Reposted by Loukas TheodosiouMing Tommy Tang @tommytang.bsky.social · 10/09/2026Mechanisms underlying disease-causing variants in promoters and enhancers www.nature.com/articles/s4... 042
Loukas Theodosiou @bioinformatician.bsky.social · 19/07/2026If you work with colour in R, take a look: Code: github.com/loukesio/ltc... Here is the explorer: loukesio.github.io/ltc-color-pa...lnkd.inLinkedInThis link will take you to a page that’s not on LinkedIn 042
Loukas Theodosiou @bioinformatician.bsky.social · 19/07/2026I never imagined it would become the foundation for the whole tidygenomics family of packages we've built since the quiet by-product of several years teaching data visualisation in genomics. 110
Loukas Theodosiou @bioinformatician.bsky.social · 19/07/2026The colour-vision-deficiency checks are inspired by pypalette by Joseph Barbier. I first made ltc for a very unglamorous reason: to make my everyday life as a bioinformatician a little easier. 100
Loukas Theodosiou @bioinformatician.bsky.social · 19/07/2026Later we added a three-colour palette from another legend who has selflessly shared so much material, Cara Thompson, and the two books I credit inside the package (A Dictionary Of Color Combinations Vol1 &2). 100
Loukas Theodosiou @bioinformatician.bsky.social · 19/07/2026 I never really posted about it, yet more than 3,500 people have already downloaded it, and hopefully put it to use in their own plots. When we first created our package, it was inspired by the legendary Wes Anderson palettes: github.com/karthik/wesa...lnkd.inLinkedInThis link will take you to a page that’s not on LinkedIn 100
Loukas Theodosiou @bioinformatician.bsky.social · 19/07/2026After 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... 216940
Reposted by Loukas TheodosiouAye @chazzersmurf.bsky.social · 03/07/2026Finished 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. 565842
Reposted by Loukas TheodosiouMichael Sieber @michaelsieber.bsky.social · 01/07/2026Have 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.deGroup Leader in Theoretical Biology (m/f/d)Experience in Theoretical Biology, Applied Mathematics, Theoretical Physics 07383
Reposted by Loukas TheodosiouC. Brandon Ogbunu @cbo.bsky.social · 26/06/20261/3 🚨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.comWhen 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 36328
Reposted by Loukas TheodosiouPaul Rainey @paulbrainey.bsky.social · 26/06/2026I 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.comDiverse Microbial Communities Assemble on Both Recalcitrant and Labile Carbon SourcesTaxonomically 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 ... 0168
Reposted by Loukas TheodosiouKWS 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.orgFrontiers | Prime editing: a new frontier in precision genome engineering for rice improvementRice (Oryza sativa) is a primary cereal crop that provides food for more than half of the global population, however, its production is increasingly threaten... 021
Reposted by Loukas TheodosiouJames McInerney @jomcinerney.bsky.social · 25/06/2026The 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.comDrift and LuckIn 1968, a Japanese geneticist named Motoo Kimura published a paper that changed how every evolutionary biologist thought about evolution. 0227
Reposted by Loukas TheodosiouAlex Selby-Boothroyd @alexselbyb.bsky.social · 25/06/2026Striking charts in this week's Briefing on AI models' values www.economist.com/briefing/202... 1147
Reposted by Loukas TheodosiouPaul Rainey @paulbrainey.bsky.social · 25/06/2026A 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. 053
Loukas Theodosiou @bioinformatician.bsky.social · 24/06/2026Thanks to @physaliacourses.bsky.social l for the opportunity to give the course, and to all the participants. It was a really nice and curious crowd that pushed the course in directions I couldn't have imagined. #dataviz #bioinformatics 111
