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 persuaded Nick Loman to join him in Birmingham. Mark tells us how they worked with George Weinstock to perform the first genome sequence analyses of Gram-negatives for genomic epidemiology—in this case of multi-drug resistant Acinetobacter baumannii. After winning an Ion Torrent sequencer in a competition, Mark and Nick then contributed some pioneerin...
Jun 23, 2022•27 min
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 from model organisms and fearsome pathogens. He recounts working with his hero David Relman on the genome sequencing of the strange slow-growing organism called Tropheryma whipplei in competition with a French team. Mark moved to Belfast in late 1999 collaborating with another Englishman working on the island of Ireland, Tim Foster in Dublin. Palle...
Jun 09, 2022•22 min
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 sometime soon.
May 26, 2022•18 min
In this episode we talk to Professor Mark Pallen, who discusses the highlights from his long career as a medical microbiologist turned bioinformatician. His bioinformatics journey began in 1977, the year Fred Sanger invented DNA sequencing-as-we know-it, when Mark was tasked with assembling some amino acid sequences under exam conditions. Mark explains how little was know about sequences at the time. Luckily he managed to gain a grasp of molecular biology and joined a group in the late 1908s at ...
May 12, 2022•40 min
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-sars-cov-2. See our previous episode for part 1 of the conversation. * Previous paper for bacterial datasets can be found at https://peerj.com/articles/3893/ * Jill can be found on Twitter at @JillHagey and jvhagey.github.io * Lingzi can be found on LinkedIn at https://www.linkedin.com/in/lingzi-xiaoli-27b87174/
Apr 29, 2022•9 min
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-sars-cov-2 * Previous paper for bacterial datasets can be found at https://peerj.com/articles/3893/ * Jill can be found on Twitter at @JillHagey and jvhagey.github.io * Lingzi can be found on LinkedIn at https://www.linkedin.com/in/lingzi-xiaoli-27b87174/
Apr 28, 2022•43 min
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 containers for public health bioinformatics. Its basically how to make biology easier for everyone! Github: https://github.com/StaPH-B
Apr 14, 2022•28 min
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 those just getting started with sequencing and understanding the data generated. The organization provid...
Mar 31, 2022•26 min
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
Mar 17, 2022•38 min
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 surveillance, UK and Clement Tsui from the Weill Cornell Medicine, Qatar. Andrew Page was the Chair, supp...
Mar 03, 2022•41 min
74 SEPIA With Henk - Soup Or Salad Yes! by Microbial Bioinformatics
Feb 03, 2022•38 min
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
Jan 20, 2022•29 min
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
Jan 06, 2022•35 min
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/assets/Taxonomy_Selective_bibliography.pdf
Dec 17, 2021•41 min
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
Dec 17, 2021•29 min
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/45db8eb57d732176449073065dbdacc88a288fe9/assets/Taxonomy_Selective_bibliography.pdf
Dec 16, 2021•26 min
68 Bacterial Taxonomy: what is a species, what is a strain? part 2 by Microbial Bioinformatics
Dec 09, 2021•41 min
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.
Nov 25, 2021•25 min
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 peers organisation websites managing publication record librarians citation metrics peer review twit...
Nov 18, 2021•45 min
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.
Nov 02, 2021•31 min
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 assistant professor in molecular microbiology at the University of Bradford.
Oct 28, 2021•34 min
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 microbiology at the University of Bradford.
Oct 14, 2021•36 min
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 related enteric microorganisms like Listeria and Vibrio. His background is in Molecular Biology and ...
Sep 30, 2021•34 min
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 microorganisms like Listeria and Vibrio. His background is in Molecular Biology and Computer Science and...
Sep 16, 2021•22 min
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 on patenting a gene - https://www.npr.org/transcripts/937167323 Beeple - https://www.theverge.com/202...
Sep 02, 2021•28 min
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
Jul 01, 2021•44 min
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
Jun 17, 2021•29 min
Andrew, Nabil, and Lee answer the Microbigal's questions for the "Microbe Moment." You can find the Microbigals at https://www.microbigals.com
Jun 03, 2021•13 min
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
May 21, 2021•40 min
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/
May 07, 2021•36 min
