Year: 2024

Nanocompore for Signal Comparison

Tommaso Leonardi from the Italian Institute of Technology (IIT) presented a lightning talk at London Calling 2019 on “signal level RNA modifications detection in eukaryotic non-coding RNAs.” Leonardi explained that there are many RNA modifications, and they developed the tool Nanocompore to compare signals from two conditions. It also takes into account replicates. Nanopore also […]
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A Thirty-year Old SIV Sample

“Looking for a needle in a haystack: nanopore sequencing of a new Simian immunodeficiency virus (SIV) from a chacma baboon (Papio usrinus)” is the title of Susan Engelbrecht’s 2019 London Calling session. Engelbrecht, from Stellenbosch University in South Africa, spoke about primate lentiviruses and their “extreme genetic variability.” SIV is a retrovirus about 9 kb […]
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Sequencing on the Farm

Charles C. Kayuki from the Tanzania Agricultural Research Institute in Mikocheni, Tanzania, presented at London Calling 2019 on “Portable DNA sequencing in remote East African farms.” They are using genomics to fight plant pathogens, focusing on cassava. Kayuki explained that it is an easy crop to grow and drought-resistant. It is susceptible to two important […]
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Molecular Tagging with Unique DNA and Squiggles

Tonight, I watched a 2019 London Calling session by Katie Doroschak from the University of Washington on “Molecular tagging with nanopore-orthogonal DNA strands.” Molecular tagging systems use DNA to identify physical objects. Doroschak shared examples of secret exchange and counterfeit pharmaceutical detection. The research team used the MinION and created digital tags and codewords with […]
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Unraveling Transcriptional Complexity with Direct RNA Sequencing

Daniel P. Depledge from New York University presented at London Calling 2019 on “Redefining the transcriptional complexity of viral pathogens using direct RNA sequencing.” Depledge started with a slide and the question: Got herpes? They are fascinated with herpes viruses and their multiple features and applications. Herpes simplex virus type 1 (HSV-1) is a 152 […]
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Sequencing Australian Plant Viruses

Monica Kehoe from the Department of Primary Industries and Regional Development in Australia presented at the 2019 London Calling meeting. The session’s title was “Nanopore sequencing and analysis of plant pathogenic viruses—more than just rapid diagnostics?” Kehoe is based in Western Australia and using Nanopore sequencing to sequence RNA plant viruses. Their focus is to […]
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nano-COP to Investigate Nascent RNA Splicing Dynamics

Heather Drexler from Harvard Medical School presented at London Calling 2019 on “Direct sequencing of nascent RNA exposes splicing kinetics and order.” For example, Drexler explained that RNA splicing is complex, with distant exons being joined. Drexler emphasized that transcription rates affect alternative splicing and that transcription and splicing are physically and mechanistically coupled. The […]
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Dark and Camouflaged Genes

Mark T.W. Ebbert from the Mayo Clinic presented at London Calling 2019 on “Long-read sequencing technologies resolve most ‘dark’ and ‘camouflaged’ gene regions.”Dark and camouflaged regions? Ebbert explained that regions can be dark because there are no reads available (“dark by depth“) or dark by low sequence quality (“dark by MAPQ“). Ebbert explained that most […]
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Mapping Heterogeneity in DNA Replicaiton

“Untangling heterogeneity in DNA replication with nanopore sequencing” was the title of the London Calling 2019 session that Michael Boemo from the University of Oxford in the UK presented. Boemo spoke about how genome replication has been studied on average and not individual cases. DNA replication can be studied with next-generation sequencing methods to identify […]
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