February 2023 – Carlos C. Goller

February 28, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

Sequencing of HCV for Identification of Resistance Mutations

Kame A. Galan-Huerta from the Autonomous University of Nuevo Leon in Mexico presented at the Nanopore Community Meeting 2022 a ten minute session entitled “Identification of resistance mutations to direct-acting antiviral agents against HCV in infected subjects in Mexico.” They spoke about adapting protocols to detect the RNA positive sense hepatitis C virus. Glan-Huerta explained […]

February 27, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections

Metagenomic Binning Considering Modifications

Soren Heidelbach spoke at the Nanopore Community Meeting 2022 about “Developing new bioinformatics methods to identify modifications from nanopore sequencing.” Heidelbach is from Aalborg University, Denmark. They did metagenomic binning: grouped contigs based on information from k-mers and coverage and also considered modification motifs. Their modification of metagenomic binning was to include base modification as […]

February 26, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing

Tilapia, ISKNV, and Tiled PCR

Shayma Alathari from the University of Exeter was the next presenter at the Nanopore Community Meeting 2022 that I watched present. Their five-minute session was very brief, and packed with information. The title of Alathari’s session was “Development and application of genomic tools for tracking viral outbreaks in fish.”Alathari is a Ph.D. student interested in […]

February 25, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing

Nanopore Sequencing to Investigate Splicing Order and Deadenylation Trends

Karine Choquet from Harvard Medical School spoke at the Nanopore Community Meeting 2022 about “Direct RNA sequencing reveals multi-intron splicing order and poly(A) tail lengths across subcellular compartments.” This five-minute session began by explaining RNA processing and removal of introns in eukaryotic gene expression. Choquet explained that “RNA processing is essential for eukaryotic gene expression” […]

February 24, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections

Strand-seq for Haplotyping and Parent-of-origin Assignments

Vahid Akbari is a Ph.D. student at BC Cancer in the Genome Sciences Centre in Canada. They presented at the Nanopore Community Meeting 2022 a session entitled “Simultaneous haplotyping and parent-of-origin assignment of homologous chromosomes without parental sequence data.” The approach they developed allows researchers to haplotype chromosomes and assign parent-of-origin without parent data. They […]

February 23, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing

The Advantages of POD5

I have been thinking and learning about POD5 files. Tonight, I watched a relevant Nanopore Community Meeting 2022 session by Alex Merry, Instrument Software Fellow at Oxford Nanopore Technologies. The session was entitled “Arrow: pointing the way forward for high-performance nanopore signal handling with POD5.” They began talking about FAST5 files to store signal data […]

February 22, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, Undergraduate Research

Fungal Symbioses and Nanopore Sequencing

Jessica Allen from Eastern Washington University presented at the Nanopore Community Meeting 2022 on “Using nanopore sequencing to investigate genome evolution in fungal symbioses: ploidy, repetitive elements, and reproduction.” Allen studies fungi and mentioned that human fungal pathogens and those affecting plant systems are on the rise. Allen studies lichens. Lichenized fungi are diverse, abundant, […]

February 21, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing

Targeted Sequencing of Mycobacterium tuberculosis Resistance Genes with Nanopore

“Profiling drug-resistant Mycobacterium tuberculosis with targeted nanopore sequencing” was the title of the sessionn Shannon Murphy from the Wadsworth Center – New York State Department of Health presented at the Nanopore Community Meeting 2022. Murphy spoke about how they are planning on using Nanopore sequencing to address some of the challenges of Mycobacterium tuberculosis (MTB). […]

February 20, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing

Branching Out to Sequence Single-cell Transcript Isoforms with Nanopore

Tonight I watched Sheridan Cavalier from The John Hopkins University School of Medicine present at the Nanopore Community Meeting 2022. The title of the session was “Single-cell transcript isoform sequencing of the activated adult mouse hippocampus with 10x Genomics and Oxford Nanopore.” Cavalier is a graduate student and developed an approach to sequence mouse hippocampus […]

Dimelo-seq and CENP-A to Determine the Centromere Protein A Landscape

Yuan (Daniel) Xu from the University of California, Santa Cruz, spoke about the “Determination of the centromere protein A landscape at single-molecule resolution” during the Nanopore Community Meeting 2022. Their five-minute session was based on their work as a graduate student. They spoke about centromere localization and how CENP-A helps determine the region. The objective […]

Month: February 2023