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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
...We evaluated four categories of deep learning architectures—CNNs, recurrent neural networks (specifically, LSTMs), dilated CNNs (dCNNs), and transformers, based on their ability to predict ATAC-seq signal at high resolution. To ensure a fair comparison, we standardized the experimental setup across models...
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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: 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: Genome variation and population structure among 1142 mosquitoes of the African malaria vector species Anopheles gambiae and Anopheles coluzzii
- The Anopheles gambiae 1000 Genomes Consortium
Genome Res. October 2020 30: 1533-1546; Published in Advance September 28, 2020, doi:10.1101/gr.262790.120
...The Anopheles gambiae 1000 Genomes Consortium1 2Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK 3MRC Centre for Genomics and Global Health, University of Oxford, Oxford OX3 7BN, UK 4Department of Vector Biology, Liverpool School of Tropical Medicine...
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Research: SWATH-MS-based proteogenomic analysis reveals the involvement of alternative splicing in poplar upon lead stress
- Fu-Yuan Zhu,
- Xin Chen,
- Yu-Chen Song,
- Lydia Pui Ying Lam,
- Yuki Tobimatsu,
- Bei Gao,
- Mo-Xian Chen,
- and Fu-Liang Cao
Genome Res. March 2023 33: 371-385; Published in Advance March 24, 2023, doi:10.1101/gr.277473.122
...-seq), including short-read RNA sequencing (srRNA-seq) and long-read RNA sequencing (lrRNA-seq), and a sequential window acquisition of all theoretical mass spectra (SWATH-MS)-based proteomic approach (i.e., proteogenomics). Transcriptomic and proteomic analyses have been individually applied in plant research...
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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
..., such as ChIP-seq and chromosome-conformation-capture methods like Hi-C, have transformed our understanding of the regulatory link between structure and function. For example, Hi-C, which probes chromosome interactions -wide, has revealed that the can be partitioned into topologically associated domains (TADs...
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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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Method: TraDIS-Xpress: a high-resolution whole-genome assay identifies novel mechanisms of triclosan action and resistance
- Muhammad Yasir,
- A. Keith Turner,
- Sarah Bastkowski,
- David Baker,
- Andrew J. Page,
- Andrea Telatin,
- Minh-Duy Phan,
- Leigh Monahan,
- George M. Savva,
- Aaron Darling,
- Mark A. Webber,
- and Ian G. Charles
Genome Res. February 2020 30: 239-249; Published in Advance February 12, 2020, doi:10.1101/gr.254391.119
...TraDIS-Xpress: a high-resolution whole- assay identifies novel mechanisms of triclosan action and resistance Muhammad Yasir1,5, A. Keith Turner1,5, Sarah Bastkowski1, David Baker1, Andrew J. Page1, Andrea Telatin1, Minh-Duy Phan2, Leigh Monahan3, George M. Savva1, Aaron Darling3, Mark A. Webber1...
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