Searching journal content for articles similar to Vaser et al. 27 (5): 737.

Displaying results 1-10 of 57

For checked items

view abstracts
download to citation manager

Select this article
Method: Geometric deep learning framework for de novo genome assembly
- Lovro Vrček,
- Xavier Bresson,
- Thomas Laurent,
- Martin Schmitz,
- Kenji Kawaguchi,
- and Mile Šikić
Genome Res. April 2025 35: 839-849; Published in Advance October 29, 2024, doi:10.1101/gr.279307.124
...haploid s.De novo assembly provides essential insights into organism's biology and evolution by reconstructing its from short DNA fragments (or reads), without the access to the original genomic sequence. The assembly process is based on intricate methods on strings and graphs which were first introduced...
Select this article
Method: Highly accurate assembly polishing with DeepPolisher
- Mira Mastoras,
- Mobin Asri,
- Lucas Brambrink,
- Prajna Hebbar,
- Alexey Kolesnikov,
- Daniel E. Cook,
- Maria Nattestad,
- Julian Lucas,
- Taylor S. Won,
- Pi-Chuan Chang,
- Andrew Carroll,
- Benedict Paten,
- Kishwar Shafin,
- and and the Human Pangenome Reference Consortium
Genome Res. July 2025 35: 1595-1608; Published in Advance May 19, 2025, doi:10.1101/gr.280149.124
...of the is increasingly essential for scientists to understand the underlying biology of any organism. Genome assembly, the process of digitally reconstructing a , is accomplished by piecing together segments of DNA (called sequencing “reads”) and obtaining a consensus. The past several years have seen a huge improvement...
Select this article
Resource: Chromosome-level subgenome-aware de novo assembly provides insight into Saccharomyces bayanus genome divergence after hybridization
- Cory Gardner,
- Junhao Chen,
- Christina Hadfield,
- Zhaolian Lu,
- David Debruin,
- Yu Zhan,
- Maureen J. Donlin,
- Tae-Hyuk Ahn,
- and Zhenguo Lin
Genome Res. November 2024 34: 2133-2146; Published in Advance September 17, 2024, doi:10.1101/gr.279364.124
...of two sets of k-mer in raw sequencing reads (Wang et al. 2024), so it provides more accurate phylogenetic inferences if the contributions of parental contents are similar. Because the parental genomic contents of different S. bayanus strains vary substantially (Langdon et al. 2019), potential bias...
Select this article
Research: Accurate genotyping of three major respiratory bacterial pathogens with ONT R10.4.1 long-read sequencing
- Nora Zidane,
- Carla Rodrigues,
- Valérie Bouchez,
- Martin Rethoret-Pasty,
- Virginie Passet,
- Sylvain Brisse,
- and Chiara Crestani
Genome Res. August 2025 35: 1758-1766; Published in Advance June 2, 2025, doi:10.1101/gr.279829.124
...bacterial de novo from short-read data is rarely possible owing to complex, repetitive genomic regions such as insertion sequences (ISs) and other repetitive elements (Ring et al. 2018). Short reads also struggle to reconstruct extrachromosomal elements, such as plasmids (Arredondo-Alonso et al. 2017...
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
...coverage Illumina short reads, Chicago, and Hi-C reads (Fig. 1; see Supplemental Table S1 for read numbers and coverage). Namely, an initial de novo assembly of >72× coverage per species from Illumina sequencing data was generated and used as input for the first HiRise scaffolding using Chicago library...
OPEN ACCESS ARTICLE
Select this article
Method: Nanopore strand-specific mismatch enables de novo detection of bacterial DNA modifications
- Xudong Liu,
- Ying Ni,
- Lianwei Ye,
- Zhihao Guo,
- Lu Tan,
- Jun Li,
- Mengsu Yang,
- Sheng Chen,
- and Runsheng Li
Genome Res. November 2024 34: 2025-2038; Published in Advance October 2, 2024, doi:10.1101/gr.279012.124
...adds complexity and increases the cost associated with bacterial DNA modification detection in nanopore sequencing. Consequently, de novo detection of bacterial DNA modifications remains a challenging task.The read accuracy of nanopores may be compromised by basecalling errors, which can be caused...
Select this article
Research: Long-read genome sequencing and variant reanalysis increase diagnostic yield in neurodevelopmental disorders
- Susan M. Hiatt,
- James M.J. Lawlor,
- Lori H. Handley,
- Donald R. Latner,
- Zachary T. Bonnstetter,
- Candice R. Finnila,
- Michelle L. Thompson,
- Lori Beth Boston,
- Melissa Williams,
- Ivan Rodriguez Nunez,
- Jerry Jenkins,
- Whitley V. Kelley,
- E. Martina Bebin,
- Michael A. Lopez,
- Anna C.E. Hurst,
- Bruce R. Korf,
- Jeremy Schmutz,
- Jane Grimwood,
- and Gregory M. Cooper
Genome Res. November 2024 34: 1747-1762; Published in Advance September 19, 2024, doi:10.1101/gr.279227.124
...@hudsonalpha.orgAbstractVariant detection from long-read sequencing (lrGS) has proven to be more accurate and comprehensive than variant detection from short-read sequencing (srGS). However, the rate at which lrGS can increase molecular diagnostic yield for rare disease is not yet precisely characterized. We performed lrGS using Pacific...
Select this article
Research: Plant genome evolution in the genus Eucalyptus is driven by structural rearrangements that promote sequence divergence
- Scott Ferguson,
- Ashley Jones,
- Kevin Murray,
- Rose Andrew,
- Benjamin Schwessinger,
- and Justin Borevitz
Genome Res. April 2024 34: 606-619; Published in Advance April 8, 2024, doi:10.1101/gr.277999.123
....3.0, 4.0.11, 4.0.14, and 4.0.15) (for per species versions, see Supplemental Results).We complemented the long-read sequencing with highly accurate Illumina short-read sequencing for later use in polishing of the long-read de novo assemblies. Illumina short-read, whole- DNA sequencing libraries were...
OPEN ACCESS ARTICLE
Select this article
Research: Long-read genome assembly of the insect model organism Tribolium castaneum reveals spread of satellite DNA in gene-rich regions by recurrent burst events
- Marin Volarić,
- Evelin Despot-Slade,
- Damira Veseljak,
- Brankica Mravinac,
- and Nevenka Meštrović
Genome Res. November 2024 34: 1878-1894; Published in Advance October 22, 2024, doi:10.1101/gr.279225.124
...and assemble, and therefore, they are underrepresented or absent even in the best assemblies (for review, see Miga 2015; Lower et al. 2018). However, with the improvement of long-read sequencing technology, especially the Oxford Nanopore platform, it has recently been demonstrated that genomic loci made of sat...
OPEN ACCESS ARTICLE
Select this article
Method: Improved assembly of noisy long reads by k-mer validation
- Antonio Bernardo Carvalho,
- Eduardo G. Dupim,
- and Gabriel Goldstein
Genome Res. December 2016 26: 1710-1720; Published in Advance October 7, 2016, doi:10.1101/gr.209247.116
...Corresponding author: bernardo1963@gmail.com Abstract Genome assembly depends critically on read length. Two recent technologies, from Pacific Biosciences (PacBio) and Oxford Nanopore, produce read lengths &gt;20 kb, which yield de novo genome assemblies with vastly greater contiguity than those...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Vaser et al. 27 (5): 737.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: