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Research: Xist upstream deletion leads to dysregulation of Xist and autosomal gene expression
- Sudeshna Majumdar,
- Lakshmi Sowjanya Bammidi,
- Hemant C. Naik,
- Avinchal Manhas,
- Runumi Baro,
- Akash Kalita,
- Amlan Jyoti Naskar,
- Sundarraj Nidharshan,
- Girija S. Bariha,
- Dimple Notani,
- and Srimonta Gayen
Genome Res. September 2025 35: 1992-2010; Published in Advance August 6, 2025, doi:10.1101/gr.279822.124
..., Bangalore-560012, India; 2Functional Genomics and Bioinformatics Unit, The University of Trans-Disciplinary Health Sciences and Technology (TDU), Bangalore 560064, India; 3National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India ↵Present addresses: 4Cell...
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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
...reconstruction of methylation landscapes often obscured in bulk analyses. Advanced computational tools are required to interpret these high-resolution methylation profiles accurately, which could offer new insights into epigenetic regulation and disease mechanisms.Improved mappability through repeats and other...
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Research: The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication
- Øystein Monsen,
- Lars Grønvold,
- Alex Datsomor,
- Thomas Harvey,
- James Kijas,
- Alexander Suh,
- Torgeir R. Hvidsten,
- and Simen Rød Sandve
Genome Res. March 2025 35: 475-488; Published in Advance February 12, 2025, doi:10.1101/gr.278931.124
...-seq reads and bias in the peak calling is a potential issue. We therefore assessed the level of multimapped ATAC-seq reads in TEs versus other genomic regions for one of the brain samples. This analysis showed that -wide multimapping levels were 14%, whereas reads mapping to TEs from larger subfamilies...
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Research: The rate and spectrum of new mutations in mice inferred by long-read sequencing
- Eugenio López-Cortegano,
- Jobran Chebib,
- Anika Jonas,
- Anastasia Vock,
- Sven Künzel,
- Peter D. Keightley,
- and Diethard Tautz
Genome Res. January 2025 35: 43-54; Published in Advance December 2, 2024, doi:10.1101/gr.279982.124
...association with sequence repetitiveness. Microsatellites and, more generally, tandem repeat sequences are known to be among the fastest evolving sequences. Consequently, when the genomic background of the aligned samples differs from the reference , short tandem repeats may be unusually susceptible...
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Review: Artificial intelligence and machine learning in cell-free-DNA-based diagnostics
- W.H. Adrian Tsui,
- Spencer C. Ding,
- Peiyong Jiang,
- and Y.M. Dennis Lo
Genome Res. January 2025 35: 1-19; doi:10.1101/gr.278413.123
..., the placenta) are the main contributors to plasma cfDNA. Using high-resolution methylation atlases, cfDNA of megakaryocyte origin has also been identified (Moss et al. 2023). However, to further extend the resolution for plasma DNA tissue mapping, a number of algorithms have recently been developed...
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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
...A, Adamovic T, Samuelson E, Helou K, Behboudi A, Levan G. 2006. Chromosome ideograms of the laboratory rat (Rattus norvegicus) based on high-resolution banding, and anchoring of the cytogenetic map to the DNA sequence by FISH in sample chromosomes. Cytogenet Genome Res 115: 158–168. doi:10...
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Resource: A chromosome-scale epigenetic map of the Hydra genome reveals conserved regulators of cell state
- Jack F. Cazet,
- Stefan Siebert,
- Hannah Morris Little,
- Philip Bertemes,
- Abby S. Primack,
- Peter Ladurner,
- Matthias Achrainer,
- Mark T. Fredriksen,
- R. Travis Moreland,
- Sumeeta Singh,
- Suiyuan Zhang,
- Tyra G. Wolfsberg,
- Christine E. Schnitzler,
- Andreas D. Baxevanis,
- Oleg Simakov,
- Bert Hobmayer,
- and Celina E. Juliano
Genome Res. February 2023 33: 283-298; Published in Advance January 13, 2023, doi:10.1101/gr.277040.122
...and Bosch 2015; Dohrmann and Wörheide 2017). The resources generated in this study, which include a browser for the H. oligactis and strain AEP H. vulgaris assemblies, a BLAST server, and an interactive portal for the AEP-mapped Hydra single-cell atlas, are available at the Hydra AEP Genome Project Portal...
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Mini-Review: Toward telomere-to-telomere cat genomes for precision medicine and conservation biology
- William J. Murphy and
- Andrew J. Harris
Genome Res. May 2024 34: 655-664; Published in Advance June 7, 2024, doi:10.1101/gr.278546.123
..., Agarwala R, Schäffer AA, Houck M, Chowdhary BP, Murphy WJ. 2009. A high-resolution cat radiation hybrid and integrated FISH mapping resource for phylogenomic studies across Felidae. Genomics 93: 299–304. doi:10.1016/j.ygeno.2008.09.010 ↵Davis BW, Li G, Murphy WJ. 2010. Supermatrix and species tree methods...
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Perspective: Ribosome decision graphs for the representation of eukaryotic RNA translation complexity
- Jack A.S. Tierney,
- Michał Świrski,
- Håkon Tjeldnes,
- Jonathan M. Mudge,
- Joanna Kufel,
- Nicola Whiffin,
- Eivind Valen,
- and Pavel V. Baranov
Genome Res. April 2024 34: 530-538; Published in Advance May 7, 2024, doi:10.1101/gr.278810.123
...E, Widjaja AA, Langley SR, Viswanathan S, Pua CJ, Zhihao NT, Harmston N, D'Agostino G, Whiffin N, et al. 2022. A high-resolution map of human RNA translation. Mol Cell 82: 2885–2899.e8. doi:10.1016/j.molcel.2022.06.023 ↵Cleary JD, Ranum LPW. 2014. Repeat associated non-ATG (RAN) translation: new...
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Research: Plant genome evolution in the genus Eucalyptus is driven by structural rearrangements that promote sequence divergence
- Scott Ferguson,
- Ashley Jones,
- Kevin Murray,
- Rose Andrew,
- Benjamin Schwessinger,
- and Justin Borevitz
Genome Res. April 2024 34: 606-619; Published in Advance April 8, 2024, doi:10.1101/gr.277999.123
...contributed equally to this work. Corresponding authors: scott.ferguson.papers@gmail.com, ashley.jones@anu.edu.auAbstractGenomes have a highly organized architecture (nonrandom organization of functional and nonfunctional genetic elements within chromosomes) that is essential for many biological functions...
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