Searching journal content for articles similar to Zhang et al. 35 (4): 850.

Displaying results 1-9 of 9

For checked items

view abstracts
download to citation manager

Select this article
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
...and comparisons of TRs in human s, with broad applications in research and clinical fields.Roughly 30% of the human consists of tandem repeats (TRs) characterized by one or more repeat motifs that are defined by their consecutive repetition (Hannan 2018). This repetitive pattern often leads to DNA instability...
OPEN ACCESS ARTICLE
Select this article
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
...that are only identified upon molecular interrogation (Sasani et al. 2022). Identifying genetic factors controlling this variation can provide insight into mutation processes and DNA repair mechanisms.Short tandem repeats (STRs), typically consisting of repeated sequence motifs of 1–6 bp, show rapid mutation...
OPEN ACCESS ARTICLE
Select this article
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
...as false positives following manual visualization of read alignments in IGV, underscoring the need for improved assembly mapping, alignment, and calling methods, particularly for long tandem repeats. In total, we report the discovery of 133 de novo SMs (61 in C3H, 39 in BL6, and 33 in FVB) (Supplemental...
OPEN ACCESS ARTICLE
Select this article
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
...be in complex copy-number polymorphic regions of the , and thus potential artifacts because of their proximity to a segdup. Of the SVs that were not fully within, partially within, or within 1000 bp of a segdup, 119,255 (46.5% of the remaining SVs) overlap a variable number tandem repeat (VNTR) region. Analysis...
OPEN ACCESS ARTICLE
Select this article
Editorial: Long reads decipher genomes and transcriptomes and offer novel insights into biology and diseases
- Ana Conesa,
- Alexander Hoischen,
- and Fritz J. Sedlazeck
Genome Res. April 2025 35: xi-xiv; doi:10.1101/gr.280665.125
...and quality, overcoming traditional challenges posed by repetitive regions. Zhang et al. (2025) present MotifScope, a tool for multisample motif discovery and tandem repeat visualization, providing insights into -wide repeat structures. Chakravarty et al. (2025) develop RAmbler, a reference-guided assembler...
Select this article
Mini-Review: A Hitchhiker's Guide to long-read genomic analysis
- Medhat Mahmoud,
- Daniel P. Agustinho,
- and Fritz J. Sedlazeck
Genome Res. April 2025 35: 545-558; doi:10.1101/gr.279975.124
...models require careful selection as they are technology-specific, optimized for particular flow cell generations, and primarily trained on human data. ii) Tandem repeats (TRs) consist of consecutive copies of DNA motifs, ranging from 1 bp or larger, with variable copy numbers. TRs span around 8...
Select this article
Perspective: Unraveling the hidden complexity of cancer through long-read sequencing
- Qiuhui Li,
- Ayse G. Keskus,
- Justin Wagner,
- Michal B. Izydorczyk,
- Winston Timp,
- Fritz J. Sedlazeck,
- Alison P. Klein,
- Justin M. Zook,
- Mikhail Kolmogorov,
- and Michael C. Schatz
Genome Res. April 2025 35: 599-620; Published in Advance March 20, 2025, doi:10.1101/gr.280041.124
...with detecting alterations in tandem repeats (TRs), and more generally, with variations found within repetitive sequences (e.g., segmental duplications, satellite sequences, transposable elements), leaving a large fraction of the inaccessible. Short-reads also have limited power to phase variants within the same...
OPEN ACCESS ARTICLE
Select this article
Research: Rates and spectra of de novo structural mutations in Chlamydomonas reinhardtii
- Eugenio López-Cortegano,
- Rory J. Craig,
- Jobran Chebib,
- Eniolaye J. Balogun,
- and Peter D. Keightley
Genome Res. January 2023 33: 45-60; Published in Advance December 12, 2022, doi:10.1101/gr.276957.122
...verification with visualization tools such as IGV should also be performed.Mechanisms underlying SM and between-strain heterogeneity of rates and spectraExcluding expansions and contractions of tandem repeats, ∼79% of SMs were associated with TEs. Of these, 84% were TE insertions and excisions, which therefore...
OPEN ACCESS ARTICLE
Select this article
Resource: A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree
- Michael A. Eberle,
- Epameinondas Fritzilas,
- Peter Krusche,
- Morten Källberg,
- Benjamin L. Moore,
- Mitchell A. Bekritsky,
- Zamin Iqbal,
- Han-Yu Chuang,
- Sean J. Humphray,
- Aaron L. Halpern,
- Semyon Kruglyak,
- Elliott H. Margulies,
- Gil McVean,
- and David R. Bentley
Genome Res. January 2017 27: 157-164; Published in Advance November 30, 2016, doi:10.1101/gr.210500.116
...includes 59,310 multiallelic variants (2728 SNVs and 56,582 indels). The indel loci include short tandem repeats such as homopolymer tracts and di- and trinucleotide repeats (Supplemental Material, section 1.5), which are known to be less stable than SNVs; hence, we expect a significant number...
OPEN ACCESS ARTICLE

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Zhang et al. 35 (4): 850.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: