Out today in Nature Microbiology: a paper that started in 2021 with an email from @sullivan-lab.bsky.social. Subject line: "Crazy ideas". www.nature.com/articles/s41... 1/23

#gbdraw v0.12.1 is now live with a massive update! Powerful new features are now available in your local environment: ​You can now generate circular comparisons (homology rings) and interactive SVG files directly on your machine 🧬 #bioinformatics #genomics

What a brilliant resource! Readers can help secure the future of the Biodiversity Heritage Library, and keep its collections free and open to the world, via the Donate button at biodiversitylibrary.org.

Why does it bother me when a manager or the CEO of my employer boasts about using Copilot to write their emails? This. This is why

I’ve officially resigned as Associate Editor for Frontiers in Systems Neuroscience. It used to be a reputable journal, but became a case study in how forced automation destroys academic integrity. 👇

Our piece about academic renewal is now out in the Times Higher Education. It deals with a familiar topic on which there have been multiple high-level declarations. We need to move beyond the symbolic. Early career researchers, pls read + ask questions! www.timeshighereducation.com/depth/academ...

I wrote about AI in academia. "PhD-level thinking", LLM bias, grunt work, alignment, AGI, data center water use, AI politics -- something for everyone.

those who enjoyed our story of 𝘐. 𝘤𝘢𝘴𝘤𝘢𝘥𝘦𝘯𝘴𝘪𝘴, which was found in Hot Springs Creek in Lassen Volcanic National Park, can prepeare for an exciting continuation! no spoiler here, but 𝘍𝘶𝘮𝘢𝘳𝘰𝘭𝘢𝘮𝘰𝘦𝘣𝘢 cousins were now found at an, well... unexpected locaction. read below👇 #ProtistsOnSky

New paper out! 🔈 Genomic Characterization of the RyC collection: 50 Multidrug Resistant Clinical Isolates of Escherichia coli and Klebsiella spp. 50 MDR gut isolates, 2 sequencing platforms, 4 “omes,” and 1 mission: provide a resource to decode AMR and MGE dynamics www.biorxiv.org/content/10.6...

Jeremy Wang developed rammap, a minimap2 rewrite in Rust. It achieves comparable or better performance than minimap2 and produces identical output to minimap2. During rewrite, Jeremy found two long-existing bugs in minimap2 which are fixed in v2.31. www.biorxiv.org/content/10.6...

It's out! The LIN code approach for genomic taxonomy of microbial strains and its applications in genomic epidemiology journals.plos.org/plosbiology/...

"In the past, research was often carried out by people working alone or in groups of two or three. In these circumstances, it seems reasonable to expect each author to take responsibility for the whole." I still expect every author to take responsibility. theconversation.com/a-key-scienc...

“Academic science is not only about productivity, it is also about deep understanding, exploring creative solutions and training critical thinkers to be the next generation of researchers.” www.nature.com/articles/d41...

"Science is not simply a sequence of tasks that can be optimized....The scientific system thrives on inefficiency: redundant efforts, failed attempts, and divergent paths. These are not costs to be eliminated but sources of discovery." Excellent essay! ⬇️ www.science.org/doi/10.1126/...

Our report on a KPC157-producing K. pneumoniae clinical isolate resistant to meropenem-vaborbactam, imipenem-relebactam and other antimicrobials has been published. We established IS-mediated signal-peptide disruption of OmpK36 as a mechanism to reduce β-lactam susceptibility doi.org/10.1186/s128...

This is from 7 years ago (merenlab.org/2019/02/24/f...). We are talking about the same things today. We will be talking about the same things 7 years from now. There is no one to blame for this apart from ourselves. I find it very depressing.

Fabulous! Will look for it when I walk through Liverpool's Bold Street next time.

🌟Great start to #TARGetAMR26! 🎙️Today we heard an inspiring keynote, insightful talks and fantastic discussions on AMR genomics Plus our Co-Directors @wvschaik.bsky.social @ksbakes.bsky.social unveiled: 🚀Launch of our Flexible Funding Initiative 📚Debut of the TARGetAMR comic ⌛️We can't wait for Day 2!

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...

This report on outbreaks of Burkholderia cepacia complex in the UK and Ireland between 2010 and 2023 has become open access: doi.org/10.1017/ice....

Seconded!!! And that’s even if an email address was included on that paper. Add your email to your orcid, lab webpage, bluesky, or use GitHub to host a really simple (and free) website with your contact details.

"Most top achievers (Nobel laureates and world-class musicians, athletes, chess players) demonstrated lower performance than many peers during their early years. Across the highest adult performance, peak performance is negatively correlated with early performance" www.science.org/doi/10.1126/...

I am not sorry. This is simply true. Academics should be able to write fluently and express themselves clearly and academics should do their own work. It’s literally our job. It’s what we trained until 22nd grade to do. This is a simple observation that should require no explanation or defense.

