Table of Contents

Research

• Select this article

  Differences in molecular sampling and data processing explain variation among single-cell and single-nucleus RNA-seq experiments

  • John T. Chamberlin,
  • Younghee Lee,
  • Gabor T. Marth,
  • and Aaron R. Quinlan

  Genome Res. February 2024 34: 179-188; Published in Advance February 14, 2024, doi:10.1101/gr.278253.123
  • Abstract
  • Full Text
  • Full Text (PDF)
  • Supplemental Material

  OPEN ACCESS ARTICLE
• Select this article

  Genomic origin, fragmentomics, and transcriptional properties of long cell-free DNA molecules in human plasma

  • Huiwen Che,
  • Peiyong Jiang,
  • L.Y. Lois Choy,
  • Suk Hang Cheng,
  • Wenlei Peng,
  • Rebecca W.Y. Chan,
  • Jing Liu,
  • Qing Zhou,
  • W.K. Jacky Lam,
  • Stephanie C.Y. Yu,
  • So Ling Lau,
  • Tak Y. Leung,
  • John Wong,
  • Vincent Wai-Sun Wong,
  • Grace L.H. Wong,
  • Stephen L. Chan,
  • K.C. Allen Chan,
  • and Y.M. Dennis Lo

  Genome Res. February 2024 34: 189-200; Published in Advance February 26, 2024, doi:10.1101/gr.278556.123
  • Abstract
  • Full Text
  • Full Text (PDF)
  • Supplemental Material

  OPEN ACCESS ARTICLE
• Select this article

  Tyrosine 1–phosphorylated RNA polymerase II transcribes PROMPTs to facilitate proximal promoter pausing and induce global transcriptional repression in response to DNA damage

  • Kamal Ajit,
  • Adele Alagia,
  • Kaspar Burger,
  • and Monika Gullerova

  Genome Res. February 2024 34: 201-216; Published in Advance March 11, 2024, doi:10.1101/gr.278644.123
  • Abstract
  • Full Text
  • Full Text (PDF)
  • Supplemental Material

  OPEN ACCESS ARTICLE
• Select this article

  Preferential formation of Z-RNA over intercalated motifs in long noncoding RNA

  • Uditi Bhatt,
  • Anne Cucchiarini,
  • Yu Luo,
  • Cameron W. Evans,
  • Jean-Louis Mergny,
  • K. Swaminathan Iyer,
  • and Nicole M. Smith

  Genome Res. February 2024 34: 217-230; Published in Advance February 14, 2024, doi:10.1101/gr.278236.123
  • Abstract
  • Full Text
  • Full Text (PDF)
  • Supplemental Material
• Select this article

  RNA Pol II–dependent transcription efficiency fine-tunes A-to-I editing levels

  • Brigitta Szabo,
  • Therese C. Mandl,
  • Bernhard Woldrich,
  • Gregor Diensthuber,
  • David Martin,
  • Michael F. Jantsch,
  • and Konstantin Licht

  Genome Res. February 2024 34: 231-242; Published in Advance March 12, 2024, doi:10.1101/gr.277686.123
  • Abstract
  • Full Text
  • Full Text (PDF)
  • Supplemental Material

  OPEN ACCESS ARTICLE
• Select this article

  Pathogenic variants in CRX have distinct cis-regulatory effects on enhancers and silencers in photoreceptors

  • James L. Shepherdson,
  • Ryan Z. Friedman,
  • Yiqiao Zheng,
  • Chi Sun,
  • Inez Y. Oh,
  • David M. Granas,
  • Barak A. Cohen,
  • Shiming Chen,
  • and Michael A. White

  Genome Res. February 2024 34: 243-255; Published in Advance February 14, 2024, doi:10.1101/gr.278133.123
  • Abstract
  • Full Text
  • Full Text (PDF)
  • Supplemental Material

  OPEN ACCESS ARTICLE
• Select this article

  Dynamic DNA N⁶-adenine methylation (6mA) governs the encystment process, showcased in the unicellular eukaryote Pseudocohnilembus persalinus

  • Yongqiang Liu,
  • Junhua Niu,
  • Fei Ye,
  • Therese Solberg,
  • Borong Lu,
  • Chundi Wang,
  • Mariusz Nowacki,
  • and Shan Gao

  Genome Res. February 2024 34: 256-271; Published in Advance March 12, 2024, doi:10.1101/gr.278796.123
  • Abstract
  • Full Text
  • Full Text (PDF)
  • Supplemental Material
• Select this article

  Modeling alternative translation initiation sites in plants reveals evolutionarily conserved cis-regulatory codes in eukaryotes

  • Ting-Ying Wu,
  • Ya-Ru Li,
  • Kai-Jyun Chang,
  • Jhen-Cheng Fang,
  • Daisuke Urano,
  • and Ming-Jung Liu

  Genome Res. February 2024 34: 272-285; Published in Advance March 13, 2024, doi:10.1101/gr.278100.123
  • Abstract
  • Full Text
  • Full Text (PDF)
  • Supplemental Material

  OPEN ACCESS ARTICLE
• Select this article

  Major impacts of widespread structural variation on sorghum

  • Zhihai Zhang,
  • Joao Paulo Gomes Viana,
  • Bosen Zhang,
  • Kimberly K.O. Walden,
  • Hans Müller Paul,
  • Stephen P. Moose,
  • Geoffrey P. Morris,
  • Chris Daum,
  • Kerrie W. Barry,
  • Nadia Shakoor,
  • and Matthew E. Hudson

  Genome Res. February 2024 34: 286-299; Published in Advance March 13, 2024, doi:10.1101/gr.278396.123
  • Abstract
  • Full Text
  • Full Text (PDF)
  • Supplemental Material