In this episode of the Micro binfie Podcast, host Andrew Page sits down with Tim Dallman at the 10th Bioinformatics Hackathon in Bethesda, Maryland. Tim shares insights from his work at Utrecht University in the Netherlands, where he focuses on genomic surveillance and machine learning models to predict disease risk and severity. They discuss the challenges of integrating genomic variation into predictive models, the importance of high-quality metadata, and the complexities of working with pathogens like Shiga toxin-producing E. coli. Tim also talks about his role at the WHO Pandemic and Epidemic Intelligence Hub and how global collaboration can drive innovation in public health genomics. Tune in to hear about cutting-edge research, the importance of interdisciplinary teamwork, and how genomic data can be harnessed for future pandemic preparedness.

130 Exploring Genomic Innovation and Machine Learning in Public Health

In this episode of the Micro Binfie Podcast, host Andrew Page catches up with Torsten Seemann at the 10th Microbial Bioinformatics Hackathon in Bethesda, Maryland. They discuss the rapid evolution of bioinformatics, the challenges faced by labs worldwide, and the explosion of tools post-COVID. Torsten shares insights into his work at Melbourne’s Microbiological Diagnostic Unit (MDU), the development of platforms like OzTracker for bacterial genomics, and how his lab plays a national and international role in data sharing. 

The conversation dives into the future of the widely-used variant calling tool Snippy, as Torsten reveals exciting updates funded by the Chan Zuckerberg Initiative, including nanopore read support and the ability to process pre-assembled genomes. They also explore the importance of maintaining open-source bioinformatics tools to prevent them from becoming obsolete. Tune in for an in-depth discussion on the state of genomics, software development, and the challenges and rewards of open-source collaboration.

131 Bioinformatics Evolution: Torsten Seemann on Snippy, Open-Source Support, and Global Genomics

In this episode of the Micro Binfie podcast, host Andrew Page is live from the 10th Microbial Bioinformatics Hackathon in Bethesda, Maryland. He sits down with David Mahoney, a PhD student from Dalhousie University in Halifax, Nova Scotia. David shares his research on characterizing antimicrobial resistance (AMR) genes and their transfer within metagenomes, focusing on metagenomic assembly graphs.

They delve into David’s background in food safety microbiology and his interest in the public health implications of genomics. He explains his exciting work on analyzing how AMR genes transfer across different environments, such as food production plants and clinical settings, using both new and existing data from Canada’s Genomics Research and Development Initiative.

David also highlights his use of innovative methods like assembly graphs and graph-based approaches to uncover AMR gene flow and lateral gene transfers, including the potential of machine learning techniques such as graph convolutional neural networks.

132 Unlocking the Secrets of Antimicrobial Resistance in Metagenomes

In this episode of the Micro Binfie podcast, host Andrew Page talks with Dr. Erin Young, a bioinformatician at the Utah Public Health Laboratory, recorded during the 10th Microbial Bioinformatics Hackathon in Bethesda, Maryland. Erin shares her journey from researching hereditary cancer predisposition to her current role in public health bioinformatics, which she entered through a prestigious CDC and APHL fellowship. The conversation delves into her work with bacterial pathogens, particularly in tracking antimicrobial resistance in organisms like Klebsiella. Erin discusses the tools she uses for genome typing, such as MASH, FastANI, and SKA, and her innovative research on the accuracy of long-read sequencing technologies like Nanopore for detecting antimicrobial resistance genes. She also provides a preview of her upcoming poster for ASM, where she examines how Nanopore reads can be used effectively in public health microbiology. This episode offers a fascinating look at how bioinformatics and genomics are advancing the fight against infectious diseases.

133 The Role of Bioinformatics in Public Health and Disease Outbreaks

In this episode of the Micro Binfie Podcast, host Andrew Page speaks with Dr. Brooke Talbot, a recent PhD graduate from Emory University, about her research on Staphylococcus aureus, with a focus on MRSA and antibiotic resistance. Brooke shares insights into her molecular epidemiology work, discussing the complexities of tracking resistant bacterial strains in clinical settings and the significance of genomic epidemiology in public health. From honeybees to foodborne outbreaks, Brooke’s diverse research background offers listeners a fascinating journey through science, microbiology, and epidemiology.

134 Diving into MRSA, Genomics, and Public Health

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.

138 Decoding Tetracycline Resistance in MRSA

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.

139 Lassa virus genomics

Discover how Daphne Koller ’s pioneering work in AI is transforming healthcare, education, and the future of machine learning applications.

Daphne Koller

Daphne Koller & Artificial Intelligence

Andrew, Lee, Torsten, and Fin muse over the future of MLST, Illumina, and Nanopore at the ASM NGS Hackathon

141 hackathon panel

Today we are talking about bioinformatics with Dr. Abel Torres Espin. Abel is an Assistant Professor and Director of the health data DRIVEN lab at the School of Public Health Sciences at the University of Waterloo in Canada. He has worked with...

More info: https://u2fp.org/get-educated/curecast/episode-125.html

SCI & AI (Episode 125)

The AI VIPs page is a tribute to those pioneers—from the early architects like Alan Turing and John McCarthy, who laid the groundwork for AI, to the modern-day innovators who continue to push the boundaries of what’s possible.

Unite 2 Fight Paralysis exists to unite and empower the international spinal cord injury community to cure paralysis through advocacy, education, and support for research. Get Educated and Get Involved.

Microbial Bioinformatics is a rapidly changing field marrying computer science and microbiology. Join us as we share some tips and tricks we’ve learnt over the years. If you’re student just getting to grips to the field, or someone who just wants to keep tabs on the latest and greatest - this podcast is for you. 

The hosts are Dr. Lee Katz from the Centres for Disease Control and Prevention (US), Dr. Nabil-Fareed Alikhan from the University of Oxford (UK), and Prof. Andrew Page from Theiagen Genomics (UK) and bring together years of experience in microbial bioinformatics.

The opinions expressed here are our own and do not necessarily reflect the views of Centres for Disease Control and Prevention, University of Oxford or Theiagen Genomics.

Intro music : Werq - Kevin MacLeod (incompetech.com)
Licensed under Creative Commons: By Attribution 3.0 License
http://creativecommons.org/licenses/by/3.0/

Outro music : Scheming Weasel (faster version) - Kevin MacLeod (incompetech.com)
Licensed under Creative Commons: By Attribution 3.0 License
http://creativecommons.org/licenses/by/3.0/

Question and comments? microbinfie@gmail.com

New tracks tagged #bioinformatics