Metagenomics

Exploring Personalized Oncogenomics with High Coverage Sequencing

Tonight I watched Kieran O’Neill from Canada’s Michael Smith Genome Sciences Centre speak about “Long-read sequencing of an advanced cancer cohort” as part of London Calling 2025. This centre, O’Neill explained is one of the largest sequencing centers in Canada. The centre has a cohort of 189 diverse advanced cancer patients. With their personalized oncogenomics […]

June 2, 2025
By Carlos C. Goller
Metagenomics, Online Learning, Reflections, Softwares

London Calling 2025 ONT Application Updates

Sissel Juul, Vice President of Applications with Oxford Nanopore Technology and Sean McKenzie, Associate Director of Genomics Applications, provided the London Calling 2025 applications update. Juul explained that the applications team is global. Haplotype-resolved genetic variation detection and interpretation has been updated to use assembly approaches. However, assembly can be very challenging, especially with two […]

June 1, 2025
By Carlos C. Goller
Metagenomics, Oxford Nanopore Technologies, Reflections, sequencing

Case Studies on 16S rRNA Sequencing in Clinical Diagnostics

Dr. Anna Smielewska, a consultant virologist in the UK, spoke at ESCMID Global about 16S rRNA sequencing in healthcare settings. The title of the session was “Implementing portable, real-time 16S rRNA sequencing in the healthcare sector enhances antimicrobial stewardship.” Smielewska works with the Liverpool University Hospitals, several hospitals with a broad range of cases. The […]

May 31, 2025
By Carlos C. Goller
Metagenomics, Oxford Nanopore Technologies, Reflections, sequencing

Antimicrobial Resistance Detection Using Nanopore Sequencing

Kim Musser, Clinical Director, Wadsworth Center, David Axelrod Institute, presented at ESCMID Global on the use of nanopore sequencing in public health investigations. The title of the session was “Implementing next generation sequencing for rapid diagnostics and public health investigations.” Musser spoke about using nanopore sequencing for antimicrobial sequencing for antibiotic resistant bacteria to characterize […]

May 28, 2025
By Carlos C. Goller
Metagenomics, Oxford Nanopore Technologies, Presentations & Talks, Reflections, sequencing

Machine Learning for Quick Leukemia Diagnosis

Tonight I watched Gabriel Griffin, Assistant Professor, Dana-Faber Cancer Institute present an Oxford Nanopore Technology session titled “Rapid epigenomic classification of acute leukemia with long-read sequencing.” Griffin spoke about leukemia diagnosis requiring multiple steps and time: morphology, flow cytometry, immuno histochemistry stains, targeted sequencing, and cytogenetics. This can take up to fourteen days. Griffin and […]

March 11, 2025
By Carlos C. Goller
Metagenomics, Oxford Nanopore Technologies, Reflections, sequencing, Softwares

Advancements in Nanopore Sequencing: Insights from PAG Workshop

Tonight I watched the PAG Industry Workshop Oxford Nanopore Technologies offered on January 14, 2025. In this session, Aaron Pomerantz presented updates along with Sean Mckenzie that improve assemblies. The title of the session is “New assemblers enable unprecedented de novo genome and metagenome contiguity and completeness…” The series of talks include amplicon to massive […]

February 16, 2025
By Carlos C. Goller
Constructivism, Course Design, DBER and SoTL, JMBE, Metagenomics, Online Learning, Reflections, Student groups, Teaching techniques

Kombucha Project in Microbiology Education: A Success Story

Tonight I watched another JMBE Live! session: Microbiology lobs with virtual and hands-on parts with Marcos Garcia-Ojeda. I skipped the JMBE discussions with editors mostly because I didn’t want to hear myself. Garcia-Ojeda does a lot of work with SABER and other groups. The research article they published in 2022 was about their virtual labs […]

Teaching Microbiology and Climate Change: Lessons from ASM Microbe 2023

Tonight I watched JMBE Live! at ASM Microbe 2023. Stanley Maloy interviewed Kelly Ramirez, Zachary Freeman, and Arpita Bose. Ramirez spoke about bringing excitement about microbiology to students and courses early on! Freeman shared how they started Schoolyard Microbiology and how they collect soils from participants and learn about their microbiomes. Bose had an interest […]

January 12, 2025
By Carlos C. Goller
KBase, Metagenomics, Reflections, sequencing, Softwares

How to Join and Utilize KBase Educators Group

Tonight I started watching the KBase Educators Orientation meeting from December 2024. Ellen Dow facilitated the session and shared resources from the KBase Educators group and handbook. Dow explained the structure of KBase narratives and how to join the KBase Educators group. The Educators Org has several narratives that can be copied. There are a […]

January 10, 2025
By Carlos C. Goller
KBase, Metagenomics, Oxford Nanopore Technologies, Reflections, sequencing, Softwares

Exploring Microbial Genomics and Lanthanide Mining

Continuing with the LISA workshop, tonight I watched another session. This one was by a postdoc, Andrew Wilson, at Pacific Northwest National Laboratory. They have been working on plasmid and microbe sequencing. The title of the session was “Leveraging Long Reads for Synthetic Biology.” Wilson and team are using Gibson assembly and synthetic biology techniques. […]