How to Design Antibodies
A step-by-step guide to making de novo binders. www.asimov.press/p/antibody-...
Nice 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...
Derived layouts build on top of those by flipping, rotating, or transforming coordinates — one extra line turns a rectangular tree into a dendrogram or an inward circular plot.
Base layouts (rectangular, slanted, circular, fan, daylight…) control the overall shape of the tree.
#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
I would just love to have a simpler way to update RStudio less frequently on macOS, Windows, and Linux, or ideally have it happen with a single click. Indeed we can discuss it over an email.
Thank you, Dirk. My statement should in no way diminish the love for R or the outstanding work the community is doing I use it every day across multiple computers.
Definitely 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
I hope you've found this post helpful.
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Study finds ChatGPT Health did not recommend a hospital visit when medically necessary in more than half of cases. www.theguardian.com/technology/2...
Want 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...
5/ 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.
1. 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!
TSniffer: unbiased de novo identification of RNA editing sites and quantification of editing activity in RNA-seq data link.springer.com/article/10....
Austria'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...
Nature Genetics: Engineering AI co-scientists for statistical genetics applications www.nature.com/articles/s41... 🧬💻🧪 read free: rdcu.be/eZ2wR
"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)
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.
🔄 Stay tuned, we're constantly updating the materials and preparing for new adventures in genomics data visualization. 𝗠𝗼𝗿𝗲 𝗶𝗱𝗲𝗮𝘀, 𝗰𝗼𝘂𝗿𝘀𝗲𝘀, 𝗰𝘂𝘀𝘁𝗼𝗺 𝗽𝗮𝗰𝗸𝗮𝗴𝗲𝘀, 𝗮𝗻𝗱 𝗮 𝗯𝗼𝗼𝗸 𝗼𝗻 𝗴𝗲𝗻𝗼𝗺𝗶𝗰𝘀 𝗱𝗮𝘁𝗮 𝘃𝗶𝘀𝘂𝗮𝗹𝗶𝘇𝗮𝘁𝗶𝗼𝗻 𝗮𝗿𝗲 𝗰𝗼𝗺𝗶𝗻𝗴.
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
Gavras at this best!
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...
