Loukas Theodosiou
Senior Bioinformatics scientist at @mpipz_cologne. Previously postdoc at the @RaineyLab in @MPI_EvolBio. Data Science, Bioinformatics, Machine Learning, R, Rcpp, Python
- Reposted by Loukas TheodosiouWant 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...
- Reposted by Loukas Theodosiou5/ 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.
- Reposted by Loukas Theodosiou1. 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!
- Reposted by Loukas TheodosiouTSniffer: unbiased de novo identification of RNA editing sites and quantification of editing activity in RNA-seq data link.springer.com/article/10....
- Reposted by Loukas TheodosiouAustria'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...
- Reposted by Loukas TheodosiouNature Genetics: Engineering AI co-scientists for statistical genetics applications www.nature.com/articles/s41... 🧬💻🧪 read free: rdcu.be/eZ2wR
- Reposted by Loukas Theodosiou"The changing roles of Escherichia coli" -- a short essay by yours truly. rdcu.be/eVtXT
- Reposted by Loukas TheodosiouAll 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 scalable transposon mutagenesis system for non-model bacteria biorxiv.org/content/10.64898/20…
- 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.
- 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.
- Reposted by Loukas TheodosiouOur 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!
- Reposted by Loukas Theodosiou💻 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
- Reposted by Loukas TheodosiouJoin our online course "Genomic Data Visualisation with R" on Dec 15-17. Learn to create impactful visuals for genomics. More info and registration: physalia-courses.org/courses-workshops/g… #course
- Reposted by Loukas TheodosiouHuman-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
- The genomic response to drought across spatiotemporal scales in Amaranthus tuberculatus biorxiv.org/content/10.1101/202…
- Reposted by Loukas TheodosiouLabour finding a monkey's paw in early 2020: "We may be 20 points behind now but we'll halve it in five years..."
- Reposted by Loukas TheodosiouA 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...
- Reposted by Loukas Theodosiou🎨 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...
- Reposted by Loukas Theodosiou{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/
- Reposted by Loukas Theodosiou📢 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
- 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. 💡
- 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 🌳
- 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
- Reposted by Loukas TheodosiouHere 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...
- 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?
- Reposted by Loukas Theodosiou#TidyTuesday week 19: Seismic Events at Mount Vesuvius 🌋 A quick one looking at the relationship between depth and duration magnitude. #Rstats #dataviz #ggplot2
- Reposted by Loukas TheodosiouDo you like potatoes? Don't miss our most recent work on tetraploid potato genome! @nature.com #potato #genomics #history #evolution
- 📢 Excited to share our work out now in @nature.com! 📢 We present the phased pan-genome of tetraploid European potato, based on 10 historical cultivars representing 85% of European potato diversity. Learn more below! 🔗 www.nature.com/articles/s41... 1/7
- Reposted by Loukas TheodosiouMatchday 3️⃣2️⃣: #LFC 2️⃣-0️⃣ West Ham United Another step closer to the title 😅 #LIVWHU #rstats #ggplot2
- Reposted by Loukas Theodosiou
[Not loaded yet] - This is my contribution for this week's #TidyTuesday 📊 I used the dataset provided and added the median household income per state — wondering if higher salaries would mean shorter emergency department wait times. Turns out, I was wrong 😅 #ggplot2 #RStats #DataViz #EmergencyCare
- Here's my contribution to this week's hashtag#TidyTuesday. This time I worked with the Pokémon dataset — fitting, since Pokémon has been a big part of both my childhood and adulthood. #R #ggplot2 #TidyTuesday #RStats #DataViz #ggplot2 #Pokemon
- Reposted by Loukas Theodosiouggpal2 dependencies have been updated to use "chores" (fka "pals")! 🗄️🧹📈
- Reposted by Loukas Theodosiou“In the current trials, we do a biopsy of the patient, sequence the tissue, send it to the pharmaceutical company, and they design a personalized vaccine that’s bespoke to that patient’s cancer. That vaccine is not suitable for anyone else. It’s like science fiction.”
- Reposted by Loukas Theodosiou🚨 Evolution Isn’t So Simple! 🚨 New research reveals that population structure can allow disadvantageous mutations to persist—challenging traditional evolutionary theory. 🧬🔬 📖 Read more: www.evolbio.mpg.de/3810220/news... #Evolution #Science #Genetics #Biology #Research
- Reposted by Loukas TheodosiouThe 1st hour of "Interactive Visual Dashboards Using R Shiny" with Adam D. Rennhoff is now on YouTube! Get started with ggplot2 and the #tidyverse, then join us April 30-May 2 to learn how to build and deploy interactive dashboards with #RShiny in #Rstats.
