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Loukas Theodosiou

@bioinformatician.bsky.social
446 followers 122 following 65 posts

Senior scientist. Previously postdoc at the @RaineyLab in @MPI_EvolBio. Data Science, Bioinformatics, Machine Learning, R, Rcpp, Python

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Reposted by Loukas Theodosiou
Ming Tommy Tang @tommytang.bsky.social · 10/09/2026
Mechanisms underlying disease-causing variants in promoters and enhancers www.nature.com/articles/s4...
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Loukas Theodosiou @bioinformatician.bsky.social · 19/07/2026
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...
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Reposted by Loukas Theodosiou
Aye @chazzersmurf.bsky.social · 03/07/2026
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.
Book: John Le Carré, Tinker tailor soldier spy.
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Reposted by Loukas Theodosiou
Michael Sieber @michaelsieber.bsky.social · 01/07/2026
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!
mpg.de
Group Leader in Theoretical Biology (m/f/d)
Experience in Theoretical Biology, Applied Mathematics, Theoretical Physics
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Reposted by Loukas Theodosiou
C. Brandon Ogbunu @cbo.bsky.social · 26/06/2026
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...
academic.oup.com
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
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Reposted by Loukas Theodosiou
Paul Rainey @paulbrainey.bsky.social · 26/06/2026
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/...
enviromicro-journals.onlinelibrary.wiley.com
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 ...
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Reposted by Loukas Theodosiou
KWS Group @kwsgroup.bsky.social · 25/06/2026
🌾 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...
frontiersin.org
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...
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Reposted by Loukas Theodosiou
James McInerney @jomcinerney.bsky.social · 25/06/2026
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...
open.substack.com
Drift and Luck
In 1968, a Japanese geneticist named Motoo Kimura published a paper that changed how every evolutionary biologist thought about evolution.
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Reposted by Loukas Theodosiou
Alex Selby-Boothroyd @alexselbyb.bsky.social · 25/06/2026
Striking charts in this week's Briefing on AI models' values www.economist.com/briefing/202...
Scatter chart showing worldviews of AI models compared with the World Values SurveyScatter chart showing replies to political questions and press freedom scoresChart showing AI models' responses to various statementsScatter chart showing views of AI models compared with American voters in 2020
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Reposted by Loukas Theodosiou
Paul Rainey @paulbrainey.bsky.social · 25/06/2026
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...
forschung-und-lehre.de
"Wettbewerb lässt sich in andere Bahnen lenken"
Warum wird Forschungsqualität zunehmend an Publikationszahlen gemessen? Ein Gespräch mit Paul Rainey über die Belohnung des Quantifizierbaren.
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Loukas Theodosiou @bioinformatician.bsky.social · 24/06/2026
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...
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Physalia-courses@ONLINE @physaliacourses.bsky.social · 22/06/2026
#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
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Isabella Velásquez @ivelasq3.bsky.social · 17/06/2026
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
meetup.com
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
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Reposted by Loukas Theodosiou
KWS Group @kwsgroup.bsky.social · 18/06/2026
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
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Reposted by Loukas Theodosiou
Stephen Turner @stephenturner.us · 18/06/2026
10 tips for getting better R code from your AI coding agent www.infoworld.com/article/4184... #Rstats
infoworld.com
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.
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Reposted by Loukas Theodosiou
Paul Rainey @paulbrainey.bsky.social · 18/06/2026
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...
academicrenewal.substack.com
Building a journal accreditation system
How journals could be assessed without favouring size, wealth or brand
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Reposted by Loukas Theodosiou
Stephen Turner @stephenturner.us · 18/06/2026
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...
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Reposted by Loukas Theodosiou
Ming Tommy Tang @tommytang.bsky.social · 18/06/2026
Multi-omic characterization of nasopharyngeal carcinoma delineates the subtype-specific landscape of response to induction chemotherapy www.nature.com/articles/s4...
