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 · 19/07/2026After 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 · 24/06/2026There'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
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 14714
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 · 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. 215177
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
Reposted by Loukas TheodosiouSergey Kryazhimskiy @skryazhi.bsky.social · 12/03/2026Nice 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.orgPutting BASIL in a BLT: A Bayesian filtering method for estimating the fitness effects of nascent adaptive mutationsAuthor 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... 0229
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 3328
Loukas Theodosiou @bioinformatician.bsky.social · 12/03/2026Definitely 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 150
Reposted by Loukas TheodosiouMing Tommy Tang @tommytang.bsky.social · 09/03/2026I hope you've found this post helpful. Follow me for more. Subscribe to my FREE newsletter chatomics to learn bioinformatics divingintogeneticsandgenomics.ck.page/profiledivingintogeneticsandgenomics.ck.pageChatomics! — The Bioinformatics NewsletterWhy 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 011
Reposted by Loukas TheodosiouCarl Zimmer @carlzimmer.com · 27/02/2026Study 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 emergenciesStudy finds ChatGPT Health did not recommend a hospital visit when medically necessary in more than half of cases 431268716
Reposted by Loukas TheodosiouPhysalia-courses@ONLINE @physaliacourses.bsky.social · 06/02/2026Want 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.orgGenomic Data Visualisation with Python15-17 June 2026 031
Reposted by Loukas TheodosiouMing Tommy Tang @tommytang.bsky.social · 07/01/20265/ 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. 121
Reposted by Loukas TheodosiouMing Tommy Tang @tommytang.bsky.social · 02/01/20261. 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.comGitHub - crazyhottommy/ROSE2: ROSE: RANK ORDERING OF SUPER-ENHANCERSROSE: RANK ORDERING OF SUPER-ENHANCERS. Contribute to crazyhottommy/ROSE2 development by creating an account on GitHub. 111
Reposted by Loukas TheodosiouMing Tommy Tang @tommytang.bsky.social · 23/01/2026TSniffer: unbiased de novo identification of RNA editing sites and quantification of editing activity in RNA-seq data link.springer.com/article/10.... 052
Reposted by Loukas TheodosiouFelix Pretis @felixpretis.bsky.social · 22/01/2026Austria'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.comFlexible use of a multi-purpose tool by a cowOsuna-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. 012
Reposted by Loukas TheodosiouStephen Turner @stephenturner.us · 21/01/2026Nature Genetics: Engineering AI co-scientists for statistical genetics applications www.nature.com/articles/s41... 🧬💻🧪 read free: rdcu.be/eZ2wR 062
Reposted by Loukas TheodosiouRichard Lenski @relenski.bsky.social · 19/12/2025"The changing roles of Escherichia coli" -- a short essay by yours truly. rdcu.be/eVtXTrdcu.beThe changing roles of Escherichia coliNature Microbiology - Richard Lenski traces the legacy of Escherichia coli and how science is evolving to use this model organism in new ways. 116359
Reposted by Loukas TheodosiouAlex Crits-Christoph @acritschristoph.bsky.social · 24/12/2025All 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) 18432
Loukas Theodosiou @bioinformatician.bsky.social · 24/12/2025𝗢𝘂𝗿 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. 250
Reposted by Loukas TheodosiouPhysalia-courses@ONLINE @physaliacourses.bsky.social · 17/12/2025Our 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! 031
Reposted by Loukas TheodosiouNextflow @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 043
Reposted by Loukas TheodosiouEvolDir @evoldir.bsky.social · 28/10/2025Join 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… #coursephysalia-courses.orgGenomic Data Visualisation with R15-17 Dember 2025 023