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Method: Early feature extraction drives model performance in high-resolution chromatin accessibility prediction
- Aayush Grover,
- Till Muser,
- Liine Kasak,
- Lin Zhang,
- Ekaterina Krymova,
- and Valentina Boeva
Genome Res. March 2026 36: 619-629; Published in Advance January 12, 2026, doi:10.1101/gr.281042.125
...of noncoding genetic variants and the decoding of regulatory element architecture (Zhou and Troyanskaya 2015; Kelley et al. 2018; Avsec et al. 2021a; Pampari et al. 2024). Accurate, high-resolution maps of chromatin accessibility are essential for downstream tasks such as identifying regulatory elements...
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Method: High-resolution spatial transcriptomics in fixed tissue using a cost-effective PCL-seq workflow
- Xue Dong,
- Mengzhu Hu,
- Xiaonan Cui,
- Wenjian Zhou,
- Jingtao Cai,
- Guangyao Mao,
- and Weiyang Shi
Genome Res. September 2025 35: 2052-2063; Published in Advance August 5, 2025, doi:10.1101/gr.279906.124
...regulation layers and the complex mechanisms controlling cellular function.Whereas PCL-seq achieves high-resolution spatial profiling within individual ROIs, broader applications are currently constrained by technical limitations in throughput and ROI discrimination. The moderate ligation efficiency (∼60...
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Research: High resolution genomes of multiple Xiphophorus species provide new insights into microevolution, hybrid incompatibility, and epistasis
- Yuan Lu,
- Edward Rice,
- Kang Du,
- Susanne Kneitz,
- Magali Naville,
- Corentin Dechaud,
- Jean-Nicolas Volff,
- Mikki Boswell,
- William Boswell,
- LaDeana Hillier,
- Chad Tomlinson,
- Kremitzki Milin,
- Ronald B. Walter,
- Manfred Schartl,
- and Wesley C. Warren
Genome Res. April 2023 33: 557-571; Published in Advance May 5, 2023, doi:10.1101/gr.277434.122
...High resolution s of multiple Xiphophorus species provide new insights into microevolution, hybrid incompatibility, and epistasis Yuan Lu1,9, Edward Rice2,9, Kang Du1, Susanne Kneitz3, Magali Naville4, Corentin Dechaud4, Jean-Nicolas Volff4, Mikki Boswell1, William Boswell1, LaDeana Hillier5, Chad...
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Method: Ultra-long sequencing for contiguous haplotype resolution of the human immunoglobulin heavy-chain locus
- Mari B. Gornitzka,
- Egil Røsjø,
- Uddalok Jana,
- Easton E. Ford,
- Alan Tourancheau,
- William D. Lees,
- Zachary Vanwinkle,
- Melissa L. Smith,
- Corey T. Watson,
- and Andreas Lossius
Genome Res. October 2025 35: 2240-2251; Published in Advance August 21, 2025, doi:10.1101/gr.280400.125
....7 per 100 kb). When we mapped the Q100 Chromosome 14 and our ONT IGH assemblies to the custom IGH reference, we observed, as expected, that large portions of the HG002 IGH locus and corresponding genes were deleted relative to the custom IGH reference (Fig. 3A,B). Notably, our assembly of haplotype 2...
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Resource: A high-resolution map of small-scale inversions in the gibbon genome
- Ludovica Mercuri,
- Donato Palmisano,
- Alberto L'Abbate,
- Pietro D'Addabbo,
- Francesco Montinaro,
- Claudia Rita Catacchio,
- Patrick Hasenfeld,
- Mario Ventura,
- Jan O. Korbel,
- Ashley D. Sanders,
- Flavia Angela Maria Maggiolini,
- and Francesca Antonacci
Genome Res. October 2022 32: 1941-1951; Published in Advance September 30, 2022, doi:10.1101/gr.276960.122
...A high-resolution map of small-scale inversions in the gibbon Ludovica Mercuri1, Donato Palmisano1, Alberto L'Abbate2, Pietro D'Addabbo1, Francesco Montinaro1,3, Claudia Rita Catacchio1, Patrick Hasenfeld4, Mario Ventura1, Jan O. Korbel4, Ashley D. Sanders5,6,7, Flavia Angela Maria Maggiolini1...
