scikit-bio is participating in #GSoC 2026 via NumFOCUS! We aim to modernize core bioinformatics algorithms to support GPU acceleration and interoperability across AI-ready libraries like JAX and CuPy. Details: github.com/scikit-bio/s... Contributors are welcome! #opensource #bioinformatics #python
This MCP server for edgePython should be useful for anyone building (comp)bio agents: github.com/pachterlab/e...
scikit-bio 0.7.2 is out -- featuring multiple genetic distance metrics like JC69 and K2P, support for PHYLIP distance matrices, and optimized algorithms for condensed (triangular) distance matrices. Also enhanced ordination plotting. scikit.bio #Bioinformatics #Microbiome #OpenSource
Introducing TM-Vec 2 and 2s -- protein language models for fast, accurate remote homology detection. Predict structural similarity from sequence alone. Major speedup, high accuracy, runs on regular hardware. Suited for proteome-scale clinical & environmental datasets. #deeplearning #bioinformatics
We introduce a Python implementation of ANCOM-BC that is 100x faster than the original R code, while preserving statistical validity. Scales to much larger omics datasets and enables ML workflows with repeated inference (feature selection, sensitivity, stability, etc.) #Bioinformatics #Microbiome
See email. Thanks for your interest!
The scikit-bio paper in online in Nature Methods! Many thanks to our collaborators, community contributors and reviewers! We couldn’t have done it without you. www.nature.com/articles/s41... #Bioinformatics #OpenSource
Excited to have our new paper on phylogenetic marker genes online!
Augmenting microbial phylogenomic signal with tailored marker gene sets www.nature.com/articles/s41... #jcampubs
ANCOM-BC in Python! scikit-bio 0.7.1 introduces a native implementation of this widely used differential abundance test. Same validated methodology, consistent results, and blazing fast! Scalable to very large datasets. Try it out: scikit.bio/docs/latest/... #Bioinformatics #Microbiome #OpenSource
@xrefugee13.bsky.social I might have an idea to "save" Bacillota by measuring phylogenetic rejection. Let me email you.
Good to know! People may say that more observations offer more chances to break a hypothesis (Bacillota's monophyly). Taxon sampling vs. method robustness is always a dilemma...
Making Bacillota monophyletic probably isn't easy. I've been thinking that a taxonomic group should be splitted only when there's strong phylogenetic evidence rejecting its monophyly (instead of supporting). This can probably resolve lots of "_A" suffixes.
(2/2) ...omic data augmentation methods, interoperability with e.g., Anndata and PyTorch, cross-release benchmarks, roadmap of development practices, enriched tutorials for non-microbiome omics.
(1/2) Announcing scikit-bio 0.7.0 (scikit.bio) -- A major upgrade for microbiome & multi-omics data science! Enhanced differential abundance testing, new sequence alignment engine, GPU-ready log-ratio transformations, scalable PCoA and PERMANOVA with binaries,...
Skin bacteria are subject to dispersal and chance across 22 amphibian species, yet contemporary and historical contingencies (e.g., #phylosymbiosis) leave strong signatures in their microbiomes even at large geographical scales.
doi.org/10.1111/mec....
Our method selects any number of markers that perform as well as or better than currently adopted markers of this number. More is better. More contains less. Paralogs okay. One can tweak it to bias toward well- or pooly-studied microbial genomes.
Thrilled to share our new preprint on finer and flexible marker gene selection for microbial phylogenomics. Given any input genomes and an arbitrary number, it will find this number of useful markers. Effective with highly incomplete MAGs. www.biorxiv.org/content/10.1...
Check out raxtax, our new open-source tool for taxonomic classification of barcoding sequences, it's 2.7-1000 times faster than competing tools and also implements fancy uncertainty scores: www.biorxiv.org/content/10.1...
Metabuli App preprint is out!
💻Taxonomic classification & interactive visualization—right on your laptop
🛠️Create new databases or update existing ones with new sequences. 🧵1/5
github.com/steineggerla...
www.biorxiv.org/content/10.1101/2025.03.10.642298v1
Happy to see a large chunk of my PhD work published today in Cell Host&Microbe: www.cell.com/cell-host-mi...
We conducted fluorescence-activated single-cell sorting of active predatory protists in the ocean and recovered symbionts with cool evolutionary positions close to animal pathogens.
I'm pleased to introduce our new paper rooting the eukaryote Tree of Life (eToL) that resulted from a collaboration led by PhD student Kelsey Williamson and a large group of collaborators doi.org/10.1038/s415...htt
Screenshot of a book cover: Bluesky for Dummies (a Wiley Brand). There a photo of a butterfly on the left. In a purple circle there’s more text: “Build your profile on Bluesky Find new friends and followers Take full control of your feed.” In the bottom right on a yellow background it lists authors as Eric Butow, Rebecca Bollwitt and a Foreword by Jay Graber, Bluesky CEO
Thanks to @jay.bsky.team for writing the foreword for Bluesky for Dummies. We can’t wait until it’s out in the world.
Pre-order now wherever you purchase books.
Vancouver friends can order from independent shops like @bookwarehouse.bsky.social @crossandcrowsbooks.bsky.social @banyen.bsky.social
A microscopy image of snowflake yeast on the cover of Nature, with the extended cells of two clusters barely touching in a manner reminiscent of Michelangelo's depiction of Adam touching God in the Sistine chapel.
Awwww yeah, check this out: snowflake yeast making their cover debut!
www.nature.com/nature/volum...
We have two papers in this issue:
1) A paper examining whole genome duplication in the MuLTEE
2) A review of long-term experiments in evolutionary biology led by @jameststroud.bsky.social 🧪
