Micro binfie podcast
Episodes
152 - Deacon part 2
09 Apr 2026
Contributed by Lukas
In this follow-up Software Deep Dive episode, we continue our conversation with Dr. Bede Constantinides (University of Birmingham) about the design an...
151 - Deacon part 1
26 Mar 2026
Contributed by Lukas
In this Software Deep Dive episode, we talk with Dr. Bede Constantinides (University of Birmingham) about Deacon, a tool for removing host DNA reads f...
150 - Genomicx
12 Mar 2026
Contributed by Lukas
In this episode, Lee, Nabil, and Andrew experiment with “vibe coding” bioinformatics tools using AI coding assistants. The goal: quickly build use...
149 - Bridging AI & Biosciences
09 Feb 2026
Contributed by Lukas
Join hosts Kieren Sharma (Artificially Ever After podcast, University of Bristol) and Andrew Page (MicroBinfie podcast) for a compelling live panel di...
148 - NextFlow debate 3
13 Nov 2025
Contributed by Lukas
Final part of our discussion/debate on NextFlow
147 - NextFlow debate 2
30 Oct 2025
Contributed by Lukas
Part two of debating NextFlow
146 - NextFlow debate 1
16 Oct 2025
Contributed by Lukas
Andrew, Nabil, and Lee debate about NextFlow!
145 - micro binfie Pathoplexus part 2
25 Sep 2025
Contributed by Lukas
Nabil and Lee bring a guest host Clint to talk with some of the people behind Pathoplexus http://pathoplexus.org/ * Dr. Emma Hodcroft - https://path...
144 - micro binfie Pathoplexus part 1
11 Sep 2025
Contributed by Lukas
Nabil and Lee bring a guest host Clint to talk with some of the people behind Pathoplexus http://pathoplexus.org/ * Dr. Emma Hodcroft - https://path...
143 - where we catch up on our professional lives
28 Aug 2025
Contributed by Lukas
143 - where we catch up on our professional lives by Microbial Bioinformatics
142 - Microbinfie - genomeqc
07 Aug 2025
Contributed by Lukas
The crew talks about the genomeqc ecosystem. Check it out at https://happykhan.github.io/qualibact/ Errata: The project name was chaned to qualibact ...
140 Exploring Clinical Metagenomics
03 Jul 2025
Contributed by Lukas
In this episode of the Podcast, hosts Lee Katz and Andrew Page delve into the intricacies of clinical metagenomics. Joined by experts Torsten Seemann ...
139 Lassa virus genomics
19 Jun 2025
Contributed by Lukas
On this episode we are joined by Sara Zufan to discuss her PhD journey and recent projects. The episode covers various research experiences and challe...
138 Decoding Tetracycline Resistance in MRSA
16 Jan 2025
Contributed by Lukas
In this episode of the Micro Binfie Podcast, host Andrew Page takes listeners to the heart of the microbial genomics hackathon in Bethesda, Maryland, ...
137 Contagion part 2
02 Jan 2025
Contributed by Lukas
In a two-part discussion, the hosts analyze the movie Contagion from their expert perspectives, focusing on the film's portrayal of epidemiology and g...
135 Assembling ATCC bacterial strains
19 Dec 2024
Contributed by Lukas
In this episode of the Micro Binfie podcast, host Andrew Page is joined by Nikhita Puthuveetil, Senior Bioinformatician at the American Type Culture C...
141 hackathon panel
18 Dec 2024
Contributed by Lukas
Andrew, Lee, Torsten, and Fin muse over the future of MLST, Illumina, and Nanopore at the ASM NGS Hackathon
136 Contagion part 1
16 Dec 2024
Contributed by Lukas
In a two-part discussion, the hosts analyze the movie Contagion from their expert perspectives, focusing on the film's portrayal of epidemiology and g...
134 Diving into MRSA, Genomics, and Public Health
05 Dec 2024
Contributed by Lukas
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 re...