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Method: NicE-C efficiently reveals open chromatin–associated chromosome interactions at high resolution
- Zhengyu Luo,
- Ran Zhang,
- Tengfei Hu,
- Yuting Zhu,
- Yueming Wu,
- Wenfei Li,
- Zhi Zhang,
- Xuebiao Yao,
- Haiyi Liang,
- and Xiaoyuan Song
Genome Res. March 2022 32: 534-544; Published in Advance February 1, 2022, doi:10.1101/gr.275986.121
..., Ewels PA, et al. 2015. Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C. Nat Genet 47: 598–606. doi:10.1038/ng.3286 ↵Mumbach MR, Rubin AJ, Flynn RA, Dai C, Khavari PA, Greenleaf WJ, Chang HY. 2016. HiChIP: efficient and sensitive analysis of protein...
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Resource: A chromosome-scale epigenetic map of the Hydra genome reveals conserved regulators of cell state
- Jack F. Cazet,
- Stefan Siebert,
- Hannah Morris Little,
- Philip Bertemes,
- Abby S. Primack,
- Peter Ladurner,
- Matthias Achrainer,
- Mark T. Fredriksen,
- R. Travis Moreland,
- Sumeeta Singh,
- Suiyuan Zhang,
- Tyra G. Wolfsberg,
- Christine E. Schnitzler,
- Andreas D. Baxevanis,
- Oleg Simakov,
- Bert Hobmayer,
- and Celina E. Juliano
Genome Res. February 2023 33: 283-298; Published in Advance January 13, 2023, doi:10.1101/gr.277040.122
...A chromosome-scale epigenetic map of the Hydra reveals conserved regulators of cell state Jack F. Cazet1, Stefan Siebert1,2, Hannah Morris Little1, Philip Bertemes3, Abby S. Primack1, Peter Ladurner3, Matthias Achrainer3, Mark T. Fredriksen4, R. Travis Moreland4, Sumeeta Singh4, Suiyuan Zhang4...
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Method: Accessible Region Conformation Capture (ARC-C) gives high-resolution insights into genome architecture and regulation
- Ni Huang,
- Wei Qiang Seow,
- Alex Appert,
- Yan Dong,
- Przemyslaw Stempor,
- and Julie Ahringer
Genome Res. February 2022 32: 357-366; Published in Advance December 21, 2021, doi:10.1101/gr.275669.121
.... Furthermore, we discover that inactive compartment interactions are dependent on H3K9 methylation. ARC-C is a powerful new tool to interrogate architecture and regulatory interactions at high resolution.The development and application of chromosome conformation capture methods have been instrumental...
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Research: Identification of the male-specific region on the guppy Y Chromosome from a haplotype-resolved assembly
- Kang Du,
- Oliver Deusch,
- Ilja Bezrukov,
- Christa Lanz,
- Yann Guiguen,
- Margarete Hoffmann,
- Anette Habring,
- Detlef Weigel,
- Manfred Schartl,
- and Christine Dreyer
Genome Res. March 2025 35: 489-498; Published in Advance March 5, 2025, doi:10.1101/gr.279582.124
...Poecilia wingei and Poecilia obscura (Nanda et al. 2014). This analysis revealed polymorphisms in heterochromatin content of the Y as well as differences in distance of the genetic marker M_229 to the physical chromosome end between populations. The sex determination locus (SDL) was mapped to the most...
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Method: High-resolution simulations of chromatin folding at genomic rearrangements in malignant B cells provide mechanistic insights into proto-oncogene deregulation
- Daniel Rico,
- Daniel Kent,
- Nefeli Karataraki,
- Aneta Mikulasova,
- Rolando Berlinguer-Palmini,
- Brian A. Walker,
- Biola M. Javierre,
- Lisa J. Russell,
- and Chris A. Brackley
Genome Res. July 2022 32: 1355-1366; Published in Advance July 21, 2022, doi:10.1101/gr.276028.121
...that dramatically changes the local environment of CCND1: it relocates to Chromosome 14 where it becomes juxtaposed with the joining region of the IGH locus. Although the t(11;14) rearrangement is common, the breakpoint has not previously been mapped in this cell line. Using paired-end read targeted DNA sequencing...
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