Yu Wan 万宇

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)…

Congratulations to you, Ed! Wonderful news.

Belgian AI scientists resist the use of AI in academia Several AI scientists have published an open letter calling for a ban on AI use by students.

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...

You made history in the lab, haha.😆

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.

Photo in my lab

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 The TidyTuesday Cookbook

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

Scrap the Bathroom Ban 🚨This is urgent🚨 Bridget Phillipson, the Minister for Women and Equalities, has a decision to make. The EHRC, a regulator mired in controversy over anti-trans views, has sent a new draft Code of Prac...

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...

Same illusion when people believe economic deflation makes life easier by reducing prices.

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

lol, Alice, this is incredible!

agtools: a software framework to manipulate assembly graphs Assembly graphs are a fundamental data structure used by genome and metagenome assemblers to represent sequences and their overlap information, facilitating the assembler to construct longer genomic f...

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

Clustering of plasmid genomes for genomic epidemiology by using rearrangement distances, with pling Integration of plasmids into genomic epidemiology is challenging, because there are no clearly defined evolving-units (equivalent to species), and because plasmids appear to evolve as much by structur...

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....

Evidence of a novel sublineage of Streptococcus agalactiae in elephants from zoo populations in Germany Streptococcus agalactiae research primarily centres on investigating human and bovine infections, although this pathogen also can be carried and cause infections in a wider range of animal species. Mo...

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...

Species interactions determine plasmid persistence in a 3-member bacterial community Microbial communities are shaped by complex forces, including interspecies interactions and the effects of mobile genetic elements such as plasmids. How these forces interact to affect community respo...

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

PhD-level abilities and character traits It's not all about intelligence

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.

Main walkway

Grassland

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.

Plasmids promote antimicrobial resistance through Insertion Sequence-mediated gene inactivation Antimicrobial Resistance (AMR) is a major threat to public health. Plasmids are mobile genetic elements that can rapidly spread across bacterial populations, promoting the dissemination of AMR genes i...

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...

University of Liverpool

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...

‘Bacteria knows no borders. The UK and Fleming Fund must ... The planned dismantling of the world’s largest fund to fight antimicrobial resistance could contribute to millions of deaths worldwide

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...

Read out all of the text on your slides I have a simple rule for better public speaking: If you’re using slides that contain text, you must read it out, word-for-word.

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...