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Jia-Xing Yue (岳家兴)

@iamphioxus.bsky.social
444 followers 733 following 30 posts

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

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Reposted by Jia-Xing Yue (岳家兴)
Dmitri Petrov @petrovadmitri.bsky.social · 17/09/2026
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...
facultypositions.stanford.edu
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...
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Jia-Xing Yue (岳家兴) @iamphioxus.bsky.social · 15/09/2026
The first written piece of our telomere work. More to come~
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Reposted by Jia-Xing Yue (岳家兴)
bioRxiv Genomics @biorxiv-genomic.bsky.social · 04/09/2026
Integrated map of somatic mosaicism across human tissues in 25 individuals www.biorxiv.org/content/10.64898/20…
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Reposted by Jia-Xing Yue (岳家兴)
Inigo Martincorena @imartincorena.bsky.social · 03/09/2026
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...
biorxiv.org
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...
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Reposted by Jia-Xing Yue (岳家兴)
Tom Sasani @tomsasani.bsky.social · 02/09/2026
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...
biorxiv.org
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
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Jia-Xing Yue (岳家兴) @iamphioxus.bsky.social · 03/08/2026
The first story coming out from a much larger experimental setup, co supervised with @jingli-0512.bsky.social.
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Jia-Xing Yue (岳家兴) @iamphioxus.bsky.social · 16/07/2026
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. 🧬🦠
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Reposted by Jia-Xing Yue (岳家兴)
Andrew Carroll @acarroll.bsky.social · 01/07/2026
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...
andrewcarroll.github.io
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...
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Jia-Xing Yue (岳家兴) @iamphioxus.bsky.social · 17/06/2026
Came back to US for the first time after my PhD to attend the @genetics-gsa.bsky.social #Yeast26 Genetics Meeting. Great to meet many colleagues from the North American yeast community, whose research I have followed through papers. Until next time~
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Jia-Xing Yue (岳家兴) @iamphioxus.bsky.social · 08/06/2026
Great to come back to Nice, an ever charming & cozy city that I’ve spent good five years of my life ! Had a lovely reunion with my postdoc advisor @litinice.bsky.social as well as both old & new friends at @ircan.bsky.social. Until next time, à bientôt ~
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Jia-Xing Yue (岳家兴) @iamphioxus.bsky.social · 15/04/2026
Proud to have played a part in this multi-lab collaboration! 😀
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Reposted by Jia-Xing Yue (岳家兴)
Saccharomyces Genome Database @yeastgenome.bsky.social · 14/04/2026
⏰ Only 2 DAYS left for early registration! Join us at #Yeast26 (June 13-17, Pacific Grove, CA) for cutting-edge research in #genetics, #genomics, #disease, #regulation, #systemsBiology, #cellBiology, #lifeCycle, #syntheticBiology, & more. Register by April 16 to save! 🧬 genetics-gsa.org/yeast-2026/
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Jia-Xing Yue (岳家兴) @iamphioxus.bsky.social · 23/03/2026
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" ~
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Reposted by Jia-Xing Yue (岳家兴)
Sishuo Wang @sishuowang.bsky.social · 12/03/2026
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.com
GitHub - evolbeginner/phyloHessianWrapper
Contribute to evolbeginner/phyloHessianWrapper development by creating an account on GitHub.
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Reposted by Jia-Xing Yue (岳家兴)
Genetics Society of America @genetics-gsa.bsky.social · 06/03/2026
The abstract submission deadline for #Yeast26 has been extended to next week, March 12! 📣 GSA is committed to meeting the needs of our genetics community and supporting our scientists through challenging times. Join us at the stunning Asilomar. Submit your abstract now: buff.ly/XmP8Z2i
buff.ly
Abstract Submission - Yeast Genetics Meeting 2026
Visit our website to learn more.
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Reposted by Jia-Xing Yue (岳家兴)
Genetics Society of America @genetics-gsa.bsky.social · 03/03/2026
David Botstein, a titan within the scientific community, died last week. GSA mourns his passing and celebrates his legacy. Read more about his significance to our community in this thread ⬇️🧵
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Reposted by Jia-Xing Yue (岳家兴)
Saccharomyces Genome Database @yeastgenome.bsky.social · 02/03/2026
We are deeply saddened to share the news of the passing of David Botstein, a towering figure in modern #genetics and a foundational force behind SGD. www.yeastgenome.org/blog/in-memo... #yeast #modelOrganism
a headshot of David Botstein
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Reposted by Jia-Xing Yue (岳家兴)
Yeast Journal @yeast-journal.bsky.social · 02/03/2026
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...
onlinelibrary.wiley.com
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.
