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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
....07.011 ↵Usdin K. 2008. The biological effects of simple tandem repeats: lessons from the repeat expansion diseases. Genome Res 18: 1011–1019. doi:10.1101/gr.070409.107 ↵Wang F, Nazarali AJ, Ji S. 2016. Circular RNAs as potential biomarkers for cancer diagnosis and therapy. Am J Cancer Res 6: 1167–1176. ↵Wirawan...
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Review: Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences
- Terence Gall-Duncan,
- Nozomu Sato,
- Ryan K.C. Yuen,
- and Christopher E. Pearson
Genome Res. January 2022 32: 1-27; Published in Advance December 29, 2021, doi:10.1101/gr.269530.120
...Project notoriously struggled with TR stretches and, in fact, there are still regions with long TRs yet to be correctly assembled—for example, the classical satellite repeats I-IV (Miga 2015). Shorter simple tandem repeats (STR), with 1- to 6-bp motif units, were also underrecognized, with recent...
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Method: CRISPR-Cas9-based repeat depletion for high-throughput genotyping of complex plant genomes
- Marzia Rossato,
- Luca Marcolungo,
- Luca De Antoni,
- Giulia Lopatriello,
- Elisa Bellucci,
- Gaia Cortinovis,
- Giulia Frascarelli,
- Laura Nanni,
- Elena Bitocchi,
- Valerio Di Vittori,
- Leonardo Vincenzi,
- Filippo Lucchini,
- Kirstin E. Bett,
- Larissa Ramsay,
- David James Konkin,
- Massimo Delledonne,
- and Roberto Papa
Genome Res. May 2023 33: 787-797; Published in Advance May 1, 2023, doi:10.1101/gr.277628.122
...-copy (high-complexity) regions, the latter comprising coding and regulatory regions that are the main targets of natural selection and thus the focus of most genotyping projects. In contrast, low-complexity regions of plant s mainly comprise transposable elements, simple sequence repeats, and tandem repeats...
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Research: Massive variation of short tandem repeats with functional consequences across strains of Arabidopsis thaliana
- Maximilian O. Press,
- Rajiv C. McCoy,
- Ashley N. Hall,
- Joshua M. Akey,
- and Christine Queitsch
Genome Res. August 2018 28: 1169-1178; Published in Advance July 3, 2018, doi:10.1101/gr.231753.117
...author: queitsch@uw.eduAbstractShort tandem repeat (STR) mutations may comprise more than half of the mutations in eukaryotic coding DNA, yet STR variation is rarely examined as a contributor to complex traits. We assessed this contribution across a collection of 96 strains of Arabidopsis thaliana...
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Research: Genome-wide evidence for selection acting on single amino acid repeats
- Wilfried Haerty and
- G. Brian Golding
Genome Res. June 2010 20: 755-760; Published in Advance January 7, 2010, doi:10.1101/gr.101246.109
...s using evolutionary signatures. Nature 450: 219–232. Usdin K. 2008. The biological effects of simple tandem repeats: Lessons from the repeat expansion diseases. Genome Res 18: 1011–1019. Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB. 2008...
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Methods: De Novo Repeat Classification and Fragment Assembly
- Paul A. Pevzner,
- Haixu Tang,
- and Glenn Tesler
Genome Res. September 2004 14: 1786-1796; doi:10.1101/gr.2395204
.... ↵ 4 The concept of an “elementary repeat,” although important, was never rigorously defined in the recent papers on repeat analysis ( Volfovsky et al. 2001 ; Bailey et al. 2002 ; Bao and Eddy 2002 ). Although it is well defined for perfectly conserved repeats (e.g., as maximal simple paths...
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Methods: Detecting heterozygosity in shotgun genome assemblies: Lessons from obligately outcrossing nematodes
- Antoine Barrière,
- Shiaw-Pyng Yang,
- Elizabeth Pekarek,
- Cristel G. Thomas,
- Eric S. Haag,
- and Ilya Ruvinsky
Genome Res. March 2009 19: 470-480; Published in Advance February 9, 2009, doi:10.1101/gr.081851.108
...Detecting heterozygosity in shotgun genome assemblies: Lessons from obligately outcrossing nematodes Antoine Barrière 1 , Shiaw-Pyng Yang 2 , Elizabeth Pekarek 1 , Cristel G. Thomas 3 , Eric S. Haag 3 , 4 and Ilya Ruvinsky 1 , 4...
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Letter: Rapid evolution of mouse Y centromere repeat DNA belies recent sequence stability
- Mark D. Pertile,
- Alison N. Graham,
- K.H. Andy Choo,
- and Paul Kalitsis
Genome Res. December 2009 19: 2202-2213; Published in Advance September 8, 2009, doi:10.1101/gr.092080.109
...microtubule attachment (Wong and Rattner 1988; Broccoli et al. 1990). Major satellite DNA is a more abundant, 234-bp tandem repeat (Horz and Altenburger 1981) that resides adjacent to a minor satellite and has a role in heterochromatin formation and sister chromatid cohesion (Guenatri et al. 2004). Neither...
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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
.... It is notable that even in compact bacterial s, long-read sequencing has led to improved indel rate estimates (Zhou et al. 2023). Copy-number variants of tandem repeats of 1–6 bp, known as simple sequences or microsatellites (Tautz 1993), have significant medical importance owing to their involvement...
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Research: Elasmobranch genome sequencing reveals evolutionary trends of vertebrate karyotype organization
- Kazuaki Yamaguchi,
- Yoshinobu Uno,
- Mitsutaka Kadota,
- Osamu Nishimura,
- Ryo Nozu,
- Kiyomi Murakumo,
- Rui Matsumoto,
- Keiichi Sato,
- and Shigehiro Kuraku
Genome Res. September 2023 33: 1527-1540; Published in Advance August 17, 2023, doi:10.1101/gr.276840.122
...for an elasmobranch fish. The sequenced shark s show a gradualism of chromosome length with remarkable length-dependent characteristics—shorter chromosomes tend to have higher GC content, gene density, synonymous substitution rate, and simple tandem repeat content as well as smaller gene length and lower interspersed...
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