Loukas Theodosiou

‘Unbelievably dangerous’: experts sound alarm after ChatGPT Health fails to recognise medical emergencies Study finds ChatGPT Health did not recommend a hospital visit when medically necessary in more than half of cases

Study finds ChatGPT Health did not recommend a hospital visit when medically necessary in more than half of cases. www.theguardian.com/technology/2...

Genomic Data Visualisation with Python 15-17 June 2026

Want to master genomics data visualization with Python?

Join our online course with @bioinformatician.bsky.social (15–17 June ) and learn to create publication-quality plots—from volcano and Manhattan plots to phylogenetic trees—using top Python libraries.
www.physalia-courses.org/courses-work...

5/ How standard tools behave depends on depth.
DESeq2, edgeR, limma-voom with size-factor or TMM normalization handle moderate depth differences fine. But artifacts explode when depth is very low or tightly confounded with condition.

GitHub - crazyhottommy/ROSE2: ROSE: RANK ORDERING OF SUPER-ENHANCERS ROSE: RANK ORDERING OF SUPER-ENHANCERS. Contribute to crazyhottommy/ROSE2 development by creating an account on GitHub.

1. phantompeakqualtools still works github.com/kundajelab/...

2. I optimized ROSE for super-enhancer identification. now it finishes within 10mins! It was 12 hours! github.com/crazyhottom... now install via pip!

TSniffer: unbiased de novo identification of RNA editing sites and quantification of editing activity in RNA-seq data link.springer.com/article/10....

Flexible use of a multi-purpose tool by a cow Osuna-Mascaró and Auersperg report flexible, multipurpose tool use in a cow, expanding the known range of mammalian tool users and underscoring overlooked cognitive capacities in livestock.

Austria's newly famous tool-using cow - maybe it should have been a co-author? "Flexible use of a multi-purpose tool by a cow" - www.cell.com/current-biol...

Nature Genetics: Engineering AI co-scientists for statistical genetics applications www.nature.com/articles/s41... 🧬💻🧪 read free: rdcu.be/eZ2wR

The changing roles of Escherichia coli Nature Microbiology - Richard Lenski traces the legacy of Escherichia coli and how science is evolving to use this model organism in new ways.

"The changing roles of Escherichia coli" -- a short essay by yours truly.

rdcu.be/eVtXT

All you want for christmas is.... transposon mutagenesis!

Our new work at @cultivarium.bsky.social screening lots of transposon vectors in lots of bacteria, from @charliegilbert.bsky.social and team.

Transposon and promoter modular parts available on Addgene (pooled library will be there soon too)

A special shout-out to the amazing people who have shaped my approach to slide design and teaching, particularly Cédric Scherer, whose work continues to inspire how I think about making complex concepts accessible and visually engaging.

🔄 Stay tuned, we're constantly updating the materials and preparing for new adventures in genomics data visualization. 𝗠𝗼𝗿𝗲 𝗶𝗱𝗲𝗮𝘀, 𝗰𝗼𝘂𝗿𝘀𝗲𝘀, 𝗰𝘂𝘀𝘁𝗼𝗺 𝗽𝗮𝗰𝗸𝗮𝗴𝗲𝘀, 𝗮𝗻𝗱 𝗮 𝗯𝗼𝗼𝗸 𝗼𝗻 𝗴𝗲𝗻𝗼𝗺𝗶𝗰𝘀 𝗱𝗮𝘁𝗮 𝘃𝗶𝘀𝘂𝗮𝗹𝗶𝘇𝗮𝘁𝗶𝗼𝗻 𝗮𝗿𝗲 𝗰𝗼𝗺𝗶𝗻𝗴.

𝗢𝘂𝗿 𝗔𝗻𝗻𝘂𝗮𝗹 𝗚𝗲𝗻𝗼𝗺𝗶𝗰𝘀 𝗩𝗶𝘀𝘂𝗮𝗹𝗶𝘇𝗮𝘁𝗶𝗼𝗻 𝗖𝗼𝘂𝗿𝘀𝗲 𝘄𝗶𝘁𝗵 Physalia courses 𝗵𝗮𝘀 𝘄𝗿𝗮𝗽𝗽𝗲𝗱 𝘂𝗽! All course materials are available: 👉 lnkd.in/gTnfFewM You'll find all the code, slides, and resources I used to prepare the course from basic ggplot2 concepts to advanced genomic visualizations using R.

