Tag: MinION

What is 16s rRNA sequencing?

What are the limitations of using 16S sequencing for taxonomic identification?4 answers16S sequencing for taxonomic identification has several limitations. The most commonly used bioinformatics tools, such as Qiime 2 and Mothur, may underestimate the accuracy of species-level taxonomic assignments. Additionally, current analytical approaches lack the ability to formalize syntheses of…

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Validation of Oxford nanopore sequencing for improved New World Leishmania species identification via analysis of 70-kDA heat shock protein | Parasites & Vectors

Akhoundi M, Downing T, Votypka J, Kuhls K, Lukes J, Cannet A, et al. Leishmania infections: molecular targets and diagnosis. Mol Aspects Med. 2017;57:1–29. Article  PubMed  Google Scholar  Akhoundi M, Kuhls K, Cannet A, Votypka J, Marty P, Delaunay P, et al. A historical overview of the classification, evolution, and…

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Gut Microbiome and Bifidobacterium Research in Zimbabwe

Introduction The Infant Gut Microbiome Untangling what constitutes a healthy gut microbiome is timely, particularly in low- and middle-income (LMIC) settings where problems of infant nutrition, chronic diarrhea, and failure to thrive are high priority.1,2 Studying the infant gut microbiome is also crucial as many of the events capable of…

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Molecular Techniques | SpringerLink

Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR et al (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456:53–59 CrossRef  CAS  PubMed  PubMed Central  Google Scholar  Büyükköroğlu G, Dora DD, Özdemir F, Hızel C (2018)…

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Revolutionizing Water Safety with MinION Genome Sequencing

Revolutionizing Water Safety with MinION Genome Sequencing Introduction Microbiology Concepts and Detection Techniques 2.1. Concept of Microbial Water Quality 2.2. Limitations of Culture-Based Methods 2.3. Introduction to NEXt-Generation Sequencing (NGS) 2.4. Shotgun Sequencing: A Powerful DNA Sequencing Technique The Need for DNA Sequencing in Water Analysis 3.1. Application of DNA…

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Resin acids play key roles in shaping microbial communities during degradation of spruce bark

Bark preparation Spruce bark was obtained from the Iggesund pulp and paper mill (Iggesund, Holmen AB, Sweden), from a bark pile resulting from stripping of spruce logs at the mill after harvest, with the average age of trees at harvest being ~70 years. The bark was left to dry at…

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Characterization of 16S rRNA of the gut microbiome in long-tailed macaque (Macaca fascicularis) with spontaneous type 2 diabetes mellitus

Ahmad A, Yang W, Chen G, Shafiq M, Javed S, Zaidi SSA, Shahid R, Liu C, Bokhari H. 2019. Analysis of gut microbiota of obese individuals with type 2 diabetes and healthy individuals. PLoS One. 14(12):1–15. doi:10.1371/ journal.pone.0226372. Arora A, Behl T, Sehgal A, Singh S, Sharma N, Bhatia S,…

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Genomic DNA extraction optimization and validation for genome sequencing using the marine gastropod Kellet’s whelk [PeerJ]

Introduction Rapidly advancing next generation sequencing technologies such as whole genome sequencing, genotyping-in-thousands by sequencing (GT-seq), and restriction-site-associated DNA sequencing (RAD-seq), are becoming more available and affordable for non-model organisms (Park & Kim, 2016; Ellegren, 2014; Van Wyngaarden et al., 2017; Bootsma et al., 2020). However, applying these technologies to…

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The Revolutionary DNA Sequencing Breakthrough

Space scientists at the University of Aberdeen have achieved a monumental breakthrough that is set to transform the field of DNA sequencing and its applications in the search for extraterrestrial life. Employing state-of-the-art technology, these researchers have developed an innovative technique capable of precisely detecting and characterizing soil DNA using…

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How to determine E. coli MLST (Multi Locus Sequence Typing ) from the sequencing of the PCR product of 7 housekeeping genes

How to determine E. coli MLST (Multi Locus Sequence Typing ) from the sequencing of the PCR product of 7 housekeeping genes 0 Hi, I am working on a project to determine antibiotic resistance origins in E. coli. We have amplified 7 housekeeping genes using PCR and sequenced the product…

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Wasatch Biolabs certified Nanopore sequencing provider

© 2008 – 2023 Oxford Nanopore Technologies plc. All rights reserved. Registered Office: Gosling Building, Edmund Halley Road, Oxford Science Park, OX4 4DQ, UK | Registered No. 05386273 | VAT No 336942382. Oxford Nanopore Technologies, the Wheel icon, EPI2ME, Flongle, GridION, Metrichor, MinION, MinIT, MinKNOW, Plongle, PromethION, SmidgION, Ubik and…

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New technique developed to rapidly detect genetic changes in malaria parasites

Scientists have developed a technique to rapidly and reliably detect genetic changes in malaria parasites in Ghana, using just a gaming laptop and portable MinION sequencer from Oxford Nanopore. Researchers from the Wellcome Sanger Institute and University of Ghana were able to demonstrate for the first time that end-to-end, real-time…

