Year: 2023

AmplideX PCR and Nanopore Sequencing for Carrier Screening

Sarah Statt presented at the Nanopore Community Meeting 2021 on “AmplideX PCR and nanopore sequencing deepens analysis and simplifies workflows for carrier screening.” Statt is an R&D Senior Manager at Asurgen, a Bio-Techne Brand. They spoke about the technologies needed for carrier screening. The company created AmplideX that includes long-range PCR and long-read sequencing to […]
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Olive Trees, Bacteria, Fungi, and High-throughput Screens

Manuel Anguita Maeso, a Ph.D. student, presented at the Nanopore Community Meeting 2021 a short session entitled: “Unravelling the whole genome of olive antagonistic xylem-inhabiting bacteria, to fight vascular plant pathogens in olive trees.” Anguita Maeso is from the Institute for Sustainable Agriculture, CSIC, in Cordoba, Spain. They began with an introduction to the two […]
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Genome-wide Protein Interactions with DiMeLo-seq

Annie Maslan from the University of California, Berkley spoke about “Mapping protein-DNA interactions genome-wide with DiMeLo-seq as part of the Nanopore Community Meeting 2021. They explained that existing methods for mapping protein binding use coverage as a proxy for binding.” Maslan noted that short-read methods obscure or complicate the interpretation of joint and independent binding […]
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Multiple Sequencing Approaches for HPV Analyses

Nicole Rossi & Michael Dean presented at Nanopore Community Meeting 2021 on: “Resolution of complex human papillomavirus and human sequences.” Rossi and Dean are from the National Cancer Institute. Rossi spoke about the impact of human papilloma virus (HPV). Cervical cancer causes numerous deaths. The HPV genome has two oncogenes and promotes genome instability. HPV […]
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Near-perfect Bacterial Genomes and MAGs

Mantas Sereika, a Ph.D. student at Aalborg University in Denmark, spoke at the Nanopore Community Meeting 2021 about “Nanopore R10.4 enables near-perfect bacterial genomes.” This topic is of interest for several of the courses I teach. Sereika spoke about the improvements in accuracy of Nanopore sequencing. Raw read accuracy has increased but there are still […]
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Bambu for Transcript Discovery

Andre Sim from the Genome Institute of Singapore (A*STAR) in Singapore spoke at the Nanopore Community Meeting 2021 about “Bambu – generating context-aware transcriptomes with Oxford Nanopore long-reads.” What a cool name! Sim explained that RNA sequencing technologies have evolved, but reference annotation for transcript analysis has remained relatively unchanged. Sim noted that fragments could […]
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Rapid-CNS2

Tonight I watched the Nanopore Community Meeting 2021 recording featuring Areeba Patel and titled “Rapid-CNS2: rapid, comprehensive adaptive nanopore sequencing of central nervous system (CNS) tumours.” Patel is at the German Cancer Research Center (DKFZ) and the University Hospital Heidelberg, Germany. Patel spoke about the use of molecular diagnostics for CNS tumors. They noted the […]
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Portable GPUs

Miles Benton from the Institute of Environmental Science and Research in New Zealand spoke at the Nanopore Community Meeting 2021 about “Affordable GPU compute makes nanopore sequencing even more disruptive and empowering.”Benton is a senior scientist, bioinformatician, and an advocate of open, reproducible science. They share their materials on GitHub. Benton spoke about the birth […]
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Cell-free DNA Analyses for Acute Lymphoblastic Leukemia Treatment

Jessica Blackburn from the University of Kentucky spoke at the Nanopore Community Meeting 2021 about “Detection of cell-free DNA in acute lymphoblastic leukemia patients to potentially identify CNS disease and monitor response to therapy.” Blackburn explained that acute lymphoblastic leukemia is the most common pediatric cancer, with ~3,000 children diagnosed each year. They explained that […]
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Undergraduate Research with the CREWS Project

Megan Radosevich from Carroll College presented at the Nanopore Community Meeting 2021 on “Analyzing regional and seasonal microbial community variation from a contaminated Montanana river.” Their project is called CREWS: Consortium for Research on Environmental Water Systems that is funded by the Montana NSF EPSCoR Partnership with several colleges and universities in Montana. A central […]
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