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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
...with long-read technologies. Conversely, bacterial DNA modifications can be of scientific interest, as they impact bacterial function, and Liu et al. (2024) introduce a novel pipeline to accurately detect DNA modifications in prokaryotes.We would like to thank all the authors, reviewers, and the Genome...
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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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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
..., by evolutionary clusters of vastly different ages and genomic diversity levels. Our results should stimulate discussions among historians and zooarcheologists regarding the relationship between humans and rats.The genus Rattus originated and diversified in eastern and central Asia, and fossil evidence (Smith...
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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
...and improvement, engineering technologies are clearly ready to have a significant impact on genomics and medicine. Functional characterization of the epigenetic modifications associated with gene regulation is now possible using these tools. This will allow high resolution functional annotation and indexed...
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Research: Natural variation of histone modification and its impact on gene expression in the rat genome
- Carola Rintisch,
- Matthias Heinig,
- Anja Bauerfeind,
- Sebastian Schafer,
- Christin Mieth,
- Giannino Patone,
- Oliver Hummel,
- Wei Chen,
- Stuart Cook,
- Edwin Cuppen,
- Maria Colomé-Tatché,
- Frank Johannes,
- Ritsert C. Jansen,
- Helen Neil,
- Michel Werner,
- Michal Pravenec,
- Martin Vingron,
- and Norbert Hubner
Genome Res. June 2014 24: 942-953; Published in Advance May 2, 2014, doi:10.1101/gr.169029.113
...Natural variation of histone modification and its impact on gene expression in the rat genome Carola Rintisch 1 , 12 , Matthias Heinig 1 , 2 , 12 , Anja Bauerfeind 1 , Sebastian Schafer 1 , Christin Mieth 1 , Giannino Patone 1...
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Research: Tandem repeat variation in human and great ape populations and its impact on gene expression divergence
- Tugce Bilgin Sonay,
- Tiago Carvalho,
- Mark D. Robinson,
- Maja P. Greminger,
- Michael Krützen,
- David Comas,
- Gareth Highnam,
- David Mittelman,
- Andrew Sharp,
- Tomàs Marques-Bonet,
- and Andreas Wagner
Genome Res. November 2015 25: 1591-1599; Published in Advance August 19, 2015, doi:10.1101/gr.190868.115
...evolutionary rates of sex chromosomes (Brawand et al. 2011). Here, we surveyed the -wide diversity of TRs in a large collection of high-quality human and nonhuman great ape Bilgin Sonay et al. 1594 Genome Research www..org s and showed for the first time their possible impact on gene expression divergence...
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Research: ACTB methylation regulates SMARCA4 genomic occupancy to promote translation and reduce adhesion in colorectal cancer cells
- Elina Abaev-Schneiderman,
- Linh Nguyen,
- Raz Shalev,
- Tzofit Elbaz Biton,
- Anand Chopra,
- Giritharan Jagadeesan,
- Daniel Sevilla-Sanchez,
- Nili Tickotsky Moskovitz,
- Liron Levin,
- Michal Feldman,
- Capucine Van Rechem,
- and Dan Levy
Genome Res. April 2026 36: 684-694; Published in Advance March 25, 2026, doi:10.1101/gr.280534.125
...polymerization and smooth muscle contraction. Here, we show that the genomic distribution of ACTB is SETD3-dependent and that this regulation modulates the transcription of genes involved in cell adhesion and mRNA translation in colorectal cancer cells. Proteomic analyses reveal that ACTB and SETD3 interact...
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Research: Degrees of convergent evolution in rodent adaptations to arid environments
- Domitille Chalopin,
- Carine Rey,
- Jeremy Ganofsky,
- Juliana Blin,
- Pascale Chevret,
- Marion Mouginot,
- Laurent Guéguen,
- Bastien Boussau,
- Sophie Pantalacci,
- and Marie Sémon
Genome Res. March 2026 36: 472-486; Published in Advance January 21, 2026, doi:10.1101/gr.280089.124
....pantalacci@ens-lyon.fr, marie.semon@ens-lyon.frAbstractSpecies adapting to a similar lifestyle may undergo convergent changes in organ structure and cellular function, themselves relying or not on these convergent genetic changes. The extent of genomic convergence is thus debated and may further depend on the interplay between...
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Research: The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance
- Santosh S. Atanur,
- İnanç Birol,
- Victor Guryev,
- Martin Hirst,
- Oliver Hummel,
- Catherine Morrissey,
- Jacques Behmoaras,
- Xose M. Fernandez-Suarez,
- Michelle D. Johnson,
- William M. McLaren,
- Giannino Patone,
- Enrico Petretto,
- Charles Plessy,
- Kathleen S. Rockland,
- Charles Rockland,
- Kathrin Saar,
- Yongjun Zhao,
- Piero Carninci,
- Paul Flicek,
- Ted Kurtz,
- Edwin Cuppen,
- Michal Pravenec,
- Norbert Hubner,
- Steven J.M. Jones,
- Ewan Birney,
- and Timothy J. Aitman
Genome Res. June 2010 20: 791-803; Published in Advance April 29, 2010, doi:10.1101/gr.103499.109
...The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance Santosh S. Atanur 1 , İnanç Birol 2 , Victor Guryev 3 , Martin Hirst 2 , Oliver Hummel 4 , Catherine Morrissey 1 , Jacques...

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