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Tricorder Tech: Pocket-sized DNA Sequencers Track Malaria Drug Resistance In Ghana In Near Real-time

Editor’s note: when you find yourself in a field situation with little resource – one where you are trying to trace the spread of a epidemic or the impact a drug has on resistance to an epidemic – being able to do fast genomic assays with equipment you can carry…

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Next Generation Sequencing Market Is Anticipated To Grow At

The global Next-generation Sequencing Market was valued at 5.4 billion in 2022 and it is anticipated to grow up to USD 18.7 billion by 2032, at a CAGR of 13.2% during the forecast period. Request free sample copy of this research study: www.globalinsightservices.com/request-sample/GIS10518/?utm_source=pranalipawar&utm_medium=Openpr&utm_campaign=04122023 Next-generation sequencing (NGS) is a type of…

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Common analysis of direct RNA sequencinG CUrrently leads to misidentification of m5C at GCU motifs

Introduction Oxford Nanopore Technologies (ONT) direct RNA sequencing (Fig 1A) enables detection of RNA modifications. A modified base produces an altered electrical current and/or dwell time relative to a canonical base that can be detected with algorithms (Garalde et al, 2018; Smith et al, 2019; Workman et al, 2019). Figure…

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Tricorder Tech: UCSC Astrobiologist David Deamer And Mark Akeson Honored For Invention Of Nanopore Sequencing

UCSC’s David Deamer and Mark Akeson won the Golden Goose award for the invention of nanopore sequencing, a transformational technology for reading DNA and RNA. Here, Deamer holds the MinION, a portable device for nanopore sequencing. (photo by Nick Gonzales) [In September 2023] two UC Santa Cruz researchers were honored…

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Portable DNA Sequencers Rapidly Detect Malaria Drug Resistance

Edem Adika loading a flow cell in Accra. Credit: William Hamilton Key points: Scientists working in Ghana developed an on-site technique to rapidly and reliably detect genetic changes in malaria parasites. The team’s genetic surveillance technique is an accessible, low cost, near real-time approach that only requires a gaming laptop…

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Compact DNA Sequencers Monitor Malaria Drug Resistance in Real-Time in Ghana

– Advertisement – Scientists have developed a technique to rapidly and reliably detect genetic changes in malaria parasites in Ghana, using just a gaming laptop and portable MinION sequencer from Oxford Nanopore. Researchers from the Wellcome Sanger Institute and University of Ghana demonstrated real-time pathogen monitoring from clinical blood samples…

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Compact DNA Sequencers Monitor Malaria Drug Resistance in Near Real-Time

Register for free to listen to this article Thank you. Listen to this article using the player above. ✖ Want to listen to this article for FREE? Complete the form below to unlock access to ALL audio articles. Scientists have developed a technique to rapidly and reliably…

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Enhanced specificity of Bacillus metataxonomics using a tuf-targeted amplicon sequencing approach

Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of Prokaryotic names with standing in nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol. 2020;70:5607–12. Article  PubMed  PubMed Central  Google Scholar  Saxena AK, Kumar M, Chakdar H, Anuroopa N, Bagyaraj DJ. Bacillus species in soil…

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Tricorder Tech: Sequencing DNA in Space

NASA is not often known for making the best use of existing COTS (commercial off the shelf technology) aboard the ISS. Then again, sometimes they are. This is an example of when the agency really grabs cutting edge biotech and sends it into space. There’s usually quite a lag time….

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POCKET-SIZED DNA SEQUENCERS TRACK MALARIA DRUG RESISTANCE IN GHANA IN NEAR REAL-TIME

For immediate release: 27 November 2023 Peer-reviewed / Observational / Cells POCKET-SIZED DNA SEQUENCERS TRACK MALARIA DRUG RESISTANCE IN GHANA IN NEAR REAL-TIME Scientists have developed a technique to rapidly and reliably detect genetic changes in malaria parasites in Ghana, using just a gaming laptop and portable MinION sequencer from…

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Sol-Gel Technologies (NASDAQ:SLGL) vs. Oxford Nanopore Technologies (OTC:ONTTF) Head-To-Head Contrast

Oxford Nanopore Technologies (OTC:ONTTF – Get Free Report) and Sol-Gel Technologies (NASDAQ:SLGL – Get Free Report) are both medical companies, but which is the better business? We will compare the two businesses based on the strength of their analyst recommendations, risk, earnings, dividends, institutional ownership, profitability and valuation. Analyst Recommendations…

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Top 5 Best Nanotech Companies In India 2024

In a world where innovation continues to shape our future, nanotechnology has emerged as a transformative force. India, with its remarkable scientific prowess and technological advancements, is at the forefront of this revolution. As we step into 2024, it’s an exciting time to explore the Top 5 Best Nanotech innovations…

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MinKNOW software installation doubt for MinION Nanopore sequencing

MinKNOW software installation doubt for MinION Nanopore sequencing 0 Hi good people, Recently in lab we have received a Nanopore MinION device and currently trying to figure out installation and other details. I am seeking a few suggestions from users and experts. The running machine spec is AMD Ryzen 9…

