Proud to share this work with @kevinchalut.bsky.social and Byron Mui. Why do some injuries scar while others regenerate? Using digit tip models, we show the ECM is a key driver. HA-rich ECM promotes regeneration, and boosting it can shift healing away from fibrosis. www.science.org/doi/10.1126/...
🚨 Why can’t mammals regenerate limbs like frog tadpoles or salamanders?
In our new paper in @science.org , we show that species-specific oxygen sensing acts as a gatekeeper for initiating limb regeneration 🐭🐸
🔗 www.science.org/doi/10.1126/... #EvoDevo
Novabrowse: A Tool for High-Resolution Synteny Analysis, Ortholog Detection, and Gene Signal Discovery www.biorxiv.org/content/10.64898/2026.03...
Novabrowse: A Tool for High-Resolution Synteny Analysis, Ortholog Detection, and Gene Signal Discovery
doi.org/10.64898/202...
DupyliCate - mining, classifying, and characterizing gene duplications
doi.org/10.1101/2025...
#Genomics #Bioinformatics #Evolution
Novabrowse: A Tool for High-Resolution Synteny Analysis, Ortholog Detection, and Gene Signal Discovery www.biorxiv.org/content/10.64898/2026.03...
Novabrowse: A Tool for High-Resolution Synteny Analysis, Ortholog Detection, and Gene Signal Discovery www.biorxiv.org/content/10.64898/2026.03...
Sounds interesting!!!
Gotta let us know what you dig up in the axolotl genome!
This looks very cool 😎
🔗 to download: github.com/RegenImm-Lab...
Check it out here: github.com/RegenImm-Lab... and get in touch if you have questions or suggestions for improving it!
18/18
Novabrowse is open source, and we have designed and documented it so that it is accessible to those without extensive bioinformatics experience. You can run it as a Jupyter notebook or via command line and it can be used with conda, Docker, or Apptainer.
17/n
As high-quality genome assemblies become available across the tree of life, the ability to evaluate missing genes becomes essential. Novabrowse helps fill that gap (pun intended 🤣)
16/n
This indicates a true gene loss in P. waltl, interestingly despite its retention in axolotl! And even more interesting given it’s a tumor suppressor gene and these animals are known to be relatively tumor resistant.
15/n
As for Rbl1, Novabrowse uncovered a chromosomal rearrangement, no putative gene signal, and extensive searching in the vast amount of transcriptomic data available for P. waltl was unable to find a putative ortholog.
14/n
Ameneh found transcripts for both Aire and Foxp3! Thus, these genes weren’t missing from the genome, just our annotation.
13/n
Aire is primarily expressed in the thymus, a tiny organ in which RNAseq data did not previously exist–potentially explaining the lack of a gene annotation. Ameneh from the lab took on the task of performing Nanopore long‑read RNAseq of the thymus to try and get transcripts for Aire.
12/n
For Foxp3 and Aire, the ability to perform clustering of hits into putative gene units convinced us that these genes were likely present in the genome, but absent from the annotation.
11/n
We put Novabrowse to the test with three conserved vertebrate genes in P. waltl: Foxp3, Aire, and Rbl1, all of which were absent in the NCBI RefSeq annotation (www.ncbi.nlm.nih.gov/datasets/gen...).
10/n
The output is both interactive and customizable and combines:
• alignment statistics
• chromosomal maps
• ribbon plots
• clustering of hits into putative gene units.
9/n
All you need to do is define a genomic region or gene of interest, select one or more comparison species, and Novabrowse retrieves sequences, runs BLAST, and integrates everything into a single interactive HTML report (see video above).
This means no more digging through BLAST text files!
8/n
So Lennart made Novabrowse!
An interactive tool for interpreting BLAST results in genomic context.
Allowing for:
• high-resolution synteny viz (great for non-traditional model organisms!)
• ortholog detection
• assessing chromosomal rearrangements
• discovery of unannotated gene signals
7/n
We needed something in between single‑gene alignment viewers and genome‑wide synteny frameworks.
We aimed to hit the middle ground, just the right info and combination of homology information, genomic location, and the ability to search for unannotated genes inside conserved loci.
6/n
Typically, we rely on two complementary approaches:
1) Sequence homology (e.g. BLAST)
2) Conservation of gene order/neighborhoods (i.e., synteny)
But existing tools had an awkward tradeoff…
5/n
That question turned out to be hard to answer.
Genomes are easier to sequence and assemble than annotate, especially in poorly sampled branches of the phylogenetic tree and/or when transcriptomic data are sparse.
4/n
This was interesting, but we were skeptical given their importance in immune function across species. So, Lennart, a former MSc student in the lab, set out to answer a “simple” question: Are these genes truly missing or just hiding unannotated in the genome?
3/n
We recently generated a high-quality genome assembly for the newt Pleurodeles waltl (www.cell.com/cell-genomic... and were puzzled to find two of our favorite immune genes, Foxp3 and Aire, were apparently absent.
2/n
New tool from the lab...check out Novabrowse: An interactive and customizable tool for interpreting BLAST results in genomic context!
www.biorxiv.org/content/10.6...
Does your favorite gene seems to be missing from your species of interest?
Are you sure?
🧵👇 1/n
Excited to share our #preprint showing that #macrophages in the regenerating #zebrafish #heart are shaped by local cardiac-immune microniches, with a fibroblast-to-macrophage signal promoting regeneration over fibrotic repair www.biorxiv.org/content/10.6...
@idrm.ox.ac.uk @oxforddpag.bsky.social
🗓️ 23-26 June 2026 🇸🇪
#PALS #summerschool in #OMICS is back!
Soon registration and info about speakers for the 3rd edition!
Organized by @claudiocantu81.bsky.social and me, @remeseiro-lab.bsky.social, with the support from @scilifelab.se and @kawresearch.bsky.social
