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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
...when multiplexing) (Sanderson et al. 2024), and the ability to circularize chromosomes and plasmids owing to its long-read nature (Lerminiaux et al. 2024). It also provides options for real-time sequencing and rapid library preparation, essential for quick outbreak responses (Wagner et al. 2023). Early...
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Research: Assessing the readiness of Oxford Nanopore sequencing for clinical genomics applications
- Judith Arres,
- Santosh Elavalli,
- Shalini Behl,
- Daniel Matias Sanchez,
- Ayesha Al Ali,
- Abdelrahman Ahmed Yehia Abdelaziz Saad,
- Azza Attia,
- Cyla Minas,
- Sharika Pariyachery,
- Shariq Ahmed,
- Fatmah Aldhuhoori,
- Nitu Thulasidharan,
- Gurunath Katagi,
- Omar Soliman,
- Shilp Purohit,
- Vinay Kusuma,
- Raony Cardenas,
- Thyago Cardoso,
- Luis F. Paulin,
- Philippe Sanio,
- Joseph Mafofo,
- Haiguo Wu,
- Val Zvereff,
- Albarah El-Khani,
- Fahed Al Marzooqi,
- Tiago R. Magalhães,
- Fritz J. Sedlazeck,
- and Javier Quilez
Genome Res. March 2026 36: 460-471; Published in Advance February 11, 2026, doi:10.1101/gr.280134.124
...Beyond comparisons to reference truth sets, we also examined systematic differences in variant calling between sequencing platforms. We noticed that for ONT, both R9 and R10, an excess of SNPs/indels around the centromeres is called compared with other parts of the chromosome (Supplemental Fig. S12). That is also...
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Review: Artificial intelligence and machine learning in cell-free-DNA-based diagnostics
- W.H. Adrian Tsui,
- Spencer C. Ding,
- Peiyong Jiang,
- and Y.M. Dennis Lo
Genome Res. January 2025 35: 1-19; doi:10.1101/gr.278413.123
...@cuhk.edu.hkAbstractThe discovery of circulating fetal and tumor cell-free DNA (cfDNA) molecules in plasma has opened up tremendous opportunities in noninvasive diagnostics such as the detection of fetal chromosomal aneuploidies and cancers and in posttransplantation monitoring. The advent of high-throughput sequencing...
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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
...and persistent challenges, including the experimental and computational requirements needed to scale to larger sample sizes, the hurdles in sequencing and analyzing complex cancer s, and opportunities for leveraging machine learning and artificial intelligence technologies for cancer informatics. We further...
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Resource: Complete sequencing of a cynomolgus macaque major histocompatibility complex haplotype
- Julie A. Karl,
- Trent M. Prall,
- Hailey E. Bussan,
- Joshua M. Varghese,
- Aparna Pal,
- Roger W. Wiseman,
- and David H. O'Connor
Genome Res. March 2023 33: 448-462; Published in Advance February 28, 2023, doi:10.1101/gr.277429.122
...of class I loci (Daza-Vamenta et al. 2004; Fukami-Kobayashi et al. 2005; Shiina et al. 2006; Watanabe et al. 2007). Sequencing of an MHC class I B haplotype from a rhesus macaque bacterial artificial chromosome (BAC) library (CHORI-250) identified 19 distinct MHC-B genes (Daza-Vamenta et al. 2004; Shiina...
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Research: Chromosome-scale assemblies of Acanthamoeba castellanii genomes provide insights into Legionella pneumophila infection–related chromatin reorganization
- Cyril Matthey-Doret,
- Morgan J. Colp,
- Pedro Escoll,
- Agnès Thierry,
- Pierrick Moreau,
- Bruce Curtis,
- Tobias Sahr,
- Matt Sarrasin,
- Michael W. Gray,
- B. Franz Lang,
- John M. Archibald,
- Carmen Buchrieser,
- and Romain Koszul
Genome Res. September 2022 32: 1698-1710; Published in Advance September 15, 2022, doi:10.1101/gr.276375.121
..., which is a hallmark of most bacterial chromosome structure (Le et al. 2013; Marbouty et al. 2017), was barely visible. Therefore, the protocol must first be improved to enrich for contacts in bacterial sequence before parallel analysis of changes in host and pathogen organization can be considered...
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Method: Chromosome assembly of large and complex genomes using multiple references
- Mikhail Kolmogorov,
- Joel Armstrong,
- Brian J. Raney,
- Ian Streeter,
- Matthew Dunn,
- Fengtang Yang,
- Duncan Odom,
- Paul Flicek,
- Thomas M. Keane,
- David Thybert,
- Benedict Paten,
- and Son Pham
Genome Res. November 2018 28: 1720-1732; Published in Advance October 19, 2018, doi:10.1101/gr.236273.118
...to explore s from a large number of species (Jarvis et al. 2014).Recently, new de novo assembly algorithms have been developed to combine high-throughput short-read sequencing data with long single-molecule sequencing reads or jumping libraries to completely assemble bacterial s (one chromosome into one...
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Method: Paired-end sequencing of Fosmid libraries by Illumina
- Louise J.S. Williams,
- Diana G. Tabbaa,
- Na Li,
- Aaron M. Berlin,
- Terrance P. Shea,
- Iain MacCallum,
- Michael S. Lawrence,
- Yotam Drier,
- Gad Getz,
- Sarah K. Young,
- David B. Jaffe,
- Chad Nusbaum,
- and Andreas Gnirke
Genome Res. November 2012 22: 2241-2249; Published in Advance July 16, 2012, doi:10.1101/gr.138925.112
...Paired-end sequencing of Fosmid libraries by Illumina Louise J.S. Williams , Diana G. Tabbaa , Na Li 1 , Aaron M. Berlin , Terrance P. Shea , Iain MacCallum , Michael S. Lawrence , Yotam Drier , Gad Getz...
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Method: High precision Neisseria gonorrhoeae variant and antimicrobial resistance calling from metagenomic Nanopore sequencing
- Nicholas D. Sanderson,
- Jeremy Swann,
- Leanne Barker,
- James Kavanagh,
- Sarah Hoosdally,
- Derrick Crook,
- The GonFast Investigators Group,
- Teresa L. Street,
- and David W. Eyre
Genome Res. September 2020 30: 1354-1363; Published in Advance September 1, 2020, doi:10.1101/gr.262865.120
...offers the potential to detect and sequence near-complete N. gonorrhoeae s directly from urine samples (Street et al. 2020). This clinical metagenomic approach has the advantage that it does not require prior bacterial culture, which typically adds two to three days to diagnostic workflows and may...
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Research: Origin and domestication of papaya Y^h chromosome
- Robert VanBuren,
- Fanchang Zeng,
- Cuixia Chen,
- Jisen Zhang,
- Ching Man Wai,
- Jennifer Han,
- Rishi Aryal,
- Andrea R. Gschwend,
- Jianping Wang,
- Jong-Kuk Na,
- Lixian Huang,
- Lingmao Zhang,
- Wenjing Miao,
- Jiqing Gou,
- Jie Arro,
- Romain Guyot,
- Richard C. Moore,
- Ming-Li Wang,
- Francis Zee,
- Deborah Charlesworth,
- Paul H. Moore,
- Qingyi Yu,
- and Ray Ming
Genome Res. April 2015 25: 524-533; Published in Advance March 11, 2015, doi:10.1101/gr.183905.114
..., and positive BACs were confirmed using PCR and BAC end sequencing. New probes were designed from these positive BACs to screen the BAC library. Chromosome walking continued until a minimum tiling path of MSY BACs spanned the entire sex determining region. Mini-prep BAC DNA isolation was performed to check...

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