Loukas Theodosiou @bioinformatician.bsky.social · 24/06/2026There'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... 151
Reposted by Loukas TheodosiouPhysalia-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 021
Loukas Theodosiou @bioinformatician.bsky.social · 22/06/2026Oooo Ritsos is one of a kind! Did not manage to follow Krasznahorkai! I sympathise and feel sorry for what happening in Colombia. Un abrazo 110
Reposted by Loukas TheodosiouIsabella Velásquez @ivelasq3.bsky.social · 17/06/2026If 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! ⚒️ #RStatsmeetup.comWorking Smarter with {dplyr} 1.2.0, Wed, Jun 24, 2026, 6:00 PM | MeetupDiscover 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 12511
Reposted by Loukas TheodosiouKWS Group @kwsgroup.bsky.social · 18/06/2026What 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 052
Reposted by Loukas TheodosiouStephen Turner @stephenturner.us · 18/06/202610 tips for getting better R code from your AI coding agent www.infoworld.com/article/4184... #Rstatsinfoworld.com10 tips for getting better R code from your AI coding agentWith 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. 0122
Reposted by Loukas TheodosiouPaul Rainey @paulbrainey.bsky.social · 18/06/2026Public 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.comBuilding a journal accreditation systemHow journals could be assessed without favouring size, wealth or brand 0116
Reposted by Loukas TheodosiouStephen Turner @stephenturner.us · 18/06/2026LifeSciBench: Evaluating Language Models on Realistic, Expert-Level Tasks in the Life Sciences (PDF): cdn.openai.com/pdf/b4299379... Blog post: openai.com/index/introd... 042
Reposted by Loukas TheodosiouMing Tommy Tang @tommytang.bsky.social · 18/06/2026Multi-omic characterization of nasopharyngeal carcinoma delineates the subtype-specific landscape of response to induction chemotherapy www.nature.com/articles/s4... 021
Reposted by Loukas TheodosiouAlex Selby-Boothroyd @alexselbyb.bsky.social · 17/06/2026This 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.frBirthplaces of every 2026 FIFA World Cup playerFully 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 ... 121
Reposted by Loukas TheodosiouJulia Silge @juliasilge.com · 16/06/2026I 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.coA brief and biased history of Posit data science agentsWhat we learned from Positron Assistant and Databot 14614
Loukas Theodosiou @bioinformatician.bsky.social · 15/06/2026Its going to be fun! Apart from traditional #dataviz we will also learn how to build your own #dataviz agend. Looking forward seeing you there 042
Reposted by Loukas TheodosiouPhysalia-courses@ONLINE @physaliacourses.bsky.social · 15/06/2026Join 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.orgGenomic Data Visualisation with Python22-24 June 2026 011
Reposted by Loukas TheodosiouKWS 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.beBreed with speed – KWS relies on innovative methods such as double-haploid productionYouTube video by KWS Group 073
Loukas Theodosiou @bioinformatician.bsky.social · 08/06/2026𝗕𝗲𝘆𝗼𝗻𝗱 𝘁𝗵𝗲 𝗹𝗼𝘃𝗲 𝗼𝗳 𝘀𝗵𝗮𝗿𝗶𝗻𝗴, 𝘁𝗵𝗲 𝗺𝗮𝗶𝗻 𝗿𝗲𝗮𝘀𝗼𝗻 𝗜'𝗺 𝗽𝗼𝘀𝘁𝗶𝗻𝗴 𝗶𝘀 𝘁𝗼 𝘀𝗲𝗲 𝗼𝘁𝗵𝗲𝗿 𝗽𝗲𝗼𝗽𝗹𝗲'𝘀 𝗽𝗿𝗲𝗱𝗶𝗰𝘁𝗼𝗿𝘀 𝗮𝗻𝗱 𝘁𝗵𝗲 𝗮𝗽𝗽𝗿𝗼𝗮𝗰𝗵𝗲𝘀 𝘁𝗵𝗲𝘆 𝘂𝘀𝗲𝗱. 𝗜'𝗺 𝗲𝘀𝗽𝗲𝗰𝗶𝗮𝗹𝗹𝘆 𝗶𝗻𝘁𝗲𝗿𝗲𝘀𝘁𝗲𝗱 𝗶𝗻 𝗠𝗟 𝗮𝗻𝗱 𝗔𝗜 𝗺𝗲𝘁𝗵𝗼𝗱𝘀, 𝗶𝘁'𝘀 𝗰𝗼𝗺𝗽𝗹𝗲𝘅 𝗱𝗮𝘁𝗮 𝘄𝗶𝘁𝗵 𝗮 𝗹𝗼𝘁 𝗼𝗳 𝗵𝗶𝘀𝘁𝗼𝗿𝘆, 𝗮𝗻𝗱 𝗮 𝗴𝗿𝗲𝗮𝘁 𝗼𝗽𝗽𝗼𝗿𝘁𝘂𝗻𝗶𝘁𝘆 𝘁𝗼 𝗹𝗲𝗮𝗿𝗻. github.com/loukesio/Wor...github.comGitHub - loukesio/WorldCup_2026Contribute to loukesio/WorldCup_2026 development by creating an account on GitHub. 010
