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Method: Unsupervised contrastive peak caller for ATAC-seq
- Ha T.H. Vu,
- Yudi Zhang,
- Geetu Tuteja,
- and Karin S. Dorman
Genome Res. July 2023 33: 1133-1144; Published in Advance May 22, 2023, doi:10.1101/gr.277677.123
...in the deep learning tools, and the approaches available for traditional methods either cannot be applied to ATAC-seq, where control samples may be unavailable, or are post hoc and do not capitalize on potentially complex, but reproducible signal in the read enrichment data. Here, we propose a novel peak...
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Resource: Quadrupia provides a comprehensive catalog of G-quadruplexes across genomes from the tree of life
- Nikol Chantzi,
- Akshatha Nayak,
- Fotis A. Baltoumas,
- Eleni Aplakidou,
- Shiau Wei Liew,
- Jesslyn Elvaretta Galuh,
- Michail Patsakis,
- Austin Montgomery,
- Camille Moeckel,
- Ioannis Mouratidis,
- Saiful Arefeen Sazed,
- Wilfried Guiblet,
- Panagiotis Karmiris-Obratański,
- Guliang Wang,
- Apostolos Zaravinos,
- Karen M. Vasquez,
- Chun Kit Kwok,
- Georgios A. Pavlopoulos,
- and Ilias Georgakopoulos-Soares
Genome Res. November 2025 35: 2578-2600; Published in Advance August 26, 2025, doi:10.1101/gr.279790.124
.... These structures have demonstrably shaped organismal evolution. However, a comprehensive, organism-wide G-quadruplex map encompassing the diversity of life has remained elusive. Here, we introduce Quadrupia, the most extensive and well-characterized G-quadruplex database to date, facilitating the exploration of G...
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Research: Mapping multitissue regulatory variants reveals a liver-centric coexpression network associated with duck egg-laying performance
- Yang Xi,
- Jingjing Qi,
- Zhao Yang,
- Yutian Zeng,
- Huicong Zhang,
- Qiuyu Tao,
- Mengru Xu,
- Anqi Huang,
- Shenqiang Hu,
- Chunchun Han,
- Lili Bai,
- Jiwei Hu,
- Jiwen Wang,
- Liang Li,
- Lingzhao Fang,
- and Hehe Liu
Genome Res. October 2025 35: 2211-2225; Published in Advance September 10, 2025, doi:10.1101/gr.280345.124
...in ducks. Future functional validation of these regulatory pathways will help elucidate the mechanistic links between hepatic metabolism and reproductive activity.In summary, we provided a comprehensive multitissue catalog of regulatory variants in ducks. By integrating this resource with GWAS data, we...
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Resource: Cell type–specific gene regulatory atlas prioritizes drug targets and repurposable medicines in Alzheimer's disease
- Yunxiao Ren,
- Ming Hu,
- Yang E. Li,
- Andrew A. Pieper,
- Jeffrey Cummings,
- and Feixiong Cheng
Genome Res. March 2026 36: 645-659; Published in Advance January 21, 2026, doi:10.1101/gr.280436.125
...) Collection and preprocessing of snRNA-seq and snATAC-seq data sets in physical space. (B) Multiple analysis to identify an AD-associated gene list including differential gene expression analysis; identification of cCRE; cell type–specific, AD-associated risk variants; and peak-to-gene linkages. (C) Two...
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Resource: The PanOryza pangene catalog of Asian cultivated rice
- Bruno Contreras-Moreira,
- Eshan Sharma,
- Shradha Saraf,
- Guy Naamati,
- Parul Gupta,
- Justin Elser,
- Dmytro Chebotarov,
- Kapeel Chougule,
- Zhenyuan Lu,
- Sharon Wei,
- Andrew Olson,
- Ian Tsang,
- Disha Lodha,
- Yong Zhou,
- Zhichao Yu,
- Wen Zhao,
- Jianwei Zhang,
- Sandeep Amberkar,
- Kawinnat Sue-Ob,
- Zhi Sun,
- Maria Martin,
- Kenneth L. McNally,
- Doreen Ware,
- Eric W. Deutsch,
- Dario Copetti,
- Rod A. Wing,
- Pankaj Jaiswal,
- Sarah Dyer,
- and Andrew R. Jones
Genome Res. January 2026 36: 226-238; Published in Advance December 12, 2025, doi:10.1101/gr.280790.125
..., with the latter being the more widely used/reference annotations (for historical reasons).To study genetic variation, significant efforts have been made to identify variants on a large scale from high-throughput short DNA read sequencing, for example, via the 3000 Rice Genomes Project (Li et al. 2014; Wang et al...
