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Research: Natural diversity of telomere length distributions across 100 Saccharomyces cerevisiae strains
- Clotilde Garrido,
- Cintia Gómez-Muñoz,
- Etienne Kornobis,
- Nicolas Agier,
- Oana Ilioaia,
- Gilles Fischer,
- and Zhou Xu
Genome Res. March 2026 36: 522-533; Published in Advance January 16, 2026, doi:10.1101/gr.281132.125
....fischer@sorbonne-universite.fr, zhou.xu@sorbonne-universite.frAbstractTelomeres gradually shorten at each cell division, and telomerase counteracts this shortening by elongating telomere sequences. This dynamic balance between elongation and shortening results in a steady-state telomere length (TL) distribution. Here, we develop...
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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
...Toward telomere-to-telomere cat s for precision medicine and conservation biology William J. Murphy1,2,3 and Andrew J. Harris1,3 1Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843-4458, USA; 2Department of Biology, Texas A&M University, College...
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Research: Contiguous and complete assemblies of Blastocystis gut microbiome–associated protists reveal evolutionary diversification to host ecology
- Abigail L. Lind,
- Nathan A. McDonald,
- Elias R. Gerrick,
- Ami S. Bhatt,
- and Katherine S. Pollard
Genome Res. June 2025 35: 1377-1390; Published in Advance April 22, 2025, doi:10.1101/gr.279080.124
...Contiguous and complete assemblies of Blastocystis gut microbiome–associated protists reveal evolutionary diversification to host ecology Abigail L. Lind1,2, Nathan A. McDonald2,3, Elias R. Gerrick4, Ami S. Bhatt5,6 and Katherine S. Pollard1,7,8 1Gladstone Institute for Data Science...
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Research: Chromosome-specific telomere lengths and the minimal functional telomere revealed by nanopore sequencing
- Samantha L. Sholes,
- Kayarash Karimian,
- Ariel Gershman,
- Thomas J. Kelly,
- Winston Timp,
- and Carol W. Greider
Genome Res. April 2022 32: 616-628; Published in Advance October 26, 2021, doi:10.1101/gr.275868.121
...repeats that do not bind Rap1 has little effect on telomere length (Henning et al. 1998; Alexander and Zakian 2003; Brevet et al. 2003; Bah et al. 2011). In addition, recent work suggests the apparent preferential elongation of short telomeres may be due to replication fork collapse in telomere repeats...
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Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
- Paul Ashford,
- Alexander M. Frankell,
- Zofia Piszka,
- Camilla S.M. Pang,
- Mahnaz Abbasian,
- Maise Al Bakir,
- Mariam Jamal-Hanjani,
- Nicholas McGranahan,
- Charles Swanton,
- and Christine A. Orengo
Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
...functional diversification during evolution. In this study, we seek to identify the diversification and potential gene neofunctionalization of lung tumors in the TRACERx cohort. We develop a novel computational protocol to identify preduplication and postduplication mutations predicted to affect protein...
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Method: Telomere-to-telomere assembly by preserving contained reads
- Sudhanva Shyam Kamath,
- Mehak Bindra,
- Debnath Pal,
- and Chirag Jain
Genome Res. November 2024 34: 1908-1918; Published in Advance October 15, 2024, doi:10.1101/gr.279311.124
...Sudhanva Shyam Kamath, Mehak Bindra, Debnath Pal and Chirag Jain Department of Computational and Data Sciences, Indian Institute of Science, Bangalore 560012, India Corresponding author: chirag@iisc.ac.inAbstractAutomated telomere-to-telomere (T2T) de novo assembly of diploid and polyploid s...
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Method: Kinetic measurement of gene-specific RNA polymerase II transcription elongation rates
- Haiyue Liu and
- Lea H. Gregersen
Genome Res. November 2025 35: 2550-2562; Published in Advance October 22, 2025, doi:10.1101/gr.280852.125
...Haiyue Liu and Lea H. Gregersen Center for Gene Expression, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark Corresponding author: leag@sund.ku.dkAbstractTranscription is regulated at multiple levels, including initiation, elongation, and termination...
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Method: Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding
- Dmitry Antipov,
- Mikko Rautiainen,
- Sergey Nurk,
- Brian P. Walenz,
- Steven J. Solar,
- Adam M. Phillippy,
- and Sergey Koren
Genome Res. July 2025 35: 1583-1594; Published in Advance May 19, 2025, doi:10.1101/gr.280383.124
...Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere assembly, phasing, and scaffolding Dmitry Antipov1,4, Mikko Rautiainen2,4, Sergey Nurk3, Brian P. Walenz1, Steven J. Solar1, Adam M. Phillippy1 and Sergey Koren1 1Genome Informatics Section...
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Research: Transposons contribute to the functional diversification of the head, gut, and ovary transcriptomes across Drosophila natural strains
- Marta Coronado-Zamora and
- Josefa González
Genome Res. September 2023 33: 1541-1553; Published in Advance October 4, 2023, doi:10.1101/gr.277565.122
...of transcripts that can be involved in diverse biological functions, and contribute to adaptive evolution and disease (e.g., Marasca et al. 2020; Kiyose et al. 2022; Singh and Ahi 2022; Verta and Jacobs 2022). The potential contribution of transposable element (TE) insertions to the diversification...
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Resource: Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental expression
- Ni-Chen Chang,
- Quirze Rovira,
- Jonathan Wells,
- Cédric Feschotte,
- and Juan M. Vaquerizas
Genome Res. July 2022 32: 1408-1423; Published in Advance January 5, 2022, doi:10.1101/gr.275655.121
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