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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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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
..., Stanford University School of Engineering, Stanford, California 94305, USA Corresponding author: geleta@berkeley.eduAbstractModern biobanks are providing numerous high-resolution genomic sequences of diverse populations. In order to account for diverse and admixed populations, new algorithmic tools...
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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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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: 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
...Accessible Region Conformation Capture (ARC-C) gives high-resolution insights into architecture and regulation Ni Huang1,2, Wei Qiang Seow1,2, Alex Appert1, Yan Dong1, Przemyslaw Stempor1 and Julie Ahringer1 1The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge CB2 1...
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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
...); this is because there is enrichment of H3K27me3 at the promoter. There are also ‘active’ H3K4me1/3 modifications, which could indicate variation between alleles or across the population, with the gene sometimes expressed and sometimes repressed. Consistent with this, publicly available RNA-seq data (The ENCODE...
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Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
...Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster Harsh G. Shukla1,2, Mahul Chakraborty3 and J.J. Emerson1,4 1Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California 92697, USA; 2Graduate Program in Mathematical...
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Research: High-resolution structural genomics reveals new therapeutic vulnerabilities in glioblastoma
- Michael J. Johnston,
- Ana Nikolic,
- Nicoletta Ninkovic,
- Paul Guilhamon,
- Florence M.G. Cavalli,
- Steven Seaman,
- Franz J. Zemp,
- John Lee,
- Aly Abdelkareem,
- Katrina Ellestad,
- Alex Murison,
- Michelle M. Kushida,
- Fiona J. Coutinho,
- Yussanne Ma,
- Andrew J. Mungall,
- Richard Moore,
- Marco A. Marra,
- Michael D. Taylor,
- Peter B. Dirks,
- Trevor J. Pugh,
- Sorana Morrissy,
- Bradley St Croix,
- Douglas J. Mahoney,
- Mathieu Lupien,
- and Marco Gallo
Genome Res. August 2019 29: 1211-1222; Published in Advance June 27, 2019, doi:10.1101/gr.246520.118
...et al. 2015) and cancer (Flavahan et al. 2016) through dysregulation of gene expression programs. The global impact of architecture on transcriptional programs in gliomas and other brain tumors has been difficult to assess because of the lack of high-resolution 3D maps for these cancers. We...
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Research: Integrating genetic variation with deep learning provides context for variants impacting transcription factor binding during embryogenesis
- Olga M. Sigalova,
- Mattia Forneris,
- Frosina Stojanovska,
- Bingqing Zhao,
- Rebecca R. Viales,
- Adam Rabinowitz,
- Fayrouz Hammal,
- Benoît Ballester,
- Judith B. Zaugg,
- and Eileen E.M. Furlong
Genome Res. May 2025 35: 1138-1153; Published in Advance April 15, 2025, doi:10.1101/gr.279652.124
...as the primary source of information. The Drosophila dm6 reference served as the input for the training process. In essence, the Basenji model seeks to generate accurate and high-resolution genomic tracks by learning the complex relationships between DNA sequences and their corresponding genomic profiles (Kelley...
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