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Reposted by Loukas Theodosiou
Alex Selby-Boothroyd @alexselbyb.bsky.social · 17/06/2026
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...
umap.openstreetmap.fr
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 ...
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Reposted by Loukas Theodosiou
Julia Silge @juliasilge.com · 16/06/2026
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...
opensource.posit.co
A brief and biased history of Posit data science agents
What we learned from Positron Assistant and Databot
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Loukas Theodosiou @bioinformatician.bsky.social · 15/06/2026
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
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Reposted by Loukas Theodosiou
Physalia-courses@ONLINE @physaliacourses.bsky.social · 15/06/2026
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...
physalia-courses.org
Genomic Data Visualisation with Python
22-24 June 2026
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Reposted by Loukas Theodosiou
KWS Group @kwsgroup.bsky.social · 08/06/2026
🌾 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?...
youtu.be
Breed with speed – KWS relies on innovative methods such as double-haploid production
YouTube video by KWS Group
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Loukas Theodosiou @bioinformatician.bsky.social · 07/06/2026
Dear network ⚽ 𝗧𝗵𝗶𝘀 𝗶𝘀 𝗺𝘆 𝗽𝗿𝗲𝗱𝗶𝗰𝘁𝗼𝗿 𝗳𝗼𝗿 𝘁𝗵𝗲 𝗙𝗜𝗙𝗔 𝗪𝗼𝗿𝗹𝗱 𝗖𝘂𝗽 𝟮𝟬𝟮𝟲, 𝗯𝘂𝗶𝗹𝘁 𝘄𝗶𝘁𝗵 𝘁𝗵𝗲 𝗵𝗲𝗹𝗽 𝗼𝗳 𝗖𝗹𝗮𝘂𝗱𝗲. loukesio.github.io/WorldCup_2026/ I decided to go with a Monte Carlo simulation: instead of predicting a single outcome. #FIFA #ML #AI #WorldCup #dataviz
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Paul Rainey @paulbrainey.bsky.social · 02/06/2026
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...
doi.org
Autogenic transitions in individuality
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Reposted by Loukas Theodosiou
Physalia-courses@ONLINE @physaliacourses.bsky.social · 01/06/2026
🧠✨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
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Reposted by Loukas Theodosiou
Richard Lenski @relenski.bsky.social · 11/05/2026
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.
worldscientific.com
A Primer for Experimental Evolution
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Paul Rainey @paulbrainey.bsky.social · 01/06/2026
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/...
science.org
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.
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Jeroen Meijer @jeroenmeijer.bsky.social · 01/06/2026
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
science.org
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.
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Stephen Turner @stephenturner.us · 01/06/2026
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...
doi.org
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
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Reposted by Loukas Theodosiou
Tan G. @tangandhara.bsky.social · 28/05/2026
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
open.substack.com
What happens when a chart goes viral?
Also: FIFA’s exorbitant World Cup tickets could backfire
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Nature Astronomy @natastron.nature.com · 16/03/2026
Samples returned from the asteroid Ryugu contain all five canonical nucleobases (A, G, C, T, U). Their presence in Ryugu and Bennu supports the hypothesis that carbonaceous asteroids contributed to the prebiotic chemical inventory of early Earth. dlvr.it/TRWtVp ☄️
dlvr.it
A complete set of canonical nucleobases in the carbonaceous asteroid (162173) Ryugu - Nature Astronomy
Samples returned from the asteroid Ryugu contain all five canonical nucleobases (A, G, C, T and U). Their presence in Ryugu and Bennu supports the hypothesis that carbonaceous asteroids contributed to the prebiotic chemical inventory of early Earth.
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Reposted by Loukas Theodosiou
Ming Tommy Tang @tommytang.bsky.social · 13/03/2026
How to Design Antibodies A step-by-step guide to making de novo binders. www.asimov.press/p/antibody-...