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Reposted by Jia-Xing Yue (岳家兴)
Genome Research @genomeresearch.bsky.social · 02/03/2026
The new issue of @genomeresearch.bsky.social is now live. Follow the link to new research on chromosome engineering in 8p syndrome, convergent evolution in arid rodents, and more! tinyurl.com/Genome-Res-3...
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Jia-Xing Yue (岳家兴) @iamphioxus.bsky.social · 25/02/2026
📢 It has been a few years since we updated LRSDAY last time, during which the downloading URLs of some of its dependencies have become inaccessible. I've just implemented a fix in GitHub make the automatic installation script work again. github.com/yjx1217/LRSDAY
github.com
GitHub - yjx1217/LRSDAY: LRSDAY: Long-read Sequencing Data Analysis for Yeasts
LRSDAY: Long-read Sequencing Data Analysis for Yeasts - yjx1217/LRSDAY
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Reposted by Jia-Xing Yue (岳家兴)
Genome Biology and Evolution @genomebiolevol.bsky.social · 11/02/2026
Jia-Xing Yue (@iamphioxus.bsky.social), principal investigator at Sun Yat-sen University, is one of the new members of the GBE editorial board. He is an expert in evolutionary genomics, genome instability, telomeres, aneuploidy, cancer, and yeast. #societyjournal
Jia-Xing Yue (Sun Yat-sen University)
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Jia-Xing Yue (岳家兴) @iamphioxus.bsky.social · 08/02/2026
Honored to serve @genomebiolevol.bsky.social and the greater @official-smbe.bsky.social community! 🫡
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Jia-Xing Yue (岳家兴) @iamphioxus.bsky.social · 30/01/2026
Honored to serve on the Yeast Genetics Meeting Program Committee of Evolution & Population Genetics. Welcome for meeting registration and abstract submission, especially on our Evolution & Population Genetics program! genetics-gsa.org/yeast-2026/ @genetics-gsa.bsky.social #Yeast26
genetics-gsa.org
Homepage - Yeast Genetics Meeting 2026
Visit our website to learn more.
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Reposted by Jia-Xing Yue (岳家兴)
Society for Molecular Biology and Evolution @official-smbe.bsky.social · 18/12/2025
SMBE is now on Weixin/WeChat! Stay up-to-date with the latest news, events, and articles published in @molbioevol.bsky.social and @genomebiolevol.bsky.social Follow the @officialSMBE account, or scan the QR code with the app. 🔗 academic.oup.com/smbejournals/pages/wechat #society
SMBE is now on Weixin/WeChat
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Jia-Xing Yue (岳家兴) @iamphioxus.bsky.social · 29/07/2025
It is great to have @petrovadmitri.bsky.social here at Sun Yat-sen University Cancer Center to give us an highly inspiring talk on “Fitness landscape of tumor suppressor genes in lung cancer ”. Tour de force experiments, mind blowing results, and exciting bench-to-bed perspectives!
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Reposted by Jia-Xing Yue (岳家兴)
Evomics Lab @evomicslab.bsky.social · 25/07/2025
First #SMBE meeting for our lab!Definitely a memorable experience. Already looking forward to the next one! @official-smbe.bsky.social #SMBE2025
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Reposted by Jia-Xing Yue (岳家兴)
Tobias Marschall @tobiasmar.bsky.social · 23/07/2025
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.
tinyurl.com
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.
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Jia-Xing Yue (岳家兴) @iamphioxus.bsky.social · 23/07/2025
Super honored to have chance to co-organize the #SMBE2025 Symposium on Experimental Evolution, together with @jingli-0512.bsky.social and Dao-Qiong Zheng. Thank @petrovadmitri.bsky.social for serving as our invited speaker. Also thank all the oral/poster presenters and audience. @OfficialSMBE
Group photo with all oral speakers.Prof. Dmitri Petrov delivering his talk.
