After four years, several updates and a handful of CRAN releases, 𝗹𝘁𝗰 𝗰𝗼𝗹𝗼𝗿 𝗽𝗮𝗹𝗲𝘁𝘁𝗲 𝗥-𝗽𝗮𝗰𝗸𝗮𝗴𝗲, reached a version I feel genuinely good about sharing with the community. github.com/loukesio/ltc...
Loukas Theodosiou
@bioinformatician.bsky.social
Senior scientist. Previously postdoc at the @RaineyLab in @MPI_EvolBio. Data Science, Bioinformatics, Machine Learning, R, Rcpp, Python
Finished this last night.Never read any Le Carré before and now I have lots to read. Such a great book. Think in my head I'd lumped him in with the Dick Francis type popular novels of my childhood. Well, I was an idiot.
Have ideas for your own, independent research program in Theoretical Biology? Then come and join us as a Group Leader at the @mpi-evolbio.bsky.social in Plön, Germany!
Group Leader in Theoretical Biology (m/f/d)
Experience in Theoretical Biology, Applied Mathematics, Theoretical Physics
mpg.de
1/3 🚨New Perspective🚨 (@genetics-gsa.bsky.social) "When evolvability meets constraint: reflections on empirical fitness landscapes after Weinreich et al. (2006)" 20 years after a seminal study, I discuss the forces that both constrain evolution + make it possible academic.oup.com/genetics/adv...
When evolvability meets constraint: reflections on empirical fitness landscapes after Weinreich et al. (2006)
Abstract. In 2006, a manuscript appeared with a provocative title: “Darwinian evolution can follow only very few mutational paths to fitter proteins.” Twen
academic.oup.com
I really value: the dynamics of community assembly on 2 contrasting C sources. Daily sampling of communities derived from compost & maintained over 8 wks. No difference in diversity maintained on simple or complex C. AmaZinG. 🙏 all enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...
Diverse Microbial Communities Assemble on Both Recalcitrant and Labile Carbon Sources
Taxonomically and functionally distinct communities assemble on cellulose and its monomer, glucose. Although single carbon sources were provided, high and comparable diversity was maintained in both ...
enviromicro-journals.onlinelibrary.wiley.com
🌾 Rice feeds more than half the world. This review shows how Prime editing can overcome key limits of other #GenomeEditing approaches, with applications such as improved grain quality, stress resilience and disease resistance. www.frontiersin.org/journals/pla...
Frontiers | Prime editing: a new frontier in precision genome engineering for rice improvement
Rice (Oryza sativa) is a primary cereal crop that provides food for more than half of the global population, however, its production is increasingly threaten...
frontiersin.org
The latest in my “what has four billion years of evolution taught us” series. Always free. Always about evolution. Take a look. open.substack.com/pub/profmcin...
Drift and Luck
In 1968, a Japanese geneticist named Motoo Kimura published a paper that changed how every evolutionary biologist thought about evolution.
open.substack.com
A short interview on research assessment and academic reform was published today by Forschung & Lehre. The article is in German, but with an English translation. This forms part of a broader initiative on Academic Renewal that can be found on Substack. www.forschung-und-lehre.de/management/w...
"Wettbewerb lässt sich in andere Bahnen lenken"
Warum wird Forschungsqualität zunehmend an Publikationszahlen gemessen? Ein Gespräch mit Paul Rainey über die Belohnung des Quantifizierbaren.
forschung-und-lehre.de
There's a persistent rumor that Python's genomics plots are ugly. It was a real pleasure working on the practical for our Python genomics visualization course and showing that simply isn't true. Follow the repo and stay tuned as we finalize the agenda 👇 github.com/loukesio/dat...
#Python is also a powerful tool for creating stunning scientific visualizations! 🚀 We are exploring how to analyse genomic data and transform complex results into beautiful, publication-ready figures with @bioinformatician.bsky.social 🧬🐍 www.physalia-courses.org/courses-work... #DataVisualisation
If you're still wondering about the slick new functions in dplyr 1.2.0, join me for a "Working smarter with dplyr 1.2.0" redux with R-Ladies Abuja! 📅 Wednesday, 24 June 2026 🕐️ 6pm WAT 🔗 www.meetup.com/rladies-abuj... See you there! ⚒️ #RStats
Working Smarter with {dplyr} 1.2.0, Wed, Jun 24, 2026, 6:00 PM | Meetup
Discover how the latest features in **{dplyr} 1.2.0** can help you write cleaner, faster, and more maintainable data transformation workflows. This session explores practic
meetup.com
What does the new EU framework on #NGTs mean for us at KWS? ➡️ After yesterday’s approval in the European Parliament, a two-year phase starts to prepare implementation. 🌱 Then: faster development of more resource-efficient, climate-tolerant crop varieties. ow.ly/ipG150Ze5UV
10 tips for getting better R code from your AI coding agent www.infoworld.com/article/4184... #Rstats
10 tips for getting better R code from your AI coding agent
With the proper setup and guidance, you can have Claude Code, Codex, Posit Assistant, and other coding agents writing R code like a pro. Here’s how.
infoworld.com
Public money should not flow automatically to journals that fail to meet acceptable standards of editorial quality, transparency and accountability. In this post I ask what a journal accreditation system might look like & how it could work. academicrenewal.substack.com/p/building-a...