133 The Role of Bioinformatics in Public Health and Disease Outbreaks
05 Dec 2024
Contributed by Lukas
In this episode of the Micro Binfie podcast, host Andrew Page talks with Dr. Erin Young, a bioinformatician at the Utah Public Health Laboratory, reco...
132 Unlocking the Secrets of Antimicrobial Resistance in Metagenomes
21 Nov 2024
Contributed by Lukas
In this episode of the Micro Binfie podcast, host Andrew Page is live from the 10th Microbial Bioinformatics Hackathon in Bethesda, Maryland. He sits ...
131 Bioinformatics Evolution: Torsten Seemann on Snippy, Open-Source Support, and Global Genomics
07 Nov 2024
Contributed by Lukas
In this episode of the Micro Binfie Podcast, host Andrew Page catches up with Torsten Seemann at the 10th Microbial Bioinformatics Hackathon in Bethes...
130 Exploring Genomic Innovation and Machine Learning in Public Health
25 Oct 2024
Contributed by Lukas
In this episode of the Micro binfie Podcast, host Andrew Page sits down with Tim Dallman at the 10th Bioinformatics Hackathon in Bethesda, Maryland. T...
129 Genomics on the Frontier: Bactopia, Bioinformatics, and Pathogen Surveillance with Robert Petit
11 Oct 2024
Contributed by Lukas
Host Andrew Page is joined by Robert Petit from the Wyoming Public Health Laboratory. Robert, a key developer of the Bactopia pipeline, shares insight...
128 Haiti cholera outbreak with Christine Lee and Cynney Walters
19 Sep 2024
Contributed by Lukas
Andrew and Lee talk with Christine and Cynney about the Haiti cholera outbreak Cynney Walters: https://www.linkedin.com/in/cynney-walters-763111190 ...
127 Minimum spanning trees
05 Sep 2024
Contributed by Lukas
Nabil and Lee have a quick chat about minimum spanning trees (MST). Eburst paper: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2...
126 Tree viz
22 Aug 2024
Contributed by Lukas
We go over tree visualizations! * Microreact https://microreact.org/,https://www.phylocanvas.gl/ * grapetree https://github.com/achtman-lab/GrapeTre...
125 Kostas Konstantinidis returns to talk to us about ANI and metagenomics
06 Jun 2024
Contributed by Lukas
125 Kostas Konstantinidis returns to talk to us about ANI and metagenomics by Microbial Bioinformatics
124 Kostas Konstantinidis talks to us about ANI and metagenomics
23 May 2024
Contributed by Lukas
We talk with Kostas! For more information please visit https://enve-omics.gatech.edu/
123 The Revolution of Hash Databases in cgMLST
21 Mar 2024
Contributed by Lukas
In this episode of the Micro Binfie Podcast, hosts Dr. Andrew Page and Dr. Lee Katz delve into the fascinating world of hash databases and their appli...
122 GAMBIT: Genomic Approximation Method for Bacterial Identification and Tracking
09 Mar 2024
Contributed by Lukas
We discuss GAMBIT, software for accurately classifying bacteria and eukaryotes using a targeted k-mer based approach. GAMBIT software: https://githu...
121 K-mers, Sourmash, and Open Source Software - More Conversations with Titus Brown
01 Feb 2024
Contributed by Lukas
In this episode, Andrew Page and Lee Katz continue their conversation with Titus Brown, diving deeper into his work on k-mers, Sourmash, and open sour...
120 Scaling Metagenomic Search with Sourmash - Conversations with Titus Brown
18 Jan 2024
Contributed by Lukas
In this final episode with Titus Brown, the conversation focuses on his work scaling metagenomic search with Sourmash: An overview of what Sourmash d...
119 The Challenges of Microbial Taxonomy - Conversations with Titus Brown
04 Jan 2024
Contributed by Lukas
In this episode, Andrew Page and Lee Katz continue their chat with Titus Brown, focusing on taxonomy assignment in metagenomics: Topics discussed: D...