Loukas Theodosiou @bioinformatician.bsky.social · 07/06/2026I simulate the entire tournament, all 104 matches, thousands of times. Counting how often each team lifts the trophy across all those runs gives its win probability. 🐙 There's also a fun tab where the winner is "predicted" purely from the first letter of each country's name (meaningless) 100
Loukas Theodosiou @bioinformatician.bsky.social · 07/06/2026Dear 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 130
Reposted by Loukas TheodosiouPaul Rainey @paulbrainey.bsky.social · 02/06/2026ETIs 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 033
Reposted by Loukas TheodosiouPhysalia-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 022
Reposted by Loukas TheodosiouRichard Lenski @relenski.bsky.social · 11/05/2026New 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.comA Primer for Experimental Evolution 511348
Reposted by Loukas TheodosiouPaul Rainey @paulbrainey.bsky.social · 01/06/2026Pleased 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.orgEco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communitiesA single bacteriophage can dominate microbial communities yet only evolves when migration changes its ecological context. 0137
Reposted by Loukas TheodosiouJeroen Meijer @jeroenmeijer.bsky.social · 01/06/2026Thrilled 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.socialscience.orgEco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communitiesA single bacteriophage can dominate microbial communities yet only evolves when migration changes its ecological context. 24419
Reposted by Loukas TheodosiouStephen Turner @stephenturner.us · 01/06/2026Anthropic 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.orgFree Claude Courses from Anthropic17 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 0155
Reposted by Loukas TheodosiouTan G. @tangandhara.bsky.social · 28/05/2026I 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 #datavizopen.substack.comWhat happens when a chart goes viral?Also: FIFA’s exorbitant World Cup tickets could backfire 0196
Reposted by Loukas TheodosiouNature Astronomy @natastron.nature.com · 16/03/2026Samples 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.itA complete set of canonical nucleobases in the carbonaceous asteroid (162173) Ryugu - Nature AstronomySamples 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. 214977
Loukas Theodosiou @bioinformatician.bsky.social · 15/03/2026Here is a short example of how to create a phylogenetic tree like the one on the left. I use data and silhouettes provided by the ggtree package — more is coming in the next days! #ggtree #rstats #phylogenetics #dataviz #bioinformatics #ggplot2 #PhyloPic code: gist.github.com/loukesio/dd3... 050
Loukas Theodosiou @bioinformatician.bsky.social · 15/03/2026thats a very interesting phylogenetic tree that reflect the avian evolution. I know its a big jump, but can we build something like this with #ggtree ? www.nature.com/articles/s41... 171
Loukas Theodosiou @bioinformatician.bsky.social · 15/03/2026Styling ggtree branches is easy; change color, linewidth, and linetype directly inside the ggtree() call. Works the same across rectangular, circular, and slanted layouts. Colors from the alger palette (ltc package). #ggtree #rstats #phylogenetics #dataviz 110
Loukas Theodosiou @bioinformatician.bsky.social · 15/03/2026thank you Trevor 😀! More stuff related to #ggtree are coming 010
Loukas Theodosiou @bioinformatician.bsky.social · 15/03/2026The cool things about ggtree don't stop here. You can use geom_text() or geom_label() to display node and tip labels simultaneously, or geom_tiplab() to show only tip labels. You can even have nodes and tips looking differently #ggtree #rstats #phylogenetics #dataviz #bioinformatics #ggplot2 173
Reposted by Loukas TheodosiouMing Tommy Tang @tommytang.bsky.social · 13/03/2026How to Design Antibodies A step-by-step guide to making de novo binders. www.asimov.press/p/antibody-... 041