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Qiyun Zhu @zhuqiyun.bsky.social · 24/09/2026

Our Python rework of ANCOM-BC(2) in scikit-bio 0.7.4 puts this sophisticated method at the fast side of available microbiome differential abundance tests. scikit.bio/docs/latest/... #metagenomics #microbiome #bioinformatics

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Qiyun Zhu @zhuqiyun.bsky.social · 22/09/2026

We are proudly delivering scikit-bio 0.7.4 -- with Numba and GPU acceleration of PERMANOVA and Mantel, native Python-built ANCOM-BC2, much faster differential abundance tests, generic multiple sequence alignment, and more! github.com/scikit-bio/s... #bioinformatics #microbiome #omics

github.com

Release scikit-bio 0.7.4 · scikit-bio/scikit-bio

We are excited to announce scikit-bio 0.7.4! Release highlights: Added ancombc2, an efficient Python implementation of ANCOM-BC2 for differential abundance analysis, including post-hoc tests. Adde...

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Qiyun Zhu @zhuqiyun.bsky.social · 30/07/2026

(My) last human-written bioinformatics algorithm (maybe). A parallel balanced minimum evolution tree-building algorithm up to 82x faster than FastME. Crunches all GTDB bacteria (190k taxa) within 40 min. Better than NJ as data size gro ws. Preprint online: www.biorxiv.org/content/10.6...

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Qiyun Zhu @zhuqiyun.bsky.social · 28/07/2026

Proud to celebrate Henry Secaira-Morocho @hsecaira.bsky.social, my first PhD graduate at ASU! He has done outstanding research in evolutionary biology, computational biology and microbiome research. I'm excited to see him advance in his academic career at NLM. Congratulations, Henry!

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Qiyun Zhu @zhuqiyun.bsky.social · 03/06/2026

We've released scikit-bio 0.7.3: github.com/scikit-bio/s... with enhanced GPU support, a refreshed MMvec algorithm for multiomics co-occurrence and embedding, robust centered log-ratio transformation, accelerated minimum evolution phylogenetics, and more! #Bioinformatics #Microbiome #OpenSource

github.com

Release scikit-bio 0.7.3 · scikit-bio/scikit-bio

We are excited to announce scikit-bio 0.7.3! Release highlights: Implemented a global mechanism for supporting the Python array API standard and GPU computing. Added mmvec (Microbe-Metabolite Vect...

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Qiyun Zhu @zhuqiyun.bsky.social · 04/03/2026

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

github.com

scikit-bio at Google Summer of Code 2026 · scikit-bio scikit-bio · Discussion #2401

We are excited to announce that scikit-bio is participating in Google Summer of Code (GSoC) 2026 as part of the NumFOCUS umbrella organization. This year, we aim to modernize fundamental bioinforma...

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Qiyun Zhu @zhuqiyun.bsky.social · 13/02/2026

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

scikit.bio

scikit-bio: Bioinformatics in Python — scikit-bio

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Qiyun Zhu @zhuqiyun.bsky.social · 12/02/2026

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

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Qiyun Zhu @zhuqiyun.bsky.social · 31/01/2026

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

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Qiyun Zhu @zhuqiyun.bsky.social · 11/12/2025

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

nature.com

Scikit-bio: a fundamental Python library for biological omic data analysis - Nature Methods

Nature Methods - Scikit-bio: a fundamental Python library for biological omic data analysis

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Qiyun Zhu @zhuqiyun.bsky.social · 16/11/2025

Excited to have our new paper on phylogenetic marker genes online!

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Qiyun Zhu @zhuqiyun.bsky.social · 29/10/2025

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

scikit.bio

skbio.stats.composition.ancombc — scikit-bio 0.7.1 documentation

Perform differential abundance test using ANCOM-BC.

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Qiyun Zhu @zhuqiyun.bsky.social · 17/07/2025

(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,...

scikit.bio

scikit-bio: Bioinformatics in Python — scikit-bio

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Reposted by Qiyun Zhu

Seth Bordenstein @symbionticism.bsky.social · 23/03/2025

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....

doi.org

Blurred Lines Between Determinism and Stochasticity in an Amphibian Phylosymbiosis Under Pathogen Infection

Selection, dispersal and drift jointly contribute to generating variation in microbial composition within and between hosts, habitats and ecosystems. However, we have limited examples of how these pr...

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Qiyun Zhu @zhuqiyun.bsky.social · 20/03/2025

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...

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Reposted by Qiyun Zhu

Alexis Stamatakis @stamatak.bsky.social · 19/03/2025

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...

biorxiv.org

raxtax: A k-mer-based non-Bayesian Taxonomic Classifier

Taxonomic classification in biodiversity studies is the process of assigning the anonymous sequences of a marker gene (barcode) to a specific lineage using a reference database that contains named seq...

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Reposted by Qiyun Zhu

Jaebeom Kim @jbeom.bsky.social · 13/03/2025

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

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Reposted by Qiyun Zhu

Fabian Wittmers @fabianwittmers.bsky.social · 12/02/2025

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.

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Reposted by Qiyun Zhu

Andrew Roger @andrewjroger.bsky.social · 14/03/2025

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

doi.org

A robustly rooted tree of eukaryotes reveals their excavate ancestry - Nature

The root of the eukaryote Tree of Life is estimated from a new, larger dataset of mitochondrial proteins including all known eukaryotic supergroups, showing it lies between two multi-supergroup assemb...

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Reposted by Qiyun Zhu

Rebecca Bollwitt @miss604.com · 03/03/2025

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

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Reposted by Qiyun Zhu

Will Ratcliff @wcratcliff.bsky.social · 19/03/2025

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 🧪

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.

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