118 Real bioinformaticians react to Jurassic Park
21 Dec 2023
Contributed by Lukas
Andrew, Nabil, and Lee react to the bioinformatics and the science overall in the 1993 film Jurassic Park. We looked at these YouTube clips: * https...
117 From Math to Metagenomics - Titus Brown on Career Journeys and Software Solutions
07 Dec 2023
Contributed by Lukas
In this episode of the Micro Binfie Podcast, Andrew Page and Lee Katz interview Titus Brown about his journey from studying math and physics as an und...
116 AI Authorship and Ethics in Academic Publishing for Genomics
23 Nov 2023
Contributed by Lukas
The podcast discusses an article co-authored by Andrew Page, examining the use of GPT-4 for research publication. The conversation focuses on the auth...
115 Write-the: speeding up software development for bioinformatics
09 Nov 2023
Contributed by Lukas
We continue our conversation with Wytamma Wirth about write-the and all things AI. It starts with discussing the usage of language models, specificall...
114 Write-the: Automating Code Documentation ChatGPT
04 Nov 2023
Contributed by Lukas
In this episode, we dive deep into the world of automated code documentation and conversion using ChatGPT through the write-the software developed by ...
113 Global Microbial Identifier conference with Ruth Timme
18 Sep 2023
Contributed by Lukas
Lee and Andrew are at the Global Microbial Identifier conference (GMI13) in Vancouver Canada. On day 3 we catch up with Dr Ruth Timme.
112 Global Microbial Identifier conference with Will Hsiao
17 Sep 2023
Contributed by Lukas
Andrew and Lee are at the Global Microbial Identifier conference (GMI13) in Vancouver Canada. We talk to Dr William Hsiao, one of the organisers of th...
111 Global Microbial Identifier with Finlay Maguire and Emma Griffiths
16 Sep 2023
Contributed by Lukas
Andrew and Lee are at the Global Microbial Identifier conference 13 in Vancouver Canada. On the first day they talked to Dr Finlay Maguire and Dr Emma...
110 ChatGPT: The Bioinformatics Calculator
06 Jul 2023
Contributed by Lukas
In this episode there is a comprehensive discussion on the influence of AI, especially GPT-4, in the sphere of microbial bioinformatics. They reflect ...
109 AI Unleashed: Navigating the Opportunities and Challenges of AI in Microbial Bioinformatics
22 Jun 2023
Contributed by Lukas
In this episode of the Micro Binfie Podcast, titled "AI Unleashed: Navigating the Opportunities and Challenges of AI in Microbial Bioinformatics", Lee...
Encore: What language should I learn?
08 Jun 2023
Contributed by Lukas
The MicroBinfie podcast discusses the top programming languages for bioinformatics. Andrew, Lee, and Nabil agree that Python is a great starting point...
108 SeqCode: a nomenclatural code for prokaryotes described from sequence data
25 May 2023
Contributed by Lukas
We are back talking about systematics, and SeqCode; a nomenclatural code for prokaryotes described from sequence data. Marike Palmer is a Postdocto...
107 Systematics and naming of prokaryotes in the era of sequencing
11 May 2023
Contributed by Lukas
Today we are talking about systematics, and specifically SeqCode; a nomenclatural code for prokaryotes described from sequence data. Joining us to t...
106 Why on earth would you do a PostDoc?
27 Apr 2023
Contributed by Lukas
An honest discussion about the up and downsides of doing a postdoc in front of an audience of first year PhD students. Guests Dr Emma Waters, Dr Heath...
105 Mobile genetic elements panel discussion
20 Apr 2023
Contributed by Lukas
This is a panel discussion on mobile genetic elements, guest chaired by Dr Muhammad Yasir with guests Dr Emma Waters, Dr Heather Felgate and Dr Andrew...
104 The Kraken software suite
06 Apr 2023
Contributed by Lukas
We talk about KRAKEN the taxonomic classification software and the software suite around it and are joined by Jennifer Lu and Natalia Rincon from John...