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Genomic characterization of SARS-CoV-2 from Uganda using MinION nanopore sequencing

In this study, we sequenced and characterized 49 SARS-CoV-2 samples from Uganda, collected between April 2020 and July 2021, using MinION Nanopore sequencing. Overall, the ARTIC protocol used was able to generate the required libraries for successful sequencing on the long-read sequencer. MinION Oxford Nanopore technology enabled the identification of…

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Away Team Report: Using DNA Analysis To Identify Bacteria On Board The International Space Station

NASA astronaut and Expedition 70 Flight Engineer Jasmin Moghbeli uses DNA analysis — NASA NASA astronaut and Expedition 70 Flight Engineer Jasmin Moghbeli uses DNA analysis to identify bacteria extracted from water samples collected aboard the International Space Station. Known as BioMole, the study is demonstrating the ability to monitor…

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A single pseudouridine on rRNA regulates ribosome structure and function in the mammalian parasite Trypanosoma brucei

Cell growth and transfections Procyclic form (PCF) T. brucei, strain 29-1354, which carries integrated genes for the T7 polymerase and the tetracycline repressor, was grown in SDM-79 medium supplemented with 10% fetal calf serum, in the presence of 50 μg/ml hygromycin. Cells were grown in the presence of 15 μg/ml G418 for…

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How Much Does Personalized Genome Sequencing Cost? Start Now!

Introduction The field of genome sequencing has revolutionized healthcare by offering personalized insights into our genetic code. With advancements in technology and decreasing costs, personalized genome sequencing has become more accessible to individuals, families, and healthcare professionals. In fact, according to the latest statistical data, the global market for personalized…

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NGS Updates from ASHG: What’s New in Sequencing?

As expected, the NGS companies were sharing their news, out in full force, at the annual American Society for Human Genetics (ASHG) meeting last week in Washington, DC. Whether the updates came from the expo booths showcasing instruments, or users sharing data in the lecture halls, each company had progress…

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DNA Barcoding: A Molecular Toolkit for Species Identification | by Saitama | Nov, 2023

Photo by SilverV 🧬DNA, or deoxyribonucleic acid, is the hereditary material in humans and almost all other organisms. It is a long, thin molecule that carries our genetic code and is coiled up tightly inside the nucleus of every cell in our body. 🧬DNA barcoding is a molecular technology that…

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Leveraging Bioinformatic Algorithms to Improve the Genomic and Metagenomic Analyses of Bacterial Pathogens

Leveraging Bioinformatic Algorithms to Improve the Genomic and Metagenomic Analyses of Bacterial Pathogens Contact: Zhao (Jack) Chen, MS, PhD zhchen29@umd.edu Overview Advances in next-generation sequencing have revolutionized genomics and metagenomics of bacterial pathogens by increasing throughput exponentially over first-generation Sanger sequencing. Short reads with a low error rate of…

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Whole genome sequencing in the palm of your hand: how to implement a MinION-Galaxy-based workflow in a food safety laboratory for rapid Salmonella spp. serotyping, virulence and antimicrobial resistance genes identificationcontrol

1Lhica, Department of Analytical Chemistry, Nutrition and Bromatology, Veterinary School, Campus Terra, Universidade da Santiago de Compostela 27002, Lugo, Spain, Spain 2Food Quality & Safety Research Group. International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal, Portugal 3Department of Animal Pathology…

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Whole transcriptome

Whole transcriptome 0 I need to do Human whole transcriptome using oxford Nanopore but I can’t to calculate the depth of coverage on long read. in short read I need 50 millions read per sample if i need the same output but by long read how can i calculate it,…

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Coca Cola, Oxford Nanopore, BP

Three things you need to know in the financial markets today from investment writer, Tony Cross. #1. Coca Cola sees strong revenue growth seen against small volume uptick Coca Cola HBC [LON:CCH] has a Q3 trading update out today, noting another strong trading period. Revenues are up by 15.3% against…

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Beyond ATGC: enzymatic synthesis and nanopore sequencing of 12-letter supernumerary DNA to unlock xenobiology’s potential

Challenging the rules of Nature with unnatural base pairing xenonucleic acids (XNAs) The 4-letter DNA code Nature utilizes (A, T, G, C) is the backbone of the central dogma and the very blueprint of life itself. Our ability to manipulate this code is also the driver of biotechnological progress; everything…

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MGA-seq: robust identification of extrachromosomal DNA and genetic variants using multiple genetic abnormality sequencing | Genome Biology

Zack TI, Schumacher SE, Carter SL, Cherniack AD, Saksena G, Tabak B, Lawrence MS, Zhang C-Z, Wala J, Mermel CH. Pan-cancer patterns of somatic copy number alteration. Nat Genet. 2013;45:1134–40. Article  CAS  PubMed  PubMed Central  Google Scholar  Dixon JR, Xu J, Dileep V, Zhan Y, Song F, Le VT, Yardımcı…

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A warming world could unleash dangerous new pathogens. Metagenomics early warning tools are vital for pandemic prevention.

