Glad to see this joint work finally out in Nature Cancer @natureportfolio.nature.com
! A truly tour-de-force multiomics quest into nasopharyngeal carcinoma subtyping and its clinical implications!
www.nature.com/articles/s43...
7/n: This work would not be possible without the long-term support of our collaborators, namely Linda Z. Holland, Jr-Kai (Sky) Yu , & Sung-Jin Cho. Many thanks to everyone involved!
6/n: Taken together, our findings illuminate the genome and gene evolution of amphixous and the Cephalochordata subphylum that they represent, as well as provide valuable resources for understanding the early evolution of chordates and the origin of vertebrates.
5/n: We also elucidated the evolutionary history of some important genes/locus underlying development & immune functions (e.g., Hox, TLRs, NLRs, MHC, RAGs) during chordate evolution.
4/n: The strong micro-synteny conservation is at least partially explained by co-transcriptional regulatory constraints, with those genes enclosed in the same micro-synteny block showing higher correlation of both gene expression profiles and molecular evolution.
3/n: We found Asymmetron has a larger genome, driven mainly by intergenic TE expansion. Despite such TE expansion, the Asymmetron genome show substantial macro- and micro-synteny conservation with other amphioxus species and even vertebrates.
2/n: In this work, we assembled a chromosome-level genome for Asymmetron lucayanum—the earliest diverging cephalochordate genus—expanding beyond the current Branchiostoma-centric view regarding cephalochordate genome evolution.
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/...
Honored to serve @genomebiolevol.bsky.social and the greater @official-smbe.bsky.social community! 🫡
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
First #SMBE meeting for our lab！Definitely a memorable experience. Already looking forward to the next one! @official-smbe.bsky.social #SMBE2025
📣 Glad to share our genome paper on an early-diverged cephalochordate (amphioxus) species, Asymmetron lucayanum! By decoding & analyzing this genome in a comparative genomics framework, we know better now regarding the genome and gene evolution in cephalochordates.
www.biorxiv.org/content/10.1...
📣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
Welcome to attend our SMBE2025 Symposium on Experimental Evolution. Co-organized by Dao-Qiong Zheng, @jingli-0512.bsky.social and myself.
📢 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!
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...
📢📢📢 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
Finally, we would like to thank @HumanPangenome
for making the #HPRC resources available, which helped us a lot in testing and perfecting our VRPG. And of course, our own ScRAP #yeast pangenome collection reported at evomicslab.org/db/ScRAPdb/ and www.nature.com/articles/s41...
Many thanks to our talented student Zepu Miao for leading the development of VRPG. Built upon VRPG, we are currently working on new development and discoveries with #pangenome graphs. Stay tuned!
To further demonstrate its functionality & scalability, we applied VRPG to the cutting-edge yeast and human reference pangenome graphs via a dedicated web portal at evomicslab.org/app/vrpg/
Especially, VRPG enables side-by-side visualization between the graph-based pangenome representation and the conventional primary-linear-reference-genome-based feature annotations, which greatly increases the Interpretability of pangenome graphs.
VRPG provides efficient & intuitive supports for exploring and annotating pangenome graphs along a linear-genome-based coordinate system and offers many highly useful features such as in-graph path highlighting, CNV and SV characterization, graph-based sequence query, etc.
To facilitate better exploration & understanding of pangenome graphs towards novel biological insights, here we present a web-based interactive Visualization and interpretation framework for linear-Reference-projected Pangenome Graphs (VRPG).
In the era of #T2T genomics, #pangenome graphs have emerged as a new paradigm for identifying, encoding, and presenting genomic variation at population levels. However, it remains challenging to dissect and interpret pangenome graphs in a biologically informative manner.
📢🧬Proud to announce our 1st work on pangenome graphs is early online @genomeresearch.bsky.social ! Here we developed an interpretative visualization framework for pangenome graphs named VRPG, which seamlessly bridges the graph and linear genomics world.
genome.cshlp.org/content/earl...
📢 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 !!!
📣 ⚠️👀Attn: The abstract submission for the #SMBE2025 meeting in Beijing @official-smbe.bsky.social
is open now!
Submission site: smbe2025.scimeeting.cn/en/web/index...
Submission Deadline: 2025.01.30
Welcome for all abstract submissions, especially for our Experimental Evolution Symposium !!!
Welcome to join our dedicated symposium on Experimental Evolution for the @MolBioEvol 2025 Beijing Meeting! See you in Beijing!
As real case demonstrations, we applied NanoTrans to the public DRS datasets of yeast, Arabidopsis, as well as human embryonic kidney and cancer cell lines to showcase its utility, effectiveness, and efficacy across diverse systems and application settings.