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Jia-Xing Yue (岳家兴) @iamphioxus.bsky.social · 22/07/2025
📣Our #SMBE 2025 Symposium (No. 3) on Experimental Evolution will be held today (7.22, Tuesday) at 10:30 in Room 4, Building No. 8. An associated poster session will be held at 14:00 (poster number: S3-P01~P16). Welcome to join! let's study evolution in action! 🥳 🎉 @official-smbe.bsky.social
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Reposted by Jia-Xing Yue (岳家兴)
Society for Molecular Biology and Evolution @official-smbe.bsky.social · 20/07/2025
📅 The day is today! #SMBE2025 in Beijing starts now, as the registration desk opens to all participants. Join us for five days full of the latest discoveries in molecular biology and evolution 🧬 We hope all attendees enjoy the many opportunities for discussion and networking among our community.
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Reposted by Jia-Xing Yue (岳家兴)
Li Zhao @lizhao.bsky.social · 15/07/2025
Our latest paper is out: rdcu.be/ev6Ym — one of my favorite projects. It began about 8 years ago when Nobel laureate Torsten Wiesel asked me: what transcription factors regulate new genes? I had no idea then. Now we have some answers.
rdcu.be
Gene regulatory networks and essential transcription factors for de novo-originated genes
Nature Ecology & Evolution - A combination of computational methods applied to single-cell RNA sequencing data and genetic experiments shows that a small number of transcription factors are...
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Jia-Xing Yue (岳家兴) @iamphioxus.bsky.social · 17/06/2025
Welcome to attend our SMBE2025 Symposium on Experimental Evolution. Co-organized by Dao-Qiong Zheng, @‪jingli-0512.bsky.social‬ and myself.
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Reposted by Jia-Xing Yue (岳家兴)
Dmitri Petrov @petrovadmitri.bsky.social · 15/05/2025
Very excited about this work by @mrazo.bsky.social in collaboration with www.madhavmani.com bsky.app/profile/mraz... I am so lucky to be able to collaborate with such brilliant people! Learned a lot. This is our first foray into ML approaches and I am quite taken with their power 1/n
madhavmani.com
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Reposted by Jia-Xing Yue (岳家兴)
Mike Schatz @mikeschatz.bsky.social · 15/05/2025
Keynote talk from Steven McCarroll from last weeks Biology of Genomes conf. My favorite talk of the whole meeting! #bog25 youtu.be/BCRAlmFv7ag?...
youtu.be
CSHL Keynote, Dr. Steven McCarroll, Harvard Medical School + Broad Institute
YouTube video by CSHL Leading Strand
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Reposted by Jia-Xing Yue (岳家兴)
Evomics Lab @evomicslab.bsky.social · 28/04/2025
📢 3 Postdoc positions available in @evomicslab.bsky.social targeting on genome instability evolution of both yeast and human genomes. Both computational genomics and experimental genomics backgrounds are welcome! 🧬🧑‍💻🧪 For more information, see evomicslab.org or send me a message!
evomicslab.org
Evomics Lab – Exploring Omics in the Light of Evolution
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Reposted by Jia-Xing Yue (岳家兴)
Nature Methods @natmethods.nature.com · 28/03/2025
Uncalled4: a toolkit for nanopore signal alignment, analysis and visualization of DNA and RNA modifications. www.nature.com/articles/s41...
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Reposted by Jia-Xing Yue (岳家兴)
Will Ratcliff @wcratcliff.bsky.social · 19/03/2025
1/35 New paper out! @jamesTstroud and I dive into why long-term studies are crucial for understanding evolution. They reveal processes impossible to detect in short timescales and capture rare events that transform our understanding of evolutionary dynamics. www.nature.com/articles/s41...
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Reposted by Jia-Xing Yue (岳家兴)
Christian Landry @christianlandry.bsky.social · 23/02/2025
We are looking for a postdoc in #EvolutionarySystemsBiology. Exciting science, amazing team, wonderful city! landrylab.ibis.ulaval.ca/research-opp... #evolution #synbio #systemsbiology #genomics
landrylab.ibis.ulaval.ca
Research opportunities | Landry Lab
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Reposted by Jia-Xing Yue (岳家兴)
Evomics Lab @evomicslab.bsky.social · 15/02/2025
Glad to see the copy-edited version of our VRPG paper formally published in the latest issue of @genomeresearch.bsky.social ! We developed VRPG as a novel visualization framework for intuitively exploring pangenome graphs in a linear-reference-projected context. genome.cshlp.org/content/35/2...
genome.cshlp.org
Interactive visualization and interpretation of pangenome graphs by linear reference–based coordinate projection and annotation integration
An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms
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Reposted by Jia-Xing Yue (岳家兴)
Genome Research @genomeresearch.bsky.social · 14/02/2025
The new issue of @genomeresearch.bsky.social is now live! Follow the link to new research on homeodomain–DNA cooperative dimerization in developmental defects, nucleic quasi-primes, and more! tinyurl.com/Genome-Res-3...
