Applications for the 2027 summer school on Computational Molecular Evolution on Crete are now open at: meetings.embo.org/event/27-com...

Riboseek is a fast RNA/DNA search. More sensitive than nhmmer at 250x speed. Structure-aware realignment produces MSAs approaching rMSA quality. Plus 1.7M precomputed RNA MSAs, and an API to search your own 📄 www.biorxiv.org/content/10.6... 💾 github.com/steineggerla... 🌐 search.foldseek.com/riboseek

Interesting new tool to extract phylogenies from images (Tremble). It is crazy that this is still something we have to do. doi.org/10.1093/bioi...

Treemble: a graphical tool to generate Newick strings from phylogenetic tree images

AbstractSummary. Phylogenetic trees are ubiquitous and central to biology, but most published trees are available only as visual diagrams and not in the ma

doi.org

Sandpiper 2 is up. 913,000 metagenomic community profiles w @ace-gtdb.bsky.social R232, 200k more than 1.0. sandpiper.qut.edu.au GlobDB coming. Thanks to @aroneys.bsky.social @thepatientwait.bsky.social @iambrettb.bsky.social and especially the new kid @nhstefan.bsky.social

Happy to share our recent work on genetic factors and clinical impact of S. aureus adhesion, published in natcomms.nature.com doi.org/10.1038/s414...

This is an incredibly relevant preprint. Your favourite pipeline and/or AMR gene database cannot be considered authoritative, but neither can others.

@bigdatabiology.bsky.social · 3mo ago

How well do ARG detection pipelines agree when applied to the same data? Spoiler: not very well. In our new preprint, we ran 10 pipelines on 270M microbial unigenes from GMGCv1. The same data can support conflicting biological conclusions! 🧵 www.biorxiv.org/content/10.6...

📣 Whelan lab is hiring 📣 We are looking for an entry level technician to help us with our culturing and DNA sequencing prep of cystic fibrosis lung microbiome samples. Applications close 20 May 2026. www.jobs.manchester.ac.uk/Job/JobDetai...

Research Technician in Microbiology and Molecular Biology:Oxford Road

jobs.manchester.ac.uk

I'm currently advertising a PhD position in my lab, to study the transition from commensal to pathogen in Staphylococcus aureus. Details available here, please share! www.keele.ac.uk/research/pos...

FacultystudentshipinSchoolofLifeSciences

keele.ac.uk

Free and open-source images, icons, and tools for creating scientific illustrations doi.org/10.59350/5zt... 🧪

Free and open-source images, icons, and tools for creating scientific illustrations

Phylopic, NIH Bioart, Bioicons, Scidraw, Open Science Art, Health Icons, Servier Medical Art, Biodiversity Heritage Library, the Noun Project, Segment Anything, Excalidraw, draw.io, Biographics

doi.org

It took years after my masters to publish BaGPipe, now it's out! It's a Nextflow pipeline to run end-to-end bacterial GWAS, heavily tested and benchmarked on different datasets, and now in good hands of the Sanger's Pathogen Informatics Team. link.springer.com/article/10.1...

BaGPipe: an automated, reproducible, and flexible pipeline for bacterial genome-wide association studies - BMC Microbiology

BMC Microbiology - Microbial genome-wide association studies (GWAS) are crucial for linking genetic variation to phenotypic traits in bacteria. However, current tools often involve complex manual...

link.springer.com

Our new preprint is out! We train a transformer on gene order and gene content of bacterial pathogens, applying it to a range of epidemiological and evolutionary analyses (1/8) www.biorxiv.org/content/10.6...

😱 Take-home message: hospital sinks are perfectly safe if you don’t run the taps! #IDSky

Alan McNally@alanmcn1.bsky.social · 3mo ago

Latest paper out today with the IPC team in Birmingham. Where we show the 2m splash zone of a hospital sink is awash with Gram negs, including a Citrobacter containing our Birmingham KPC-2 plasmid pQEB1 www.sciencedirect.com/science/arti...

Nature research paper: Demography and life histories across the Roman frontier in Germany 400–700 ce go.nature.com/4cHRUb6

Demography and life histories across the Roman frontier in Germany 400–700 ce - Nature

Analysis of 258 ancient genomes from southern Germany reveals a major demographic shift during the late fifth century, yet family structures persisted from Late Roman times, demonstrating cultural continuity despite profound demographic reorganization.

go.nature.com

Happy to share our latest work on “In Host Mutational Adaptation of Mycobacterium Tuberculosis Complex Strains During Tuberculosis Infection” published in @jidjournal.bsky.social doi.org/10.1093/infd...

We're recruiting! We're looking for two graduate students to join us at UBC in Vancouver. Fully funded and open to global applicants, with flexible start-date. Topics include theory, bioinformatics, and microbiology. More details: asherleeks.com/apply #socialviruses #evosky #virosky 🧪

This preprint on #Shigella flexneri covers a new genotyping scheme + tool, #AMR and analysis of 13k genomes from ~1925-current day 🦠 #MicroSky #microbiology 🧪 www.biorxiv.org/content/10.6...

