Searching journal content for articles similar to Antonarakis 32 (4): 599.

Displaying results 1-10 of 87

For checked items

view abstracts
download to citation manager

Select this article
Research: Mitotic chromosomes harbor cell type– and species-specific structural features within a universal loop array conformation
- Marlies E. Oomen,
- A. Nicole Fox,
- Inma Gonzalez,
- Amandine Molliex,
- Thaleia Papadopoulou,
- Pablo Navarro,
- and Job Dekker
Genome Res. August 2025 35: 1733-1744; Published in Advance June 6, 2025, doi:10.1101/gr.280648.125
...of each chromosome, per definition, the q-arm, rather than plotting the full chromosome lengths. Indeed, when we compare the q-arm length between these three species, we find that chicken has very short q-arms with an average length of 11 Mb, followed by human chromosomes with an average q-arm length...
OPEN ACCESS ARTICLE
Select this article
Research: De novo genome assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover novel 3D genome folding in amniotes
- Basanta Bista,
- Laura González-Rodelas,
- Lucía Álvarez-González,
- Zhi-qiang Wu,
- Eugenia E. Montiel,
- Ling Sze Lee,
- Daleen B. Badenhorst,
- Srihari Radhakrishnan,
- Robert Literman,
- Beatriz Navarro-Dominguez,
- John B. Iverson,
- Simon Orozco-Arias,
- Josefa González,
- Aurora Ruiz-Herrera,
- and Nicole Valenzuela
Genome Res. October 2024 34: 1553-1569; Published in Advance October 16, 2024, doi:10.1101/gr.279443.124
...a fragment of the short- and long-arm of a chromosome, respectively, whereas “b” denotes a fragment of an acrocentric chromosome or of the same chromosome arm. (B) Ideograms depicting BAC positions and chromosomal homology across species (Badenhorst et al. 2015). (C) Major chromosomal fusions and fissions...
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
...al. 2024). Excluding isolated scaffolds of the distal satellite, spanning from the short-arm telomere into the rDNA array, all nine remaining acrocentric chromosomes were resolved in the trio assembly (five as gapless contigs). In comparison, a total of 6 out of 10 distal satellites were resolved...
Select this article
Method: OMKar automates genome karyotyping using optical maps to identify constitutional abnormalities
- Siavash Raeisi Dehkordi,
- Zhaoyang Jia,
- Joey Estabrook,
- Jen Hauenstein,
- Neil Miller,
- Naz Güleray-Lafci,
- Jürgen Neesen,
- Alex Hastie,
- Alka Chaubey,
- Andy Wing Chun Pang,
- Paul Dremsek,
- and Vineet Bafna
Genome Res. December 2025 35: 2671-2681; Published in Advance November 14, 2025, doi:10.1101/gr.280536.125
...Genomics 2018, 2024). In particular, Robertsonian translocations involving rearrangements of the short arms of acrocentric chromosomes are not currently detected by OGM. Recent studies have suggested the use of long-read technologies like Oxford Nanopore Technologies for detecting them (Mostovoy et al...
OPEN ACCESS ARTICLE
Select this article
Method: Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding
- Dmitry Antipov,
- Mikko Rautiainen,
- Sergey Nurk,
- Brian P. Walenz,
- Steven J. Solar,
- Adam M. Phillippy,
- and Sergey Koren
Genome Res. July 2025 35: 1583-1594; Published in Advance May 19, 2025, doi:10.1101/gr.280383.124
...-ligation-based haplotype phasing and scaffolding, and adds support for multiple long-read data types. These enhancements allow Verkko2 to assemble all regions of a diploid human , including the short arms of the acrocentric chromosomes and both sex chromosomes. Together, these changes increase the number of telomere...
OPEN ACCESS ARTICLE
Select this article
Research: Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species
- Charles Plessy,
- Michael J. Mansfield,
- Aleksandra Bliznina,
- Aki Masunaga,
- Charlotte West,
- Yongkai Tan,
- Andrew W. Liu,
- Jan Grašič,
- María Sara del Río Pisula,
- Gaspar Sánchez-Serna,
- Marc Fabrega-Torrus,
- Alfonso Ferrández-Roldán,
- Vittoria Roncalli,
- Pavla Navratilova,
