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Research

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  Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection

  • Jian-Hai Chen,
  • Patrick Landback,
  • Deanna Arsala,
  • Alexander Guzzetta,
  • Shengqian Xia,
  • Jared Atlas,
  • Dylan Sosa,
  • Yong E. Zhang,
  • Jingqiu Cheng,
  • Bairong Shen,
  • and Manyuan Long

  Genome Res. March 2025 35: 379-392; Published in Advance February 14, 2025, doi:10.1101/gr.279498.124
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  Estrogen-induced chromatin looping changes identify a subset of functional regulatory elements

  • Hosiana Abewe,
  • Alexandra Richey,
  • Jeffery M. Vahrenkamp,
  • Matthew Ginley-Hidinger,
  • Craig M. Rush,
  • Noel Kitchen,
  • Xiaoyang Zhang,
  • and Jason Gertz

  Genome Res. March 2025 35: 393-403; Published in Advance March 3, 2025, doi:10.1101/gr.279699.124
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  Nucleosome binding by TP53, TP63, and TP73 is determined by the composition, accessibility, and helical orientation of their binding sites

  • Patrick D. Wilson,
  • Xinyang Yu,
  • Christopher R. Handelmann,
  • and Michael J. Buck

  Genome Res. March 2025 35: 404-416; Published in Advance February 10, 2025, doi:10.1101/gr.279541.124
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  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
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  Ancient dog introgression into the Iberian wolf genome may have facilitated adaptation to human-dominated landscapes

  • Diana Lobo,
  • Hernán E. Morales,
  • Cock Van Oosterhout,
  • José Vicente López-Bao,
  • Pedro Silva,
  • Luis Llaneza,
  • Carolina Pacheco,
  • Diana Castro,
  • Germán Hernández-Alonso,
  • George Pacheco,
  • John Archer,
  • M. Thomas P. Gilbert,
  • Nuno Ferrand,
  • and Raquel Godinho

  Genome Res. March 2025 35: 432-445; Published in Advance February 14, 2025, doi:10.1101/gr.279093.124
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  Variation in the fitness impact of translationally optimal codons among animals

  • Florian Bénitière,
  • Tristan Lefébure,
  • and Laurent Duret

  Genome Res. March 2025 35: 446-458; Published in Advance February 10, 2025, doi:10.1101/gr.279837.124
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  Vertebrates show coordinated elevated expression of mitochondrial and nuclear genes after birth

  • Hadar Medini and
  • Dan Mishmar

  Genome Res. March 2025 35: 459-474; Published in Advance March 4, 2025, doi:10.1101/gr.279700.124
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  The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication

  • Øystein Monsen,
  • Lars Grønvold,
  • Alex Datsomor,
  • Thomas Harvey,
  • James Kijas,
  • Alexander Suh,
  • Torgeir R. Hvidsten,
  • and Simen Rød Sandve

  Genome Res. March 2025 35: 475-488; Published in Advance February 12, 2025, doi:10.1101/gr.278931.124
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  Identification of the male-specific region on the guppy Y Chromosome from a haplotype-resolved assembly

  • Kang Du,
  • Oliver Deusch,
  • Ilja Bezrukov,
  • Christa Lanz,
  • Yann Guiguen,
  • Margarete Hoffmann,
  • Anette Habring,
  • Detlef Weigel,
  • Manfred Schartl,
  • and Christine Dreyer

  Genome Res. March 2025 35: 489-498; Published in Advance March 5, 2025, doi:10.1101/gr.279582.124
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  The genomic consequences and persistence of sociality in spiders

  • Jilong Ma,
  • Jesper Bechsgaard,
  • Anne Aagaard,
  • Palle Villesen,
  • Trine Bilde,
  • and Mikkel Heide Schierup

  Genome Res. March 2025 35: 499-511; Published in Advance February 20, 2025, doi:10.1101/gr.279503.124
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  Transcriptomic and proteomic effects of gene deletion are not evolutionarily conserved

  • Yang Li and
  • Jianzhi Zhang

  Genome Res. March 2025 35: 512-521; Published in Advance February 18, 2025, doi:10.1101/gr.280008.124
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  Atypical epigenetic and small RNA control of degenerated transposons and their fragments in clonally reproducing Spirodela polyrhiza

  • Rodolphe Dombey,
  • Daniel Buendía-Ávila,
  • Verónica Barragán-Borrero,
  • Laura Diezma-Navas,
  • Arturo Ponce-Mañe,
  • José Mario Vargas-Guerrero,
  • Rana Elias,
  • and Arturo Marí-Ordóñez

  Genome Res. March 2025 35: 522-544; Published in Advance March 4, 2025, doi:10.1101/gr.279532.124
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