The first version of FigTree was released nearly 20 years ago and it is still widely used (including by me). But there are currently 85 issues on the GitHub repo (github.com/rambaut/figt...) and some of them I don’t really like the look of.

Looking forward to sharing our recent work on population metabolism of #klebsiella pneumoniae this week. Join me to learn about metabolic diversity within species, featuring work by @bananabenana.bsky.social @helena-bethany.bsky.social and a sneak peak at our latest from @kalanip.bsky.social

Thanks @theviin.bsky.social for the invite to join this great meeting, and share our work on Kaptive for capsule typing, and how we can apply it to inform #klebsiella vaccines: tinyurl.com/npaj4vzr With @tomstantonmicro.bsky.social @shaunkeegan.bsky.social @katholt.bsky.social and many others

🧫 Our publication,“Global perspectives on Klebsiella epidemiology and biology: conference report on the KLEBS 2024 symposium,” is now out! 📄 Link to paper: www.nature.com/articles/s44... @kelwyres.bsky.social @katholt.bsky.social @sylvainbrisse.bsky.social @pasteur.fr

Why so many co-circulating #Klebsiella pneumoniae clones? By studying >7000 isolates, @bananabenana.bsky.social @kelwyres.bsky.social &co identify structured, clone-specific #metabolic specialisation across the population that enables reciprocal cross-feeding @plosbiology.org 🧪 plos.io/4qdC2B2

Ditto, ditto, ditto! We are thrilled this is now available in @plosbiology.org 🎉🎉🎉 Our analysis of metabolic diversity in #klebsiella pneumoniae, showing clone specific metabolism. 🦠 Fantastic work by @bananabenana.bsky.social, summarised beautifully below. 🤩

📣🦠Check out our new Editor’s Spotlight! Senior MGEN editor Jesse Shapiro tells us about a recently published paper on the bystander effect on the evolution of Bordetella parapertussis, a non-target species of the pertussis vaccine #MGEN Read the full blog here: microb.io/48zfOlJ

#AMR #Klebsiella cause >100,000 neonatal deaths globally each year. Our new preprint shows more than half of #Klebsiella pneumoniae neonatal sepsis cases in African and South Asian are nosocomial, acquired through transmission in neonatal units. #WAAW doi.org/10.1101/2025...

Huge preprint if you are interested in bacterial strain taxonomy! The why and how of cgMLST LIN codes: An extensively revised and expanded version doi.org/10.1101/2024... I will summarize it for you in this thread 👇

Want to learn about #klebsiella genomics? Check out our free online resource, developed as part of the @klebnet.bsky.social project and in collaboration with ECDC Gen-Epi Bio train. #genomics #amr #sero-epi #hypervirulence #LINcodes

Registration is open for the Microbial Genomics of Eukaryotes meeting in Glasgow! This event will showcase diverse scientific achievements in eukaryotic genome research. Register now and submit your abstract by 12 August: microb.io/MicroGenomic...

Pleased to say that our preprint benchmarking Nanopore data for MLST, cgMLST, cgSNP & AMR typing from bacterial isolates is out! TL;DR you can get almost perfect results from 50x depth using live SUP basecalling with a GPU in under 20 hours #microsky#IDsky 🦠🧬🖥️ /1 www.medrxiv.org/content/10.1...

🚨 New preprint 🚨 My phage annotation tool, Phynteny, finally has a preprint and a brand new version powered by a cool AI transformer architecture and protein language models! #phagesky www.biorxiv.org/content/10.1...

AlphaGEM Enables Precise Genome-Scale Metabolic Modelling by Integrating Protein Structure Alignment with deep-learning-based Dark Metabolism Mining https://www.biorxiv.org/content/10.1101/2025.07.21.665674v1

Our new #klebsiella O type nomenclature, codesigned with Chris Whitfield, is now live in @pathogenwatch.bsky.social! Need a quick explainer on the new names? Check out my blog post: tinyurl.com/y8yb3rbb (+link to full review article) #MicroSky @klebnet.bsky.social @tomstantonmicro.bsky.social

Woohoo Kaptive is now integrated within BIGSdb for #Klebsiella and #Acinetobacter. Thanks @kjolley.bsky.social! Also like to acknowledge that the Acineto dbs were developed and maintained by Johanna Kenyon and team at Griffith Uni.

🦋Hello BlueSky!🦋 Let's get right into it. MicroSeq is back September 3-4, 2025! Stay tuned for more details on registration and abstract submission coming soon here and at www.microseqconference.com. 🌟Save the date!🌟 #MicroSeq2025

First paper on our projects on #Klebsiella transmission in the hospital environment; I'm so lucky to get to work with the wonderful teams@ Malawi Liverpool Wellcome Program, Kamuzu University, Queen Elizabeth Central Hospital🇲🇼 #MicroSky #IDSky #GlobalHealth 🧬💻🧪 (1/3) www.medrxiv.org/content/10.1...

So excited that this is now online. It's been a huge collaborative effort to estimate the prevalence of capsule and O antigens associated with #klebsiella neonatal sepsis in Africa and South Asia. The first step to prioritising antigens for a vaccine to protect 1000s of newborns. #MicroSky #AMR

Working on #klebsiella genomes? ✅ Want to collaborate globally to advance Klebs genomic epi? ✅ Please join us via the KlebNET-GSP Epidemiology consortium ⬇️ #microsky #AMR

Great night at the ASM VIC branch student and ECR awards. Such a high standard of scientific talks, and broad range of science. Congrats to all of the speakers and winners! 🎉🎉🎉 @aussocmic.bsky.social

Interested in a PhD focusing on Streptococcus pneumoniae or pyogenes? Our group is looking for new PhD students to join our lab! Apply here: career10.successfactors.com/sfcareer/job...