Our final course of the year is a wrap! 🎉

Huge thanks to @bioinformatician.bsky.social and to all the participants who joined us this week to level up their #Genomics #DataViz skills.

We can’t wait to see your beautiful figures making their way into papers, posters, and presentations!

💻 Discover all the latest features of Nextflow on Dec 11, , including the new Plugin Registry, workflow inputs & outputs, and static types.

Plus, don't miss the opportunity to ask the creator of Nextflow (@paoloditommaso.bsky.social) anything! 🌟

🌟 Register now: hubs.la/Q03W12B90

Genomic Data Visualisation with R 15-17 Dember 2025

Join our online course "Genomic Data Visualisation with R" on Dec 15-17. Learn to create impactful visuals for genomics. More info and registration: https://www.physalia-courses.org/courses-workshops/genomic-data-viz/ #course

Human-mediated land-use and climate change occur simultaneously, but how do they interact to shape adaptive dynamics? Super excited to share the first paper from the Kreiner lab, led by postdoc extraordinaire @rpineau.bsky.social

Gavras at this best!

Britain, voting intention, %

Labour finding a monkey's paw in early 2020: "We may be 20 points behind now but we'll halve it in five years..."

Diverse microbial communities assemble on both recalcitrant and labile carbon sources Microbial community assembly is shaped by the nature of available resources, with labile carbon sources such as glucose often expected to support low diversity due to rapid growth and competitive excl...

A new preprint! Data from a huge experiment by @prczhaoyansong.bsky.social show that similar microbial communities diverge depending on whether the carbon source is glucose or its polymer, cellulose. Diversity is comparable, but biomass, functions and taxonomy differ:
www.biorxiv.org/content/10.1...

Genomic Data Visualisation with R 10-12 November 2025

🎨 Turn your genomic data into stunning visuals – with R!

Join us online for our course:🧬 Genomic Data Visualisation with R

📅 10–12 November | 🕐 1–6 PM (Berlin time)

🧑‍🍳 Instructor: @bioinformatician.bsky.social

www.physalia-courses.org/courses-work...

{ralger} #rstats package looks like an absolute game changer in the task of web scraping for people with very occasional need in this rather nerdy task 🤩
Instead of drilling manually through cached HTML, one can use intuitively named functions that just do it ✨
🔗 feddelegrand7.github.io/ralger/

📢 deeptime 📦 v. 2.2.0 is now on #CRAN:

- geom_text_phylo() for adding labels to radial phylogenies 🏷️
- timescales updated to ICS 2024/12 🗓️
- compatibility with ggplot2 4.0.0 📈

Patch notes 👉 williamgearty.com/deeptime/news/

Docs 👉 williamgearty.com/deeptime/

#rstats #dataviz #geology #deeptime

#R #Rpackage #bioinformatics #ggplot2 #blast #blastar

Feel free to check it out, ⭐ star the repo, and contribute here:

👉 lnkd.in/dXTyDn-m

A paper like this one:
lnkd.in/dV2Ea3ga
...could have been easily done with Blastr within a day

It’s a fun and very user-friendly tool that allows you to:
🔹 Easily download sequences from NCBI
🔹 Align them quickly 🧬
🔹 Seamlessly draw phylogenetic trees 🌳

Some years ago, together with Eva, we developed Blastr (βλαστάρι) 🌱 as a project — but we never got paid for it. So we decided to release it for free. 💡

An example solution to the [Taxi Trips] exercise.

Here is a repository with the exercises I use in my data visualization class. We cover ggplot2/shiny and then consider different types of data (network, text, ...) and models (clustering, ...). I've tried to make the problems somewhat realistic. Feel free to reuse! github.com/krisrs1128/d...

Thank you ☺️

Which Five you have in mind? I know only 3

Hello network #bioinformatics @tommytang.bsky.social
Which are the best tools to take an AlphaFold model and extract:
➢ secondary structure types (helices, sheets)
➢ bond types (e.g. disulfide bonds)
➢ amino acids at critical positions
➢ possible subunits, function & cellular localization?