Loukas Theodosiou
@bioinformatician.bsky.social
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 Theodosiou
Join our online course "Genomic Data Visualisation with R" on Dec 15-17. Learn to create impactful visuals for genomics. More info and registration: https://www.physalia-courses.org/courses-workshops/genomic-data-viz/ #course
Genomic Data Visualisation with R
15-17 Dember 2025
www.physalia-courses.org
October 28, 2025 at 6:04 PM
Join our online course "Genomic Data Visualisation with R" on Dec 15-17. Learn to create impactful visuals for genomics. More info and registration: https://www.physalia-courses.org/courses-workshops/genomic-data-viz/ #course
Reposted by Loukas Theodosiou
Human-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
October 6, 2025 at 3:13 PM
Human-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
Reposted by Loukas Theodosiou
Labour finding a monkey's paw in early 2020: "We may be 20 points behind now but we'll halve it in five years..."
October 3, 2025 at 8:38 PM
Labour 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 Theodosiou
A 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...
www.biorxiv.org/content/10.1...
Diverse microbial communities assemble on both recalcitrant and labile carbon sources
Microbial community assembly is shaped by the nature of available resources, with labile carbon sources such as glucose often expected to support low diversity due to rapid growth and competitive excl...
www.biorxiv.org
August 11, 2025 at 2:59 PM
A 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...
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...
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...
Genomic Data Visualisation with R
10-12 November 2025
www.physalia-courses.org
August 7, 2025 at 3:31 AM
🎨 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...
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/
Instead of drilling manually through cached HTML, one can use intuitively named functions that just do it ✨
🔗 feddelegrand7.github.io/ralger/
July 12, 2025 at 7:37 PM
{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/
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
- 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
June 23, 2025 at 3:20 PM
📢 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
- 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. 💡
June 19, 2025 at 6:57 PM
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. 💡
Reposted by Loukas Theodosiou
Here 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...
![An example solution to the [Taxi Trips] exercise.](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:z22hox63epnsh4x474uqqkqj/bafkreigpfdnxva6mp32oim6nm6tuj6jwlewjlr367xgvz45suluzc3fn7a@jpeg)
May 20, 2025 at 2:37 AM
Here 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?
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?
May 18, 2025 at 1:52 PM
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?
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
A quick one looking at the relationship between depth and duration magnitude.
#Rstats #dataviz #ggplot2
May 18, 2025 at 10:02 AM
#TidyTuesday week 19: Seismic Events at Mount Vesuvius 🌋
A quick one looking at the relationship between depth and duration magnitude.
#Rstats #dataviz #ggplot2
A quick one looking at the relationship between depth and duration magnitude.
#Rstats #dataviz #ggplot2
Reposted by Loukas Theodosiou
Do you like potatoes? Don't miss our most recent work on tetraploid potato genome!
@nature.com
#potato #genomics #history #evolution
@nature.com
#potato #genomics #history #evolution
April 20, 2025 at 10:51 AM
Do you like potatoes? Don't miss our most recent work on tetraploid potato genome!
@nature.com
#potato #genomics #history #evolution
@nature.com
#potato #genomics #history #evolution
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
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
April 11, 2025 at 11:06 PM
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
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
Reposted by Loukas Theodosiou
ggpal2 dependencies have been updated to use "chores" (fka "pals")! 🗄️🧹📈
March 21, 2025 at 1:12 AM
ggpal2 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.”
Covid Vaccines Have Paved the Way for Cancer Vaccines
The mRNA technology behind coronavirus vaccines is now being used to create bespoke vaccines for cancer patients.
www.wired.com
March 15, 2025 at 7:15 PM
“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
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
March 11, 2025 at 8:26 AM
🚨 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
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 Theodosiou
The 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.
R Shiny & Interactive Visual Dashboards: An Intro with Adam D. Rennhoff
YouTube video by Code Horizons
youtu.be
March 5, 2025 at 3:04 PM
The 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.
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.
Enabling evolvability to evolve
A multilevel population architecture enables bacteria to evolve increased adaptability
www.science.org
March 4, 2025 at 6:15 PM
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.
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...
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...
February 20, 2025 at 7:40 PM
🚀 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...
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 Theodosiou
Quantitative 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...
www.cell.com/cell-systems...
Should biology put complexity first?
The dictum “Everything should be made as simple as possible, but no simpler” poses
a problem for biology. How simply can it be told without doing damage to its complex
nature? The answer might be foun...
www.cell.com
February 22, 2025 at 12:38 PM
Quantitative 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...
www.cell.com/cell-systems...
Reposted by Loukas Theodosiou
My 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.
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.
December 12, 2024 at 2:03 AM
My 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.
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.