Micro binfie podcast

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 the popular SARS-CoV-2 pipeline cecret. Website: staphb.org/ Cecret Pipeline: github.com/CDCgov/SC2CLIA Kelsey explains that StaPH-B was created to facilitate collaborations between bioinformaticians in state public health laboratories, especially thos...

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 Group Leader at the European Bioinformatics Institute and Dr. Grace Blackwell who is jointly at the European Bioinformatics Institute, in Zam’s group and Nick Thomson’s team at Wellcome Sanger Institute

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 Bioinformatics hackathon run in conjunction with JPIAMR, PHA4GE and CLIMB. The panel were: Mark Pallen from the Quadram Institute Bioscience, UK, Finlay Maguire from Dalhousie University, Canada, Anthony Underwood from the Centre for genomic pathogen surve...

74 SEPIA With Henk - Soup Or Salad Yes! by Microbial Bioinformatics

We are again joined by Dr Robert Petit from the Wyoming Public Health Laboratory who is talking to us about BACTOPIA, a bioinformatics workflow specifically for bacterial genomes. Docs: https://bactopia.github.io/ Repo: https://github.com/bactopia/bactopia/ Pub: https://doi.org/10.1128/mSystems.00190-20

We are joined by Dr Robert Petit from the Wyoming Public Health Laboratory who is talking to us about BACTOPIA, a bioinformatics workflow specifically for bacterial genomes. Docs: https://bactopia.github.io/ Repo: https://github.com/bactopia/bactopia/ Pub: https://doi.org/10.1128/mSystems.00190-20

We finish our discussion on bacterial taxonomy, this time looking at new approaches of naming the multitudes of unnamed uncultured organisms and the controversial renaming of phyla. With guests Professor Phil Hugenholtz, Professor Iain Sutcliffe and Professor Mark Pallen. Selective bibliography: https://github.com/MicroBinfie/MicroBinfie.github.io/blob/45db8eb57d732176449073065dbdacc88a288fe9/asse...

We continue our discussion on bacterial taxonomy, this time looking at how genomics has changed taxonomy with: Professor Phil Hugenholtz, Professor Iain Sutcliffe and Professor Mark Pallen. Selective bibliography: https://github.com/MicroBinfie/MicroBinfie.github.io/blob/45db8eb57d732176449073065dbdacc88a288fe9/assets/Taxonomy_Selective_bibliography.pdf

There has been a lot of discussion about bacterial taxonomy recently announced regarding phyla, and this revealed a lot of misconceptions around taxonomy in general. Today we discuss the background to bacterial taxonomy with: Professor Phil Hugenholtz, Professor Iain Sutcliffe and Professor Mark Pallen. Selective bibliography: https://github.com/MicroBinfie/MicroBinfie.github.io/raw/45db8eb57d7321...

68 Bacterial Taxonomy: what is a species, what is a strain? part 2 by Microbial Bioinformatics

We’re navigating the twisted world of bacterial taxonomy. We have some excellent guides to help us! Our guests today are: Dr. Leighton Pritchard: Who is a Strathclyde Chancellor's Fellow at Strathclyde Institute of Pharmacy and Biomedical Sciences in the University of Strathclyde Dr. Conor Meehan: Dr. Conor Meehan is an assistant professor in molecular microbiology at the University of Bradford.

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 communicating themselves or their science to the wider world, so we have a chat about it, specifically with bioinformaticians in mind. Topics include: Online presence/ scholarly communications for bioinformatics Google scholar/Scopus Marketing to a set of...

We discuss how to effectively review bioinformatics papers, what to look out for and tips for researchers to when writing bioinformatics or microbial genomics papers to ease their way through review.

We’re continuing our series where we examine a particular microbial species in some depth. We’re continuing our look at Mycobacterium tuberculosis, focusing more on bioinformatics, genomics and typing. Our guests are Dr. Suzie Hingley-Wilson Lecturer in Bacteriology at the University of Surrey, Dr. Dany Beste Senior Lecturer in Microbial Metabolism at the University of Surrey and Dr. Conor Meehan...

We’re continuing our series where we examine a particular microbial species in some depth. We’re talking about mycobacterium tuberculosis, the forgotten pandemic. Our guests are Dr. Suzie Hingley-Wilson Lecturer in Bacteriology at the University of Surrey, Dr. Dany Beste Senior Lecturer in Microbial Metabolism at the University of Surrey and Dr. Conor Meehan assistant professor in molecular microb...

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 20 years since the publication of the first reference genome in 1999. Ozan leads the foodborne enteric pathogen group at the London school of hygiene and tropical medicine. Where they study the physiology and pathogenesis of Campylobacter and other...

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 undercooked chicken, Campy is probably the cause. Ozan leads the foodborne enteric pathogen group at the London school of hygiene and tropical medicine. Where they study the physiology and pathogenesis of Campylobacter and other related enteric micr...

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 bioinformatics. We propose a way of replacing all the central genome databases and our own cryptocurrency (BioBucks or maybe GenomeCoin). Myriad genetics SCOTUS decision - https://www.supremecourt.gov/opinions/12pdf/12-398_1b7d.pdf Planet money episode o...

Torsten Seemann joins us to discuss how to write good bioinformatics software. Torsten is the author of many popular bioinformatics tools such as Prokka, Snippy, Barrnap, Abricate, Shovill, and Nullarbor. Links: https://github.com/tseemann

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 have? Primer on ANI: https://www.pnas.org/content/102/7/2567.short Wikipedia on Salmonella serovars: https://en.wikipedia.org/wiki/Kauffman%E2%80%93White_classification Nabil's viral tweet: https://twitter.com/happy_khan/status/1387804862830809091?s=20

Andrew, Nabil, and Lee answer the Microbigal's questions for the "Microbe Moment." You can find the Microbigals at https://www.microbigals.com

We dive deeper into Curtis's and Kevin's career! Relevant links: https://www.skypeascientist.com/ https://www.aphl.org/fellowships/Pages/Bioinformatics.aspx https://www.jmu.edu/genomics/index.shtml jmu.edu/biology

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 repository: https://github.com/StaPH-B/docker-builds * StaPH-B DockerHub container repositories: https://hub.docker.com/u/staphb * Guide for contributing: https://staph-b.github.io/docker-builds/contribute/

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 Kai Blin and Tue Jorgensen, both from the Technical University of Denmark. The preprint: www.medrxiv.org/content/10.1101/2….03.27.21252266v1 The protocol: www.protocols.io/view/sanger-sequ…-2-spik-bsbdnai6 The software: github.com/kblin/covid-spike-cl...

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 method Kai Blin and Tue Jorgensen, both from the Technical University of Denmark. The preprint: https://www.medrxiv.org/content/10.1101/2021.03.27.21252266v1 The protocol: https://www.protocols.io/view/sanger-sequencing-of-a-part-of-the-sars-cov-2-spik-...