evolved exons By mapping mouse expressed sequences onto the 12,419 genes that are listed in the HomoloGene database ( ftp...
  8. Letter: Tracking the past: Interspersed repeats in an extinct Afrotherian mammal, Mammuthus primigenius
    • Fangqing Zhao,
    • Ji Qi,
    • and Stephan C. Schuster
    Genome Res. August 2009 19: 1384-1392; Published in Advance June 9, 2009, doi:10.1101/gr.091363.109
    ...subfamilies was investigated. The unprecedented expansion of LINE/RTE elements may contribute to an increase of mammoth size. Results Comparison of mammoth, human, and opossum repeats Interspersed repeats were identified and classified using homologybased and de novo methods as described in the Methods...
  9. Research: KRAB zinc-finger proteins regulate endogenous retroviruses to sculpt germline transcriptomes and genome evolution
    • Kai Otsuka,
    • Akihiko Sakashita,
    • So Maezawa,
    • Richard M. Schultz,
    • and Satoshi H. Namekawa
    Genome Res. March 2025 35: 417-431; Published in Advance March 12, 2025, doi:10.1101/gr.279924.124
    ...to the evolution of gene regulatory networks in mammals (Imbeault et al. 2017; Senft and Macfarlan 2021), we first evaluated the amino acid sequence similarity of mouse and human KZFP proteins across mammalian species using the BioMart web tool. Notably, a subset of mouse KZFPs was present only in mice...
  10. LETTER: Divergent V1R repertoires in five species: Amplification in rodents, decimation in primates, and a surprisingly small repertoire in dogs
    • Janet M. Young,
    • Marijo Kambere,
    • Barbara J. Trask,
    • and Robert P. Lane
    Genome Res. February 2005 15: 231-240; Published in Advance January 14, 2005, doi:10.1101/gr.3339905
    ...in human, and 54 in dog. Primate and dog pseudogenes are distributed among almost all V1R subfamilies seen in rodents, indicating that the common ancestor of these species had a diverse V1R repertoire. We find that V1R genes were subject to strikingly different fates in different species and in different...
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