New Atlanticist October 30, 2023 • 8:36 am ET A warming world could unleash dangerous new pathogens. Metagenomics early warning tools are vital for pandemic prevention. By Oluwayemisi Ajumobi The world is experiencing a rapid rise in average global temperatures and climate change is increasingly recognized as a health security threat…

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Sequencing and Genotyping / Technological Facilities / Facilities / CRI – Fondazione E. Mach

Instruments MISEQ ILLUMINA NGS sequencing platform that allows to generate up to 25 million reads from 25 to 300 nucleotides in paired end mode (PE 2X300)  MinION ONT Portable real time device for DNA and RNA sequencing by nanopore technology 3730xl GENETIC ANALYZER Capillary electrophoresis platform for high throughput genetic…

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MinION | Oxford Nanopore Technologies

Your browser does not support the video tag. Small but mighty < 450 g Sequence anywhere, pocket-sized devices From $1,000 Low-cost sequencing for every lab Up to 48 Gb* Real-time sequencing data * Theoretical max output when system is run for 72 hours at 400 bases / second. Outputs may…

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Genetic diversity and phylogenetic analyses of Asian lineage Zika virus whole genome sequences derived from Culex quinquefasciatus mosquitoes and urine of patients during the 2020 epidemic in Thailand

Hayes, E. B. Zika virus outside Africa. Emerg. Infect. Dis. 15(9), 1347–1350. doi.org/10.3201/eid1509.090442 (2009). Article  PubMed  PubMed Central  Google Scholar  Faye, O. et al. Molecular evolution of Zika virus during its emergence in the 20th century. PLoS Negl. Trop. Dis. 8(1), e2636. doi.org/10.1371/journal.pntd.0002636 (2014). Article  CAS  PubMed  PubMed Central  Google…

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DNA Sequence Analysis Software Market Intelligence Report:

The research study on Global DNA Sequence Analysis Software Market offers a detailed outline of the factors influencing the worldwide business scope. DNA Sequence Analysis Software Market research report shows the new market insights, current situation examination with upcoming trends, and breakdown of the products and services. The report provides…

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That New Nanopore Protein Sequencing Paper

There’s a new nanopore protein sequencing BioRxiv out! It’s well worth a read. But here are my high level thoughts… They design a bunch of synthetic proteins with a bit on the end which the ClpX unfoldase can attach to. This allows them to use ClpX to ratchet the protein…

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Comparison of methylation estimates obtained via MinION nanopore sequencing and sanger bisulfite sequencing in the TRPA1 promoter region | BMC Medical Genomics

Repeated measurements in one DNA sample revealed congruent results for methylation calling between the methods Sanger bisulfite and nanopore sequencing Mean methylation rates and the methylation rates of individual replicates were congruent between bisulfite and nanopore sequencing (Fig. 1), although the number of calls per site varied in nanopore sequencing. The…

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Microbiome variations among age classes and diets of captive Asian elephants (Elephas maximus) in Thailand using full-length 16S rRNA nanopore sequencing

Phuangkum, P., Lair, R. C. & Angkawanith, T. Elephant Care Manual for Mahouts and Camp Managers (FAO Regional Office for Asia and the Pacific, 2005). Google Scholar  Sukumar, R. The Asian Elephant: Ecology and Management (Cambridge University Press, 1992). Google Scholar  Bansiddhi, P., Brown, J. L., Thitaram, C., Punyapornwithaya, V….

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A Pinoy innovation on HIV research

A Filipino HIV research project is a finalist for Innovation of the Year at IDWeek CLINICAL MATTERS   When I returned to the Philippines as a Balik Scientist in 2009, little did I know I would be playing a major role in fighting HIV in our country. When I graduated…

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Microbiome Sequencing Market Update 2023 : to Reach USD 3.4 Billion Revenue by 2031, Claims Report

The microbiome sequencing market size was valued for $859.42 million in 2021 and is estimated to reach $3,417.09 million by 2031, exhibiting a CAGR of 14.8% from 2022 to 2031. Understanding the Microbiome Before delving into the technological advancements, it’s essential to understand what the microbiome is. The microbiome refers…

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OmicsSuite: Tailored Pipeline for Multi-Omics Big Data Analysis

Abstract: With the advancements in high-throughput sequencing technologies such as Illumina, PacBio, and 10X Genomics platforms, and gas/liquid chromatography-mass spectrometry, large volumes of biological data in multiple formats can now be obtained through multi-omics analysis. Bioinformatics is constantly evolving and seeking breakthroughs to solve multi-omics problems, however it is challenging…

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Timeline Of DNA Sequencing Technology On The International Space Station

iss057e000185 (10/8/2018) – Biomolecule Sequencer for the BEST experiment floating in front of Window 7 in the Cupola module. Earth is in the background. The Biomolecule Sequencer seeks to demonstrate, for the first time, that DNA sequencing is feasible in an orbiting spacecraft. A space-based DNA sequencer could identify microbes,…

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Researchers develop nanopore sequencing method for mapping disease biomarkers

