DNA

AMRs in Complex Environmental Matrices

Rob James from the University of Warwick in the UK presented a session titled “From amplicons to metagenomes: long-read sequencing the environment” at London Calling 2019. James spoke about complex environmental matrices such as soil, sediment, and excreta that are often impure and biologically and chemically contaminated. Different extraction methods are used depending on the […]
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Spider Silk and Arachnid Genomes

Sarah Stellwagen from the University of Maryland, Baltimore County, spoke at the Nanopore Community Meeting 2019 on arachnids! The title of the session is “Advances in arachnid genomics using Oxford Nanopore’s MinION.” They study spider silk genetics and also harvestmen. Stellwagen explained that there are several different types of silk to make egg sacs, joints, […]
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Detecting the Epigenome with ONT

Chen Yong from Oxford Nanopore helped facilitate the Knowledge Exchange session I watched tonight: “Decoding the epigenome with Oxford Nanopore real-time methylation detection.” This webinar was recorded. Sayonika Mohanta from ONT explained that methylation is central to gene expression. They spoke about the role of methylation in gene expression: her or hypo methylation can affect […]
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A Nanopore-based Approach to Detect and Analyze Repeat Anomalies

Hagar Mor-Shaked from the Hadassah Medical Organization and Faculty of Medicine, Hebrew University of Jerusalem, presented a lightning talk at London Calling 2023. The title of the session is “Pathological short tandem repeats analysis by long-read sequencing in affected individuals.” They were also an employee of the Geneyx company that did genomic analysis. Mor-Shaked spoke […]
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Use of Long-read Sequencing in a Contract Food Laboratory

Andrzej A. Benkowski from Eurofins Microbiology Laboratories in Madison, WI, presented at London Calling 2023 a lightning talk on the “Practical uses of nanopore long-read sequencing in a high-throughput contract food laboratory.” They presented a few case studies from the contract lab. The first case study was from a client who experienced an increase in […]
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Mitochondrial Genome Sequencing Reveals Variants

“Single-cell full-length nanopore sequencing for quantitative variant analysis of native and genome-edited mitochondria” is the title of the London Calling 2023 lightning talk I watched tonight. The presenter was Mo Li from King Abdullah University of Science and Technology (KAUST) in Saudi Arabia. Li spoke about the human mitochondrial genome (mtDNA) and the challenges in […]
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Studying Centromere Structure with ONT

I continue to watch the YouTube “Assembly” playlist from the Oxford Nanopore Technologies (ONT) channel. Tonight, I watched session #8! Ian Henderson from the University of Cambridge in the UK presented at the Nanopore Community Meeting 2021. The session was titled “Assembling the centromeres – the ‘black holes’ of the genome.” Henderson said the centromeres […]
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Liftoff and Novel Gene Annotation

Alaina Shumate from Johns Hopkins University was a speaker at the Nanopore Community Meeting 2021. Shumate was a graduate student and worked on “The annotation of novel genes in a complete human genome.” They noted that in 2003, scientists “finished” the human genome, but reions were still incomplete. In 2021, the Telomere-to-Telomere (T2T) Consortium was […]
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CanSeq150 to Sequence Canada’s Most Endangered Species

The London Calling 2021 session “CanSeq150: high-resolution genomic sequencing and assembly of 150 Canadian species” caught my attention today. Jahanshah Ashkani from Canada’s Michael Smith Genome Sciences Center was the speaker. The goal is to save Canada’s rich biodiversity by sequencing unique species. Loss of biodiversity is an issue: there are over 700 species at […]
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