103 Release the Kraken
23 Mar 2023
Contributed by Lukas
We are talking about KRAKEN - the taxonomic classification software and in the hot seat are Dr Jennifer Lu and Natalia Rincon from Johns Hopkins Unive...
102 Early days of MLST
09 Mar 2023
Contributed by Lukas
Ed Feil is a professor of bacterial evolution at the University of Bath, and Natacha Couto, a data scientist at the Center of Genomic Pathogen Surveil...
101 One Health with Natacha Couto and Ed Feil
23 Feb 2023
Contributed by Lukas
The hosts of the MicroBinfie podcast invite Dr Natacha Couto (University of Oxford) and Professor Ed Feil (University of Bath) as special guests to di...
100 The 100th episode
09 Feb 2023
Contributed by Lukas
We celebrate having 100 episodes! We look back at the history of our podcast and then talk about what the future might hold. Then: Lee gets his reve...
99 Stories from the frontlines of bioinformatics
26 Jan 2023
Contributed by Lukas
At the 8th Microbial Bioinformatics Hackathon in Bath we talked to a live panel with Kristy Horan, Torsten Seemann, Finlay Maguire and Andrew Page abo...
98 Nomadic bioinformatics with Frank
12 Jan 2023
Contributed by Lukas
We interview Frank Ambrosio. He is embarking on a lifestyle of nomadic bioinformatics, living his best life. * https://www.linkedin.com/in/francis-a...
97 Advances in sequencing technologies
29 Dec 2022
Contributed by Lukas
We discuss recent advancements in genome sequencing technologies, based on what we've been hearing at conferences and within the community. The Micro...
96 IMMEM XIII and ASM NGS conference roundup
22 Dec 2022
Contributed by Lukas
We've been busy attending in-person conferences such as IMMEM XIII and ASM NGS so we thought we'd give you some of our reflections. We discuss waste w...
95 Lost in Translation with Torsten Seemann
08 Dec 2022
Contributed by Lukas
For the first time ever all 3 MicroBinfies are together in person to record an episode. We are joined by Torsten Seemann for a conversation about how ...
94 The great scientific Mastodon migration
17 Nov 2022
Contributed by Lukas
Over the past few weeks scientists have been swapping Twitter for Mastodon. Our very own Nabil-Fareed Alikhan talks about his experience with setting ...
93 Roary Troubleshooting And Issues
10 Nov 2022
Contributed by Lukas
We go through bug reports and issues and give insights into how bioinformaticians dig into them. We suggest the underlying problems and possible solut...
92 Avoid dependency hell and get up and running fast
27 Oct 2022
Contributed by Lukas
Often the hard part of bioinformatics isnt the analysis, its getting all of the software you need setup and installed. Come with us on this journey an...
91 What language should I learn?
13 Oct 2022
Contributed by Lukas
The MicroBinfie podcast discusses the top programming languages for bioinformatics. Andrew, Lee, and Nabil agree that Python is a great starting point...
90 Public health bioinformatics on the cloud with WDL + Terra.bio
29 Sep 2022
Contributed by Lukas
90 Public health bioinformatics on the cloud with WDL + Terra.bio by Microbial Bioinformatics
89 What do we do with WDL?
15 Sep 2022
Contributed by Lukas
Today on the @microbinfie podcast, we talk about WDL with @sevinsky and @DannyJPark. We learn what widdle means to Andrew and his kids. Joel takes a s...
88 Sepia directors cut
04 Aug 2022
Contributed by Lukas
This is an extended directors cut of our chat with Dr Henk den Bakker about Sepia. Its a summer holiday bonus. Some URLs Get Sepia here: https://gith...
