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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
...and Campbell 2024) and may also provide a buffer for the continuous accumulation of deleterious mutations in essential genes (López et al. 2020). Conceivably, tumor WGD and gene duplication events may also broaden the cellular evolutionary potential of cancer cells, permitting divergence in duplicated genes...
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Method: Accurate detection of tandem repeats from error-prone sequences with EquiRep
- Zhezheng Song,
- Tasfia Zahin,
- Xiang Li,
- and Mingfu Shao
Genome Res. December 2025 35: 2714-2721; Published in Advance August 21, 2025, doi:10.1101/gr.280750.125
...in genetic diversity and gene regulation, and are associated with various neurological and developmental disorders. They can also arise in sequencing reads generated by certain technologies, such as those used for sequencing circular molecules. A key challenge in analyzing tandem repeats is reconstructing...
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Method: Targeted, programmable, and precise tandem duplication in the mammalian genome
- Yaoge Jiao,
- Min Li,
- Xingyu He,
- Yanhong Wang,
- Junwei Song,
- Yun Hu,
- Li Li,
- Lifang Zhou,
- Lurong Jiang,
- Junyan Qu,
- Lifang Xie,
- Qiang Chen,
- and Shaohua Yao
Genome Res. May 2023 33: 779-786; Published in Advance June 9, 2023, doi:10.1101/gr.277261.122
...al. 2019), single-nucleotide conversions (Anzalone et al. 2019; Adikusuma et al. 2021; Zhuang et al. 2022), and large fragment deletions (Anzalone et al. 2022; Choi et al. 2022; Jiang et al. 2022; Tao et al. 2022a,b), but not gene duplication. Here, we designed a novel editing strategy, named tandem...
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Method: Read-level genotyping of short tandem repeats using long reads and single-nucleotide variation with STRkit
- David R. Lougheed,
- Tomi Pastinen,
- and Guillaume Bourque
Genome Res. March 2026 36: 578-588; Published in Advance January 15, 2026, doi:10.1101/gr.280766.125
...Institute, Kansas City, Missouri 64108, USA; 4Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec H3A 0G1, Canada Corresponding authors: david.lougheed@mail.mcgill.ca, guil.bourque@mcgill.caAbstractVariation in short tandem repeats (STRs) is implicated in Mendelian...
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Method: Estimating the size of long tandem repeat expansions from short reads with ScatTR
- Rashid Al-Abri and
- Gamze Gürsoy
Genome Res. December 2025 35: 2701-2713; Published in Advance August 21, 2025, doi:10.1101/gr.280563.125
...nucleotide sequence motifs that are widespread throughout the human . Studying TR variation in the human population is important owing to the high mutation rate and polymorphic nature of TRs (Press et al. 2014). TRs influence key biological processes, including gene regulation, and are implicated in a range...
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Method: Taurine pangenome uncovers a segmental duplication upstream of KIT associated with depigmentation in white-headed cattle
- Sotiria Milia,
- Alexander S. Leonard,
- Xena Marie Mapel,
- Sandra Milena Bernal Ulloa,
- Cord Drögemüller,
- and Hubert Pausch
Genome Res. April 2025 35: 1041-1052; Published in Advance December 18, 2024, doi:10.1101/gr.279064.124
...-associated bubble upstream of the KIT gene. (A) Bandage plots showing the paths traversed for the three observed alleles (two for white-headed breeds and one for color-headed) through the pan. Unless stated otherwise, n = 1 for the breed. The gray arrow paths indicate the segmental duplication regions, whereas...
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Method: Enabling efficient and robust analysis of tandem repeats in genomic data using wavefront-based string decomposer
- Junhai Qi,
- Zhidong Yang,
- Ting Yu,
- and Guojun Li
Genome Res. April 8, 2026 gr.281346.125; Published in Advance April 8, 2026, doi:10.1101/gr.281346.125
...University5 of Science and Technology, Hong Kong S.A.R., China, 9990776 ∗Correspondence to: tingy@sdu.edu.cn and gjli@sdu.edu.cn7 Abstract8 Tandem repeats (TRs) analysis is crucial for understanding structure and variation. However, string de-9 composition, a key challenge in TRs analysis, remains...
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Method: Multisample motif discovery and visualization for tandem repeats
- Yaran Zhang,
- Marc Hulsman,
- Alex Salazar,
- Niccolò Tesi,
- Lydian Knoop,
- Sven van der Lee,
- Sanduni Wijesekera,
- Jana Krizova,
- Erik-Jan Kamsteeg,
- and Henne Holstege
Genome Res. April 2025 35: 850-862; Published in Advance November 13, 2024, doi:10.1101/gr.279278.124
...Nijmegen, The Netherlands; 5Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, 1081HV Amsterdam, The Netherlands Corresponding author: h.holstege@amsterdamumc.nlAbstractTandem repeats (TRs) occupy a significant portion of the human and are a source...
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Research: Diversity, duplication, and genomic organization of homeobox genes in Lepidoptera
- Peter O. Mulhair,
- Liam Crowley,
- Douglas H. Boyes,
- Amber Harper,
- Owen T. Lewis,
- Darwin Tree of Life Consortium,
- and Peter W.H. Holland
Genome Res. January 2023 33: 32-44; Published in Advance December 8, 2022, doi:10.1101/gr.277118.122
...between the zen and pb Hox genes. This presence of unusual “special homeobox” (Shx) genes within the Hox gene cluster was later confirmed in several other Lepidoptera, most of which were found to possess four Shx genes, ShxA, ShxB, ShxC, and ShxD, derived by tandem duplication and divergence from zen...
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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
...period following doubling.The two most influential mutational mechanisms that have shaped eukaryotic evolution are whole- duplications (WGDs) and transposable element (TE) activity. Both WGDs and TEs drive size evolution. However, as mobile genetic elements with capacity to replicate (Feschotte...

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