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Research: Epigenetic and evolutionary features of ape subterminal heterochromatin
- DongAhn Yoo,
- Katherine M. Munson,
- and Evan E. Eichler
Genome Res. January 2026 36: 38-49; Published in Advance October 22, 2025, doi:10.1101/gr.280987.125
...to the pericentromeric and SDs at the boundaries of inversions [Linardopoulou et al. 2005; Porubsky et al. 2020; Yoo et al. 2025]) may function as an incubator for the birth of new genes in ape s. This implicit genomic instability may confer a long-term selective advantage if the genes evolve function important...
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Method: BayesRVAT enhances rare-variant association testing through Bayesian aggregation of functional annotations
- Antonio Nappi,
- Liubov Shilova,
- Theofanis Karaletsos,
- Na Cai,
- and Francesco Paolo Casale
Genome Res. December 2025 35: 2682-2690; Published in Advance October 24, 2025, doi:10.1101/gr.280689.125
...of -wide variants. Nat Biotechnol doi:10.1038/s41587-024-02511-w ↵Brandes N, Linial N, Linial M. 2020. PWAS: proteome-wide association study—linking genes and phenotypes by functional variation in proteins. Genome Biol 21: 173. doi:10.1186/s13059-020-02089-x ↵Brandes N, Goldman G, Wang CH, Ye CJ, Ntranos V...
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Research: Molecular and genetic landscapes of retina and brain microglia in neurodegenerative diseases
- Khang Ma and
- Rinki Ratnapriya
Genome Res. October 2025 35: 2143-2157; Published in Advance August 26, 2025, doi:10.1101/gr.280554.125
...that genetic variants associated with AMD and AD are linked to microglia-specific gene signatures. Furthermore, integrating regulatory annotations with GWAS data shows that susceptibility loci for both AMD and AD are notably enriched in the open chromatin regions of microglia from the brain and retina...
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Method: Resolving the chromatin impact of mosaic variants with targeted Fiber-seq
- Stephanie C. Bohaczuk,
- Zachary J. Amador,
- Chang Li,
- Benjamin J. Mallory,
- Elliott G. Swanson,
- Jane Ranchalis,
- Mitchell R. Vollger,
- Katherine M. Munson,
- Tom Walsh,
- Morgan O. Hamm,
- Yizi Mao,
- Andre Lieber,
- and Andrew B. Stergachis
Genome Res. December 2024 34: 2269-2278; Published in Advance December 9, 2024, doi:10.1101/gr.279747.124
...-in of an illustrative locus showing m6A events (purple ticks) across individual fibers.ResultsTo assess the chromatin impact of variants across extended genomic loci, we designed targeted Fiber-seq to simultaneously capture multiple 100–250 kb genomic loci using a CRISPR–Cas9 targeting approach. Specifically, four...
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Resource: A map of enhancer regions in primary human neural progenitor cells using capture STARR-seq
- Sophia C. Gaynor-Gillett,
- Lijun Cheng,
- Manman Shi,
- Jason Liu,
- Gaoyuan Wang,
- Megan Spector,
- Qiuyu Guo,
- Le Qi,
- Mary Flaherty,
- Martha Wall,
- Ahyeon Hwang,
- Mengting Gu,
- Zhanlin Chen,
- Yuhang Chen,
- PsychENCODE Consortium,
- Jennifer R. Moran,
- Jing Zhang,
- Donghoon Lee,
- Mark Gerstein,
- Daniel Geschwind,
- and Kevin P. White
Genome Res. August 2025 35: 1887-1901; Published in Advance July 11, 2025, doi:10.1101/gr.279584.124
.... 2022; Deng et al. 2024; Farrow et al. 2024) and large-scale eQTL analyses from the Genotype-Tissue Expression (GTEx) project (GTEx Consortium 2017). Eight of the significant variants are located within the 17q21.31 region, which is a 1.5-Mb inversion region (Bowles et al. 2022). Two major haplotypes, H...
