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Research: Ancient dog introgression into the Iberian wolf genome may have facilitated adaptation to human-dominated landscapes
- Diana Lobo,
- Hernán E. Morales,
- Cock Van Oosterhout,
- José Vicente López-Bao,
- Pedro Silva,
- Luis Llaneza,
- Carolina Pacheco,
- Diana Castro,
- Germán Hernández-Alonso,
- George Pacheco,
- John Archer,
- M. Thomas P. Gilbert,
- Nuno Ferrand,
- and Raquel Godinho
Genome Res. March 2025 35: 432-445; Published in Advance February 14, 2025, doi:10.1101/gr.279093.124
...Tree.Whole- sequencing approachWhole- sequences and SNP callingTo attain the requisite high resolution for detecting small genomic dog blocks and confirming the presence of the Δblock in Chromosome 2 of Iberian wolves, we generated whole-s for 12 of the contemporary Iberian wolves used in the SNP chip data set (Fig. 1B...
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Method: High-resolution genotype-free mapping of genetic variation with CRI-SPA-Map
- Sheila Lutz,
- Megan Lawler,
- Samuel Amidon,
- and Frank W Albert
Genome Res. March 23, 2026 gr.281514.125; Published in Advance March 23, 2026, doi:10.1101/gr.281514.125
...High-resolution, genotype-free mapping of genetic 1 variation with CRI-SPA-Map 2 3 Sheila Lutz*, Megan Lawler†, Samuel Amidon†, Frank W. Albert* 4 Department of Genetics, Cell Biology, & Development, 5 University of Minnesota, 6 6-160 Jackson Hall, 321 Church St SE 7 Minneapolis, MN 55455, USA 8...
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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
..., or attention mechanisms, drive performance in these high-resolution predictions. To address these knowledge gaps, we systematically evaluate classic architectural choices and introduce ConvNeXt V2 blocks, originally developed for computer vision, as high-resolution feature extractors in deep learning models...
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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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Resource: Haplotype-resolved genome and population genomics of the threatened garden dormouse in Europe
- Paige A. Byerly,
- Alina von Thaden,
- Evgeny Leushkin,
- Leon Hilgers,
- Shenglin Liu,
- Sven Winter,
- Tilman Schell,
- Charlotte Gerheim,
- Alexander Ben Hamadou,
- Carola Greve,
- Christian Betz,
- Hanno J. Bolz,
- Sven Büchner,
- Johannes Lang,
- Holger Meinig,
- Evax Marie Famira-Parcsetich,
- Sarah P. Stubbe,
- Alice Mouton,
- Sandro Bertolino,
- Goedele Verbeylen,
- Thomas Briner,
- Lídia Freixas,
- Lorenzo Vinciguerra,
- Sarah A. Mueller,
- Carsten Nowak,
- and Michael Hiller
Genome Res. November 2024 34: 2094-2107; Published in Advance November 14, 2024, doi:10.1101/gr.279066.124
...Alpine ridge to be strongly differentiated from all other sampling regions, as evidenced in our study by both model-based (STRUCTURE), and non-model-based (PCA) approaches. This strong signal of genetic differentiation displayed by the Alpine population further confirms prior mtDNA genetic distance...
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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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Research: A high resolution A-to-I editing map in the mouse identifies editing events controlled by pre-mRNA splicing
- Konstantin Licht,
- Utkarsh Kapoor,
- Fabian Amman,
- Ernesto Picardi,
- David Martin,
- Prajakta Bajad,
- and Michael F. Jantsch
Genome Res. September 2019 29: 1453-1463; Published in Advance August 19, 2019, doi:10.1101/gr.242636.118
...Biology PhD Program at Vienna BioCenter. Sequencing was performed at the VBCF NGS Unit (www.viennabiocenter.org/facilities). We thank the European Elixir infrastructure (https://www.elixir-europe.org/) and Elixir-ITA for supporting the development and maintenance of REDIportal, Interomics, and PRACE (Pra...
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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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Corrigendum: Corrigendum: 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. June 2022 32: 1229_2; doi:10.1101/gr.276968.122
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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
...conformation capture to enable robust and cost-effective detection of open chromatin interactions at high resolution, especially enhancer–promoter interactions. Using TNF stimulation and mouse kidney aging as models, we applied NicE-C to reveal characteristics of dynamic enhancer–promoter interactions...

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