Today I am very proud to announce the release of the Antibiotic Resistance Microbiology Dataset - Mass General Brigham (ARMD-MGB; physionet.org/content/armd...) , as part of an NIH-funded collaboration led by Jonathan Chen at Stanford. (1/6)

Defunding scientists for the nationality of who they co-author with or who they train. One of the most radical attack on freedom of speech in US history. A far right nationalist destruction of US science. Such a shameful time to be an American that this racist stupidity has become mainstream.

Hi, I'm setting up a peer support platform for ECRs in ecology & evolution in China, aiming to address a huge problem --- academic burnout driven by hyper-competition and a system that often prioritizes elite background/title over actual research. #ECR #AcademicSupport #科研互助 #ecology #evolution

Service of Remembrance in Liverpool this morning.

Apart from the AI junk part… the notion that one should not offer a potential mechanistic explanation for an observation, without first spending years & (unavailable) $$ trying to test possibilities before sharing the observation with others (who may be better equipped to investigate the mechanism)…

Belgian AI scientists are advocating *against* the use of AI in academia. “If independent thinking is no longer encouraged at university, where would it?” apache.be/2025/10/24/b...

Our pipeline for years has used PoreChop for adapter clipping because dorado doesn’t remove all barcodes. Mainly troubling if the Dorado demultiplexing/trimming leads to an appreciable % of reads demtiplexed into the wrong sample before PoreChop, but doesn’t look like that happens at a high rate.

Celebrating the first wet-lab experiment in my group. Successfully carried out by Sophie, my first MRes student and research assistant in Liverpool @liverpooluni.bsky.social, and me. Thanks to colleagues in the APT group of ISMIB @livuni-ismib.bsky.social for sharing their experience. #nanopore

The Art of Data Visualization with ggplot2: A free online book by @nrennie.bsky.social that guides us through the entire process of creating plots, including why certain decisions were made, using real datasets that have been part of #TidyTuesday. Very excited to get stuck into this one. #rstats

Here we go! 📝📝📝 🚽 Scrap the Bathroom Ban🚨🏳️‍⚧️ Our work so far is already working (see here: archive.ph/gaCN4) Now we’re demanding that any new Code must outline how providers can lawfully *include* trans folk in their services. ✍️ Write to your MP with our easy tool: actionnetwork.org/letters/scra...

Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols. Thread 1/n

Excited to share our latest preprint on agtools, an open-source Python framework for analysing and manipulating assembly graphs. (1/n) www.biorxiv.org/content/10.1... #Bioinformatics #genomics #assembly #assemblygraphs #software

For anyone who has used pling for comparing plasmids using rearrangement distances ("how many structural events apart are these plasmids"), here's how to tweak parameters, and integrate it with typing info, and the host phylogeny www.biorxiv.org/content/10.1... github.com/iqbal-lab-or...

I am so glad to see our paper on two nationwide healthcare-associated outbreaks of Burkholderia cepacia complex linked to product contamination in the UK and Ireland, 2010–2023, is finally published. The UKHSA team has exhibited great resilience in the delivery of this work. doi.org/10.1017/ice....

Delighted to share our recent publication on group B Streptococcus: Evidence of a novel sublineage of Streptococcus agalactiae in elephants from zoo populations in Germany. It is a great pleasure to contribute to this collaboration. doi.org/10.1099/mgen...

Plasmids can be lost from a bacterial community even under positive environmental selection: doi.org/10.1101/2025...

My latest blog posts: The abilities and character traits required to do well in a PhD program. blog.genesmindsmachines.com/p/phd-level-...

Along with this: it's tempting to collect technical skills like pokemon, and there certainly is focus on work with breadth that rewards this. But don't forget about the value of depth. Hard to do good science without deep understanding of what you're doing. That only comes from years of immersion.

🧵 So you want to be a computational biologist? 1/ It’s not about pushing buttons. It’s late nights, failed scripts, breakthroughs, and detective work with data. Let’s dive.

Sefton Park, #Liverpool

Fun fact: In reference 28 here, I used the word strain to mean something similar to the lineage level because a reviewer refused to let me use the word lineage. There is still a lot of confusion in this space, and I strongly recommend defining whatever terminology you use.

New paper out! 🔈🔈📣📣 Plasmids promote antimicrobial resistance through Insertion Sequence-mediated gene inactivation. Combining experimental and computational approaches, we unveil how two of the most prevalent bacterial MGE accelerate the evolution of AMR. 🧵👇🏻 www.biorxiv.org/content/10.1...

The iconic Victoria Gallery & Museum at the University of Liverpool, 8 August 2025

Jesus, I thought we were past this. The only measure of success we have in academia is authorship. I don’t assess tenure, but in my view authorship should be given to anyone who made the study possible. Every paper is a huge collaboration. Authorship costs you nothing, so best to acknowledge it.

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...

Prof Lord Ara Darzi, writing in @observeruk.bsky.social, warns that axing the Fleming Fund, Britain’s landmark antimicrobial resistance initiative ( #AMR ), would be a deadly retreat. With 5 million annual global deaths, the stakes couldn’t be higher. observer.co.uk/news/nationa...

A simple rule for better public speaking: If you’re using slides that contain text, you must read it out, word-for-word. clauswilke.substack.com/p/read-out-a...