Evomics Lab

First #SMBE meeting for our lab！Definitely a memorable experience. Already looking forward to the next one! @official-smbe.bsky.social #SMBE2025

The genome of the early diverged amphioxus, Asymmetron lucayanum, illuminates the evolution of genome architecture and gene repertoires in cephalochordates Cephalochordates (amphioxus or lancelet) are considered as living proxies for ancestral chordates due to their key phylogenetic position and slow evolutionary rate. The genomes of living amphioxus thu...

📣 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!

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

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!

GitHub - yjx1217/NanoTrans: An integrated computational framework for comprehensive transcriptome analyses with Nanopore direct-RNA sequencing data An integrated computational framework for comprehensive transcriptome analyses with Nanopore direct-RNA sequencing data - yjx1217/NanoTrans

The code of NanoTrans can be freely accesible via @github
at github.com/yjx1217/Nano...

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.

Starting from the raw sequencing reads, NanoTrans can perform read basecalling, isoform clustering & quantification, differential gene expression & splicing, RNA modification, poly(A) tail length profiling, and fusion gene detection in a highly streamlined fashion.

NanoTrans: an integrated computational framework for comprehensive transcriptome analysis with nanopore direct RNA sequencing Nanopore direct RNA sequencing (DRS) provides the direct access to native RNA strands with full-length information, shedding light on rich qualitative…

The copy-edited version of our NanoTrans paper has been recently published @JGenetGenomics ! Here we developed an all-in-one pipeline for comprehensive data analysis for @nanoporetech.com direct-RNA sequencing (#DRS). www.sciencedirect.com/science/arti...

ScRAPdb: an integrated pan-omics database for the Saccharomyces cerevisiae reference assembly panel Abstract. As a unicellular eukaryote, the budding yeast Saccharomyces cerevisiae strikes a unique balance between biological complexity and experimental tr

Excited to introduce the ScRAPdb work that we recently published at Nucleic Acids Research, in which we assembled a #pangenome x #multi-omics database for #yeast. This is one step forward for a pan-multi-omics understanding of genome & trait evolution. Read more > academic.oup.com/nar/advance-...