A nanopore sequencing method that can map dozens of biomarkers at the same time has the potential to transform testing for heart disease and other conditions, say researchers. Scientists at Imperial College London have revealed the results of a research collaboration with Oxford Nanopore Technologies (ONT) in Nature Nanotechnology. The…

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Ultra-fast deep-learned CNS tumour classification during surgery

Data simulation Short nanopore sequencing runs yield sparse and random coverage of the genome. To enable model training, we generate simulated sparse nanopore runs based on microarray data. To this end, N simulated reads are randomly sampled from the read length distribution (D) and assigned a start mapping position in…

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Oxford Nanopore collaboration makes classroom DNA sequencing accessible

An ambition to make in-classroom DNA sequencing routinely available, more user-friendly, and more egalitarian in U.S. universities and schools has been set out by a leading genetics educator. David Micklos, founder and executive director of Cold Spring Harbor Laboratory’s DNA Learning Center (DNALC), said that sequencing technology could prove “revolutionary”…

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Adapters finder

Adapters finder 0 Hi, I am currently studying RNA-seq analysis and have been primarily using the Minion algorithm to find and trim adapters. While this algorithm does not have a large community, it is capable of discovering adapter motifs de novo in addition to finding adapters from a library. I…

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Issues with featureCounts

Dear community, I have been struggling finding the problem for the past few days now. I work on making a differential expression analysis (DEA) with direct RNA nanopore long reads from the minion platform. I ran into this wall and I would really appreciate your help! I sequenced the RNA…

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Somatic evolution of marine transmissible leukemias in the common cockle, Cerastoderma edule

Murchison, E. P. Clonally transmissible cancers in dogs and Tasmanian devils. Oncogene 27, S19–S30 (2009). Article  Google Scholar  Metzger, M. J. & Goff, S. P. A sixth modality of infectious disease: contagious cancer from devils to clams and beyond. PLoS Pathog. 12, e1005904 (2016). Article  PubMed  PubMed Central  Google Scholar …

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A maximum severity Pytorch TorchServe vulnerability

What comes to mind when you hear names like Google, Facebook, and Microsoft? Giants in the tech industry, right? And when such giants trust a particular tool, you’d expect it to be rock solid, especially when it’s about securing sensitive data and machine learning models. However, a recent vulnerability discovery…

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Issues with featureCounts (No

Dear community, i have been struggling finding the problem for the past few days now. I work on making a differential expression analysis (DEA) with direct RNA nanopore long reads from the minion platform. I ran into this wall and i would really appreciate your help! I sequenced the RNA…

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UCSC’s David Deamer and Mark Akeson honored for invention of nanopore sequencing

David Deamer (left) and Mark Akeson in Santa Cruz in 2023 after receiving the inaugural UCSC Chancellor’s Innovation Impact Award for inventing nanopore sequencing. (photo by Nestor Guerrero) September 27, 2023 By Emily Cerf UCSC’s David Deamer and Mark Akeson won the Golden Goose award for the invention of nanopore sequencing, a…

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Solved We are working with the fastq files in this

Transcribed image text: We are working with the fastq files in this directory: Generate a fastqc report for each fastq file in that directory. Look at the “Per base sequence quality” file and compare them, then choose the correc answers below. The mean quality of the illumina reads is higher…

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Even Tiny Amounts of DNA on Mars Will Be Detectable

The Search for Life is focused on the search for biosignatures. Planetary life leaves a chemical fingerprint on a planet’s atmosphere, and scientists are trying to work out which chemicals in what combinations and amounts are a surefire indicator of life. Martian methane is one they’re puzzling over right now….

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Nanopore sequencing and DNA barcoding method gives hope of personalized medicine

With the ability to map dozens of biomarkers at once, a new method could transform testing for conditions including heart disease and cancer. Currently, many diseases are diagnosed from blood tests that look for one biomarker (such as a protein or other small molecule) or, at most, a couple of…

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Scientists Develop New Method Using DNA Sequencing to Test for Life on Mars

Scientists from the University of Aberdeen have developed a groundbreaking method for testing for life on Mars and Earth. They used a MinION DNA sequencer developed by Oxford Nanopore Technologies to detect microorganisms in minuscule amounts of soil. The researchers were able to characterize soil DNA with as little as…

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DNA Barcoding Allows Nanopore Sequencing to Identify Dozens of Biomarkers in One Test

Credit: Oxford Nanopore Technologies Researchers at Imperial College London (ICL) working with commercial partner Oxford Nanopore Technologies have developed a method for DNA barcoding that allow nanopore sequencing to identify dozens of biomarkers in one test. The new method, reported today in Nature Nanotechnology, shows promise to identify specific biomarkers…

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Nanopore sequencing and DNA barcoding method gives hope of personalised medicine | Imperial News

With the ability to map dozens of biomarkers at once, a new method could transform testing for conditions including heart disease and cancer. Currently, many diseases are diagnosed from blood tests that look for one biomarker (such as a protein or other small molecule) or, at most, a couple of…

Continue Reading Nanopore sequencing and DNA barcoding method gives hope of personalised medicine | Imperial News

capTEs enables locus-specific dissection of transcriptional outputs from reference and nonreference transposable elements

