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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
...of RNA modifications and read mapping with high-accuracy nanopore RNA basecalling models. Genome Res (this issue) 34: 1865–1877. doi:10.1101/gr.278849.123 ↵Eisfeldt J, Ameur A, Lenner F, de Boer ETB, Ek M, Wincent J, Vaz R, Ottosson J, Jonson T, Ivarsson S, et al. 2024a. A national long-read sequencing...
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Resource: Haplotype-resolved genome and population genomics of the threatened garden dormouse in Europe
- Paige A. Byerly,
- Alina von Thaden,
- Evgeny Leushkin,
- Leon Hilgers,
- Shenglin Liu,
- Sven Winter,
- Tilman Schell,
- Charlotte Gerheim,
- Alexander Ben Hamadou,
- Carola Greve,
- Christian Betz,
- Hanno J. Bolz,
- Sven Büchner,
- Johannes Lang,
- Holger Meinig,
- Evax Marie Famira-Parcsetich,
- Sarah P. Stubbe,
- Alice Mouton,
- Sandro Bertolino,
- Goedele Verbeylen,
- Thomas Briner,
- Lídia Freixas,
- Lorenzo Vinciguerra,
- Sarah A. Mueller,
- Carsten Nowak,
- and Michael Hiller
Genome Res. November 2024 34: 2094-2107; Published in Advance November 14, 2024, doi:10.1101/gr.279066.124
...Haplotype-resolved and population genomics of the threatened garden dormouse in Europe Paige A. Byerly1,2,16, Alina von Thaden1,2,16, Evgeny Leushkin1,3, Leon Hilgers1,3, Shenglin Liu1,3, Sven Winter4,5, Tilman Schell1,3, Charlotte Gerheim1,3, Alexander Ben Hamadou1,3, Carola Greve1,3, Christian...
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Resource: Construction and evaluation of a new rat reference genome assembly, GRCr8, from long reads and long-range scaffolding
- Kai Li,
- Melissa L. Smith,
- J. Chris Blazier,
- Kelli J. Kochan,
- Jonathan M.D. Wood,
- Kerstin Howe,
- Anne E. Kwitek,
- Melinda R. Dwinell,
- Hao Chen,
- Julia L. Ciosek,
- Patrick Masterson,
- Terence D. Murphy,
- Theodore S. Kalbfleisch,
- and Peter A. Doris
Genome Res. November 2024 34: 2081-2093; Published in Advance November 8, 2024, doi:10.1101/gr.279292.124
...and adds more than 1100 new protein coding genes. PacBio Iso-Seq data have been acquired from multiple tissues of the subject animal and are released concurrently with the new assembly to aid further analyses.The laboratory rat, Rattus norvegicus, provides an important model organism for genetic, genomic...
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Research: Identification of a transcriptional signature found in multiple models of ASD and related disorders
- Samuel Thudium,
- Katherine Palozola,
- Éloïse L'Her,
- and Erica Korb
Genome Res. September 2022 32: 1642-1654; Published in Advance September 14, 2022, doi:10.1101/gr.276591.122
...regulation of gene expression. The down-regulated transcriptional signature is also observed within multiple mouse models of NDDs that result in ASD, but not those only associated with intellectual disability. Finally, the down-regulated transcriptional signature can distinguish between control...
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Research: Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits
- Peter Orchard,
- Nandini Manickam,
- Christa Ventresca,
- Swarooparani Vadlamudi,
- Arushi Varshney,
- Vivek Rai,
- Jeremy Kaplan,
- Claudia Lalancette,
- Karen L. Mohlke,
- Katherine Gallagher,
- Charles F. Burant,
- and Stephen C.J. Parker
Genome Res. December 2021 31: 2258-2275; Published in Advance November 23, 2021, doi:10.1101/gr.268482.120
...ATAC-seq), and multiomic profiling (joint snRNA-seq + snATAC-seq) on the 10x Genomics platform to profile gene expression and chromatin accessibility of frozen skeletal muscle cell populations in human and rat. To our knowledge, this represents the first snATAC-seq data from rat skeletal muscle tissue and the first joint...
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Research: Brown rat demography reveals pre-commensal structure in eastern Asia before expansion into Southeast Asia
- Emily E. Puckett and
- Jason Munshi-South
Genome Res. May 2019 29: 762-770; Published in Advance March 25, 2019, doi:10.1101/gr.235754.118
...to corroborate genomic inferences, although the house mouse, domestic dogs, and livestock are notable exceptions. Thus, we paired these data sources to test how well demographic models of a rapid and recent global expansion match historic records on rat invasions.Research into the global expansion of brown rats...
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Perspective: Enabling functional genomics with genome engineering
- Isaac B. Hilton and
- Charles A. Gersbach
Genome Res. October 2015 25: 1442-1455; doi:10.1101/gr.190124.115
...comprehensive and valuable definitions of regulatory element functionality will use several independent approaches, including sequence disruption and manipulation of activity across varied biological contexts. Genome engineering to model disease and develop therapeutics ZFs, TALEs, and the CRISPR/Cas9 system...
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Resource: Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set
- Joana Damas,
- Rebecca O'Connor,
- Marta Farré,
- Vasileios Panagiotis E. Lenis,
- Henry J. Martell,
- Anjali Mandawala,
- Katie Fowler,
- Sunitha Joseph,
- Martin T. Swain,
- Darren K. Griffin,
- and Denis M. Larkin
Genome Res. May 2017 27: 875-884; Published in Advance November 30, 2016, doi:10.1101/gr.213660.116
...as they are the most studied phylogenetic Class of organisms in the scientific literature. Reasons for this include human interest (e.g., clinical studies), biomedical models (e.g., mouse, rat, rabbit, pig), companion animals (e.g., cat, dog), and agricultural mammals (pig, sheep, cattle, etc.). Many are on the CITES...
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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
...BioSciences, Richmond, California 94804, USA; 6genOway, Lyon F69007, France The generation of genetically modified animals is important for both research and commercial purposes. The rat is an important model organism that until recently lacked efficient genetic engineering tools. Sequence...
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PERSPECTIVE: Impact of genomics on research in the rat
- Jozef Lazar,
- Carol Moreno,
- Howard J. Jacob,
- and Anne E. Kwitek
Genome Res. December 2005 15: 1717-1728; doi:10.1101/gr.3744005
...positioned the rat as an invaluable animal model for genomic research. The significant increase in genomic resources in recent years has had an immediate functional application in the rat. Many of the resources for translational research are already in place and are ready to be combined with the years...

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