- www.science.org/doi/10.1126/.... The original paper Experimental Evolution of Evolvability by M. Barnett from Paul Rainey’s group, along with Edo Kussell’s story, are both fascinating. A brilliant example of experimental evolution at its finest.
- Reposted by Loukas Theodosiou🚀 New Study: Can evolution have foresight? 🧬🔬 A new study shows natural selection can shape genetic systems for future adaptation—challenging the idea that evolution is blind. Find out more: www.evolbio.mpg.de/3807853/news...
- Reposted by Loukas Theodosiou
- Reposted by Loukas TheodosiouQuantitative genetics is poorly understood by many biologists, and that's surely a failure in how it is taught. But teaching biology as 'fundamentally complex' seems like one of the least promising educational ideas since those 1970s schools that made lessons optional. www.cell.com/cell-systems...
- Reposted by Loukas TheodosiouMy Tidyverse local synteny visualizer is up on GitHub: github.com/cxli233/Tidy... GitHub page contains 2 example datasets, as well as step-by-step instruction & explanations on how it works. Details on required input data are discussed in the GitHub page. Let me know if you run into issues.
- Reposted by Loukas TheodosiouFor the "Working with Colors" 🎨 chapter of my book, I am also talking about good and bad color choices. Likely the most problematic color choice remains data encoded by the rainbow and jet colormaps. Here is a figure I am working on as an illustrative example plus some potential alternatives.
- Reposted by Loukas TheodosiouWhat's the problem? The rainbow and jet colors are problematic as the change in color is not perceptually uniform, leading to distinct 'bands' of certain colors. This causes misleading jumps and emphasizes certain values, most likely without the intention to highlight them.
- Reposted by Loukas TheodosiouYES
- Reposted by Loukas TheodosiouDo you want to learn how to visualise your genomic data with R? Do not look any further! Check out our new course with @bioinformatician.bsky.social in November: physalia-courses.org/courses-work... #Genomics #DataViz #RStats
- Dear friends, 🌋 𝐠𝐠𝐯𝐨𝐥𝐜 I'm excited to share some new features I've added to my 𝐠𝐠𝐯𝐨𝐥𝐜 R package for making volcano plots! 👩🔬 Have a look in here github.com/loukesio/ggv... and feel free to ⭐ the repo!
- ggvolc has: 💠 New function for easily customizing volcano plots to your preferences! You can now easily change colors, axis labels, plot titles, etc. 🔥 💠Ability to accompany your volcano plot with a table listing key genes of interest! I'm working on making these tables look extra polished. 📊
- There's more to come too! I'm continuing to improve the aesthetics of the gene tables and adding handy new functionality. Stay tuned! ⏳ #ggvolc #bioinformatics #RNAseq #Rstats
- 🚦Dear Blooskies, We have an updated version of our ltc package, which contains, among other enhancements, colour palettes based on the life and art of Pablo Picasso! Find it here: github.com/loukesio/ltc... 🎨🖌️
- Reposted by Loukas TheodosiouNew work from my group, led by Michael Miller. In this paper, we assess the effectiveness of cooperation enforcement in Dictyostelium (social amoeba) www.biorxiv.org/content/10.1...
- Reposted by Loukas Theodosiou@mrebolleda.bsky.social and I are very excited to host the US West Hub of the MEEHubs24 conference (meehubs.org) in San Diego Jan 9-11, 2024. We have an outstanding lineup of speakers across all hubs! Registration is open until Sept 29. Please apply! It's free. #evolution #ecology
- Reposted by Loukas TheodosiouPublication alert! 🚨 Our work on identifying mobile elements in evolving compost communities is out in ISME communications! 🦠🧬 Link: rdcu.be/dkAsc Let me briefly summarise the paper in my first Bluesky thread:
- Presenting bioinformatics pipelines visually takes time. I wish there was a flowchart tool to easily generate SVG diagrams! It takes me about an hour to make one manually. If anyone knows of a tool to streamline this, please share! I am sharing one in SVG in case it helps someone to save time!
- Reposted by Loukas TheodosiouDecided to post this here. It seems good that my first post is also the first preprint with an author from my lab! We used previously identified metabolic rules to predict microbial community assembly along a temperature gradient (1/12). www.biorxiv.org/content/10.1...
