"The changing roles of Escherichia coli" -- a short essay by yours truly. rdcu.be/eVtXT

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)

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.

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!

💻 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

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

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

Labour finding a monkey's paw in early 2020: "We may be 20 points behind now but we'll halve it in five years..."

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...

🎨 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...

{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/

📢 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. 💡

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?

#TidyTuesday week 19: Seismic Events at Mount Vesuvius 🌋 A quick one looking at the relationship between depth and duration magnitude. #Rstats #dataviz #ggplot2

Do you like potatoes? Don't miss our most recent work on tetraploid potato genome! @nature.com #potato #genomics #history #evolution

Matchday 3️⃣2️⃣: #LFC 2️⃣-0️⃣ West Ham United Another step closer to the title 😅 #LIVWHU #rstats #ggplot2

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

ggpal2 dependencies have been updated to use "chores" (fka "pals")! 🗄️🧹📈

“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.”

🚨 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

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.

🚀 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...

Animated Maps in R youtu.be/ra3BrCW5o54?... #rstats #ggplot2

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...

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.

For 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.

What'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.

YES

Do 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!

🚦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... 🎨🖌️

New 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...

@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

Publication 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!

Decided 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...

Dear blskyers, In collaboration with Kristian Ullrich, I'd like to present SNPless, a Nextflow pipeline developed for time series analysis of microbial genomics data 🧬. github.com/kullrich/snp...

🙀 Microsoft has integrated Python into Excel, which opens up powerful new capabilities. 🙀 😎 This means you can now leverage the full power of Python - including AI, ML, advanced calculations and more - directly within Excel spreadsheets. 📹 check the video, CRAZY www.youtube.com/watch?v=FbBX...