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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
...disparities and promote equity in precision medicine (Rhead et al. 2023). This creates a need for new, efficient, and accurate data-driven algorithmic tools to store, visualize, and characterize high-dimensional genomic data. Whereas many traditional statistical techniques for genomic data like hidden Markov...
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Method: Read-level genotyping of short tandem repeats using long reads and single-nucleotide variation with STRkit
- David R. Lougheed,
- Tomi Pastinen,
- and Guillaume Bourque
Genome Res. March 2026 36: 578-588; Published in Advance January 15, 2026, doi:10.1101/gr.280766.125
...motif composition can also affect phenotype: insertion of a stretch of a noncanonical motif into a noncoding STR in the DAB1 gene is responsible for a form of spinocerebellar ataxia (Seixas et al. 2017). Beyond expansion detection, precisely determining copy number and motif composition in disease...
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Method: Automated interpretable artificial intelligence genomic prediction with AlGP
- Lei Wei,
- Ziqin Jiang,
- Baoliang Fan,
- Yidan Yan,
- Zhenqiang Xu,
- Xiaoxiang Hu,
- and Yuzhe Wang
Genome Res. March 5, 2026 ; Published in Advance March 5, 2026, doi:10.1101/gr.281006.125
....] Using genomic mutations to predict phenotypes and explain phenotypic variation is one of the primary objectives of precision medicine, as well as contemporary animal and plant breeding (Wiggans et al. 2011; Moon et al. 2023). The process of genomic prediction (GP), which encompasses the transition from...
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Research: Modest increase in the de novo single-nucleotide mutation rate in house mice born by assisted reproduction
- Laura Blanco-Berdugo,
- Alexis Garretson,
- and Beth L. Dumont
Genome Res. January 2026 36: 50-60; Published in Advance November 13, 2025, doi:10.1101/gr.281180.125
...not precisely replicate those encountered in the maternal reproductive tract (Konstantogianni et al. 2024); exposure to either hyperoxic or hypoxic culture conditions can promote DNA damage and genomic instability (Gille et al. 1994; Bristow and Hill 2008). Additionally, compounds such as glucocorticoids...
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Resource: The ggRibo single-gene viewer reveals insights into translatome and other nucleotide-resolution omics data
- Hsin-Yen Larry Wu,
- Isaiah D. Kaufman,
- and Polly Yingshan Hsu
Genome Res. September 2025 35: 2130-2142; Published in Advance July 22, 2025, doi:10.1101/gr.280480.125
...) now offer opportunities to develop specialized software packages for multiomic data visualization.Ribo-seq is a widely used technique for studying noncanonical open reading frames (ORFs) and mechanisms of mRNA translation at single-nucleotide resolution (Ingolia et al. 2009; Brar and Weissman 2015; Wu...
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Method: Robust and efficient annotation of cell states through gene signature scoring
- Laure Ciernik,
- Agnieszka Kraft,
- Florian Barkmann,
- Josephine Yates,
- and Valentina Boeva
Genome Res. March 2026 36: 630-644; Published in Advance February 18, 2026, doi:10.1101/gr.280926.125
...phenotype (Nevins and Potti 2007). One key application of signature scoring is cell annotation, as it offers a highly efficient and reliable method for classifying cells into types and states (Neftel et al. 2019). Notably, the quality of gene signatures plays a critical role in this process, as the accuracy...
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Method: Targeted, programmable, and precise tandem duplication in the mammalian genome
- Yaoge Jiao,
- Min Li,
- Xingyu He,
- Yanhong Wang,
- Junwei Song,
- Yun Hu,
- Li Li,
- Lifang Zhou,
- Lurong Jiang,
- Junyan Qu,
- Lifang Xie,
- Qiang Chen,
- and Shaohua Yao
Genome Res. May 2023 33: 779-786; Published in Advance June 9, 2023, doi:10.1101/gr.277261.122
...RNA (sgRNA) to promote the reannealing of the edited DNA strands and the duplication of the fragment in between. We showed that TD-PE produced robust and precise in situ tandem duplications of genomic fragments ranging from ∼50 bp to ∼10 kb, with a maximal efficiency up to 28.33%. By fine...
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Method: Efficient gene targeting by homology-directed repair in rat zygotes using TALE nucleases
- Séverine Remy,
- Laurent Tesson,
- Séverine Menoret,
- Claire Usal,
- Anne De Cian,
- Virginie Thepenier,
- Reynald Thinard,
- Daniel Baron,
- Marine Charpentier,
- Jean-Baptiste Renaud,
- Roland Buelow,
- Gregory J. Cost,
- Carine Giovannangeli,
- Alexandre Fraichard,
- Jean-Paul Concordet,
- and Ignacio Anegon
Genome Res. August 2014 24: 1371-1383; Published in Advance July 2, 2014, doi:10.1101/gr.171538.113
...-specific nucleases, such as ZFNs, TALE nucleases, and CRISPR/Cas9 have allowed the creation of rat knockout models. Genetic engineering by homology-directed repair (HDR) is utilized to create animals expressing transgenes in a controlled way and to introduce precise genetic modifications. We applied TALE nucleases...
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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
...provides novel insights into the genomic regulatory landscape underlying antiviral 33 immunity in a farmed fish with a complex . 34 Introduction 35 The innate immune response to viral infection, which is mainly based on the type I interferon 36 (type I IFN) pathway is crucial to both disease progression...
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Method: Structure-optimized sgRNA selection with PlatinumCRISPr for efficient Cas9 generation of knockouts
- Irmgard U. Haussmann,
- Thomas C. Dix,
- David W.J. McQuarrie,
- Veronica Dezi,
- Abdullah I. Hans,
- Roland Arnold,
- and Matthias Soller
Genome Res. December 2024 34: 2279-2292; Published in Advance December 3, 2024, doi:10.1101/gr.279479.124
...to the genomic target site (protospacer), which also requires the protospacer adjacent motif (PAM) at the 3′end, comprised of an NGG sequence (whereby N is any nucleotide and G is guanine). In addition to the target complementary sequence (spacer), the gRNA also contains a constant CRISPR RNA (crRNA) sequence...
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