Month: June 2024

Nanopore Sequencing Advancements: Optimizing Metagenome Assemblies

It was great to see Lauren Lui from the Lawrence Berkley National Laboratory present at London Calling 2024 on “An unprecedented metagenomic landscape of European and North American coastal samples.” Lui is a research scientist and, while at Miten Jain’s lab at Northeastern University, loaded 34 PromethION flow cells, generating 5 Tbases of data! Lui […]
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Intraoperative Brain Tumor Diagnosis

“Robbing the array to feed the pore: exploring ultra-fast brain tumor diagnosis” is the title of the session Dr. Simon Paine from Nottingham University Hospitals NHS Trust in the UK presented at London Calling 2024. What a creative title! Paine is a clinical consultant and neuropathologist. Paine explained that neuropathologists are trying to predict tumor […]
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Flames and Blaze: Advancing Long-Read scRNA-seq for Brain Development Research

Mike Clark from The University of Melbourne in Australia presented at London Calling 2024 on “Igniting single-cell analysis of full-length RNA isoforms in brain development.” Clark works on RNA isoforms and developing single-cell analysis methods. They noted that almost all human genes express multiple RNA isoforms. Clark emphasized that alternative splicing modifies which exons are […]
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Understanding Drug Resistance in Multiple Myeloma: Insights from Tomas di Domenico

Tonight, I watched Tomas di Domenico from the National Cancer Research Center in Spain present at London Calling 2024 on “An (epi-)genomics analysis of drug resistance in multiple myeloma.” Di Domenico explained how multiple myeloma affects the bone marrow and thickens the blood. Multiple myeloma also causes bone issues. There are several treatments and a […]
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SamnSero Workflow: Real-time Bacterial Genome Analysis

Tonight, I watched the London Calling EPI2ME product demo: “EPI2ME: democratising bioinformatics—from point-and-click analysis to custom integrations.” Natalia Garcia, a Bioinformatics Workflow Developer with Oxford Nanopore Technologies, explained how workflows use Nextflow and Docker containers. Seventeen workflows were available at the time of the recording during London Calling. Workflows can be run via the command […]
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Long-Read Sequencing Innovations in Neurodegenerative Disease Research

Tonight, I watched the London Calling 2024 session on “breaking boundaries in neurodegenerative disease research.” Cora Vacher from Oxford Nanopore Technologies (ONT) introduced the speakers and facilitated the question and answer session. Joanne Trinh from the Institute of Neurogenetics at the University of Lubeck in Germany was the first presenter. Trinh works with a research […]
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Blood Group Genome Targeted Sequencing for Precision Typing | London Calling 2024

Morgan Gueuning from the Blood Transfusion Service in Switzerland presented at London Calling 2024 on “Targeted sequencing of the entire blood group genome by adaptive sampling.” They noted that there are over 45 blood group systems coded by fifty genes and with over 350 antigens. Precise typing and matching are essential to minimize alloimmunization. Current […]
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Genome Assembly Challenge: Sequencing Variants of Feline Coronavirus in Cyprus

Amanda Warr from The Roslin Institute in the UK presented at London Calling 2024 on “What the cat dragged in: emergence of a highly pathogenic feline/canine recombinant coronavirus.” Warr explained that feline coronavirus (FCoV) is common. In a subset of cases, it mutates once in the cat host. This is called feline infectious peritonitis (FIP). […]
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Long-Read Sequencing Reveals Diverse Intergenerational Epigenetic Patterns in Mice

The IPERT workshops finished today. I am tired and ready for rest. Tonight, I watched the London Calling 2024 session “Long-read sequencing reveals diverse patterns of epigenetic inheritance in mice.” Adam Davidovich, a Ph.D. student at Johns Hopkins, presented their work. They worked on studying intergenerational epigenetic patterns using a mouse model. The work involved […]
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Conservation Genomics and Biodiversity Crisis: Insights from Org.one Program | London Calling 2024

The Org. One program is fascinating. I would love to be involved. Tonight, I watched the London Calling 2024 session titled “Org.one to 10.” Kara Dicks, Program Manager at Conservation Genomics with Org.one, spoke about the biodiversity crisis. The Org.one program supports local sequencing. The program has supported over ninety projects. Participants receive kits and […]
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