87 Nextstrain, SARSCOV2 and dealing with a data deluge
21 Jul 2022
Contributed by Lukas
87 Nextstrain, SARSCOV2 and dealing with a data deluge by Microbial Bioinformatics
86 What's next for nextstrain?
07 Jul 2022
Contributed by Lukas
86 What's next for nextstrain? by Microbial Bioinformatics
85 Breaking the dogma with bioinformatics
23 Jun 2022
Contributed by Lukas
We are joined again by Prof Mark Pallen who takes us through his early experiences in high-throughput microbial genomics. Mark was pleased that he per...
84 Bioinformatics in the noughties with Mark Pallen
09 Jun 2022
Contributed by Lukas
Mark Pallen explains how exciting it was to be in microbial bioinformatics around the turn of the millennium, as we gained genomes for the first time ...
83 A short journey into mobile genetic elements
26 May 2022
Contributed by Lukas
We discuss mobile genetic elements in bacteria and find, its really hard. Its just a short chat as Lee lost power, but we will be back with a part 2 s...
82 Bioinformatics moments before the millennium
12 May 2022
Contributed by Lukas
In this episode we talk to Professor Mark Pallen, who discusses the highlights from his long career as a medical microbiologist turned bioinformaticia...
81 The people behind the benchmark datasets for SARS-CoV-2
29 Apr 2022
Contributed by Lukas
We bring on Lingzi Xiaoli and Jill Hagey to talk about their benchmark datasets for SARS-CoV-2. Find out more at https://github.com/CDCgov/datasets-s...
80 Benchmark datasets for SARS-CoV-2
28 Apr 2022
Contributed by Lukas
We bring on Lingzi Xiaoli and Jill Hagey to talk about their benchmark datasets for SARS-CoV-2. Find out more at https://github.com/CDCgov/datasets-s...
79 StaPH-B: Stable containers for public health bioinformatics
14 Apr 2022
Contributed by Lukas
Dr Erin Young from the Utah Department of Health and Dr Kelsey Florek from the Wisconsin State Laboratory of Hygiene join us to talk about StaPH-B c...
78 StaPH-B: state public health bioinformatics
31 Mar 2022
Contributed by Lukas
Dr. Erin Young and Dr Kelsey Florek join us to talk about StaPH-B, a US state public health bioinformatics group. They also give some insights into th...
77 Genomics for a new era
17 Mar 2022
Contributed by Lukas
Today we’re talking about some exciting new developments in the area of comparative genomics. We are joined by Dr. Zamin Iqbal who is a Research Gro...
76 What are the major challenges for getting AMR genomics into the clinic?
03 Mar 2022
Contributed by Lukas
What are the major challenges for getting AMR genomics into the clinic? This was the question poised to a panel of experts at the 7th Microbial Bioin...
74 SEPIA With Henk - Soup Or Salad Yes!
03 Feb 2022
Contributed by Lukas
74 SEPIA With Henk - Soup Or Salad Yes! by Microbial Bioinformatics
73 Bactopia and using workflow managers in bioinformatics part 2
20 Jan 2022
Contributed by Lukas
We are again joined by Dr Robert Petit from the Wyoming Public Health Laboratory who is talking to us about BACTOPIA, a bioinformatics workflow specif...
72 Bactopia and using workflow managers in bioinformatics part 1
06 Jan 2022
Contributed by Lukas
We are joined by Dr Robert Petit from the Wyoming Public Health Laboratory who is talking to us about BACTOPIA, a bioinformatics workflow specifically...
71 Bacterial taxonomy: Into the unknown, SeqCode, naming uncultured multitudes and renaming of phyla
17 Dec 2021
Contributed by Lukas
We finish our discussion on bacterial taxonomy, this time looking at new approaches of naming the multitudes of unnamed uncultured organisms and the c...
70 Bacterial Taxonomy: the grand vista is ahead of us
17 Dec 2021
Contributed by Lukas
We continue our discussion on bacterial taxonomy, this time looking at how genomics has changed taxonomy with: Professor Phil Hugenholtz, Professor Ia...
69 Background to bacterial taxonomy
16 Dec 2021
Contributed by Lukas
There has been a lot of discussion about bacterial taxonomy recently announced regarding phyla, and this revealed a lot of misconceptions around taxon...
