Lightnews — Scholar-powered news

Yu Wan 万宇 @wanyuac.bsky.social · 11d

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

Reposted by Yu Wan 万宇

Zamin Iqbal @zaminiqbal.bsky.social · 13d

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.
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Yu Wan 万宇 @wanyuac.bsky.social · 18d

lol, Alice, this is incredible!

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Reposted by Yu Wan 万宇

Vijini Mallawaarachchi @vijinim.bsky.social · 21d

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

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...

www.biorxiv.org

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Reposted by Yu Wan 万宇

Zamin Iqbal @zaminiqbal.bsky.social · Sep 7

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...

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...

www.biorxiv.org

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Yu Wan 万宇 @wanyuac.bsky.social · Sep 7

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....

Two concurrent nationwide healthcare-associated outbreaks of Burkholderia cepacia complex linked to product contamination, UK and Ireland, 2010–2023 | Infection Control & Hospital Epidemiology | C...

Two concurrent nationwide healthcare-associated outbreaks of Burkholderia cepacia complex linked to product contamination, UK and Ireland, 2010–2023

doi.org

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Yu Wan 万宇 @wanyuac.bsky.social · Sep 6

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...

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...

doi.org

Reposted by Yu Wan 万宇

Kaitlin Schaal @evokait.bsky.social · Sep 3

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

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...

doi.org

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Reposted by Yu Wan 万宇

Claus Wilke @clauswilke.com · Sep 1

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

PhD-level abilities and character traits

It's not all about intelligence

blog.genesmindsmachines.com

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Reposted by Yu Wan 万宇

Abby Polter @ampolter.bsky.social · Sep 1

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.

Michael Baym @baym.lol · Sep 1

Same with bioinformatics, honestly. Doing a two-month rotation in a lab that uses computation is going to give you a taste, but don't fool yourself into thinking you'll develop meaningful transferrable skill in that time

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Reposted by Yu Wan 万宇

Ming Tommy Tang @tommytang.bsky.social · Aug 30

🧵 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.

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Yu Wan 万宇 @wanyuac.bsky.social · Aug 24

Sefton Park, #Liverpool

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Reposted by Yu Wan 万宇

Tami Lieberman @contaminatedsci.bsky.social · Aug 18

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.

Adrià Auladell @adriaula.bsky.social · Aug 18

I love this diagram

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Reposted by Yu Wan 万宇

Jorge Sastre Domínguez @jorgesastred.bsky.social · Aug 13

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...

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...

www.biorxiv.org

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Yu Wan 万宇 @wanyuac.bsky.social · Aug 8

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

Reposted by Yu Wan 万宇

Steven Robbins @stevenjrobbins.bsky.social · Aug 7

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.

Elinne Becket, PhD @bielleogy.bsky.social · Aug 6

Question for Cell Bio folks: does having a lower number of authors per publication affect your tenure/promotion guidelines at all?

I heard this from a postdoc re: why they weren't added on a paper, and as a genomics person this is an asinine concept.

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Reposted by Yu Wan 万宇

Hugh Cottingham @hughcottingham.bsky.social · Jul 30

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...

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Reposted by Yu Wan 万宇

Imperial Medicine @imperialmed.bsky.social · Jul 22

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...

‘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

observer.co.uk

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Reposted by Yu Wan 万宇

Claus Wilke @clauswilke.com · Jul 20

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...

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.

clauswilke.substack.com

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Yu Wan 万宇 @wanyuac.bsky.social · Jul 20

Health research saves lives, while the wars kill people. One T-90 tank costs about $4.5 million. With the money spent on killing each other, how many research projects we can conduct to save patients? How many future skilled professionals we can support? How much healthcare expense we can avoid?

Antimicrobial resistance #AMR @antimicrobial.bsky.social · Jul 20

UK has shut down the £265 million #FlemingFund, which supported #AMR surveillance in 25 LMICs, due to aid budget cuts tied to increased defense spending. This move will harm global health and damage UK's reputation as a reliable international partner in fighting AMR.

observer.co.uk/news/science...

Budget cuts close UK body tackling antimicrobial resistance

Move to close Fleming Fund also threatens standing as a reliable global partner

observer.co.uk

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Reposted by Yu Wan 万宇

Dr Zoë Ayres @zjayres.bsky.social · Jun 28

Just out: latest blog for Voices of Academia ✍️📖

"I thrive in my job, and I am good at it. However, my fixed-term contract is harming my mental health."

voicesofacademia.com/2025/06/28/h...

Help! Universities won’t commit! Why fixed-term contracts are harmful to mental health by Anonymous

Recent research reveals that around two thirds of University Research Staff in the UK are employed on fixed-term contracts, which are usually less than two years. This practice has no end in sight.…

voicesofacademia.com

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Yu Wan 万宇 @wanyuac.bsky.social · Jun 23

Recommend an insightful paper: "Are reads required? High-precision variant calling from bacterial genome assemblies" by @rrwick.bsky.social et al. doi.org/10.1099/acmi...

Are reads required? High-precision variant calling from bacterial genome assemblies

Accurate nucleotide variant calling is essential in microbial genomics, particularly for outbreak tracking and phylogenetics. This study evaluates variant calls derived from genome assemblies compared...

doi.org

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Reposted by Yu Wan 万宇

Julie Johnston @queermsfrizzle.bsky.social · Jun 19

Protect Trans Scientists.

cowritten with a lot of amazing people (I tagged those I could find but there are so many more incredible folks)
www.science.org/doi/10.1126/...
@thepunkscientist.bsky.social @jlw-ecoevo.bsky.social @bfrancescol.bsky.social @drsueishaq.bsky.social

Protect transgender scientists

Transgender and gender nonconforming (TGnC) people are a primary target of the Trump administration. Multiple executive orders seek to erase TGnC protections; mandate denial of gender identity; and ba...

www.science.org

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Yu Wan 万宇 @wanyuac.bsky.social · Jun 19

Biosciences Building, University of Liverpool

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Reposted by Yu Wan 万宇

Mike Inouye @mikeinouye.bsky.social · Jun 16

Your Brain on ChatGPT: Accumulation of Cognitive Debt when Using an AI Assistant for Essay Writing Task arxiv.org/abs/2506.08872

h\t @gmeric.bsky.social

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