Chao Yang

Minibwa is a hybrid of bwa-mem and minimap2 and the successor of bwa-mem for short-read mapping. ~4X/2.5X as fast as bwa-mem/bwa-mem2 for WGS reads at comparable accuracy. Native support of directional bisulfite-seq. Applicable to long reads. Preprint at arxiv.org/abs/2606.15357

Our paper "Gene ancestries reveal diverse microbial associations during eukaryogenesis.” is finally out in Nature. Eukaryogenesis was likely a gradual process shaped by multiple microbial partners and virus-mediated gene transfer, rather than a single binary symbiosis. doi.org/10.1038/s415...

Vibriophiles! Come join us in Berlin this September! Still time to register and submit your abstract

Read 'Evolution of Pandemic Cholera at its Global Source’ from @sangerinstitute.bsky.social, @amberbarton.bsky.social, icddr,b, PGIMER, and others in @nature.com, here ⤵️ www.nature.com/articles/s41...

How diverse is bacterial immunity ? We report in @science.org how language models allowed us to predict 2.4M antiphage proteins spanning >23K novel potential systems. 👏 @emordret.bsky.social, @alexhv.bsky.social & al doi.org/10.1126/scie... Explore them here defensefinder.mdmlab.fr/wiki/refseq_...

Grateful to share our paper on gene-specific selective sweeps in human gut microbiomes, now out in Nature! It has been a joy to work with @rwolff.bsky.social, whose insights and hard work made this possible. www.nature.com/articles/s41...

Nature Reviews Genetics Focus issue: Eco-evolutionary genomics of microorganisms www.nature.com/collections/... 🧬🖥️🧪🦠 🧵 1/

Absolutely stoked to have this published in @plosbiology.org We looked at the metabolism of #Klebsiella pneumoniae 🦠🧫. We not only demonstrated lineage-specific #metabolism, but that lineages can cross-feed and support each other. journals.plos.org/plosbiology/... #MicroSky #microbiology 🧬 🧪 💊

metaTraits: a large-scale integration of microbial phenotypic trait information academic.oup.com/nar/advance-...

Huge preprint if you are interested in bacterial strain taxonomy! The why and how of cgMLST LIN codes: An extensively revised and expanded version doi.org/10.1101/2024... I will summarize it for you in this thread 👇

Combination of large-scale phylogenomic analysis, mouse lethality experiments and bacterial growth assays shows sheds light on how a pandemic clone of Vibrio parahaemolyticus was able to spread worldwide www.nature.com/articles/s41...

Beautiful work on the emergence of the pandemic clone of V. parahaemolyticus

Our “Less is more” story is out! 🚀 We reveal how gene loss shaped the adaptive evolution of pandemic Vibrio parahaemolyticus, highlight a potentially general mechanism across bacteria. Huge thanks @danielfalush.bsky.social @campy-bara.bsky.social @jaimemurtaza.bsky.social & all coauthors

How to get introgressed fragments in genomic data? Everything you always wanted to know you find in our review in @cp-trendsgenetics.bsky.social, led by Xin Huang: doi.org/10.1016/j.ti...

Molassodon! Excited to post my research group's first laboratory project. We identify a phenotype and a putative ecological strategy for the Molassodon ecospecies of Vibrio parahamolyticus, thanks to the hard work of our lab team led by @campy-bara.bsky.social www.biorxiv.org/content/10.1...

Delighted to present our Macrogenetics atlas of prokaryotes. www.biorxiv.org/content/10.1... This is a herculean effort from Chao Yang, which has a previous existence as a preprint first posted in 2018 "why panmictic bacteria are rare?" www.biorxiv.org/content/10.1...