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Jia-Xing Yue (岳家兴)

@iamphioxus.bsky.social

PI of @EvomicsLab.bsky.social (www.evomicslab.org) at Sun Yat-sen University Cancer Center Editor of @genomebiolevol.bsky.social and @yeast-journal.bsky.social Alumni of @cnrs.fr @ircan.bsky.social @RiceUniversity @NanjingUniversity

30 Posts455 Follower743 Folgt
Joe Hanly@hanliconius.bsky.social · 2d ago

An attempt to explain what this does, using a simple case. How much 'tangle' in a synteny plot comes how we chose to order chromosomes, and how much is unavoidable because it represents accurate crossings in the data? 1/

a tangled synteny plot with 55 crossings on the left, and its solved partner on the right with only 9 crossings
Joe Hanly@hanliconius.bsky.social · 6d ago

I've complained on here a few times about synteny plots that are harder to read than they need to be. I decided it was time to actaully do something about it: introducing SynTangle, a tool for untangling whole-genome synteny plots github.com/Hanliconius/... 1/

Dmitri Petrov@petrovadmitri.bsky.social · last mo.

We are searching for an Assistant Professor in Evolutionary Biology! Looking for colleagues asking fundamental questions relating to evolutionary processes and drivers of evolutionary patterns. If you think it is you, please do apply! And please repost. facultypositions.stanford.edu/jobs/assista...

Assistant Professor in Evolutionary Biology - Stanford University, California, United States

The Department of Biology at Stanford University seeks applicants for a tenure-track Assistant Professor in Evolutionary Biology. A successful candidate will conduct research that asks fundamental que...

facultypositions.stanford.edu

Inigo Martincorena@imartincorena.bsky.social · 2mo ago

Big paper alert! This project has been years in the making. A comprehensive description of somatic mutation rates and signatures across 53 tissues or cell types using NanoSeq. A large collective effort led by Mimy Pham, Mike Stratton and @r-rahbari.bsky.social. www.biorxiv.org/content/10.6...

A comprehensive atlas of somatic mutation rates and mutational signatures in normal human cells

Over the course of a lifetime, somatic mutations accrue in normal human cells, causing variation in cell phenotype and engendering somatic evolution with outcomes ranging from the adaptive immune syst...

biorxiv.org

Tom Sasani@tomsasani.bsky.social · 2mo ago

How long does DNA damage last? @aaronquinlan.bsky.social and I found evidence that lesions are transmitted from parent (P0) to offspring (F1) in C. elegans. If they segregate unrepaired for multiple cell divisions, lesions generate multi-allelism in the F1 germline. www.biorxiv.org/content/10.6...

Inherited DNA damage generates multi-allelic mutations in C. elegans

Exogenous and endogenous mutagens generate a wide variety of DNA lesions, including bulky adducts, chemical modifications, and single- or double-stranded breaks. A phenomenon called “lesion segregation,” in which lesions evade repair and persist for multiple cell divisions, has recently been documented in tumors and healthy somatic tissues from mice and humans, respectively. Persistent lesions can generate multi-allelic variants (MAVs) by serving as templates for multiple rounds of error-prone replication. By reanalyzing data from a large C. elegans mutagenesis experiment, we observed robust evidence for MAVs at a small fraction (∼0.2%) of mutated sites in the offspring of strains treated with alkylating agents. Because these sequencing data were derived from the progeny of a single F1 animal — itself the offspring of a mutagenized P0 — all mutations should be biallelic. The presence of multi-allelic variation implies that some DNA lesions are transmitted to the F1 zygote, evade repair, and are repeatedly bypassed by error-prone polymerases during embryogenesis. We suspect that many more lesions are inherited than is suggested by MAV prevalence, and that a large fraction of biallelic mutations are also caused by inherited lesions. Our results demonstrate that DNA lesions serve as durable, transgenerational templates for mutagenesis in C. elegans . We speculate that lesion segregation in the early embryo may be a source of mosaicism and genetic diversity in humans, as well. ### Competing Interest Statement The authors have declared no competing interest. National Institutes of Health, https://ror.org/01cwqze88, R01HG012252

biorxiv.org

Jia-Xing Yue (岳家兴)@iamphioxus.bsky.social · 3mo ago

Great collaboration with Dr. Na Liu and Dr. Jun Ma's teams! It was a fun journey to expand our research footprint into cancer-associated microorganisms. Special thanks to @simonemozzachiodi.bsky.social for critically reading our manuscript and providing valuable feedback. 🧬🦠

Evomics Lab@evomicslab.bsky.social · 3mo ago

Glad to see this joint work on nasopharyngeal microbiota culturomics published in #ScienceTranslationalMedicine, featured as a cover story! By building this local bacterial catalog, we characterized a Fusobacterium-Prevotella mutualism in nasopharyngeal tumors. www.science.org/doi/10.1126/...