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Jia-Xing Yue (岳家兴) @iamphioxus.bsky.social · 12/02/2025
📢📢📢 The FINAL COUNT DOWN for the extended abstract submission deadline of #SMBE2025! Please submit your abstract by 23:59 (GMT +8) of February 15, 2025 [Saturday]! And shout out again for our symposium on Experimental Evolution ! 🎉🎉🎉 @OfficialSMBE #LTEE #ExperimentalEvolution
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Reposted by Jia-Xing Yue (岳家兴)
Gilles FISCHER @gillesfischer.bsky.social · 06/02/2025
A very significant step forward for synthetic genomics www.nature.com/articles/s41...
nature.com
Engineering a genomically recoded organism with one stop codon - Nature
Ochre, a strain of Escherichia coli engineered to have a single stop codon, enables reassignment of four codons for non-degenerate functions, such as incorporation of non-standard amino acids into pro...
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Reposted by Jia-Xing Yue (岳家兴)
Society for Molecular Biology and Evolution @official-smbe.bsky.social · 27/01/2025
📢📢📢 #SMBE2025 Abstract Submission EXTENDED to Saturday, February 15, 2025 We also invite you to register at www.smbe2025.org @SMBEmeetings
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Reposted by Jia-Xing Yue (岳家兴)
Gilles FISCHER @gillesfischer.bsky.social · 14/01/2025
📢 #Yeast2025 News! Registration and abstract submission are NOW OPEN! Join us at the 32nd ICYGMB 📅 Save the Date: 21-24 July 2025 📍 Location: Paris @sorbonne-universite.fr 🔗 Submit: premc.org/yeast2025/su... 🕒 Register now to take advantage of the Early Bird fee premc.org/yeast2025/re...
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Reposted by Jia-Xing Yue (岳家兴)
Genome Research @genomeresearch.bsky.social · 22/01/2025
The new issue of @genomeresearch.bsky.social is now live! Follow the link to new research on AI in cell-free DNA diagnostics, disease progression insights using single-cell/-nucleus genomics, and more! tinyurl.com/Genome-Res-3...
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Jia-Xing Yue (岳家兴) @iamphioxus.bsky.social · 21/01/2025
The last 10-day countdown for abstract submission! Welcome to spread the word and of course welcome to submit the abstract!!! 📢😃⏰
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Reposted by Jia-Xing Yue (岳家兴)
Harmit Singh Malik @harmitmalik.bsky.social · 17/01/2025
Cool paper on evolutionary constraints and trajectories shaping point centromere evolution in budding yeasts by @helsenjana.bsky.social @gautamdey.bsky.social @gsherloc.bsky.social www.biorxiv.org/content/10.1...
biorxiv.org
Centromeres evolve progressively through selection at the kinetochore interface
During mitosis, stable but dynamic interactions between the centromere DNA and kinetochore complex enable accurate and efficient chromosome segregation. Even though many proteins of the kinetochore ar...
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Jia-Xing Yue (岳家兴) @iamphioxus.bsky.social · 14/01/2025
Introducing VRPG, our recent work on the pangenome graph visualization & interpretation @genomeresearch.bsky.social !We posted our initial idea years ago and continuously improved it with many added features. Appreciate the great suggestions from all 3 reviewers. It is so much better now!
evomicslab.org
VRPG
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Jia-Xing Yue (岳家兴) @iamphioxus.bsky.social · 10/01/2025
📢 2nd-round abstract submission call for the 2025 @OfficialSMBE annual meeting in #Beijing . Where: smbe2025.scimeeting.cn/en/web/index... When: now - 2025/01/30. Welcome for all abstract submissions, especially for our Experimental Evolution Symposium !!!
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Sholto David @sholtodavid.bsky.social · 10/01/2025
You can use my webapp to identify similar, overlapping, and duplicate images in PDFs of scientific papers: sholtodavid.pythonanywhere.com
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