Micro binfie podcast

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

twitter

blogs

personal webpage

github for personal webpages

sign up to github

--help citation and name

making your code public as you develop it.

links in your signature

self promote at end of slides

just starting out

Links: How to pronounce ORCID - https://info.orcid.org/how-should-orcid-be-pronounced/#:~:text=But%2C%20for%20those%20who%20want,pronounced%20%E2%80%9Coar%2Dkid%E2%80%9D.

Phil Ashtons blog: https://bitsandbugs.org/

Publons: https://publons.com/about/home/

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 assistant professor in molecular microbiology at the University of Bradford.

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.

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 Computer Science and he completed his PhD at LSHTM (London School of Hygiene & Tropical Medicine) in 2011.

www.lshtm.ac.uk/aboutus/people/gundogdu.ozan

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 he completed his PhD at LSHTM (London School of Hygiene & Tropical Medicine) in 2011.

https://www.lshtm.ac.uk/aboutus/people/gundogdu.ozan

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/2021/3/11/22325054/beeple-christies-nft-sale-cost-everydays-69-million

Make NFT - https://www.coindesk.com/how-to-create-buy-sell-nfts

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