Check out our latest Kaptive update for highly sensitive and accurate identification of surface polysaccharide loci from WGS of #AMR pathogens, #Klebsiella and #Acinetobacter baumanii. Led by the awesome @tomstantonmicro.bsky.social 🦠🧫

🧬🖥️ 🦠🧫 🧪🔬 Hey BSky Bioinformatics and Genomics! Some years ago many people were compiling 𝐥𝐢𝐬𝐭𝐬 𝐨𝐟 𝐰𝐨𝐦𝐞𝐧 𝐢𝐧 𝐬𝐜𝐢𝐞𝐧𝐜𝐞 as an effort to break biases when looking for reviewers and collaborators... Is there anything like that for Bioinformatics and Genomics? #WomenInSTEM

📣Our latest paper is out now in mSystems: Not quite as it may seem - investigating #plasmid diversity and evolution in #Klebsiella pneumoniae at a single institution over time. A short thread 🧵 @zaminiqbal.bsky.social

Great thread

This scheme was how Zong and I first established our collaboration. Led to two MRC grants and 33 papers. Can’t encourage people enough to go for this.

What do you think are the critical features pathogen genomic data-sharing platforms require to meet the public health need? Please participate in this public consultation!

Interested in predicting AMR in bacteria? We show ignoring phylogenetic structure in genome collections leads to overly optimistic evaluations of machine learning methods for AMR prediction. With @nwheeler443.bsky.social and former PhD student Yanying Yu. 🦠🧫🧬🖥️🧪 www.biorxiv.org/content/10.1...

Time to say 'Au revoir Paris' after a fantastic #KLEBS2024. Great science and great people. So proud to have @tomstantonmicro.bsky.social @kalanip.bsky.social @bananabenana.bsky.social representing the lab, and congrats to Tom and Kalani for their poster prizes! 👏

Ziyaad Dangor talking on Klebsiella pneumoniae as an important infectious cause of death in infants in LMIC settings. K. pneumoniae contributes to "pathway to death" in almost a quarter of infants between months 1 and 59 months of life. #KLEBS2024

(1/6) Our new short paper on incidental bacterial domestication between patient isolation and creation of frozen stock. Geno/phenotype changes are obscured by rich media and more prevalent than we previously thought. #MicroSky

Here we go! #KLEBS2024 400 in person and 400 online participants from 71 countries...... Wow!

Finally time for #KLEBS2024! Starting with the genomics workshop before we kick off the main event: 2 whole days of #klebsiella 🦠 Looking forward to catching up with great collaborators and friends, and making new connections with Klebs aficionados. 🎉🎉🎉

Let's increase #klebclub chatter on 🔵🦋! Klebsiella aficionados add your handle below and we will build a starter pack. 🔁 to spread the word

Ever wondered why there are so many co-circulating #klebsiella pneumo clones? ... me too! So I'm thrilled to present this new preprint from my lab, where we explore this very question. The culmination of 3+ yrs hard work by @bananabenana.bsky.social! doi.org/10.1101/2024...

Are you a fan of #klebsiella genomics? Looking for a post-doc role? ...🥁 ... I'm recruiting! Join my team in Melbourne (Australia) to help us build the first Klebsiella clone risk framework. See details here tinyurl.com/yrka232h Applications close June 9th. #klebNET @klebclub.bsky.social

📢 The One Health Microbiome Symposium is extending the deadline for registration and abstract submission to March 22nd! If you would like to attend and potentially give a talk or poster presentation, now's your last chance! Tickets are going quickly‼️ www.eventbrite.com/e/one-health...

AlphaFind: Discover structure similarity across the entire known proteome https://www.biorxiv.org/content/10.1101/2024.02.15.580465v1

Are you an early-stage researcher seeking support to attend ASM Microbe? 🧪🧬 The ASM Peggy Cotter Travel Award Program provides funds for outstanding early career Branch members to attend ASM Microbe. asm.org/Travel-Award...

Back to the socials after the holidays and first post is an absolute joy--> 📣📣📣 Congratulations to twitter.com/helena_betha... for preprinting the first chapter of her PhD thesis 🎉🎉🎉 doi.org/10.1101/2023...

The evolution and international spread of extensively drug resistant Shigella sonnei. The international outbreak (England, France, Belgium, USA, Australia) was ciprofloxacin, azithromycin, and ceftriaxone resistant - three of four WHO recommended antibiotic treatment options for shigellosis. 🖥️🧪🧬🦠🧫

New 🧫🦠🧪 paper from the lab: Targeted deletion of Pf prophages from diverse Pseudomonas aeruginosa isolates impacts quorum sensing and virulence traits doi.org/10.1101/2023... #phagesky #microsky

Hot off the press - Longitudinal analysis within one hospital in sub-Saharan Africa over 20 years reveals repeated replacements of dominant clones of Klebsiella pneumoniae and stresses the importance to include temporal patterns for vaccine design considerations 🖥️ 🧬 www.medrxiv.org/content/10.1...

We have published a manuscript describing a software tool to reduce ambiguity and improve interpretability in microbial GWAS, called panfeed. Here's a quick explainer: www.microbial-pangenomes-lab.org/2023/11/09/M... And here's the link to the paper: www.microbiologyresearch.org/content/jour...