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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 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: 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
...to the expected size of species from this genus (Table 1). Primary scaffolding of the assembled contigs was accomplished with the aid of DNA restriction enzyme site-based imaging (BioNano) for X. maculatus and X. couchianus and proximity ligation maps (Hi-C) for X. helleri. The final assemblies display similar...
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Method: Nanopore-based consensus sequencing enables accurate multimodal tumor cell-free DNA profiling
- Li-Ting Chen,
- Myrthe Jager,
- Dàmi Rebergen,
- Geertruid J. Brink,
- Tom van den Ende,
- Willem Vanderlinden,
- Pauline Kolbeck,
- Marc Pagès-Gallego,
- Ymke van der Pol,
- Nicolle Besselink,
- Norbert Moldovan,
- Nizar Hami,
- Wigard P. Kloosterman,
- Hanneke van Laarhoven,
- Florent Mouliere,
- Ronald Zweemer,
- Jan Lipfert,
- Sarah Derks,
- Alessio Marcozzi,
- and Jeroen de Ridder
Genome Res. April 2025 35: 886-899; Published in Advance January 13, 2025, doi:10.1101/gr.279144.124
...of sequencing platforms are used for -wide cfDNA sequencing, including Illumina sequencing, Oxford Nanopore Technologies (nanopore) sequencing, and PacBio sequencing (Cristiano et al. 2019; Choy et al. 2022; Lau et al. 2023), with Illumina sequencing being the predominant platform owing to its low-cost per base...
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Research: Xist upstream deletion leads to dysregulation of Xist and autosomal gene expression
- Sudeshna Majumdar,
- Lakshmi Sowjanya Bammidi,
- Hemant C. Naik,
- Avinchal Manhas,
- Runumi Baro,
- Akash Kalita,
- Amlan Jyoti Naskar,
- Sundarraj Nidharshan,
- Girija S. Bariha,
- Dimple Notani,
- and Srimonta Gayen
Genome Res. September 2025 35: 1992-2010; Published in Advance August 6, 2025, doi:10.1101/gr.279822.124
...to the WT (Fig. 7A). Concordant with the increased contacts between Xist and Ftx loci in D1ΔXp cells, we found increased occupancy of RAD21 encompassing the Xist and Ftx loci (Fig. 7B). On the other hand, we observed loss of few CTCF peaks at these loci (Fig. 7C). Taken together, we conclude that deletion...
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Research: Multiple paralogs and recombination mechanisms contribute to the high incidence of 22q11.2 deletion syndrome
- Lisanne Vervoort,
- Nicolas Dierckxsens,
- Marta Sousa Santos,
- Senne Meynants,
- Erika Souche,
- Ruben Cools,
- Tracy Heung,
- Koen Devriendt,
- Hilde Peeters,
- Donna M. McDonald-McGinn,
- Ann Swillen,
- Jeroen Breckpot,
- Beverly S. Emanuel,
- Hilde Van Esch,
- Anne S. Bassett,
- and Joris R. Vermeesch
Genome Res. April 2025 35: 786-797; Published in Advance November 13, 2024, doi:10.1101/gr.279331.124
...scored, by assessing the presence or absence of the spectrum orange fluorescent probe targeting the 22q11.2 HIRA region.Targeted interphase-FISHBAC DNA was extracted from BAC clones (BacPac Resources, CHORI, Oakland) using the Nucleobond Xtra BAC kit (Macherey-Nagel) and subsequently labeled (Nick...
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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
...translocation in Z-138 cells revealed that an oncogenic fusion TAD is created, encompassing CCND1 and the IGH super-enhancers. We predicted how the structure and expression of CCND1 changes in these different cell lines, validating this using qPCR and fluorescence in situ hybridization microscopy. Our work...
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Method: STCC enhances spatial domain detection through consensus clustering of spatial transcriptomics data
- Congcong Hu,
- Nana Wei,
- Jiyuan Yang,
- Hua-Jun Wu,
- and Xiaoqi Zheng
Genome Res. June 2025 35: 1415-1428; Published in Advance May 12, 2025, doi:10.1101/gr.280031.124
...analyzing tumor samples that display scattered cell type distribution patterns, integration of a single baseline method yields satisfactory performance. For consensus strategies, average-based and hypergraph-based approaches demonstrate optimal precision and stability. Overall, STCC provides a scalable...
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Method: SLIC-CAGE: high-resolution transcription start site mapping using nanogram-levels of total RNA
- Nevena Cvetesic,
- Harry G. Leitch,
- Malgorzata Borkowska,
- Ferenc Müller,
- Piero Carninci,
- Petra Hajkova,
- and Boris Lenhard
Genome Res. December 2018 28: 1943-1956; Published in Advance November 7, 2018, doi:10.1101/gr.235937.118
...data for -wide promoterome with 1000-fold less material than required by existing CAGE methods, by generating a complex, high-quality library from mouse embryonic day 11.5 primordial germ cells.Cap analysis of gene expression (CAGE) is used for -wide quantitative identification of polymerase II...
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