Searching journal content for articles similar to Kihara and Kanehisa 10 (6): 731.

Displaying results 1-10 of 810

For checked items

view abstracts
download to citation manager

Select this article
Method: Identification of the shortest species-specific oligonucleotide sequences
- Ioannis Mouratidis,
- Maxwell A. Konnaris,
- Nikol Chantzi,
- Candace S.Y. Chan,
- Michail Patsakis,
- Kimonas Provatas,
- Austin Montgomery,
- Fotis A. Baltoumas,
- Congzhou M. Sha,
- Manvita Mareboina,
- Georgios A. Pavlopoulos,
- Dionysios V. Chartoumpekis,
- and Ilias Georgakopoulos-Soares
Genome Res. February 2025 35: 279-295; Published in Advance January 2, 2025, doi:10.1101/gr.280070.124
...often contain gaps in which sequences are unknown owing to technical limitations. Initial assemblies might have ambiguous or poorly resolved regions because of complex genetic structures or repetitive DNA sequences such as tandem repeats that require longer read sequencing. As sequencing technologies...
OPEN ACCESS ARTICLE
Select this article
Resource: Visualization and analysis of medically relevant tandem repeats in nanopore sequencing of control cohorts with pathSTR
- Wouter De Coster,
- Ida Höijer,
- Inge Bruggeman,
- Svenn D'Hert,
- Malin Melin,
- Adam Ameur,
- and Rosa Rademakers
Genome Res. November 2024 34: 2074-2080; Published in Advance August 15, 2024, doi:10.1101/gr.279265.124
...version includes 1040 individuals of The 1000 Genomes Project cohort sequenced on the Oxford Nanopore Technologies PromethION. A comprehensive set of medically relevant tandem repeats has been genotyped using STRdust and LongTR to determine the tandem repeat length and sequence composition. Path...
OPEN ACCESS ARTICLE
Select this article
Method: Gapless assembly of complete human and plant chromosomes using only nanopore sequencing
- Sergey Koren,
- Zhigui Bao,
- Andrea Guarracino,
- Shujun Ou,
- Sara Goodwin,
- Katharine M. Jenike,
- Julian Lucas,
- Brandy McNulty,
- Jimin Park,
- Mikko Rautiainen,
- Arang Rhie,
- Dick Roelofs,
- Harrie Schneiders,
- Ilse Vrijenhoek,
- Koen Nijbroek,
- Olle Nordesjo,
- Sergey Nurk,
- Mike Vella,
- Katherine R. Lawrence,
- Doreen Ware,
- Michael C. Schatz,
- Erik Garrison,
- Sanwen Huang,
- William Richard McCombie,
- Karen H. Miga,
- Alexander H.J. Wittenberg,
- and Adam M. Phillippy
Genome Res. November 2024 34: 1919-1930; Published in Advance November 6, 2024, doi:10.1101/gr.279334.124
..., Haikou, Hainan 571101, China Corresponding authors: sergey.koren@nih.gov, adam.phillippy@nih.govAbstractThe combination of ultra-long (UL) Oxford Nanopore Technologies (ONT) sequencing reads with long, accurate Pacific Bioscience (PacBio) High Fidelity (HiFi) reads has enabled the completion of a human...
Select this article
Research: Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements
- Luis E. Valentin-Alvarado,
- Ling-Dong Shi,
- Kathryn E. Appler,
- Alexander Crits-Christoph,
- Valerie De Anda,
- Benjamin A. Adler,
- Michael L. Cui,
- Lynn Ly,
- Pedro Leão,
- Richard J. Roberts,
- Rohan Sachdeva,
- Brett J. Baker,
- David F. Savage,
- and Jillian F. Banfield
Genome Res. October 2024 34: 1595-1609; Published in Advance October 15, 2024, doi:10.1101/gr.279480.124
...on the same strand. The features a CT-rich intergenic tandem repeat region with six, seven, eight, or nine units of 8 bp in length (variants identified using mapped reads). MGE-9917 encodes at least 14 proteins with transmembrane domains, two of which are 1402 and 1202 amino acids in length and lack related...
OPEN ACCESS ARTICLE
Select this article
Mini-Review: Evolution of genome-wide methylation profiling technologies
- Carolina Montano and
- Winston Timp
Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
...:10.1038/s41587-022-01652-0 ↵Gall-Duncan T, Sato N, Yuen RKC, Pearson CE. 2022. Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences. Genome Res 32: 1–27. doi:10.1101/gr.269530.120 ↵Genner R, Akeson S, Meredith M, Jerez PA, Malik L...
OPEN ACCESS ARTICLE
Select this article
Resource: CGC1, a new reference genome for Caenorhabditis elegans
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Dae-Eun Jeong,
- Chie Owa,
- Haruka Kobayashi,
- Yoshihiko Suzuki,
- Manami Kanamori,
- Yu Toyoshima,
- Yuichi Iino,
- Ann E. Rougvie,
- Lamia Wahba,
- Andrew Z. Fire,
- Erich M. Schwarz,
- and Shinichi Morishita
Genome Res. August 2025 35: 1902-1918; Published in Advance July 15, 2025, doi:10.1101/gr.280274.124
...derivative of the N2 strain. We use improved long-read sequencing and manual assembly of 43 recalcitrant genomic regions to overcome deficiencies of prior N2 and VC2010 assemblies and to assemble tandem repeat loci, including a 772 kb sequence for the 45S rRNA genes. Although many differences from earlier...
OPEN ACCESS ARTICLE
Select this article
Research: The human ribosomal DNA array is composed of highly homogenized tandem clusters
- Yutaro Hori,
- Akira Shimamoto,
- and Takehiko Kobayashi
Genome Res. November 2021 31: 1971-1982; Published in Advance August 18, 2021, doi:10.1101/gr.275838.121
...sequencing. The length of this read was ∼110 kb, corresponding to two and a half tandem copies of rDNA, that is, IGS–45S–IGS–45S–IGS. From the visualization, we could identify that all the copies had the same duplicated regions in the Butterfly/Long repeat region. Therefore, this split-and-map visualizing...
OPEN ACCESS ARTICLE
Select this article

Commentary: Implications of the first complete human genome assembly Genome Res. April 2022 32: 595-598; Published in Advance March 31, 2022, doi:10.1101/gr.276723.122

...sequencing, the T2T Consortium has been able to resolve gaps even across centromeres that are hotbeds of tandem satellite arrays. In the new T2T complete reference from CHM13hTERT cells with a normal karyotype, repetitive elements are found to comprise more of the than previously thought, with satellite...
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
.... Corresponding author: mgymrek@ucsd.eduAbstractShort tandem repeats (STRs) are a class of rapidly mutating genetic elements typically characterized by repeated units of 1–6 bp. We leveraged whole- sequencing data for 152 recombinant inbred (RI) strains from the BXD family of mice to map loci that modulate -wide...
OPEN ACCESS ARTICLE
Select this article
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
...sequencing (De Roeck et al. 2019).Recent studies highlighted the need for LRS-specific algorithms for analysis of LRS data (DeJesus-Hernandez et al. 2021; Guo et al. 2021; Miller et al. 2021). While various combinations of base-caller algorithms and tandem-genotypes could provide estimates for the ABCA7 VNTR...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Kihara and Kanehisa 10 (6): 731.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: