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Research: Centromeric instability and chromoanasynthesis observed in nine supernumerary marker chromosomes resolved with long-read genome sequencing
- Kristine Bilgrav Saether,
- Angelo Salazar Mantero,
- Marlene Ek,
- Maria Pettersson,
- Elisabeth Syk Lundberg,
- Christopher M. Grochowski,
- Claudia M.B. Carvalho,
- Jesper Eisfeldt,
- and Anna Lindstrand
Genome Res. April 2026 36: 661-670; Published in Advance March 25, 2026, doi:10.1101/gr.281175.125
...-Martin B, Yilmaz F, Ebler J, Hallast P, Maggiolini M, Harvey FA, et al. 2022. Recurrent inversion polymorphisms in humans associate with genetic instability and genomic disorders. Cell 185: 1986–2005.e26. doi:10.1016/j.cell.2022.04.017 ↵Porubsky D, Harvey WT, Rozanski AN, Ebler J, Höps W, Ashraf H...
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Research: Lambdoid phages with abundant Chi recombination hotspots reflect diverse viral strategies for recombination-dependent growth
- Clarence Zheng,
- Sherwood R. Casjens,
- Alan R. Davidson,
- Susan K. Amundsen,
- and Gerald R. Smith
Genome Res. August 2025 35: 1767-1780; Published in Advance July 10, 2025, doi:10.1101/gr.280248.124
...enteric bacteria is a complex helicase-nuclease with multiple enzymatic activities (for review, see Amundsen and Smith 2023). During its rapid unwinding of DNA (up to 1 kb/sec), RecBCD produces single-stranded loops and tails. Upon encountering a properly oriented crossover hotspot instigator (Chi) site 5...
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Research: Adaptation of centromeres to breakage through local genomic and epigenomic remodeling in wheat
- Jingwei Zhou,
- Yuhong Huang,
- Huan Ma,
- Yiqian Chen,
- Chuanye Chen,
- Fangpu Han,
- and Handong Su
Genome Res. November 2025 35: 2461-2471; Published in Advance September 30, 2025, doi:10.1101/gr.280913.125
...Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; 3State Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy...
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Research: Unexpectedly low recombination rates and presence of hotspots in termite genomes
- Turid Everitt,
- Tilman Rönneburg,
- Daniel Elsner,
- Anna Olsson,
- Yuanzhen Liu,
- Tuuli Larva,
- Judith Korb,
- and Matthew T. Webster
Genome Res. May 2025 35: 1124-1137; Published in Advance March 20, 2025, doi:10.1101/gr.279180.124
...termite species with varying social complexity both have relatively low genomic average rates of meiotic recombination; (2) both s possess recombination hotspots and likely contain full-length copies of PRDM9; and (3) there are reduced levels of recombination in genomic regions depleted in CpG sites. Our...
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Research: Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
- Dongying Xie,
- Pohao Ye,
- Yiming Ma,
- and Zhongying Zhao
Genome Res. March 2026 36: 506-521; Published in Advance February 17, 2026, doi:10.1101/gr.280885.125
...Pan analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility Dongying Xie1,2,3, Pohao Ye1,3, Yiming Ma1 and Zhongying Zhao1 1Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China; 2Institute for Research...
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Method: Autoencoders for genomic variation analysis
- Margarita Geleta,
- Daniel Mas Montserrat,
- Xavier Giro-i-Nieto,
- and Alexander G. Ioannidis
Genome Res. February 2026 36: 348-360; Published in Advance January 20, 2026, doi:10.1101/gr.280086.124
..., Barcelona 08034, Spain; 3Department of Electrical Engineering and Computer Science, University of California, Berkeley, Berkeley, California 94720, USA; 4Genomics Institute, University of California, Santa Cruz, Santa Cruz, California 95060, USA; 5Institute for Computational and Mathematical Engineering...
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Method: Automated interpretable artificial intelligence genomic prediction with AIGP
- Lei Wei,
- Ziqin Jiang,
- Baoliang Fan,
- Yidan Yan,
- Zhenqiang Xu,
- Xiaoxiang Hu,
- and Yuzhe Wang
Genome Res. April 2026 36: 814-826; Published in Advance March 5, 2026, doi:10.1101/gr.281006.125
....edu.cnAbstractPredicting phenotypes from genomic mutations remains a major genetic challenge. Traditional statistical methods (such as GBLUP and BayesR) have limitations, including reliance on artificial prior assumptions, and hard to capture epistatic effects. Machine learning (ML) has emerged as a powerful alternative for genomic...
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Method: A full-proteome, interaction-specific characterization of mutational hotspots across human cancers
- Siwei Chen,
- Yuan Liu,
- Yingying Zhang,
- Shayne D. Wierbowski,
- Steven M. Lipkin,
- Xiaomu Wei,
- and Haiyuan Yu
Genome Res. January 2022 32: 135-149; Published in Advance December 28, 2021, doi:10.1101/gr.275437.121
...Hospital, Boston, MA 02114, USA Corresponding author: haiyuan.yu@cornell.eduAbstractRapid accumulation of cancer genomic data has led to the identification of an increasing number of mutational hotspots with uncharacterized significance. Here we present a biologically informed computational framework...
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Method: Localizing unmapped sequences with families to validate the Telomere-to-Telomere assembly and identify new hotspots for genetic diversity
- Brianna Chrisman,
- Chloe He,
- Jae-Yoon Jung,
- Nate Stockham,
- Kelley Paskov,
- Peter Washington,
- Juli Petereit,
- and Dennis P. Wall
Genome Res. October 2023 33: 1734-1746; Published in Advance October 25, 2023, doi:10.1101/gr.277175.122
...divergence from their aligned region in T2T-CHM13, highlighting new hotspots for genetic diversity.The human reference has been one of the major successes of modern genomics and has been heavily relied on to study how genetic variation contributes to disease (Lander et al. 2001; International Human Genome...
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Method: Predicting human genes susceptible to genomic instability associated with Alu/Alu-mediated rearrangements
- Xiaofei Song,
- Christine R. Beck,
- Renqian Du,
- Ian M. Campbell,
- Zeynep Coban-Akdemir,
- Shen Gu,
- Amy M. Breman,
- Pawel Stankiewicz,
- Grzegorz Ira,
- Chad A. Shaw,
- and James R. Lupski
Genome Res. August 2018 28: 1228-1242; Published in Advance June 15, 2018, doi:10.1101/gr.229401.117
...or genomic interval to AAMR events.The potential biological and clinical utility for delineating genomic instability due to AAMR hotspots is indicated from studies focusing on disease loci. For example, 45.5% (20/43) of the CNVs described in 17p13.3 were mediated by Alu pairs (Gu et al. 2015), 56% (9...

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