Qiyun Zhu
@zhuqiyun.bsky.social
Assistant Professor @ ASU | Studying #microbiome, #evolution, #bioinformatics, #multiomics | Developing scikit-bio (https://scikit.bio) | Open-source enthusiast
Pinned
Qiyun Zhu
@zhuqiyun.bsky.social
· Jul 17
scikit-bio: Bioinformatics in Python — scikit-bio
scikit.bio
(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,...
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
skbio.stats.composition.ancombc — scikit-bio 0.7.1 documentation
Perform differential abundance test using ANCOM-BC.
scikit.bio
October 29, 2025 at 5:36 PM
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
(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: Bioinformatics in Python — scikit-bio
scikit.bio
July 17, 2025 at 8:20 PM
(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,...
Reposted by Qiyun Zhu
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/10.1111/mec....
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...
doi.org
March 23, 2025 at 4:07 PM
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/10.1111/mec....
Reposted by Qiyun Zhu
A decade of waiting has led to this!
After a Decade of Waiting, GIMP 3.0.0 is Finally Here!
At last, GIMP 3.0 has arrived.
news.itsfoss.com
March 20, 2025 at 9:46 PM
A decade of waiting has led to this!
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...
March 20, 2025 at 5:12 PM
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...
Reposted by Qiyun Zhu
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...
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...
www.biorxiv.org
March 19, 2025 at 8:25 AM
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...
Reposted by Qiyun Zhu
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
💻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
March 13, 2025 at 8:51 AM
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
💻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
Reposted by Qiyun Zhu
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.
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.
February 12, 2025 at 6:01 PM
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.
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.
Reposted by Qiyun Zhu
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
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...
doi.org
March 14, 2025 at 11:38 AM
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
Reposted by Qiyun Zhu
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
Pre-order now wherever you purchase books.
Vancouver friends can order from independent shops like @bookwarehouse.bsky.social @crossandcrowsbooks.bsky.social @banyen.bsky.social
March 3, 2025 at 9:26 PM
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
Pre-order now wherever you purchase books.
Vancouver friends can order from independent shops like @bookwarehouse.bsky.social @crossandcrowsbooks.bsky.social @banyen.bsky.social
Reposted by Qiyun Zhu
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 🧪
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 🧪
March 19, 2025 at 6:32 PM
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 🧪
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 🧪