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Method: Chromosome engineering to correct a complex rearrangement on Chromosome 8 reveals the effects of 8p syndrome on gene expression and neural differentiation
- Sophia N. Lee,
- Erin C. Banda,
- Lu Qiao,
- Sarah L. Thompson,
- Karan Singh,
- Ryan A. Hagenson,
- Teresa Davoli,
- Stefan F. Pinter,
- and Jason M. Sheltzer
Genome Res. March 2026 36: 547-560; Published in Advance January 12, 2026, doi:10.1101/gr.280425.125
....05 for defining differentially expressed genes.Whole- sequencing and copy number alteration detectionGenomic DNA was isolated as described above. Sequencing was performed using short-read human WGS services provided by GENEWIZ from Azenta Life Sciences, as previously described (https://www.genewiz.com). After...
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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
...approximately once in every 4000 births (Wei et al. 2022), with a higher rate in cancer cells (Ju et al. 2015; Wei et al. 2022), leading to high NUMT diversity across the human population. The insertion of mtDNA into the nuclear can cause genomic instability via mutations or disruption of normal gene function...
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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
...method. (Right) Comparative genomic features between interspecific and intraspecific strains, including sizes (A), gene numbers (B), repeat content as a percentage of the (C), proportions of repeat types among total repeats (D), gene length distributions (E), and coding DNA sequence (CDS) length...
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Review: Recent advances in methods to characterize archaic introgression in modern humans
- David Peede,
- Mayra M. Bañuelos,
- Jazeps Medina Tretmanis,
- Miriam Miyagi,
- and Emilia Huerta-Sánchez
Genome Res. February 2026 36: 239-256; Published in Advance January 16, 2026, doi:10.1101/gr.278993.124
...DNA suggested minimal to no Neanderthal contribution to the genetic diversity of modern human populations (Krings et al. 1997, 1999; Caramelli et al. 2003; Currat and Excoffier 2004; Serre et al. 2004). However, in 2010, the publication of the draft Neanderthal revealed that non-African populations...
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Research: Characterization of DNA methylation reader proteins in Arabidopsis thaliana
- Jonathan Cahn,
- James P.B. Lloyd,
- Ino D. Karemaker,
- Pascal W.T.C. Jansen,
- Jahnvi Pflueger,
- Owen Duncan,
- Jakob Petereit,
- Ozren Bogdanovic,
- A. Harvey Millar,
- Michiel Vermeulen,
- and Ryan Lister
Genome Res. December 2024 34: 2229-2243; Published in Advance December 4, 2024, doi:10.1101/gr.279379.124
...catalyzing DNA demethylation (erasers). Investigation of DNA methyltransferases in Arabidopsis thaliana has revealed sequence context-specific activity for these enzymes: MET1 is responsible for maintaining mCG, being recruited to hemimethylated sites after replication (Finnegan et al. 1996; Ronemus et al...
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Research: Leveraging the T2T assembly to resolve rare and pathogenic inversions in reference genome gaps
- Kristine Bilgrav Saether,
- Jesper Eisfeldt,
- Jesse D. Bengtsson,
- Ming Yin Lun,
- Christopher M. Grochowski,
- Medhat Mahmoud,
- Hsiao-Tuan Chao,
- Jill A. Rosenfeld,
- Pengfei Liu,
- Marlene Ek,
- Jakob Schuy,
- Adam Ameur,
- Hongzheng Dai,
- Undiagnosed Diseases Network,
- James Paul Hwang,
- Fritz J. Sedlazeck,
- Weimin Bi,
- Ronit Marom,
- Josephine Wincent,
- Ann Nordgren,
- Claudia M.B. Carvalho,
- and Anna Lindstrand
Genome Res. November 2024 34: 1785-1797; Published in Advance November 1, 2024, doi:10.1101/gr.279346.124
..., undetected by srGS and linked read sequencing (lirGS) in GRCh37 (Pettersson et al. 2020). No DNA was available for lrGS, but the inversion was identified in T2T-CHM13 (Fig. 1B; Supplemental Fig. S2), where it was visible by both srGS and de novo lirGS assembly. The 10q11 breakpoint, located in a region...
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Resource: A systems view on DNA damage response kinetics in Tetrahymena
- Emily Nischwitz,
- Vivien Schoonenberg,
- Rachel Mullner,
- Albert Fradera-Sola,
- Susanne Zimbelmann,
- Joshua J Smith,
- and Falk Butter
Genome Res. January 28, 2026 gr.281000.125; Published in Advance January 28, 2026, doi:10.1101/gr.281000.125
...excision 506 repair in yeast and mammals: Translational implications1. Cancer Res 63: 549–54. 507 Kovalchuk I. 2016. Chapter 38 - Conserved and Divergent Features of DNA Repair: 508 Future Perspectives in Genome Instability Research. In Genome Stability (eds. I. 509 Kovalchuk and O. Kovalchuk), pp. 651...
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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
...“logistic mixing,” a neural network without hidden layers that uses a simple update rule to adjust the output probabilities for better bitstream coding. This idea has been brought to genomic compression of sequencing reads with GeCo3 (Silva et al. 2020). Another recent use of neural networks for DNA...
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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. March 5, 2026 gr.281006.125; Published in Advance March 5, 2026, doi:10.1101/gr.281006.125
...prediction (GP), which 45 encompasses the transition from DNA variants to phenotypes, spans the entire central dogma 46 of molecular biology and incorporates various non-genetic factors, such as environmental 47 influences (Yao et al. 2025), and is one of the most challenging tasks in biological prediction...
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Research: Comprehensive functional annotation of ESR1-driven enhancers in breast cancer reveals hierarchical activity independent of genomic and epigenomic contexts
- Yanis Zekri,
- Sebastian Gregoricchio,
- Elif Yapıcı,
- Chia-Chi Flora Huang,
- Tunç Morova,
- Umut Berkay Altıntaş,
- Gozde Korkmaz,
- Nathan A. Lack,
- and Wilbert Zwart
Genome Res. July 2025 35: 1530-1543; Published in Advance June 10, 2025, doi:10.1101/gr.280320.124
...). Briefly, a custom oligonucleotide probe pool was designed to capture ESR1 binding regions from both clinical breast tumors and T-47D cell line ESR1 ChIP-seq. Pooled human genomic DNA was sheared, captured, PCR-amplified, and cloned into the hSTARR-ORI plasmid (Addgene, plasmid 99296). The ESR1-focused...

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