Cell culture All cell lines were grown in 6 cm dishes at 37 °C in a 5% CO2 incubator. The K562, MDA-MB-231 and HCT 116 cell lines were cultured in high-glucose DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin antibiotics (pen-strep). NCM460 cells were cultured in RPMI 1640 medium supplemented…

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Genome-Based Prediction of Bacterial Antibiotic Resistance

Abdelbary M, Basset P, Blanc D et al (2017) In: Tibayrenc M (ed) Genetics and evolution of infectious diseases: the evolution and dynamics of methicillin-resistant Staphylococcus aureus, 2nd edn. Elsevier, pp 553–572. ISBN: 9780127999425 CrossRef  Google Scholar  Allard MW, Stevens EL, Brown EW (2019) All for one and one for…

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DNA sequencing at the picogram level to investigate life on Mars and Earth

All the extractions, dilutions and library preparation for sequencing were carried out inside the clean room environment of ISO (International Organization for Standardization) level 5 (ECSS-Q-ST-70-55C standard)32. An ISO 5 Class clean room is a semi-closed ultra clean environment that utilises High Efficiently Particle Air (HEPA) filtration systems to maintain…

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Morphological and physiological adaptations of psychrophilic Pseudarthrobacter psychrotolerans YJ56 under temperature stress

Bacterial isolation from Antarctic soil Soil samples were collected from the Cape Burk area (1: 74° 45′ 19.6″ S, 136° 48′ 44.6″ W)51. The soil (1 g) was inoculated in a Reasoner’s 2A (R2A) liquid (composed of 0.5% proteose peptone, 0.05% casamino acid, 0.05% yeast extract, 0.05% dextrose, 0.05% soluble starch,…

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DNA Sequencing Equipment market research report provides critical insights that can help shape business development by providing a CAGR of 7.3% from 2023 to 2030

This &ldquo;DNA Sequencing Equipment Market” highlights key external drivers that affect the industry and assesses the current performance and revenue growth of the industry. This report helps to collect industry information for target audiences before commencing any advertising campaign. The DNA Sequencing Equipment market is expected to grow annually by…

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Isolation of Spirosoma foliorum sp. nov. from the fallen leaf of Acer palmatum by a novel cultivation technique

Locey, K. J. & Lennon, J. T. Scaling laws predict global microbial diversity. PNAS 113, 5970–5975. doi.org/10.1073/pnas.1521291113 (2016). Article  ADS  CAS  PubMed  PubMed Central  Google Scholar  Hahn, M. W., Koll, U. & Schmidt, J. The Structure and Function of Aquatic Microbial Communities (Springer International Publishing, 2019). Rosenberg, E., DeLong, E….

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Targeted DNA Sequencing Market Forecast from 2023 – 2030 Growing at a CAGR of 9% with Key Players and Market Analysis

The “Targeted DNA Sequencing Market” report draws on various inferences to analyze the challenges within the industry. The final draught highlights the industry’s typical problems as well as the businesses facing them. This report is of 143 pages. The Targeted DNA Sequencing market is expected to grow annually by 9%…

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Characterisation and comparative genomics of three new Varanus-associated Borrelia spp. from Indonesia and Australia | Parasites & Vectors

The following results clearly demonstrate that the Borrelia spp. identified in ticks collected from V. salvator, V. varius, and V. giganteus are distinct species. Therefore, for clarity, we herein refer to these Borrelia spp. by their proposed names: Borrelia salvatorii (from V. salvator), ‘Ca. Borrelia undatumii’ (from V. varius), and…

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Whole-genome sequencing for One Health surveillance of antimicrobial resistance in conflict zones: a case study of Salmonella spp. and Campylobacter spp. in the West Bank, Palestine

Antimicrobial resistance (AMR) is a critical global concern driven by the overuse, misuse, and/or usage of inadequate antibiotics on humans, animals’ agriculture, and as a result of contaminated environments. This study is the first One Health survey in the Middle East that incorporated whole-genome sequencing (WGS) to examine the spread…

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Emergence of putative energy parasites within Clostridia revealed by genome analysis of a novel endosymbiotic clade

Cryan JF, O’Riordan KJ, Cowan CSM, Sandhu KV, Bastiaanssen TFS, Boehme M, et al. The microbiota-gut-brain axis. Physiol Rev. 2019;99:1877–2013. Article  CAS  PubMed  Google Scholar  Lopetuso LR, Scaldaferri F, Petito V, Gasbarrini A. Commensal clostridia: leading players in the maintenance of gut homeostasis. Gut Pathog. 2013;5:e23. Article  Google Scholar  Collins…

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Functional annotation and comparative genomics analysis of Balamuthia mandrillaris reveals potential virulence-related genes

Levinson, S. et al. Balamuthia mandrillaris brain infection: A rare cause of a ring-enhancing central nervous system lesion. Illustrative case. J. Neurosurg Case Lessons 3, 25 (2022). Google Scholar  Wu, X. et al. Diagnosing Balamuthia mandrillaris encephalitis via next-generation sequencing in a 13-year-old girl. Emerg. Microbes Infect. 9, 1379–1387 (2020)….

