144 - micro binfie Pathoplexus part 1

Final part of our discussion/debate on NextFlow

Part two of debating NextFlow

Andrew, Nabil, and Lee debate about NextFlow!

Nabil and Lee bring a guest host Clint to talk with some of the people behind Pathoplexus http://pathoplexus.org/ * Dr. Emma Hodcroft - https://pathoplexus.org/about/eb * Dr. Theo Sanderson - https://pathoplexus.org/about/development-team * Mr. Arthur Shem Kasambula - https://pathoplexus.org/about/development-team

Nabil and Lee bring a guest host Clint to talk with some of the people behind Pathoplexus http://pathoplexus.org/ * Dr. Emma Hodcroft - https://pathoplexus.org/about/eb * Dr. Theo Sanderson - https://pathoplexus.org/about/development-team * Mr. Arthur Shem Kasambula - https://pathoplexus.org/about/development-team

143 - where we catch up on our professional lives by Microbial Bioinformatics

The crew talks about the genomeqc ecosystem. Check it out at https://happykhan.github.io/qualibact/ Errata: The project name was chaned to qualibact and is no longer genomeqc as mentioned on the episode.

In this episode of the Podcast, hosts Lee Katz and Andrew Page delve into the intricacies of clinical metagenomics. Joined by experts Torsten Seemann and Finlay Maguire, they explore the challenges and methodologies involved in identifying pathogens in clinical samples when traditional diagnostic methods fail. They discuss the types of samples analyzed, the impact of low DNA concentrations, and the complexities of sequencing data interpretation. The conversation highlights the importance of interdisciplinary collaboration between bioinformaticians and clinicians in managing difficult infections. Despite the hurdles, clinical metagenomics is presented as a complementary tool aiding in diagnosis, emphasizing the need for genomic literacy among healthcare professionals.

On this episode we are joined by Sara Zufan to discuss her PhD journey and recent projects. The episode covers various research experiences and challenges in the field, including the rapid detection of AMR using nanopore sequencing, COVID-19 projects, hepatitis A outbreak investigations, and Lassa virus surveillance in Liberia. The guests share insights into their professional journeys, their experiences working across different continents, and the future of microbial bioinformatics research.

In this episode of the Micro Binfie Podcast, host Andrew Page takes listeners to the heart of the microbial genomics hackathon in Bethesda, Maryland, for an engaging conversation with special guest Megan Phillips, a PhD student from Emory University. Megan delves into her research on Staphylococcus aureus (MRSA), highlighting its fascinating dual nature as both a harmless and potentially serious pathogen. Megan discusses the complexities of tetracycline resistance, particularly focusing on plasmid-mediated mechanisms involving the pt181 plasmid. She explains how this plasmid’s efflux pump, encoded by the gene tetK, contributes to variable resistance levels and the factors influencing MIC (Minimum Inhibitory Concentration) variability. Listeners will learn about the intricacies of plasmid copy numbers, their global spread across clonal complexes, and the occurrence of horizontal and vertical gene transfer. Throughout the episode, Megan shares insights on working with short-read sequencing data and the strategies she employs to detect plasmid presence using tools like BLAST. She also touches on the challenges and fascinating discoveries of tracking historical sample data and integrating findings from older research papers, showcasing her appreciation for the poetic style of scientific writing from the 1940s. For those interested in antimicrobial resistance, evolutionary microbiology, and the subtleties of bacterial genome analysis, this episode offers a compelling blend of technical details and engaging storytelling. Tune in to hear more about Megan’s upcoming publications, her experiences navigating complex genomic data, and her thoughts on antimicrobial stewardship and historical perspectives on drug resistance.