Building a journal accreditation system
How journals could be assessed without favouring size, wealth or brand
academicrenewal.substack.com
LifeSciBench: Evaluating Language Models on Realistic, Expert-Level Tasks in the Life Sciences (PDF): cdn.openai.com/pdf/b4299379... Blog post: openai.com/index/introd...
Multi-omic characterization of nasopharyngeal carcinoma delineates the subtype-specific landscape of response to induction chemotherapy www.nature.com/articles/s4...
This is great (h/t @owenwntr.bsky.social). Incidentally, I wonder if "slop-free" will be the online equivalent of "organic" or "unprocessed food" umap.openstreetmap.fr/en/map/birth...
Birthplaces of every 2026 FIFA World Cup player
Fully handmade, slop-free, every item checked manually. Some players could be tracked down to the city, some to the neighborhood, it's all specified in the description. Messi has the hospital he was ...
umap.openstreetmap.fr
I want to publicly thank @jcheng5.bsky.social for being willing to write this post, laying out how our AI tooling has evolved (including those eyebrow-raising product names)! 😅 opensource.posit.co/blog/2026-06...
A brief and biased history of Posit data science agents
What we learned from Positron Assistant and Databot
opensource.posit.co
Its going to be fun! Apart from traditional #dataviz we will also learn how to build your own #dataviz agend. Looking forward seeing you there
Physalia-courses@ONLINE@physaliacourses.bsky.social · 2mo agoJoin us next week and learn how to turn complex genomic data into clear, publication-ready figures using Python. From exploratory plots to advanced visual analytics with @bioinformatician.bsky.social www.physalia-courses.org/courses-work...
Join us next week and learn how to turn complex genomic data into clear, publication-ready figures using Python. From exploratory plots to advanced visual analytics with @bioinformatician.bsky.social www.physalia-courses.org/courses-work...
Genomic Data Visualisation with Python
22-24 June 2026
physalia-courses.org
🌾 Speed matters in plant breeding! Developing a new variety takes about 10–12 years. To respond faster to disease pressure and the changing climate, one of the tools we use to speed up breeding is double‑haploid production. Watch how it works 👇 youtu.be/goFaLR_GMVg?...
Breed with speed – KWS relies on innovative methods such as double-haploid production
YouTube video by KWS Group
youtu.be
ETIs are usually framed as mergers among already-existing Darwinian entities. I suggest another route: lineages that generate, from within, a component that becomes part of a higher-level individual. Transmissible cancers reveal the boundary. Human–AI systems may test it. doi.org/10.5802/crbi...
Autogenic transitions in individuality
doi.org
🧠✨Course announcement: AI-Assisted Coding for Bioinformatics with Python 📅 1–2 July - Online In this hands-on course, we’ll explore how to integrate AI into Python-based research in a practical and reproducible way. www.physalia-courses.org/courses-work... #Python #AI
New book "A Primer for Experimental Evolution" with coauthors Michael Rose, Margarida Matos, and Joe Graves. www.worldscientific.com/worldscibook... A compact primer for students and colleagues interested in planning and designing experiments to address questions in evolutionary biology.
A Primer for Experimental Evolution
worldscientific.com
Pleased to see this beautiful paper out. Kudos to @jeroenmeijer.bsky.social who took @stevenquistad.bsky.social data and dug deep, revealing a new phage that erupts to astonishing abundance. As theory predicts, the life of SGEs is fuelled by encounters with new hosts www.science.org/doi/10.1126/...
Eco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communities
A single bacteriophage can dominate microbial communities yet only evolves when migration changes its ecological context.
science.org
Thrilled that our paper "Eco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communities" is out! 🎉🦠🧬 www.science.org/doi/10.1126/... w/ @paulbrainey.bsky.social, Petros Skiadas, Paulien Hogeweg, @bedutilh.bsky.social
Eco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communities
A single bacteriophage can dominate microbial communities yet only evolves when migration changes its ecological context.
science.org
Anthropic has a bunch of (free) online courses covering Claude, Claude Code, the API, MCP, agent skills, and subagents, plus AI fluency tracks for educators, students, and nonprofits doi.org/10.59350/wsh...
Free Claude Courses from Anthropic
17 free, self-paced courses from Anthropic covering Claude, Claude Code, the API, MCP, agent skills, and subagents, plus AI fluency tracks for educators, students, and nonprofits
doi.org
I like understanding how ideas for charts come about and it’s interesting to read @owenwntr.bsky.social’s explainer on that local election chart I saw everywhere. #rstats #dataviz
What happens when a chart goes viral?
Also: FIFA’s exorbitant World Cup tickets could backfire
open.substack.com