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Research: Common cis-regulatory variation modifies the penetrance of pathogenic SHROOM3 variants in craniofacial microsomia
- Hao Zhu,
- Jiao Zhang,
- Soumya Rao,
- Matthew D. Durbin,
- Ying Li,
- Ruirui Lang,
- Jiqiang Liu,
- Baichuan Xiao,
- Hailin Shan,
- Ziqiu Meng,
- Jinmo Wang,
- Xiaokai Tang,
- Zhenni Shi,
- Liza L. Cox,
- Shouqin Zhao,
- Stephanie M. Ware,
- Tiong Y. Tan,
- Michelle de Silva,
- Lyndon Gallacher,
- Ting Liu,
- Jie Mi,
- Changqing Zeng,
- Hou-Feng Zheng,
- Qingguo Zhang,
- Stylianos E. Antonarakis,
- Timothy C. Cox,
- and Yong-Biao Zhang
Genome Res. May 2025 35: 1065-1079; Published in Advance April 15, 2025, doi:10.1101/gr.280047.124
...PMods). We additionally show that rs344131, located within a regulatory enhancer region of SHROOM3, demonstrates allele-specific effects on enhancer activity and thus impacts expression levels of the associated SHROOM3 allele harboring any rare coding variant. Our findings also suggest that CePMods may serve...
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Method: methyl-ATAC-seq measures DNA methylation at accessible chromatin
- Roman Spektor,
- Nathaniel D. Tippens,
- Claudia A. Mimoso,
- and Paul D. Soloway
Genome Res. June 2019 29: 969-977; Published in Advance June 3, 2019, doi:10.1101/gr.245399.118
.... For example, assay for transposase accessible chromatin sequencing (ATAC-seq) identifies nucleosome-depleted (open) chromatin, which harbors potentially active gene regulatory sequences; and bisulfite sequencing (BS-seq) quantifies DNA methylation. When two distinct chromatin features like these are assayed...
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Method: Iterative improvement of deep learning models using synthetic regulatory genomics
- André M. Ribeiro-dos-Santos and
- Matthew T. Maurano
Genome Res. November 2025 35: 2539-2549; Published in Advance October 22, 2025, doi:10.1101/gr.280540.125
...ESCs for all three payloads (Fig. 3C). The HPRT1 payload only showed accessibility by ATAC-seq at the gene promoter, and both the reversed payloads (SynHPRT1R and SynHPRT1RnoCpG) showed no accessibility at all. In comparison, Enformer predicted false-positive peaks in both HPRT1 and SynHPRT1RnoCpG payloads...
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Research: Ruminant-specific retrotransposons shape regulatory evolution of bovine immunity
- Conor J. Kelly,
- Carol G. Chitko-McKown,
- and Edward B. Chuong
Genome Res. August 2022 32: 1474-1486; Published in Advance August 10, 2022, doi:10.1101/gr.276241.121
...window Figure 2. Contribution of ruminant-specific TEs to the IFNG-inducible regulatory landscape. (A) Proportion of IFNG-inducible (n = 4198), IFNG-down-regulated (n = 1548), and nonresponsive H3K27ac peaks (n = 3494) where the internal ATAC-seq summit overlaps a TE. (B) Volcano plot visualizing family...
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Research: A gene regulatory element modulates myosin expression and controls cardiomyocyte response to stress
- Taylor Anglen,
- Irene M. Kaplow,
- Baekgyu Choi,
- Enya Dewars,
- Robin M. Perelli,
- Kevin T. Hagy,
- Duc Tran,
- Megan E. Ramaker,
- Svati H. Shah,
- Inkyung Jung,
- Andrew P. Landstrom,
- Ravi Karra,
- Yarui Diao,
- and Charles A. Gersbach
Genome Res. November 2025 35: 2418-2432; Published in Advance October 22, 2025, doi:10.1101/gr.280825.125
...for transposase-accessible chromatin using sequencing (ATAC-seq) and RNA sequencing (RNA-seq) on human induced pluripotent stem cell–derived cardiomyocytes (iPSC-CMs) to nominate cCREs (Corces et al. 2017). We then linked key regulatory elements to MYH6 and MYH7. We characterize the effects of epigenetic editing...
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