Searching journal content for articles similar to Hamanaka et al. 33 (3): 435.

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  1. 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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  2. Research: Genome-wide evaluation of the effect of short tandem repeat variation on local DNA methylation
    • Alejandro Martin-Trujillo,
    • Paras Garg,
    • Nihir Patel,
    • Bharati Jadhav,
    • and Andrew J. Sharp
    Genome Res. February 2023 33: 184-196; Published in Advance December 28, 2022, doi:10.1101/gr.277057.122
    ...↵2 Present address: Admera Health, South Plainfield, NJ 07080, USA Corresponding author: andrew.sharp@mssm.eduAbstractShort tandem repeats (STRs) contribute significantly to genetic diversity in humans, including disease-causing variation. Although the effect of STR variation on gene expression has...
  3. Research: A novel quantitative trait locus implicates Msh3 in the propensity for genome-wide short tandem repeat expansions in mice
    • Mikhail O. Maksimov,
    • Cynthia Wu,
    • David G. Ashbrook,
    • Flavia Villani,
    • Vincenza Colonna,
    • Nima Mousavi,
    • Nichole Ma,
    • Lu Lu,
    • Jonathan K. Pritchard,
    • Alon Goren,
    • Robert W. Williams,
    • Abraham A. Palmer,
    • and Melissa Gymrek
    Genome Res. May 2023 33: 689-702; Published in Advance May 1, 2023, doi:10.1101/gr.277576.122
    ...allele, particularly at tetranucleotide repeats. Our results suggest an important role for inherited variants in Msh3 in modulating -wide patterns of germline mutations at STRs.Studies of germline and somatic mutations have shown considerable variation across individuals and species in both the rate...
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  4. Method: Characterizing tandem repeat complexities across long-read sequencing platforms with TREAT and otter
    • Niccoló Tesi,
    • Alex Salazar,
    • Yaran Zhang,
    • Sven van der Lee,
    • Marc Hulsman,
    • Lydian Knoop,
    • Sanduni Wijesekera,
    • Jana Krizova,
    • Anne-Fleur Schneider,
    • Maartje Pennings,
    • Kristel Sleegers,
    • Erik-Jan Kamsteeg,
    • Marcel Reinders,
    • and Henne Holstege
    Genome Res. November 2024 34: 1942-1953; Published in Advance October 15, 2024, doi:10.1101/gr.279351.124
    ...These authors contributed equally to this work. Corresponding authors: n.tesi@amsterdamumc.nl, a.n.salazar@amsterdamumc.nl, h.holstege@amsterdamumc.nlAbstractTandem repeats (TRs) play important roles in genomic variation and disease risk in humans. Long-read sequencing allows for the accurate characterization...
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  5. Research: Genome-wide mapping reveals R-loops associated with centromeric repeats in maize
    • Yang Liu,
    • Qian Liu,
    • Handong Su,
    • Kunpeng Liu,
    • Xue Xiao,
    • Wei Li,
    • Qianwen Sun,
    • James A. Birchler,
    • and Fangpu Han
    Genome Res. August 2021 31: 1409-1418; Published in Advance July 9, 2021, doi:10.1101/gr.275270.121
    ...characteristics of the R-loop pattern in the maize . We studied the relationships between R-loops and repetitive sequences in maize, such as tandem repeats and TEs. We also provide the first R-loop observation by atomic force microscopy (AFM) in plants.ResultsGenome-wide identification of R-loops in maize...
  6. Research: Characterizing nucleotide variation and expansion dynamics in human-specific variable number tandem repeats
    • Meredith M. Course,
    • Arvis Sulovari,
    • Kathryn Gudsnuk,
    • Evan E. Eichler,
    • and Paul N. Valdmanis
    Genome Res. August 2021 31: 1313-1324; Published in Advance July 9, 2021, doi:10.1101/gr.275560.121
    ..., Jazin E. 2005. Genome-wide prediction of human VNTRs. Genomics 85: 24–35. doi:10.1016/j.ygeno.2004.10.009 ↵Örd T, Puurand T, Örd D, Annilo T, Möls M, Remm M, Örd T. 2020. A human-specific VNTR in the TRIB3 promoter causes gene expression variation between individuals. PLoS Genet 16: e1008981. doi:10...