Andrew Carroll@acarroll.bsky.social · 4mo ago

How good is MiniBWA, the successor to BWA? To test it, I ran MiniBWA on sequencing from 76 different species, comparing mapping speed, rate and accuracy with BWA MEM. In short, it's really good. If you map short reads, it's well worth your time. andrewcarroll.github.io/2026/06/30/t...

The Best of Both Worlds - Assessing MiniBWA

Recently, Heng Li released MiniBWA (GitHub) alongside a paper by Heng Li and Nils Homer describing the method (paper). MiniBWA builds on the approaches in Minimap2 (also by Heng Li), but falls back on...

andrewcarroll.github.io

Jia-Xing Yue (岳家兴)@iamphioxus.bsky.social · 7mo ago

Such a big relief to see my much belated PhD project finally wrapped up, after so many years and so much ups and downs ... "It is a long way from amphioxus, but we all came from there" ~

Evomics Lab@evomicslab.bsky.social · 7mo ago

Excited to share our PNAS paper on the genome evolution of an early-diverging #amphioxus, Asymmetron lucayanum! There is a long and twisty story behind this work, which also explains the username choice of the lab PI @iamphioxus.bsky.social . 😀 @pnas.org www.pnas.org/doi/10.1073/...

Sishuo Wang@sishuowang.bsky.social · 8mo ago

very happy to have this work published in mbe @molbioevol.bsky.social can now use phyloHessian to get a (hopefully) improved div time & subs rate estimate, particularly for deep-time or fast‑evolving lineages github.com/evolbeginner... #julialang #iqtree #mcmctree #molecularclock

GitHub - evolbeginner/phyloHessianWrapper

Contribute to evolbeginner/phyloHessianWrapper development by creating an account on GitHub.

github.com

Molecular Biology and Evolution@molbioevol.bsky.social · 8mo ago

@sishuowang.bsky.social & Meade introduce phyloHessian, using complex mixture substitution models in molecular dating. Empirical analysis of ancient symbiont lineages leads to a revised understanding of their host association origins. 🔗 doi.org/10.1093/molbev/msag039 #evobio #molbio #compbio

Yeast Journal@yeast-journal.bsky.social · 8mo ago

ANNOUNCEMENT: The webpage for the upcoming yeast meetings of 2026 has recently been updated. Have a look at it to find out which exciting #yeast #conferences are ahead!!! 😀 onlinelibrary.wiley.com/page/journal...

Yeast | Microbiology Journal | Wiley Online Library

Yeast is a microbiology journal for research in the rapidly moving field of yeast biology. We publish the most significant developments in unicellular fungi.

onlinelibrary.wiley.com

Jia-Xing Yue (岳家兴)@iamphioxus.bsky.social · 9mo ago

Honored to serve @genomebiolevol.bsky.social and the greater @official-smbe.bsky.social community! 🫡

Genome Biology and Evolution@genomebiolevol.bsky.social · 9mo ago

GBE proudly welcomes seven new Associate Editors to its Editorial Board! These researchers bring vast experience in genomic sciences and evolutionary biology, and will provide a great service to the SMBE community. We will be presenting these colleagues throughout the coming days. #societyjournal

New GBE Associate Editors Maria Dulcetti Vibranovski (Universidade de São Paulo) Xiaoshu Chen (Sun Yat-sen University) Josué Barrera Redondo (Cinvestav Irapuato) Patrícia Beldade (Universidade de Lisboa) Jia-Xing Yue (Sun Yat-sen University) J. J. Emerson (University of California, Irvine) Choongwon Jeong (Seoul National University)
Tobias Marschall@tobiasmar.bsky.social · last yr.

Two papers in today's issue of @nature.com ‬: 1) we assemble 65 genomes to near completion, including centromeres and the MHC. tinyurl.com/3huhax6w. 2) we sequence 1,019 genomes from the 1kGP with long reads, revealing SVs down to low allele frequencies tinyurl.com/wbx3we9x.

Complex genetic variation in nearly complete human genomes - Nature

Using sequencing and haplotype-resolved assembly of 65 diverse human genomes, complex regions including the major histocompatibility complex and centromeres are analysed.

tinyurl.com