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Method: Highly accurate assembly polishing with DeepPolisher
- Mira Mastoras,
- Mobin Asri,
- Lucas Brambrink,
- Prajna Hebbar,
- Alexey Kolesnikov,
- Daniel E. Cook,
- Maria Nattestad,
- Julian Lucas,
- Taylor S. Won,
- Pi-Chuan Chang,
- Andrew Carroll,
- Benedict Paten,
- Kishwar Shafin,
- and and the Human Pangenome Reference Consortium
Genome Res. July 2025 35: 1595-1608; Published in Advance May 19, 2025, doi:10.1101/gr.280149.124
...it was trained on (DeepConsensus v1.2). This includes Sequel II, DeepConsensus v0.2, and Revio with DeepConsensus v1.1 (Supplemental Figs. 1, 2; Supplemental Tables 3, 8).We stratified the GIAB variant-calling errors by genomic region and found that the majority of indel errors removed by DeepPolisher were...
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Research: Birth of protein-coding exons by ancient domestication of LINE-1 retrotransposon
- Koichi Kitao,
- Kenji Ichiyanagi,
- and So Nakagawa
Genome Res. June 2025 35: 1287-1300; Published in Advance May 8, 2025, doi:10.1101/gr.280007.124
...isoform by transposon exonization, which is involved in the primate-specific immune response (Pasquesi et al. 2024). Thus, the emergence of transposon-derived exons has been revealed with higher resolution. Future comparative genomic analyses will elucidate the extent to which these exons are fixed...
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Research: Continuous infiltration and evolutionary trajectory of nuclear organelle DNA in Oryza
- Chenbo Gong,
- Yicheng Huang,
- Mengmeng Liu,
- Yong Zhou,
- Yinwei Xu,
- Nahed Mohammed,
- Xintong Qiao,
- Andrea Zuccolo,
- Weibo Xie,
- Rod A. Wing,
- Jianwei Zhang,
- Fei Zhou,
- and Yongjun Lin
Genome Res. June 2025 35: 1349-1363; Published in Advance April 25, 2025, doi:10.1101/gr.279609.124
...,E; Supplemental Table S8), which are difficult to explain by c-NHEJ- or alt-EJ-mediated mechanisms. In addition to DSBR pathways, RBMs such as FoSTeS/MMBIR could explain nonrecurrent structural variants such as complex genomic rearrangements containing multiple breakpoints, insertions of DNA segments...
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Research: Multiple paralogs and recombination mechanisms contribute to the high incidence of 22q11.2 deletion syndrome
- Lisanne Vervoort,
- Nicolas Dierckxsens,
- Marta Sousa Santos,
- Senne Meynants,
- Erika Souche,
- Ruben Cools,
- Tracy Heung,
- Koen Devriendt,
- Hilde Peeters,
- Donna M. McDonald-McGinn,
- Ann Swillen,
- Jeroen Breckpot,
- Beverly S. Emanuel,
- Hilde Van Esch,
- Anne S. Bassett,
- and Joris R. Vermeesch
Genome Res. April 2025 35: 786-797; Published in Advance November 13, 2024, doi:10.1101/gr.279331.124
..., resulting in reciprocal deletions, duplications, and inversions (Inoue and Lupski 2002; Porubsky et al. 2022). These recurrent genomic rearrangements often cause genomic disorders, forming collectively an important cause of disabling diseases in the general population (Angelis et al. 2015).The 22q11...
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Mini-Review: A Hitchhiker's Guide to long-read genomic analysis
- Medhat Mahmoud,
- Daniel P. Agustinho,
- and Fritz J. Sedlazeck
Genome Res. April 2025 35: 545-558; doi:10.1101/gr.279975.124
...variants, and deeper insights into the interplay between epigenetics and genomic variation. This mini-review provides a comprehensive overview of the latest developments in long-read DNA sequencing analysis, encompassing reference-based and de novo assembly approaches. We explore the entire workflow, from...

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