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Mini-Review: Evolution of genome-wide methylation profiling technologies
- Carolina Montano and
- Winston Timp
Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
...comprehensive genomic and epigenomic profiles of patients. Instances of ultrarapid sequencing in critical care settings have demonstrated the effectiveness of same-day LRS workflows for clinical genetics, as shown by Gorzynski et al. (2022) and Goenka et al. (2022).LRS technologies have now reached levels...
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Research: Assessing the readiness of Oxford Nanopore sequencing for clinical genomics applications
- Judith Arres,
- Santosh Elavalli,
- Shalini Behl,
- Daniel Matias Sanchez,
- Ayesha Al Ali,
- Abdelrahman Ahmed Yehia Abdelaziz Saad,
- Azza Attia,
- Cyla Minas,
- Sharika Pariyachery,
- Shariq Ahmed,
- Fatmah Aldhuhoori,
- Nitu Thulasidharan,
- Gurunath Katagi,
- Omar Soliman,
- Shilp Purohit,
- Vinay Kusuma,
- Raony Cardenas,
- Thyago Cardoso,
- Luis F. Paulin,
- Philippe Sanio,
- Joseph Mafofo,
- Haiguo Wu,
- Val Zvereff,
- Albarah El-Khani,
- Fahed Al Marzooqi,
- Tiago R. Magalhães,
- Fritz J. Sedlazeck,
- and Javier Quilez
Genome Res. March 2026 36: 460-471; Published in Advance February 11, 2026, doi:10.1101/gr.280134.124
...Bio) and Oxford Nanopore Technologies (ONT), both advancing toward clinical applications (for review, see Oehler et al. 2023). With the growing adoption of LRS, several population-scale initiatives are under way (De Coster et al. 2021), and programs such as All of Us and Genomics England have implemented ONT...
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Method: Iterative improvement of deep learning models using synthetic regulatory genomics
- André M. Ribeiro-dos-Santos and
- Matthew T. Maurano
Genome Res. November 2025 35: 2539-2549; Published in Advance October 22, 2025, doi:10.1101/gr.280540.125
...by the standing genetic variation and the effects of selection. A synthetic regulatory genomic approach is uniquely able to uncover novel biology, and these new technologies will move the field toward consideration of regulatory function at a locus scale.Recent work applying synthetic regulatory genomics has...
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Research: Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis-regulatory modules acting during vertebrate organogenesis
- Daniela M. Riley,
- Randa Elsayed,
- Mark D. Walsh,
- Simaran Johal,
- Ying Lin,
- Harry Walton,
- Till Bretschneider,
- Sascha Ott,
- and Andrew C. Nelson
Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
...Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cisregulatory modules acting during vertebrate organogenesis Daniela M. Riley,1,7 Randa Elsayed,1,7 Mark D. Walsh,2,7 Simaran Johal,2 Ying Lin,3,4 Harry Walton,1 Till Bretschneider,5 Sascha Ott,1...
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Method: Spatial domain detection using contrastive self-supervised learning for spatial multi-omics technologies
- Jianing Yao,
- Jinglun Yu,
- Brian Caffo,
- Stephanie C. Page,
- Keri Martinowich,
- and Stephanie C. Hicks
Genome Res. July 2025 35: 1621-1632; Published in Advance May 20, 2025, doi:10.1101/gr.279380.124
...; Maniatis et al. 2019; Chen et al. 2020; Ji et al. 2020). Examples of these types of multi-omics technologies include measuring RNA and protein (DBiT-seq [Liu et al. 2020] or the 10x Genomics Visium Spatial Proteogenomics [SPG] [https://www.10xgenomics...
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Review: k-mer approaches for biodiversity genomics
- Katharine M. Jenike,
- Lucía Campos-Domínguez,
- Marilou Boddé,
- José Cerca,
- Christina N. Hodson,
- Michael C. Schatz,
- and Kamil S. Jaron
Genome Res. February 2025 35: 219-230; Published in Advance January 31, 2025, doi:10.1101/gr.279452.124
...available s displays a wonderful diversity in size, composition, and structure and is quickly expanding thanks to several global biodiversity genomics initiatives. However, sequencing of s, even with the latest technologies, can still be challenging for both technical (e.g., small physical size...
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Research: Long-read genomics reveal extensive nuclear-specific evolution and allele-specific expression in a dikaryotic fungus
- Rita Tam,
- Mareike Möller,
- Runpeng Luo,
- Zhenyan Luo,
- Ashley Jones,
- Sambasivam Periyannan,
- John P. Rathjen,
- and Benjamin Schwessinger
Genome Res. June 2025 35: 1364-1376; Published in Advance April 11, 2025, doi:10.1101/gr.280359.124
...-resolved assemblies have become the norm in eukaryotic genomics with advances in long-read sequencing technologies. Complete assemblies are fundamental for addressing key questions in biology that were previously hidden in the “dark matter” of s. Key breakthroughs have revolved around centromeres and the embedded...
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Editorial: Revolutionizing genomics and medicine—one long molecule at a time
- Ana Conesa,
- Alexander Hoischen,
- and Fritz J. Sedlazeck
Genome Res. November 2024 34: ix-xi; doi:10.1101/gr.280179.124
...and broad interest in the technologies and the next round of revolutionary genomic science enabled by them. This interest is rooted in that all long-read technologies combine the core benefit of utilizing much longer DNA molecules (from tens of kb to Mb-scale), which offers several benefits common to most...
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Perspective: The impact of long-read sequencing on human population-scale genomics
- Tobias Rausch,
- Tobias Marschall,
- and Jan O. Korbel
Genome Res. April 2025 35: 593-598; doi:10.1101/gr.280120.124
...progress, challenges remain in scaling long-read technologies to large populations due to cost, computational complexity, and the lack of tools to facilitate the efficient interpretation of SVs in graphs. This perspective provides a succinct review on the current state of long-read sequencing in genomics...
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Method: Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease
- Tanner D. Jensen,
- Bohan Ni,
- Chloe M. Reuter,
- John E. Gorzynski,
- Sarah Fazal,
- Devon Bonner,
- Rachel A. Ungar,
- Pagé C. Goddard,
- Archana Raja,
- Euan A. Ashley,
- Jonathan A. Bernstein,
- Stephan Zuchner,
- Undiagnosed Diseases Network,
- Michael D. Greicius,
- Stephen B. Montgomery,
- Michael C. Schatz,
- Matthew T. Wheeler,
- and Alexis Battle
Genome Res. April 2025 35: 914-928; Published in Advance March 20, 2025, doi:10.1101/gr.279323.124
...University, Stanford, California 94305, USA; 4Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California 94305, USA; 5Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University...
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