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 - a bioinformatician in the United States, Dr. Nabil-Fareed Alikhan from the University of Oxford (UK), and Prof. Andrew Page from Origin Sciences (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 University of Oxford or Origin Sciences.
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
156 - Ancient problems require ancient solutions - part 2
In Part 2 of Ancient problems require ancient solutions, host Nabil Ali Khan brings James Fellows Yates back to the mic to go deeper into how ancient metagenomics actually gets done.
They dig into dental calculus — mineralised plaque whose bone-like hydroxyapatite locks DNA in place for tens of thousands of years (James recovered a microbiome from a 100,000-year-old Neanderthal), what it tells us about diet, dysbiosis and the rise of dental disease after the Neolithic, and even a coming paper on a famous historical Briton with the highest ancient-DNA yield ever seen from calculus.
Then it's onto the tooling: the origin story of nf-core/eager, why ancient DNA still needs a 10-year-deprecated GATK unified genotyper, the birth of the now-ubiquitous nf-core Metro-Map pipeline diagrams, and how James and the SPAAM community wrote the open textbook Introduction to Ancient Metagenomics as a practical guide for anyone — bioinformatician or historian — walking into the field.
Guest: James Fellows Yates Hosts: Dr Nabil Ali Khan, Dr Lee Katz, Prof Andrew Page
Introduction to Ancient Metagenomics (open textbook) — https://www.spaam-community.org/intro-to-ancient-metagenomics-book/
SPAAM community — https://spaam-community.org
nf-core/eager — https://nf-co.re/eager
AncientMetagenomeDir — https://github.com/SPAAM-community/AncientMetagenomeDir
AMDirT — https://github.com/SPAAM-community/AMDirT
nf-core Metro-Map guide — https://nf-co.re/docs/contributing/tutorials/creating_with_nf_core_tools#metro-map
17 Sept 2026
155 - Ancient problems require ancient solutions - part 1
What can DNA recovered from bones, teeth and paleofaeces tell us that living samples can't — and how do you keep modern contamination from drowning out a 1,000-year-old signal?
In Part 1, host Nabil Ali Khan is joined by James Fellows Yates (bioinformatician, biomolecular archaeologist, and editor of the new open textbook Introduction to Ancient Metagenomics) for a tour of the field. They cover why ancient DNA arrives as 30–70 bp fragments with characteristic C→T "smiley plot" damage, how endogenous yields as low as 1% still count as a good sample, and the wet-lab lengths (bodysuits, UV, no kits) needed to keep libraries clean.
They also dig into the big questions ancient microbial DNA is now answering — plague and TB origins, oral-microbiome loss since the Neolithic, AMR trends read from historical bear calculus — and how the SPAAM community, NF-core/eager and AncientMetagenomeDir grew up to support the work.
Guest: James Fellows Yates Hosts: Dr Nabil Ali Khan, Dr Lee Katz, Prof Andrew Page
SPAAM community — https://spaam-community.org
nf-core/eager — https://nf-co.re/eager
AncientMetagenomeDir — https://github.com/SPAAM-community/AncientMetagenomeDir
Introduction to Ancient Metagenomics (open textbook) — https://www.spaam-community.org/intro-to-ancient-metagenomics-book/
20 Aug 2026
154 - Boston women in bioinformatics
Nabil, Andrew, and Lee talk with Liyang Diao and Valisha Shah from the nonprofit organization, Boston Women in Bioinformatics, a community that supports bioinformaticians in the Greater Boston area. We discuss the organization’s mission, the resources it provides, and what’s coming next for the group. boston-wib.org/
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