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  Delayed DNA replication in haploid human embryonic stem cells

  • Matthew M. Edwards,
  • Michael V. Zuccaro,
  • Ido Sagi,
  • Qiliang Ding,
  • Dan Vershkov,
  • Nissim Benvenisty,
  • Dieter Egli,
  • and Amnon Koren

  Genome Res. December 2021 31: 2155-2169; Published in Advance November 22, 2021, doi:10.1101/gr.275953.121
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  Decoding the function of bivalent chromatin in development and cancer

  • Dhirendra Kumar,
  • Senthilkumar Cinghu,
  • Andrew J. Oldfield,
  • Pengyi Yang,
  • and Raja Jothi

  Genome Res. December 2021 31: 2170-2184; Published in Advance October 19, 2021, doi:10.1101/gr.275736.121
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  Epstein–Barr virus nuclear antigen 2 extensively rewires the human chromatin landscape at autoimmune risk loci

  • Ted Hong,
  • Sreeja Parameswaran,
  • Omer A. Donmez,
  • Daniel Miller,
  • Carmy Forney,
  • Michael Lape,
  • Mariana Saint Just Ribeiro,
  • Jun Liang,
  • Lee E. Edsall,
  • Albert F. Magnusen,
  • William Miller,
  • Iouri Chepelev,
  • John B. Harley,
  • Bo Zhao,
  • Leah C. Kottyan,
  • and Matthew T. Weirauch

  Genome Res. December 2021 31: 2185-2198; Published in Advance November 19, 2021, doi:10.1101/gr.264705.120
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  A multi-enhancer RET regulatory code is disrupted in Hirschsprung disease

  • Sumantra Chatterjee,
  • Kameko M. Karasaki,
  • Lauren E. Fries,
  • Ashish Kapoor,
  • and Aravinda Chakravarti

  Genome Res. December 2021 31: 2199-2208; Published in Advance November 15, 2021, doi:10.1101/gr.275667.121
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  Individualized VDJ recombination predisposes the available Ig sequence space

  • Andrei Slabodkin,
  • Maria Chernigovskaya,
  • Ivana Mikocziova,
  • Rahmad Akbar,
  • Lonneke Scheffer,
  • Milena Pavlović,
  • Habib Bashour,
  • Igor Snapkov,
  • Brij Bhushan Mehta,
  • Cédric R. Weber,
  • Jose Gutierrez-Marcos,
  • Ludvig M. Sollid,
  • Ingrid Hobæk Haff,
  • Geir Kjetil Sandve,
  • Philippe A. Robert,
  • and Victor Greiff

  Genome Res. December 2021 31: 2209-2224; Published in Advance November 23, 2021, doi:10.1101/gr.275373.121
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  Mutagenesis of human genomes by endogenous mobile elements on a population scale

  • Nelson T. Chuang,
  • Eugene J. Gardner,
  • Diane M. Terry,
  • Jonathan Crabtree,
  • Anup A. Mahurkar,
  • Guillermo L. Rivell,
  • Charles C. Hong,
  • James A. Perry,
  • and Scott E. Devine

  Genome Res. December 2021 31: 2225-2235; Published in Advance November 12, 2021, doi:10.1101/gr.275323.121
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  Alu insertion variants alter gene transcript levels

  • Lindsay M. Payer,
  • Jared P. Steranka,
  • Maria S. Kryatova,
  • Giacomo Grillo,
  • Mathieu Lupien,
  • Pedro P. Rocha,
  • and Kathleen H. Burns

  Genome Res. December 2021 31: 2236-2248; Published in Advance November 19, 2021, doi:10.1101/gr.261305.120
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  Structural variants are a major source of gene expression differences in humans and often affect multiple nearby genes

  • Alexandra J. Scott,
  • Colby Chiang,
  • and Ira M. Hall

  Genome Res. December 2021 31: 2249-2257; Published in Advance September 20, 2021, doi:10.1101/gr.275488.121
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  Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits

  • Peter Orchard,
  • Nandini Manickam,
  • Christa Ventresca,
  • Swarooparani Vadlamudi,
  • Arushi Varshney,
  • Vivek Rai,
  • Jeremy Kaplan,
  • Claudia Lalancette,
  • Karen L. Mohlke,
  • Katherine Gallagher,
  • Charles F. Burant,
  • and Stephen C.J. Parker

  Genome Res. December 2021 31: 2258-2275; Published in Advance November 23, 2021, doi:10.1101/gr.268482.120
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  Evolutionary rewiring of the wheat transcriptional regulatory network by lineage-specific transposable elements

  • Yuyun Zhang,
  • Zijuan Li,
  • Yu'e Zhang,
  • Kande Lin,
  • Yuan Peng,
  • Luhuan Ye,
  • Yili Zhuang,
  • Meiyue Wang,
  • Yilin Xie,
  • Jingyu Guo,
  • Wan Teng,
  • Yiping Tong,
  • Wenli Zhang,
  • Yongbiao Xue,
  • Zhaobo Lang,
  • and Yijing Zhang

  Genome Res. December 2021 31: 2276-2289; Published in Advance September 9, 2021, doi:10.1101/gr.275658.121
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  Transcriptional activity and epigenetic regulation of transposable elements in the symbiotic fungus Rhizophagus irregularis

  • Alexandra Dallaire,
  • Bethan F. Manley,
  • Maya Wilkens,
  • Iliana Bista,
  • Clement Quan,
  • Edouard Evangelisti,
  • Charles R. Bradshaw,
  • Navin B. Ramakrishna,
  • Sebastian Schornack,
  • Falk Butter,
  • Uta Paszkowski,
  • and Eric A. Miska

  Genome Res. December 2021 31: 2290-2302; Published in Advance November 12, 2021, doi:10.1101/gr.275752.121
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  Intergenic ORFs as elementary structural modules of de novo gene birth and protein evolution

  • Chris Papadopoulos,
  • Isabelle Callebaut,
  • Jean-Christophe Gelly,
  • Isabelle Hatin,
  • Olivier Namy,
  • Maxime Renard,
  • Olivier Lespinet,
  • and Anne Lopes

  Genome Res. December 2021 31: 2303-2315; Published in Advance November 22, 2021, doi:10.1101/gr.275638.121
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  Different trajectories of polyploidization shape the genomic landscape of the Brettanomyces bruxellensis yeast species

  • Chris Eberlein,
  • Omar Abou Saada,
  • Anne Friedrich,
  • Warren Albertin,
  • and Joseph Schacherer

  Genome Res. December 2021 31: 2316-2326; Published in Advance November 23, 2021, doi:10.1101/gr.275380.121
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