Postdoctoral Position (Please re-post)
A funded postdoctoral position for a recent graduate to study aspects of Neisseria gonorrhoeae pathogenesis, antigenic variation, genetics, or physiology.
Please contact Hank Seifert h-seifert@northwestern.edu
#Microsky, #Microbiology, #MicrobialEvolution
#pneumococci continue to be the leading cause of LRI deaths globally: Global burden of lower respiratory infections and aetiologies, 1990–2023: a systematic analysis for the Global Burden of Disease Study 2023 - The Lancet Infectious Diseases www.thelancet.com/journals/lan...
Here I would like to introduce a genome downloading tool: GenomeFetch 👇🧬
This is a Linux tool written in pure Shell/Bash for downloading bacterial genomes (genome assemblies) from RefSeq or GenBank 🧫
I had the opportunity to present my research at #AIR2026 (Wellcome Genome Campus), focusing on how lactate shapes host-microbe interactions in the lung
It was a great experience to share this work, receive valuable feedback, and engage with researchers across microbiology and immunology.
#microbiome
Here we go then, lab website at last! Still some gaps to fill and I've definitely not caught all the broken links yet but here we are.
www.lungmicrobiome.org
Hellow world!
Minor update on genomics of the menB outbreak. UKHSA have updated with four more outbreak isolates, and a high quality assembly of the earlier genome.
tl;dr ran ska+gubbins again, same results, all of these genomes look basically identical
www.bacpop.org/blog/menb_up...
Thought provoking article: Improving scientific mentoring with history and philosophy of science url: royalsocietypublishing.org/rspb/article...
Now sat at the front of a lecture room … something that NEVER happened when I was here as a student
Back at my old stomping ground @uniofsurrey.bsky.social with my eldest for an offer holder day. Forgotten how nice the campus was …
Some provisional analysis on one of the genomes from the menB outbreak detailed below:
johnlees.me/posts/menb-o...
I did my PhD on bacterial meningitis, finding whether there are genetic factors which make meningitis more likely.
Wrote down some initial thoughts on the current outbreak in Kent: johnlees.me/posts/menb-o...
I tried to think of factors and their likelihood to explain why this is happening now
It’s the hope that gets you. C’mon 🏴 #GuinnessM6N #IREvSCO
Magdalena is a white woman with short curly ginger hair and is wearing a bright yellow raincoat over a mint green top. She’s smiling at the camera with a mechanical bull statue of Ozzy the bull behind her
A white mug with a dark blue logo and orange writing. The logo shows a laptop screen with a DNA and microbes, and code underneath, the writing above reads Analysing Microbial Genomic Data
Saying goodbye to Birmingham after a brilliant week of learning about microbial genomic analysis at #AMGDMar26 🧫🧬 @unibirmingham.bsky.social with the best teachers and cohort!
And a special thank you to all of you for following along and helping me win the most coveted prize of the AMGD mug! ☕️
Final day (day 5) of #AMGDMar26 at @unibirmingham.bsky.social as @pathogenomenick.bsky.social gave an amazing talk on the applications of bacterial genomics in pandemics.
Phylogenetic tree on a white background, light reflecting off of one of the lines associated to a clade
#AMGDMar26 Bairn’s first phylogenetic tree, please ignore the reflection of the light at one of the nodes it’s not a clade experiencing a damascene intervention it’s purely the reflection from the ceiling.
University of Birmingham medical school big old brick/stone building with clock tower towards the back of the shot.
Small lecture room with a white title slide with the text Analysing Microbial Genomic Data. Day 4 part 1. David behind the lecturn on the right and Izzie on the left.
Day 4 of Analysing Microbial Genomic data #AMGDMar26
Working with Core and Pangenomes and building phylogenetic arboretums.
More overcast today and being battered by the wind but lovely conditions for coding!
Happy Bon Jovi Day, it’s day 3 at #AMGDMar26
Today was a belter, moving from the small sample work to the bigger datasets. Working through quality checks of assemblies, incorporating mlst and annotations. Big win for me getting the looped bakta annotation sorted. Alexa play Heather Small!
Day 4 of #AMGDMar26 and on to pangenomes with @izziepotterill.bsky.social
I am unashamedly pleased about getting a Proclaimers song into a sequence alignment tutorial #AMGDMar26
A pack of stickers in front of a computer screen with blurred code. The sticker pack is branded MicrobesNG and the visible sticker at the front reads: Relax it’s just a phage
A fruit stall with a blue sky and clouds above, the building behind read Queen Elisabeth Hospital Birmingham
Day 3 of #AMGDMar26 🧬 learning about alignments through song lyrics, loops starting to make sense, a trip the market in the sunshine & shiny microbe stickers thanks to @helenmcneil.bsky.social @microbesng.bsky.social 🧫
Midway through the #AMGDMar26 course and grateful to @helenmcneil.bsky.social of @microbesng.bsky.social for coming along and talking to attendees. Also gives them a much needed rest from hearing my voice!!!
Central station main entry facing northbound toward the clock reading 05:10
Early start Monday morning to travel down to Birmingham for #AMGDMar26
Intentions of updating the timeline on the train were derailed by having minimal arm space and musical chairs. Nutrition provided by Greggs.
A blue sky with some clouds above a red brick building to the left and a grey building in the centre with the university of Birmingham crest
A computer screen showing a terminal inside a browser running fastqc on a number of samples
Day 2 of #AMGDMar26 🧬 was a lovely sunny day on campus @unibirmingham.bsky.social ☀️
Which alongside cake and the aim of saving the world (see Day 1) provided ample motivation for learning a whole lot about what to do with Illumina sequencing outputs 💻
Tidy desk set up. On the left; white coursework book and notebook with the course logo on the front. On the right the laptop with desert lock screen.
Brown envelope with red top secret stamp beside course notebook
Plenty of merch #AMGDMar26 including a tote bag, j’adore a tote bag. Notebook and laptop sticker all with the course logo on. #yesplease
Also looking forward to completing a top secret task. Applying skills to a fictional scenario. Once more. #yesplease
Flat lay of a tote bag and booklet branded with the Analysing Microbial Genomic Data logo (a laptop showing a DNA double helix and microbes) and a sheet of paper that reads Human Bingo
A folded letter marked as classified with portions blacked out, suggesting the participants of the course must solve a fictional act of bioterrorism
Day 1 of #AMGDMar26 🧬 started with an icebreaker that was actually fun 😱!
And I cannot wait to live my science fiction dreams over the next few days 🤩
Oh and a tote bag?! Great start to the week!
Mags is a white woman and has short curly ginger hair and is wearing a yellow raincoat, she is smiling at the camera and pointing upwards with her left hand. She is pointing at a brick building behind her with a railways sign, university, and the university of Birmingham crest
Made it to Birmingham @unibirmingham.bsky.social for a week of microbial genomics fun! 🧫🧬💻 #AMGDMar26
Today is the start of the 5th Analysing Microbial Genomic Data course at @unibirmingham.bsky.social #AMGDMar26 - in the last three years we’ve trained nearly 80 attendees from six countries and multiple UK universities
“If you hear a voice within you say ‘you cannot paint,’ then by all means paint, and that voice will be silenced.”
Vincent Van Gogh