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Sergey Kryazhimskiy @skryazhi.bsky.social · 12/03/2026
Nice to see this published at @PLoS Comp Bio. Big improvements after peer review and important input from @gsherloc.bsky.social! Hopefully, this tool will be helpful for those interested in using barcodes for detecting new beneficial mutations. journals.plos.org/ploscompbiol...
journals.plos.org
Putting BASIL in a BLT: A Bayesian filtering method for estimating the fitness effects of nascent adaptive mutations
Author summary Beneficial mutations are rare but they are the ultimate drivers of evolution by natural selection. Evolutionary biologists seek to understand how many beneficial mutations an organism h...
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Loukas Theodosiou @bioinformatician.bsky.social · 12/03/2026
#ggtree has a relatively steep learning curve. But after looking at a few Python alternatives eg., toytree, ETE, Bio.Phylo it's hard to match its layout versatility. 21 tree variants with just a few lines of code. #rstats #phylogenetics #bioinformatics
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Loukas Theodosiou @bioinformatician.bsky.social · 12/03/2026
Definitely not the biggest problem in the world right now, but constantly installing new versions of RStudio, R and R packages is getting old fast. 😤 #RStats #DataScience
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Ming Tommy Tang @tommytang.bsky.social · 09/03/2026
I hope you've found this post helpful. Follow me for more. Subscribe to my FREE newsletter chatomics to learn bioinformatics divingintogeneticsandgenomics.ck.page/profile
divingintogeneticsandgenomics.ck.page
Chatomics! — The Bioinformatics Newsletter
Why Subscribe?✅ Curated by Tommy Tang, a Director of Bioinformatics with 100K+ followers across LinkedIn, X, and YouTube✅ No fluff—just deep insights and working code examples✅ Trusted by grad students, postdocs, and biotech professionals✅ 100% free
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Carl Zimmer @carlzimmer.com · 27/02/2026
Study finds ChatGPT Health did not recommend a hospital visit when medically necessary in more than half of cases. www.theguardian.com/technology/2...
theguardian.com
‘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
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Physalia-courses@ONLINE @physaliacourses.bsky.social · 06/02/2026
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...
physalia-courses.org
Genomic Data Visualisation with Python
15-17 June 2026
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Ming Tommy Tang @tommytang.bsky.social · 07/01/2026
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.
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Ming Tommy Tang @tommytang.bsky.social · 02/01/2026
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!
github.com
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.
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Ming Tommy Tang @tommytang.bsky.social · 23/01/2026
TSniffer: unbiased de novo identification of RNA editing sites and quantification of editing activity in RNA-seq data link.springer.com/article/10....
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Felix Pretis @felixpretis.bsky.social · 22/01/2026
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...
cell.com
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.
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Stephen Turner @stephenturner.us · 21/01/2026
Nature Genetics: Engineering AI co-scientists for statistical genetics applications www.nature.com/articles/s41... 🧬💻🧪 read free: rdcu.be/eZ2wR
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Richard Lenski @relenski.bsky.social · 19/12/2025
"The changing roles of Escherichia coli" -- a short essay by yours truly. rdcu.be/eVtXT
rdcu.be
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.
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Alex Crits-Christoph @acritschristoph.bsky.social · 24/12/2025
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)
Figure 2. Himar1 transposon variant screen on a cohort of 92 bacterial species.
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Loukas Theodosiou @bioinformatician.bsky.social · 24/12/2025
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.
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Physalia-courses@ONLINE @physaliacourses.bsky.social · 17/12/2025
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!
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Nextflow @nextflow.io · 27/11/2025
💻 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
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EvolDir @evoldir.bsky.social · 28/10/2025
Join our online course "Genomic Data Visualisation with R" on Dec 15-17. Learn to create impactful visuals for genomics. More info and registration: www.physalia-courses.org/courses-wo… #course
physalia-courses.org
Genomic Data Visualisation with R
15-17 Dember 2025
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