Kate Baker@ksbakes.bsky.social · 4mo ago

@yekwah.bsky.social launches FlexIt: the S. flexneri genotyping scheme at @shigellameeting.bsky.social 🎉

Really happy to have played a small part in this cool piece of work led by @guido-valverde.bsky.social and @msabrysarhan.bsky.social. We characterised S. pyogenes in a pre-Columbian Bolivian mummy (suggesting circulation before European contact) #VivaBolivianMummies www.nature.com/articles/s41...

Until now, scientists have identified only a few dozen variants that went through natural selection in humans in the past 10,000 years. A new study claims to find hundreds--maybe thousands. Here's my story on the provocative research, and the mixed reception it's getting. Gift link: nyti.ms/4tSJH9G

New in @science.org ‼️ In the most comprehensive study to date, we show that wildlife trade is driving animal-to-human zoonotic spillover at a planetary scale, with +1 spillover per host every 10 years. Live animal markets and illegal trade pose even greater risks. 🔓 www.science.org/doi/10.1126/...

Myloasm, our long-read metagenome assembler, is now published! w/ @mgmarin.bsky.social and @lh3lh3.bsky.social Very rewarding after > a year of development and countless hours thinking about assembly. Thanks to beta testers, Li lab, and reviewers who gave very helpful feedback. rdcu.be/famFj

High-resolution metagenome assembly for modern long reads with myloasm

Nature Biotechnology - A long-read metagenome assembly method recovers circular and complete genomes better than existing tools.

rdcu.be

Nature Biotechnology@natbiotech.nature.com · 4mo ago

High-resolution metagenome assembly for modern long reads with myloasm - @lh3lh3.bsky.social @jimshaw.bsky.social @danafarber.bsky.social @harvardmed.bsky.social go.nature.com/3PBEwvR

PhD available with @overtonlab.bsky.social Sara Jabbari and me associated with our BBSRC sLoLa project! www.findaphd.com/phds/project... (UK students only)

Improving the solvent tolerance of E. coli by understanding the rules of accumulation at University of Birmingham on FindAPhD.com

PhD Project - Improving the solvent tolerance of E. coli by understanding the rules of accumulation at University of Birmingham, listed on FindAPhD.com

findaphd.com

Am stoked and thrilled that our latest paper is now out. A longitudinal study of invasive E. coli from children in the Netherlands over 50 years www.sciencedirect.com/science/arti...

Lineage dynamics of invasive Escherichia coli isolates in the Netherlands from 1975 to 2021: a retrospective longitudinal genomic analysis

Escherichia coli is a common cause of invasive infections such as bloodstream and cerebrospinal fluid infections in neonates. Strains positive for the…

sciencedirect.com

ARTIC are hiring! Postdoctoral opportunity in metagenomics at the University of Birmingham edzz.fa.em3.oraclecloud.com/hcmUI/Candid...

Research Fellow (Postdoctoral) - School of Biosciences - 107071 - Grade 7

This post-doctoral position will contribute to both complementary programmes, developing ‘broadband’ metagenomic sequencing capabilities for rapid detection and characterisation of emerging and unknow...

edzz.fa.em3.oraclecloud.com

Great work by Jamie Gorzynski and Josh-Harling-Lee from the group providing insights into the evolutionary origins of bacterial lineages. A collaboration with @jrpenades.bsky.social @wfigueroac3.bsky.social. #Staph Cell Reports www.cell.com/cell-reports...

Bacterial defense systems and host ecology drive the evolution of intra-species lineages

Staphylococcus aureus lineages vary widely in the frequency of gene exchange and the diversity of genome content. Gorzynski and Harling-Lee et al. show that both host ecology and the horizontal acquis...

cell.com

I am seeking a postdoc to join my group at UCLA -- ideally the candidate would have some experience in either population genetics or microbes/microbiome (computational background needed). We have a range of projects and are happy to tailer to your interests. Please dm/email me if interested.

A tour de force in 1) genomic epidemiology, 2) global equity of access and representation, and 3) phylogenetic wizardry. Congrats Zam and Viridian team on this tremendous resource!

Zamin Iqbal@zaminiqbal.bsky.social · 6mo ago

A long time ago in a galaxy far away, there was a SARS-CoV-2 pandemic. Our paper, led by @martibartfast.bsky.social a) correcting errors in 4.5 million genomes & their phylogeny b) improving representation of the Global South in public data www.nature.com/articles/s41... (thread 1/n)

At long last, my final PhD chapter is out: we developed a novel evolutionary simulator of bacterial pangenomes, Pansim, fitting it to data from >600K genomes using a likelihood-free framework, PopPUNK-mod, to explore neutral and adaptive pangenome dynamics www.biorxiv.org/content/10.6...

New blog post: ONT read QC strategies for assembly rrwick.github.io/2026/02/05/r... Mini-study comparing a few QC/subsampling approaches, plus practical notes from my experience.

We're Hiring! We're looking for a postdoc with bioinformatics/modelling skills to join us in an exciting microbiome ecology project in Manchester (deadline 1st March) www.jobs.manchester.ac.uk/Job/JobDetai...

Have you ever paused and wondered about the many different ways in which computing infrastructure and activities impact the environment? @loiclnlg.bsky.social and our own Flaminia Zane have created a free guide dedicated to sustainable computing in science: www.ebi.ac.uk/training/onl... 🧬🖥️📊🌱