Year: 2023

Afterwork Genome Sequencing and CRISPRoff

Sung won Lim from Binomica Labs in the USA did a flash talk at the Nanopore Community Meeting in 2022 about “MinION outcome in amateur research: three genomes from 2018 to 2022.” They started using MinION for fun as a “weekend project.” They sequenced Deinococcus radiophilus GCF 020889623.1 and compared it to other genomes deposited […]
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Influenza WGS Surveillance and Direct RNA Sequencing of Brain Samples!

Tonight I watched two short Nanopore Community Meeting 2022 recordings. I started with Sarah Scott from the the Minnesota Public Health Laboratory, USA who presented on the “Exploration of Oxford Nanopore long-read sequencing to contribute to influenza surveillance at the state level.” Scott is an APHL and CDC Fellow. Scott explained that genomic surveillance of […]
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NAb-seq to Confirm Antibodies

Kathleen Zeglinski from the Walter and Eliza Hall Institute of Medical Research in Australia presented the ten minute recorded session entitled “NAb-seq: an accurate, rapid, and cost-effective method for antibody long-read sequencing in hybridoma cell lines and single B cells” at the Nanopore Community Meeting 2022. Zeglinski explained that hybridomas and B cells are common […]
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Stereo Duplex Nanopore Sequencing

Katherine Lawrence, a Machine Learning Bioinformatician with Oxford Nanopore, spoke at the Nanopore Community Meeting 222 about “Advances in duplex basecalling.” They defined duplex sequencing as both ends of the DNA with adaptor motor proteins and two reads from the same molecule. Duplex basecalling incorporates information from both reads’ signals and improves accuracy with the […]
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The Mortino Genome

Karla Estefania Rojas Lopez presented at the Nanopore Community Meeting 2022 a ten-minute session entitled “Draft genome of mortino (Vaccinium florib), a wild berry species of the Andean paramo.” Rojas Lopez works at the Universidad de San Francisco de Quito in Ecuador. This is the second session I watch presented by a researcher from this […]
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Cell Line Sequencing and HPV Research

Isabel Rodriguez from the National Cancer Institute, USA spoke at the Nanopore Community Meeting 2022 on “Analysis of viral and human oncogene expression in human papillomavirus-driven cancer.” Rodriguez shared that human pipillomavirus (HPV) is responsible for almost all cervical cancer cases, the fourth most common cancer worldwide. I also didn’t realize that the incidence is […]
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Sequencing the Genome of the Brown-Headed Spider Monkey

Gabriela Pozo spoke at the Nanopore Community Meeting 2022 about “Whole-genome sequencing of the Ecuadorian brown-headed spider monkey (Ateles fusciceps fusciceps), a critically endangered species. Pozo is from the Universidad San Francisco de Quito, Ecuador. Pozo mentioned that this is a diurnal primate, with a mostly ripe fruit diet and also mushrooms and insects, and […]
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The Remora Update

Marcus Stoiber, a Principle Algorithms Researcher with Oxford Nanopore Technologies, presented at the Nanopore Community Meeting 2022 the “Nanopore modified base update.” Stoiber explained Oxford Nanopore sequencing allows for powerful epigenetics research because it can “directly detect methylation with high reproducibility and low bias.” You can sequence native DNA and RNA to assess modification. The […]
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Learning to Troubleshoot by Exploring the Capabilities of Adaptive Sampling

Continuing with Devin M. Drown’s work, today I watched their Nanopore Community Meeting 2022 session entitled “Portable genomics hackathon for pathogen detection: a practical application of adaptive sampling to engage undergraduate learning.” Drown is at the University of Alaska Fairbanks. Drown explained that the MinION can be used to engage students in problem-solving and applications […]
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DART and VolTRAX

Danielle Wrenn from the Institute of Artic Biology at the University of Alaska Fairbanks presented at the Nanopore Community Meeting 2022 on “DART: a toolbox for the rapid detection of antibiotic resistance.” Wrenn acknowledged the 2022 Genomics Hackathon in January 2022. They used Nanopore and adaptive sampling. Wrenn explained that DART’s purpose is “the rapid […]
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