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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
...Evolution of -wide methylation profiling technologies Carolina Montano1,2 and Winston Timp1 1Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA; 2Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia...
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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
...a moderate signal for habitat-related convergent evolution of gene expression levels, whereas the Murinae_expr data set displays a stronger signal.Transcriptome convergence is associated with convergent shifts in kidney cell compositionTissue bulk RNA-seq data reflect variation in both expression per cell...
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Research: Transcriptome-wide systematic search does not detect A-to-I RNA editing in cis-antisense RNA duplexes
- Zohar Rosenwasser,
- Roni Cohen-Fultheim,
- Ofir Shliefer,
- Erez Y. Levanon,
- and Eli Eisenberg
Genome Res. March 12, 2026 gr.280820.125; Published in Advance March 12, 2026, doi:10.1101/gr.280820.125
...of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression. Genome Res 22: 1775–1789. Diaz Quiroz JF, Ojha N, Shayhidin EE, De Silva D, Dabney J, Lancaster A, Coull J, Milstein S, Fraley AW, Brown CR, et al. 2023. Development of a selection assay for small guide RNAs...
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Research: Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species
- Daniel Siqueira de Oliveira,
- Anaïs Larue,
- William Vilas Boas Nunes,
- Francois Sabot,
- Alejandra Bodelón,
- María Pilar García Guerreiro,
- Cristina Vieira,
- and Claudia Marcia Aparecida Carareto
Genome Res. March 2026 36: 487-505; Published in Advance February 10, 2026, doi:10.1101/gr.280463.125
...adaptation because of their ability to generate mutations. In most cases, mutations caused by TEs are likely to be deleterious or neutral. Throughout evolutionary time, TEs that remain in the tend to be silenced by epigenetic control and/or small RNA pathways (Aravin et al. 2007), accumulating mutations...
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Method: A new compression strategy to reduce the size of nanopore sequencing data
- Kavindu Jayasooriya,
- Sasha P. Jenner,
- Pasindu Marasinghe,
- Udith Senanayake,
- Hassaan Saadat,
- David Taubman,
- Roshan Ragel,
- Hasindu Gamaarachchi,
- and Ira W. Deveson
Genome Res. July 2025 35: 1574-1582; Published in Advance May 15, 2025, doi:10.1101/gr.280090.124
...by half without impacting downstream analyses, including basecalling and detection of modified DNA or RNA bases. Ex-zd compression saves hundreds of gigabytes on a single ONT sequencing experiment, thereby increasing the scalability, portability, and accessibility of nanopore sequencing...
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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
..., compression, classification, and simulation of genomic data with several worldwide whole data sets from both humans and canids, and evaluate the performance of the proposed applications with and without ancestry conditioning. The unsupervised setting of autoencoders allows for the detection and learning...
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Corrigendum: Corrigendum: A mosquito small RNA genomics resource reveals dynamic evolution and host responses to viruses and transposons
- Qicheng Ma,
- Satyam P. Srivastav,
- Stephanie Gamez,
- Gargi Dayama,
- Fabiana Feitosa-Suntheimer,
- Edward I. Patterson,
- Rebecca M. Johnson,
- Erik M. Matson,
- Alexander S. Gold,
- Douglas E. Brackney,
- John H. Connor,
- Tonya M. Colpitts,
- Grant L. Hughes,
- Jason L. Rasgon,
- Tony Nolan,
- Omar S. Akbari,
- and Nelson C. Lau
Genome Res. January 2024 34: 160; doi:10.1101/gr.278898.123
.... Lau Genome Research 31: 512–528 (2021)The authors would like to correct the omission of the following statement from the “Competing interest statement” section of the initial publication of this article:“O.S.A. is a founder of Agragene, Inc., with equity interest. The terms of this arrangement have...
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Research: Stable genome structures in living fossil fishes
- Cheng Wang,
- Chase D. Brownstein,
- Wenjun Chen,
- Zufa Ding,
- Dan Yu,
- Yu Deng,
- Chenguang Feng,
- Thomas J. Near,
- Shunping He,
- and Liandong Yang
Genome Res. February 2026 36: 318-329; Published in Advance January 13, 2026, doi:10.1101/gr.280800.125
...of the has contributed to the genomic stasis observed in Lepisosteidae. In other vertebrates, principally humans, epigenetic mechanisms (Slotkin and Martienssen 2007; Deniz et al. 2019) and microRNAs (Shalgi et al. 2010) appear to regulate TE proliferation and activity. In a sense, TE proliferation...
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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
...aspect of host defence 409 mechanisms conserved across vertebrates. In this study, we combined RNA-seq, ATAC-seq 410 and ChIP-seq to investigate the regulatory landscape underlying the antiviral response in 411 Atlantic salmon following poly I:C stimulation, a mimic of double-stranded RNA viruses. Our...
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Research: Loss of multilevel 3D genome organization during breast cancer progression
- Roberto Rossini,
- Saleh Oshaghi,
- Maxim Nekrasov,
- Aurélie Bellanger,
- Renae Domaschenz,
- Yasmin Dijkwel,
- Mohamed Abdelhalim,
- Rahul Agrawal,
- Marit Ledsaak,
- Philippe Collas,
- Ragnhild Eskeland,
- David Tremethick,
- and Jonas Paulsen
Genome Res. January 2026 36: 20-37; Published in Advance October 9, 2025, doi:10.1101/gr.280791.125
...six different genomic deletions spanning RE1–3 (Supplemental Fig. S48B) or sgRNAs for mCherry or EGFP as controls. The Cas9 protein was equally expressed from all vectors in C1 cells compared with GAPDH (Supplemental Fig. S48C). After 2 days of puromycin selection for Cas9-expressing C1 cells, we...

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