68 Bacterial Taxonomy: what is a species, what is a strain? part 2
09 Dec 2021
Contributed by Lukas
68 Bacterial Taxonomy: what is a species, what is a strain? part 2 by Microbial Bioinformatics
67 Bacterial Taxonomy: what is a species, what is a strain?
25 Nov 2021
Contributed by Lukas
We’re navigating the twisted world of bacterial taxonomy. We have some excellent guides to help us! Our guests today are: Dr. Leighton Pritchard: W...
66 Scholarly Communications for Bioinformaticians
18 Nov 2021
Contributed by Lukas
Have you ever read a paper and wondered why the author buried their key result on page 39 of a 50 page paper? Bioinformaticians aren't great at commun...
75 How to review a bioinformatics paper in 10 days or less
02 Nov 2021
Contributed by Lukas
We discuss how to effectively review bioinformatics papers, what to look out for and tips for researchers to when writing bioinformatics or microbial ...
65 Genomics of Mycobacterium tuberculosis
28 Oct 2021
Contributed by Lukas
We’re continuing our series where we examine a particular microbial species in some depth. We’re continuing our look at Mycobacterium tuberculosis...
64 Mycobacterium tuberculosis: the forgotten pandemic
14 Oct 2021
Contributed by Lukas
We’re continuing our series where we examine a particular microbial species in some depth. We’re talking about mycobacterium tuberculosis, the for...
63 A dive into Campylobacter genomics
30 Sep 2021
Contributed by Lukas
Our guest today is Dr Ozan Gundogdu for a deeper dive into the food borne pathogen Campylobacter and how genomics has informed the field over the past...
62 Campylobacter: the fussy little pathogen
16 Sep 2021
Contributed by Lukas
Our guest today is Dr Ozan Gundogdu and he gives us a crash course in food borne pathogen Campylobacter. If you've ever had a dodgy tummy after eating...
61 Non FUNGIble tokens: you too can own BRCA1
02 Sep 2021
Contributed by Lukas
We look at the crazy world of NFTs (non fungible tokens) and blockchain and explore in a light hearted way how they could be used in genomics and bioi...
Encore: 06 - What software not to write
01 Jul 2021
Contributed by Lukas
Torsten Seemann joins us to discuss how to write good bioinformatics software. Torsten is the author of many popular bioinformatics tools such as Prok...
60 Whats in a name: Salmonella and E. Coli
17 Jun 2021
Contributed by Lukas
Today we’re talking about getting your head around our favourite enteric microbes. E. coli and Salmonella. Why do they have some of the names they h...
59 - Microbe Moment Micro Binfie
03 Jun 2021
Contributed by Lukas
Andrew, Nabil, and Lee answer the Microbigal's questions for the "Microbe Moment." You can find the Microbigals at https://www.microbigals.com
58 - StaPH-B careers with Curtis Kapsak and Kevin Libuit
21 May 2021
Contributed by Lukas
We dive deeper into Curtis's and Kevin's career! Relevant links: https://www.skypeascientist.com/ https://www.aphl.org/fellowships/Pages/Bioinformati...
57 StaPH-B - Docker containers for Public Health bioinformatics Part 1
07 May 2021
Contributed by Lukas
The crew talks to Curtis Kapsak and Kevin Libuit about the StaPH-B containers. What a valuable resource! Some URLS: * StaPH-B docker-builds code re...
56 SARS-CoV-2 And Sequencing Spike With Sanger Sequencing part 2
21 Apr 2021
Contributed by Lukas
Part 2 going through a new method for identifying variants of concern using Sanger sequencing, and we’re joined by two of the authors of this method...
55 SARS-CoV-2 And Sequencing Spike With Sanger Sequencing - Welcome To 1995
08 Apr 2021
Contributed by Lukas
Today we’re going through a new method for identifying variants of concern using Sanger sequencing, and we’re joined by two of the authors of this...