Journal Français d Ophtalmologie, Journal Year: 2025, Volume and Issue: 48(5), P. 104509 - 104509
Published: April 6, 2025
Language: Английский
Nature Reviews Methods Primers, Journal Year: 2023, Volume and Issue: 3(1)
Published: July 20, 2023
Language: Английский
Citations
63
Journal of Translational Medicine, Journal Year: 2024, Volume and Issue: 22(1)
Published: Jan. 28, 2024
Abstract The study of microbial communities has undergone significant advancements, starting from the initial use 16S rRNA sequencing to adoption shotgun metagenomics. However, a new era emerged with advent long-read (LRS), which offers substantial improvements over its predecessor, short-read (SRS). LRS produces reads that are several kilobases long, enabling researchers obtain more complete and contiguous genomic information, characterize structural variations, epigenetic modifications. current leaders in technologies Pacific Biotechnologies (PacBio) Oxford Nanopore Technologies (ONT), each offering distinct set advantages. This review covers workflow metagenomics sequencing, including sample preparation (sample collection, extraction, library preparation), processing (quality control, assembly, binning), analysis (taxonomic annotation functional annotation). Each section provides concise outline key concept methodology, presenting original as well how it is challenged or modified context LRS. Additionally, introduces range tools compatible can be utilized execute process. aims present metagenomics, highlight transformative impact LRS, provide selection suitable for this task.
Language: Английский
Citations
32
MedComm, Journal Year: 2023, Volume and Issue: 4(4)
Published: July 10, 2023
Abstract Since the development of Sanger sequencing in 1977, technology has played a pivotal role molecular biology research by enabling interpretation biological genetic codes. Today, nanopore is one leading third‐generation technologies. With its long reads, portability, and low cost, widely used various scientific fields including epidemic prevention control, disease diagnosis, animal plant breeding. Despite initial concerns about high error rates, continuous innovation platforms algorithm analysis effectively addressed accuracy. During coronavirus (COVID‐19) pandemic, critical detecting severe acute respiratory syndrome coronavirus‐2 virus genome containing pandemic. However, lack understanding this may limit popularization application. Nanopore poised to become mainstream choice for preventing controlling COVID‐19 future epidemics while creating value other such as oncology botany. This work introduces contributions during pandemic promote public use emerging outbreaks worldwide. We discuss application microbial detection, cancer genomes, genomes summarize strategies improve
Language: Английский
Citations
34
Coordination Chemistry Reviews, Journal Year: 2024, Volume and Issue: 510, P. 215816 - 215816
Published: April 1, 2024
Language: Английский
Citations
12
Journal of the American Chemical Society, Journal Year: 2024, Volume and Issue: 146(19), P. 13356 - 13366
Published: April 11, 2024
The crucial roles that glycans play in biological systems are determined by their structures. However, the analysis of glycan structures still has numerous bottlenecks due to inherent complexities. nanopore technology emerged as a powerful sensor for DNA sequencing and peptide detection. This significant impact on development related research area. Currently, nanopores beginning be applied detection simple glycans, but complex this is challenging. Here, we designed an engineered α-hemolysin M113R/T115A achieve sensing at micromolar concentrations under label-free conditions. By extracting characteristic features depict three-dimensional (3D) scatter plot, with different numbers functional groups, various chain lengths ranging from disaccharide decasaccharide, distinct glycosidic linkages could distinguished. Molecular dynamics (MD) simulations show behaviors β1,3- or β1,4-glycosidic bonds nanopores. More importantly, system permitted discrimination each isomer mixture separation ratio over 0.9. work represents proof-of-concept demonstration can analyzed using technology.
Language: Английский
Citations
12
Chemical Science, Journal Year: 2024, Volume and Issue: 15(17), P. 6229 - 6243
Published: Jan. 1, 2024
This perspective outlines three potential routes for nanopore-based glycan sequencing, highlighting their applications and offering insights to meet associated challenges. It also introduces the concept of sequencer.
Language: Английский
Citations
9
Nature Reviews Methods Primers, Journal Year: 2023, Volume and Issue: 3(1)
Published: July 20, 2023
Language: Английский
Citations
18
Sensors, Journal Year: 2024, Volume and Issue: 24(9), P. 2904 - 2904
Published: May 1, 2024
Demand is strong for sensitive, reliable, and cost-effective diagnostic tools cancer detection. Accordingly, bead-based biosensors have emerged in recent years as promising platforms based on wide-ranging biomarkers owing to the versatility, high sensitivity, flexibility perform multiplexing of beads. This comprehensive review highlights trends innovations development cancer-biomarker We introduce various types such optical, electrochemical, magnetic biosensors, along with their respective advantages limitations. Moreover, summarizes latest advancements, including fabrication techniques, signal-amplification strategies, integration microfluidics nanotechnology. Additionally, challenges future perspectives field detection are discussed. Understanding these can greatly contribute improvements diagnostics, thereby facilitating early personalized treatments.
Language: Английский
Citations
8
Molecular Ecology Resources, Journal Year: 2024, Volume and Issue: unknown
Published: Oct. 10, 2024
It is a global priority to better manage the biosphere, but action must be informed by comprehensive data on abundance and distribution of species. The acquisition such information currently constrained high costs. DNA barcoding can speed registration unknown animal species, most diverse kingdom eukaryotes, as BIN system automates their recognition. However, inexpensive sequencing protocols are critical census all species likely require analysis billion or more specimens. Barcoding involves extraction followed PCR with last step dominating costs until 2017. By enabling highly multiplexed samples, Sequel platforms from Pacific BioSciences slashed 90%, these instruments only deployed in core facilities because expense. Sequencers Oxford Nanopore Technologies provide an escape capital service costs, low sequence fidelity has, recently, adoption. improved performance its latest flow cells (R10.4.1) erases this barrier. This study demonstrates that MinION cell characterise amplicon pool derived 100,000 specimens while Flongle process one several thousand. At $0.01 per specimen, now least expensive barcode workflow.
Language: Английский
Citations
8
Human Genetics, Journal Year: 2024, Volume and Issue: 143(9-10), P. 1005 - 1020
Published: May 24, 2024
Abstract Long-read single-cell transcriptomics (scRNA-Seq) is revolutionizing the way we profile heterogeneity in disease. Traditional short-read scRNA-Seq methods are limited their ability to provide complete transcript coverage, resolve isoforms, and identify novel transcripts. The protocols developed for long-read sequencing platforms overcome these limitations by enabling characterization of full-length techniques initially suffered from comparatively poor accuracy compared short read scRNA-Seq. However, with improvements accuracy, accessibility, cost efficiency, long-reads gaining popularity field This review details advances scRNA-Seq, an emphasis on library preparation downstream bioinformatics analysis tools.
Language: Английский
Citations
6