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Oxford Nanopore, IQVIA form nanopore sequencing partnership

Oxford Nanopore Technologies and IQVIA have struck a partnership to broaden access to nanopore sequencing technology, saying it will boost genomics research and patient care. The two companies will launch proof-of-concept projects in Europe, including an initial pilot in Romania, as well as in the Middle East, Africa, and India….

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Iso-Seq method outperforms other long-read methods in benchmarking consortium study

A benchmarking of long-read RNA sequencing methods and analysis tools The Long-read RNA-Seq Genome Annotation Assessment Project (LRGASP) consortium, an initiative to systematically evaluate methods for transcript identification and quantification, recently released their final assessment of long-read sequencing technologies and tools in the preprint “Systematic assessment of long-read RNA-seq methods…

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The Key to Unlocking Our Genetic Heritage

Exploring the Future: DNA Sequencing Technologies and Our Genetic Heritage DNA sequencing technologies are revolutionizing our understanding of the human genome, offering unprecedented insights into our genetic heritage and potential. These technologies, which decode the order of nucleotides in a DNA molecule, are unlocking the secrets of our genetic makeup,…

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Post-doctoral Research Fellow, School of Biomolecular and Biomedical Science job with UNIVERSITY COLLEGE DUBLIN (UCD)

Applications are invited for a Temporary post of a Post-doctoral Research Fellow Level 1 within UCD School of Biomolecular and Biomedical Science. This position is part of a research project in Professor Geraldine Butler’s laboratory in UCD Conway Institute, funded by a grant from Science Foundation Ireland. Its goals are…

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16S rRNA gene primer choice impacts off-target amplification in human gastrointestinal tract biopsies and microbiome profiling

The problem of off-target amplification The widely used standardized protocol for 16S rRNA gene amplicon sequencing7,14 turned out to be inadequate due to robust off-target amplification of human DNA during the analysis of bacteriome in samples of different biopsy sites from the upper gastrointestinal (GI) tract. In samples from all…

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Next-Generation Sequencing in Plant Breeding: Challenges and Possibilities

Abdi, H. (2007). Discriminant correspondence analysis. In N. J. Salkind (Ed.), Encyclopedia of measurement and statistic (pp. 270–275). Sage. Google Scholar  Ando, K., Carr, K. M., & Grumet, R. (2012). Transcriptome analyses of early cucumber fruit growth identifies distinct gene modules associated with phases of development. BMC Genomics, 13, 518….

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Rapid gene content turnover on the germline-restricted chromosome in songbirds

This work was carried out in accordance with ethical animal research requirements of Poland according to Polish law (the Act On the Protection of Animals used for Scientific or Educational Purposes, 15.01.2015, item 266, implementing Directive 2010/63/EU of the European Parliament and of the European Council of 22.09.2010). Experiments on…

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Bioinformatics Engineer in Fort Detrick, MD (Hybrid Remote)

Description The Military & Veteran’s Health Operation of Leidos is currently looking for a Bioinformatics Engineer to support biological research at the Biological Defense Research Directorate (BDRD) at the Naval Medical Research Center (NMRC) in Frederick, MD.  The BDRD within NMRC facilitates biological research for the rapid detection of infectious…

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Transcriptome assembler comparisons-Getting vastly different results

Transcriptome assembler comparisons-Getting vastly different results 0 Hi there I am comparing RNABLOOM2 (with and without Illumina shorts reads for polishing) and RATTLE for transcript assembly using reads from minion long read seq. The number of transcripts are extremely different. For RATTLE-50 000 transcripts; for RNABLOOM-about 160 000 transcripts (with…

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The potential role of the microbiota in prostate cancer pathogenesis and treatment

Lynch, S. V. & Pedersen, O. The human intestinal microbiome in health and disease. N. Engl. J. Med. 375, 2369–2379 (2016). Article  CAS  PubMed  Google Scholar  Qin, J. et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59–65 (2010). Article  CAS  PubMed  PubMed Central  Google…

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Increased interregional virus exchange and nucleotide diversity outline the expansion of chikungunya virus in Brazil

Mourad, O., Makhani, L. & Chen, L. H. Chikungunya: an emerging public health concern. Curr. Infect. Dis. Rep. 24, 217–228 (2022). Article  PubMed  PubMed Central  Google Scholar  Chala, B. & Hamde, F. Emerging and re-emerging vector-borne infectious diseases and the challenges for control: a review. Front. Public Health 9, 715759…

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Long-read sequence analysis of MMEJ-mediated CRISPR genome editing reveals complex on-target vector insertions that may escape standard PCR-based quality control

Overview of the targeting strategy Figure 1A presents an overview of the MMEJ-mediated genome-editing system PITCh12,13. The full-length sequence of the targeting vector is shown in Supplementary Fig. 1. The PITCh method can be classified into three types according to the number of cutting sites in the genome and the targeting vector….

