Searching journal content for articles similar to Rico et al. 32 (7): 1355.

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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
...performer, better preserving the signal’s shape. Our codebase and benchmarks provide practical tools for high-resolution chromatin modeling.Predicting chromatin accessibility from DNA sequence is one of the central challenges in regulatory genomics, with applications including the interpretation...
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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: 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: Dynamic barriers modulate cohesin positioning and genome folding at fixed occupancy
- Hadi Rahmaninejad,
- Yao Xiao,
- Maxime M.C. Tortora,
- and Geoffrey Fudenberg
Genome Res. August 2025 35: 1745-1757; Published in Advance July 8, 2025, doi:10.1101/gr.280108.124
...background because a global background leads to high scores along any enriched contact stripe or at the edge of any domain. We considered dot strengths across genomic distances between 100 kb and 5 Mb, a range based on the amount of simulated chromatin that enables quantification in simulations with either...
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Research: Genomic regulatory landscape underlying the antiviral response of Atlantic salmon
- Shahmir Naseer,
- Thomas C Clark,
- Bertrand Collet,
- Pooran Dewari,
- Damir Baranasic,
- Daniel J Macqueen,
- Pierre Boudinot,
- and Samuel A.M. Martin
Genome Res. October 22, 2025 gr.280579.125; Published in Advance October 22, 2025, doi:10.1101/gr.280579.125
...activation of regulatory regions during 313 the antiviral response. These findings provide a high-resolution view of chromatin state 314 13 dynamics, illustrating the diversity of regulatory landscapes and their functional relevance in 315 response to poly I:C stimulation. 316 To identify transcription...
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Research: Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation
- Kevin Moyung,
- Yulong Li,
- Heather K. MacAlpine,
- Alexander J. Hartemink,
- and David M. MacAlpine
Genome Res. January 2026 36: 115-128; Published in Advance December 9, 2025, doi:10.1101/gr.279637.124
...-based transcriptional regulatory networks. Overall, these results illustrate the power of an approach combining genetic perturbation with high-resolution epigenomic profiling; the latter enables a close examination of the interplay between TFs and nucleosomes -wide, providing a deeper, more mechanistic understanding...
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Mini-Review: The chromatin tapestry as a framework for neurodevelopment
- Ben Nolan,
- Timothy E. Reznicek,
- Christopher T. Cummings,
- and M. Jordan Rowley
Genome Res. October 2024 34: 1477-1486; doi:10.1101/gr.278408.123
...of this chromatin landscape in healthy neurodevelopment, as well as the diseases that occur with aberrant chromatin architecture. We discuss insights into the fundamental mechanistic relationship between histone modifications, DNA methylation, and organization. We then discuss findings that reveal how...
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Research: Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
- Dongying Xie,
- Pohao Ye,
- Yiming Ma,
- and Zhongying Zhao
Genome Res. March 2026 36: 506-521; Published in Advance February 17, 2026, doi:10.1101/gr.280885.125
...Pan analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility Dongying Xie1,2,3, Pohao Ye1,3, Yiming Ma1 and Zhongying Zhao1 1Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China; 2Institute for Research...
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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
...regulatory elements. We previously defined 15,714 promoter and 19,231 enhancer elements in C. elegans (Jänes et al. 2018). To identify chromatin interactions between these and other genomic elements at high resolution, we separated the into 500-bp bins and identified those that interacted significantly...
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