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  Whole-genome long-read sequencing downsampling and its effect on variant-calling precision and recall

  • William T. Harvey,
  • Peter Ebert,
  • Jana Ebler,
  • Peter A. Audano,
  • Katherine M. Munson,
  • Kendra Hoekzema,
  • David Porubsky,
  • Christine R. Beck,
  • Tobias Marschall,
  • Kiran Garimella,
  • and Evan E. Eichler

  Genome Res. December 2023 33: 2029-2040; Published in Advance December 7, 2023, doi:10.1101/gr.278070.123
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  A DNA methylation haplotype block landscape in human tissues and preimplantation embryos reveals regulatory elements defined by comethylation patterns

  • Yan Feng,
  • Zhiqiang Zhang,
  • Yuyang Hong,
  • Yi Ding,
  • Leiqin Liu,
  • Siqi Gao,
  • Hai Fang,
  • and Jiantao Shi

  Genome Res. December 2023 33: 2041-2052; Published in Advance November 8, 2023, doi:10.1101/gr.278146.123
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  A naturally occurring variant of MBD4 causes maternal germline hypermutation in primates

  • Alexandra M. Stendahl,
  • Rashesh Sanghvi,
  • Samuel Peterson,
  • Karina Ray,
  • Ana C. Lima,
  • Raheleh Rahbari,
  • and Donald F. Conrad

  Genome Res. December 2023 33: 2053-2059; Published in Advance November 20, 2023, doi:10.1101/gr.277977.123
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  De novo transcriptome assembly of mouse male germ cells reveals novel genes, stage-specific bidirectional promoter activity, and noncoding RNA expression

  • Mark E. Gill,
  • Alexia Rohmer,
  • Serap Erkek-Ozhan,
  • Ching-Yeu Liang,
  • Sunwoo Chun,
  • Evgeniy A. Ozonov,
  • and Antoine H.F.M. Peters

  Genome Res. December 2023 33: 2060-2078; Published in Advance December 21, 2023, doi:10.1101/gr.278060.123
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  Revisiting chromatin packaging in mouse sperm

  • Qiangzong Yin,
  • Chih-Hsiang Yang,
  • Olga S. Strelkova,
  • Jingyi Wu,
  • Yu Sun,
  • Sneha Gopalan,
  • Liyan Yang,
  • Job Dekker,
  • Thomas G. Fazzio,
  • Xin Zhiguo Li,
  • Johan Gibcus,
  • and Oliver J. Rando

  Genome Res. December 2023 33: 2079-2093; Published in Advance December 21, 2023, doi:10.1101/gr.277845.123
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  Cohesin and CTCF do not assemble TADs in Xenopus sperm and male pronuclei

  • Gregor Jessberger,
  • Csilla Várnai,
  • Roman R. Stocsits,
  • Wen Tang,
  • Georg Stary,
  • and Jan-Michael Peters

  Genome Res. December 2023 33: 2094-2107; Published in Advance December 21, 2023, doi:10.1101/gr.277865.123
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  Spatiotemporal kinetics of CAF-1-dependent chromatin maturation ensures transcription fidelity during S-phase

  • Boning Chen,
  • Heather K. MacAlpine,
  • Alexander J. Hartemink,
  • and David M. MacAlpine

  Genome Res. December 2023 33: 2108-2118; Published in Advance December 11, 2023, doi:10.1101/gr.278273.123
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  tRNA-derived small RNAs are embedded in the gene regulatory network instructing Drosophila metamorphosis

  • Junling Shi,
  • Jiaqi Xu,
  • Jun Ma,
  • and Feng He

  Genome Res. December 2023 33: 2119-2132; Published in Advance November 16, 2023, doi:10.1101/gr.278128.123
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  Evidence for selfing in a vertebrate from whole-genome sequencing

  • Astrid Böhne,
  • Zeynep Oğuzhan,
  • Ioannis Chrysostomakis,
  • Simon Vitt,
  • Denis Meuthen,
  • Sebastian Martin,
  • Sandra Kukowka,
  • and Timo Thünken

  Genome Res. December 2023 33: 2133-2142; Published in Advance December 7, 2023, doi:10.1101/gr.277368.122
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