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Nanopore long-read next-generation sequencing for detection of mitochondrial DNA large-scale deletions

. 2023 Jun 29;14:1089956. doi: 10.3389/fgene.2023.1089956. eCollection 2023. Affiliations Expand Affiliations 1 Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy. 2 Department of Pathophysiology and Transplantation (DEPT), University of Milan, Milan, Italy. Item in Clipboard Chiara Frascarelli et al. Front Genet. 2023. Show details Display…

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Oxford Nanopore Technologies Flags 22% Rise in H1 Revenue, Maintains FY23 Guidance

Oxford Nanopore Technologies plc is engaged in the generation of molecular sensing technology based on nanopores. The Company has developed a deoxyribonucleic (DNA)/ ribonucleic acid (RNA) sequencing technology. Its segments include Life Science Research Tools (LSRT) and COVID-19 Testing. The LSRT segment offers products and services for research use. The…

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Bioinformatics Analyst at Leidos | The Muse

Description The Military & Veteran’s Health Operation of Leidos is currently looking for a Bioinformatics Analyst to support biological research at the Biological Defense Research Directorate (BDRD) at the Naval Medical Research Center (NMRC) in Frederick, MD. The BDRD within NMRC facilitates biological research for the rapid detection of infectious…

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hypervariable region of 16s rrna

The mock community was created from pure cultures, whose 16S rRNA genes were determined through Sanger sequencing to be >3% different (Table S1). Bartram, Andrea. WebWhile 16S hypervariable region analysis is a powerful tool for bacterial taxonomic studies, it struggles to differentiate between closely related species. Limited by sequencing Rarefaction…

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Metagenomic surveillance for bacterial tick-borne pathogens using nanopore adaptive sampling

Albertsen, M. Long-read metagenomics paves the way toward a complete microbial tree of life. Nat. Methods 20, 30–31 (2023). Article  CAS  PubMed  Google Scholar  van Dijk, E. L., Auger, H., Jaszczyszyn, Y. & Thermes, C. T. years of next-generation sequencing technology. Trends Genet. 30, 418–426 (2014). Article  PubMed  Google Scholar …

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the MinION changing the future of medicine

You can listen to the podcast by clicking the play button above. You can watch most recordings of the podcast on Schroders Youtube channel. You can also subscribe, download, rate and review the Investor Download via Podbean, Apple Podcasts, Spotify, Google and other podcast players. New shows are available every…

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Intragenomic rDNA variation – the product of concerted evolution, mutation, or something in between?

Adams KL, Wendel JF (2005) Polyploidy and genome evolution in plants. Curr Opin Plant Biol 8(2):135–141 Article  CAS  PubMed  Google Scholar  Ambrose CD, Crease TJ (2011) Evolution of the nuclear ribosomal DNA intergenic spacer in four species of the Daphnia pulex complex. BMC Genet 12:13 Article  CAS  PubMed  PubMed Central …

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Drug resistance-associated mutations of M.TB

Introduction Tuberculosis (TB) is one of the most common causes of death and the leading cause of a single infectious agent.1 According to the 2022 Global TB Report of the World Health Organization (WHO), 10.6 million people were infected with TB in 2021, and although the annual number of deaths…

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The Complete Sequence of the Almond Genome

The consortium for sequencing the “Texas” almond genome was created and led by Dr. Arús in 2013. This project included an international team of scientists from Spain, France, Australia, the USA, and UK. Although preliminary versions of the genome were internally available for the members of the consortium in 2015,…

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Impact of nanopore-based metagenome sequencing on tick-borne virus detection

. 2023 May 30;14:1177651. doi: 10.3389/fmicb.2023.1177651. eCollection 2023. Koray Ergunay  1   2   3   4 , Ender Dincer  5 , Silvia A Justi  1   2   3 , Brian P Bourke  1   2   3 , Suppaluck P Nelson  1   2   3 , Hsiao-Mei Liao  6   7 , Mehmet…

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Batch correction for Nanopore RNAseq

Batch correction for Nanopore RNAseq 0 I have 3 RNAseq experiments that were sequenced on a MinION and I am trying to do some differential expression analysis with them. This is my pipeline: Basecalling with Guppy Cleaning using chopper Aligning to the genome (mouse) with minimap2 Counting using featureCounts At…

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The genome of Acorus deciphers insights into early monocot evolution

Lughadha, E. N. et al. Counting counts: revised estimates of numbers of accepted species of flowering plants, seed plants, vascular plants and land plants with a review of other recent estimates. Phytotaxa 272, 82–88 (2016). Article  Google Scholar  Group, A. P. An update of the Angiosperm Phylogeny Group classification for…

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Using nanopore sequencing to identify fungi from clinical samples with high phylogenetic resolution

Fungal genomic DNA DNA extracted from Aspergillus niger (kindly provided by Dr. Takamitsu Imoto, Medical Research Institute, Kitano Hospital, Osaka, Japan) and a mock community DNA standard (Mycobiome Genomic DNA Mix, MSA-1010; ATCC, Manassas, VA, USA) were used to evaluate the validity of the sequencing methodology. The mock community standard…

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