- Eric M. Thompson,
- Takeshi Onuma,
- Hiroki Nishida,
- Cristian Cañestro,
- and Nicholas M. Luscombe
Genome Res. March 2024 34: 426-440; Published in Advance April 15, 2024, doi:10.1101/gr.278295.123
...pointed to chromosome arms as the primary scale of macrosynteny conservation, to better understand chromosomal evolution in O. dioica, we investigated the distribution of breakpoint regions, operon sizes, and mutation rate at the chromosome level (Fig. 5A–D). Our analysis revealed that short chromosome...
OPEN ACCESS ARTICLE
Select this article
Research: Leveraging the T2T assembly to resolve rare and pathogenic inversions in reference genome gaps
- Kristine Bilgrav Saether,
- Jesper Eisfeldt,
- Jesse D. Bengtsson,
- Ming Yin Lun,
- Christopher M. Grochowski,
- Medhat Mahmoud,
- Hsiao-Tuan Chao,
- Jill A. Rosenfeld,
- Pengfei Liu,
- Marlene Ek,
- Jakob Schuy,
- Adam Ameur,
- Hongzheng Dai,
- Undiagnosed Diseases Network,
- James Paul Hwang,
- Fritz J. Sedlazeck,
- Weimin Bi,
- Ronit Marom,
- Josephine Wincent,
- Ann Nordgren,
- Claudia M.B. Carvalho,
- and Anna Lindstrand
Genome Res. November 2024 34: 1785-1797; Published in Advance November 1, 2024, doi:10.1101/gr.279346.124
...with repetitive regions. Inversions represent about 1/20 of all balanced structural chromosome aberrations and can lead to disease by gene disruption or altering regulatory regions of dosage-sensitive genes in cis. Short-read sequencing (srGS) can only resolve ∼70% of cytogenetically visible inversions referred...
OPEN ACCESS ARTICLE
Select this article
Research: Transposable element accumulation drives size differences among polymorphic Y Chromosomes in Drosophila
- Alison H. Nguyen,
- Weixiang Wang,
- Emily Chong,
- Kamalakar Chatla,
- and Doris Bachtrog
Genome Res. June 2022 32: 1074-1088; Published in Advance May 2, 2022, doi:10.1101/gr.275996.121
...(relative to the X Chromosome, which is derived from the sequenced reference strain in each Y-replacement line), and Y shape (ratio of long vs. short arm length) to identify different Y types (Fig. 1B; Supplemental Table S2). Consistent with Dobzhansky's studies (Dobzhansky 1935, 1937), we find large...
Select this article
Resource: Construction and evaluation of a new rat reference genome assembly, GRCr8, from long reads and long-range scaffolding
- Kai Li,
- Melissa L. Smith,
- J. Chris Blazier,
- Kelli J. Kochan,
- Jonathan M.D. Wood,
- Kerstin Howe,
- Anne E. Kwitek,
- Melinda R. Dwinell,
- Hao Chen,
- Julia L. Ciosek,
- Patrick Masterson,
- Terence D. Murphy,
- Theodore S. Kalbfleisch,
- and Peter A. Doris
Genome Res. November 2024 34: 2081-2093; Published in Advance November 8, 2024, doi:10.1101/gr.279292.124
...in the production of mRatBN7.2, reference-assisted assembly of subchromosomal scaffolds into single chromosomes (Alonge et al. 2022), assembly of existing CLR data into contigs for use in assembly gap filling, polishing of the assembly with Illumina short reads, and rapid curation of the assembly using Hi-C heat...
Select this article
Research: Gaps and complex structurally variant loci in phased genome assemblies
- David Porubsky,
- Mitchell R. Vollger,
- William T. Harvey,
- Allison N. Rozanski,
- Peter Ebert,
- Glenn Hickey,
- Patrick Hasenfeld,
- Ashley D. Sanders,
- Catherine Stober,
- Human Pangenome Reference Consortium,
- Jan O. Korbel,
- Benedict Paten,
- Tobias Marschall,
- and Evan E. Eichler
Genome Res. April 2023 33: 496-510; Published in Advance May 10, 2023, doi:10.1101/gr.277334.122
...-Mbp segments (>75%) map within centromeric satellite repeats, most likely owing to the lower density of uniquely mapped single-nucleotide variants (SNVs) (Supplemental Fig. S5). There was only one sample (HG01891) with large-scale switch errors on a short arm of Chromosome 9 (∼42 Mbp) and one...
OPEN ACCESS ARTICLE

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Antonarakis 32 (4): 599.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: