Shing
@szhan.bsky.social
Studying microbes using genomics and computers | Views my own | https://ecoevo.social/@shzhan | https://scholar.google.ca/citations?user=2nS6Z44AAAAJ&hl=en
A long time ago in a galaxy far away, there was a SARS-CoV-2 pandemic. Our paper, led by @martibartfast.bsky.social a) correcting errors in 4.5 million genomes & their phylogeny b) improving representation of the Global South in public data www.nature.com/articles/s41... (thread 1/n)
Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny - Nature Methods
This Resource paper presents a global SARS-CoV-2 phylogenetic tree of 4,471,579 high-quality genomes consistently constructed by Viridian, an efficient amplicon-aware assembler.
nature.com
FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social. 📄 www.science.org/doi/10.1126/... 🌐 search.foldseek.com/foldmason 💾 github.com/steineggerla...
Multiple protein structure alignment at scale with FoldMason
Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended ou...
science.org
www.biorxiv.org/content/10.1... We finally submitted the earlier preprint to a journal after massive restructuring. We've expanded the REML section for those interested in the method. We clarify that ARG-LMM estimates mutational variance and not additive variance.
Genetic prediction with ARG-powered linear algebra
Ancestral recombination graphs (ARGs) are an attractive means for quantitative genetic analysis of complex traits because they encode the realized genetic relatedness between a sample of individuals i...
biorxiv.org
With @szhan.bsky.social, @yulinzhang.bsky.social, Chao Zhang and Bingjie Chen, we wrote a Perspective about unifying the tree-based method across phylogenetics, population genetics and cell biology: arxiv.org/abs/2512.05499. Reposts are greatly appreciated!
Tree Thinking in the Genomic Era: Unifying Models Across Cells, Populations, and Species
The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and ...
arxiv.org
Come one come all! Come get involved in stdpopsim and help us decide where to go from here!
Dan Schrider@samurscicop.bsky.social · last yr.The PopSim Consortium wants you! Please join us on zoom on May 27 at noon Eastern Time (1600 UTC) to tell us you would like to see in the next version of stdpopsim! DM me for meeting link, or just sign up for our email list: lists.uoregon.edu/mailman/list... (1/3)
#NatureMicroPicks Microbial integrons in focus 🦠🧬 Two studies showing microbial integrons encoding phage defense systems #MicroSky www.science.org/doi/10.1126/... www.science.org/doi/10.1126/...
Mobile integrons encode phage defense systems
Integrons are bacterial genetic elements that capture, stockpile, and modulate the expression of genes encoded in integron cassettes. Mobile integrons (MIs) are borne on plasmids, acting as a vehicle ...
science.org
Fungi shape genome evolution of bacteria even in the absence of major growth phenotypes #ISMEJournal from @benwolfe.bsky.social Penicillium camemberti and Geotrichum candidum on Pseudomonas carnis evolution academic.oup.com/ismej/advanc...
Fungi shape genome evolution of bacteria even in the absence of major growth phenotypes
Abstract. Studies of microbial interactions often emphasize interactions with large, easily measurable growth differences and short-term ecological outcome
academic.oup.com
In the phosphorus-limited Sargasso Sea, microbes partition phosphorus uptake by time of day—bacteria in the morning, phytoplankton by day, and cyanobacteria at dusk—revealing a temporal niche strategy. www.pnas.org/doi/10.1073/...
Diel partitioning in microbial phosphorus acquisition in the Sargasso Sea | PNAS
The daily cycle of photosynthetic primary production at the base of marine food webs is often limited by the availability of scarce nutrients. Micr...
pnas.org
This meeting will be great! Abstract submission open now See you 26-27 Nov in Liverpool microbiologysociety.org/event/societ...
Understanding and predicting microbial evolutionary dynamics - 2025 meeting
microbiologysociety.org
Hey! That's me! Check out my latest where I develop a method for pinpointing where mutation spectra change along phylogenies. Striking, nodes with large changes are significantly enriched for protein changes in the RdRp (catalytic domain of the polymerase) suggesting a causal role.
Molecular Biology and Evolution@molbioevol.bsky.social · last yr.Using ~8M SARS-CoV-2 genomes, a new phylogenetic algorithm by @russcd.bsky.social detects 10 shifts in mutation patterns, some of them linked to changes in viral polymerase. This provides new perspectives on the evolution of mutational processes. 🔗 doi.org/10.1093/molb... #molbio #evobio #covid
300 billion years of angiosperm evolution at risk of extinction doi.org/10.1101/2025... Evolutionary blocks to anthocyanin accumulation in betalain-pigmented Caryophyllales doi.org/10.1101/2022... #Biodiversity #Evolution #PlantSci
300 billion years of angiosperm evolution at risk of extinction
Extinction results in not only loss of species, but also loss of the unique evolutionary history that they represent and the irreplaceable features they exhibit. There is broad consensus regarding the...
doi.org
Ancestral sequence reconstruction often assumes unrealistic homogeneous substitution models; however @rmuniztrejo.bsky.social et al. find that reconstruction accuracy is determined by phylogenetic signal, not model choice. 🔗 doi.org/10.1093/molb... #evobio #molbio
Robustness of Ancestral Sequence Reconstruction to Among-site and Among-lineage Evolutionary Heterogeneity
Abstract. Ancestral sequence reconstruction is typically performed using homogeneous evolutionary models, which assume that the same substitution propensit
doi.org
Code for PopPIPE here: github.com/bacpop/PopPIPE Thanks to some thorough editing in review we ironed out some errors that can arise, made the installation simpler, and added more automated output from the transmission pipline steps
GitHub - bacpop/PopPIPE: Population analysis PIPEline 🛠🧬
Population analysis PIPEline 🛠🧬. Contribute to bacpop/PopPIPE development by creating an account on GitHub.
github.com
John Lees@johnlees.bacpop.org · last yr.Our subclustering and transmission pipeline, PopPIPE has now been published: www.microbiologyresearch.org/content/jour...
Ancient polyploidy and low rate of chromosome loss explain the high chromosome numbers of homosporous ferns https://www.biorxiv.org/content/10.1101/2024.09.23.614530v1
Ancient polyploidy and low rate of chromosome loss explain the high chromosome numbers of homosporous ferns https://www.biorxiv.org/content/10.1101/2024.09.23.614530v1
A longstanding question in plant evolution is why ferns have many more chromosomes than angiosperms.
biorxiv.org
If you're interesting in the #H5N1 outbreak in cattle in the US, please have a look at our preliminary analyses just posted. Part 1 of 2: virological.org/t/preliminar...
As Prof. Priyanga Amarasekare's heartbreaking saga at UCLA drags into another year, I've compiled a thread of articles written about the situation. My sardonic take: Some people didn't like to be accused of racism and decided to destroy her career over their hurt feelings. 1/21