  7. 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...
  8. Method: Accurate typing of short tandem repeats from genome-wide sequencing data and its applications
    • Arkarachai Fungtammasan,
    • Guruprasad Ananda,
    • Suzanne E. Hile,
    • Marcia Shu-Wei Su,
    • Chen Sun,
    • Robert Harris,
    • Paul Medvedev,
    • Kristin Eckert,
    • and Kateryna D. Makova
    Genome Res. May 2015 25: 736-749; Published in Advance March 30, 2015, doi:10.1101/gr.185892.114
    ...Accurate typing of short tandem repeats from genome-wide sequencing data and its applications Arkarachai Fungtammasan 1 , 2 , 3 , 4 , 8 , Guruprasad Ananda 1 , 3 , 4 , 5 , 8 , 9 , Suzanne E. Hile 3 , 6 , Marcia Shu-Wei Su 2 , 3...
  9. Resource: Pangenome-genotyped structural variation improves molecular phenotype mapping in cattle
    • Alexander S. Leonard,
    • Xena M. Mapel,
    • and Hubert Pausch
    Genome Res. February 2024 34: 300-309; Published in Advance February 14, 2024, doi:10.1101/gr.278267.123
    ...-021-00865-4 ↵Bhati M, Mapel XM, Lloret-Villas A, Pausch H. 2023. Structural variants and short tandem repeats impact gene expression and splicing in bovine testis tissue. Genetics 225: 2023.06.07.543773. doi:10.1093/genetics/iyad161 ↵Bray NL, Pimentel H, Melsted P, Pachter L. 2016. Near-optimal probabilistic RNA...
  10. Resource: High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation
    • Jonas A. Gustafson,
    • Sophia B. Gibson,
    • Nikhita Damaraju,
    • Miranda P.G. Zalusky,
    • Kendra Hoekzema,
    • David Twesigomwe,
    • Lei Yang,
    • Anthony A. Snead,
    • Phillip A. Richmond,
    • Wouter De Coster,
    • Nathan D. Olson,
    • Andrea Guarracino,
    • Qiuhui Li,
    • Angela L. Miller,
    • Joy Goffena,
    • Zachary B. Anderson,
    • Sophie H.R. Storz,
    • Sydney A. Ward,
    • Maisha Sinha,
    • Claudia Gonzaga-Jauregui,
    • Wayne E. Clarke,
    • Anna O. Basile,
    • André Corvelo,
    • Catherine Reeves,
    • Adrienne Helland,
    • Rajeeva Lochan Musunuri,
    • Mahler Revsine,
    • Karynne E. Patterson,
    • Cate R. Paschal,
    • Christina Zakarian,
    • Sara Goodwin,
    • Tanner D. Jensen,
    • Esther Robb,
    • The 1000 Genomes ONT Sequencing Consortium,
    • University of Washington Center for Rare Disease Research (UW-CRDR),
    • Genomics Research to Elucidate the Genetics of Rare Diseases (GREGoR) Consortium,
    • William Richard McCombie,
    • Fritz J. Sedlazeck,
    • Justin M. Zook,
    • Stephen B. Montgomery,
    • Erik Garrison,
    • Mikhail Kolmogorov,
    • Michael C. Schatz,
    • Richard N. McLaughlin, Jr.,
    • Harriet Dashnow,
    • Michael C. Zody,
    • Matt Loose,
    • Miten Jain,
    • Evan E. Eichler,
    • and Danny E. Miller
    Genome Res. November 2024 34: 2061-2073; Published in Advance October 2, 2024, doi:10.1101/gr.279273.124
    ...). Furthermore, there was minimal variation among the 100 assemblies in interspersed repeat content.Among the youngest polymorphic interspersed repeats that are too long to resolve with short reads (Chaisson et al. 2019), LINE-1s (∼6000 bp) are the only types that are actively expanding in the human . We found...
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