January 2023 – Carlos C. Goller

January 31, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, Why

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 […]

January 30, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections

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 […]

January 29, 2023
By Carlos C. Goller
Diversity, Oxford Nanopore Technologies, Presentations & Talks, Reflections, sequencing

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 […]

January 28, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Presentations & Talks, Reflections, sequencing, Softwares, Website, Why

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 […]

January 27, 2023
By Carlos C. Goller
Instructor Behaviors, Mentoring, Oxford Nanopore Technologies, Reflections, sequencing, Teaching techniques, Undergraduate Research, Why, Workshop

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 […]

January 26, 2023
By Carlos C. Goller
Diversity, Oxford Nanopore Technologies, Reflections, Softwares, Undergraduate Research, Website, Why

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 […]

January 25, 2023
By Carlos C. Goller
Diversity, Oxford Nanopore Technologies, Presentations & Talks, QM, Reflections, sequencing

Sequencing FCGR

Sarah Frampton from the University of Southampton, UK spoke at the Nanopore Community Meeting 2022 on “Shinning a light on the FCGRs: deconvoluting their challenging (epi)genomic organisation and consequences in immune oncology research.” Frampton is a Ph.D. student and spoke about monoclonal antibodies and their therapeutic potential. The Fc gamma receptors, Frampton explained, are important […]

January 24, 2023
By Carlos C. Goller
Diversity, Oxford Nanopore Technologies, Presentations & Talks, Softwares, Why

SLOW5 for Indigenous Genomics

Andre Reis from the Garvan Institute of Medical Research in Australia presented at the Nanopore Community Meeting 2022 on “A long-read nanopore sequencing platform for Indigenous genomics.” Their efforts to increase efforts to increase representation of Indigenous people in Australia. Reis spoke about indigenous Australians and the lack of representation in current catalogues. Thus, there […]

January 23, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Presentations & Talks, Publishing, Reflections

New Diagnostic Approaches Using Nanopore Sequencing

Professor Laurent Mesnard from from the Medecine Sorbonne Universite spoke at the Nanopore Community Meeting 2022 about “Rapid genomic analysis for thrombotic microangiopathies (TMA) diagnosis.” Their approach combined Nanopore adaptive sampling, EPI2ME, and SeqOne approach. They described TMA and the need to detect early. Mesnard explained that the biggest challenge for TMA is early intervention. […]

January 22, 2023
By Carlos C. Goller
Delftia, Molecular Biology Education Research, Oxford Nanopore Technologies, Reflections, sequencing, Softwares, Undergraduate Research

New Oxford Nanopore Technologies

I am now watching videos from the Oxford Nanopore Technologies (ONT) YouTube playlist that includes sessions from the NCM 2022. I want to learn more about what others are doing with Nanopore and how to use automation and pipelines more efficiently. The first session I watched tonight was on “End-to-End human genome nanopore sequencing and […]

Month: January 2023