New Pre-Print Alert!
Evolving initial conditions: an alternative developmental route to morphological diversity
with Shannon Taylor and @jamesehammond.bsky.social
www.biorxiv.org/content/10.6...
As mentioned elsewhere, I've been dreaming of solving this problem for a looooooooong time. Nice to see that my dreams were also the dreams of a very talented team! Slightly different approach, same problem, similar logic. Loving this!
We just need the downstream probe to start with a ligation incompetent base, for example a 5'OH. Then Bst will grow the other probe close to this one, chop away the first nucleotide and expose a ligatable phosphate only if and when the gap is fully closed.
Unclear? here's a drawing!
The solution came from another activity of Bst. It's called nick translation. When a growing strand encounters another oligo, Bst eats the 5' nucleotides away from it and fills it back from the growing strand.
Still, incomplete gaps would sometimes be ligated by the promiscuous ligases, resulting in low capture accuracy close to the downstream oligo.
So, how did we pull this off? First we found a DNA polymerase that could also do RT, but without strand displacement activity (Bst, the old Bst...).
Second, RNA-templated DNA ligases are famously dirty, they love to ligate the wrong junction, and can sometimes even ligate across small spaces, for example non-completely filled gaps
Except, it's not simple at all. To begin with, you need a reverse transcriptase and these enzymes are very good at kicking oligos out of the way (aka "strand displacement")
The solution? Design a pair of flanking probes and try to fill the gap using a polymerase. Simple, right?
Capturing somatic mutations in single-cell probe-based assays (ie. 10X Flex) is a hard task, especially if you don't know *exactly* the mutations you want to capture, or if your target sequence is a mutational hotspot with many possible alternative alleles. Here's the way we pulled this off. Enjoy!
Why so serious? 🃏
Marco Grillo, Anna Nam and yours truly 𝗚𝗼𝗧 𝗮 𝗙𝗶𝗹𝗹𝗶𝗻𝗴 that will make you happy 😃
No more limitations. Maximum flexibility.
Something is coming. Stay tuned.
#singlecellwithaplus
Pinging here @dshb-antibodies.bsky.social, for example, who nicely shared their list with me!
Let me introduce you to KaroSpace, which is a rapid-access framework for interactive exploration of multi-sample spatial omics data. The preprint can be accessed here: www.biorxiv.org/content/10.6...
The core idea was stolen from @michalis-averof.bsky.social, the source of most of my stolen core ideas :P
I "vibe coded" the app as a fun project in about 20 minutes, based on an old script I had around my Desktop for years. Have fun!
The tool returns a per-epitope hit list, including any other info the Ab manufacturer shared with you (ie. catalogue number), that you can use to order your favorite antibody right away.
No proteome? no problem! the tool will also accept a transcriptome (or genome), compute the 6-frame translation on the go, and scan the epitope list against the 6-frame translation.
If you ask nicely, Ab manufacturers will share the epitope information for all their monoclonal epitope-mapped antibodies. These epitopes can be searched against a new species' proteome and return potential hits, revealing potential reactivity.
Do you work with a strange model species and are frustrated by the lack of antibodies for immunos? Here's a web app that does some computational pre-screening for you.
sixpack-abscan.serve.scilifelab.se
In animals with large genomes, finding cis-regulatory elements can be very challenging. Enhancers can be located tens/hundreds of kb away from their target promoters. We face this challenge in Parhyale, with >3 Gbp genome.
We just published a preprint describing how we are tackling this problem. /1
I am very happy (and a bit scared) to present to you what we have been working on over the last 4 years. This manuscript is exactly what I dreamt of when I started the lab and I could not be happier and prouder of the outcome!
Mastodon: the Command Center for Large-Scale Lineage-Tracing Microscopy Datasets www.biorxiv.org/content/10.64898/2025.12...
A cloning strategy as depicted in the OpenCloning website
#OpenCloning is a an Open Source alternative to SnapGene/Benchling that supports automation and integration with other software
✅ Free
🔓 Open Source
🧬 More cloning methods than SnapGene
🤖 Can be automated with python
👨🔬 Built by a researcher — for researchers!
👉 Check it out at opencloning.org
Thrilled to share my main postdoc work with @jamesbriscoe.bsky.social
We used genomic barcoding + scRNAseq in chick & human embryos to reveal a lineage architecture that reshapes how we understand neural tube development & cell fate decisions
🧵👇
www.biorxiv.org/content/10.1...
There is still “an urgent need for donations from the community,” says Eric Lai, president of the Fly Board.
By @callimcflurry.bsky.social
#neuroskyence
www.thetransmitter.org/community/fl...
Here it is! Postdoctoral position to identify the progenitors sensory organs in the regenerating legs of Parhyale
apply here: www.averof-lab.org/pages/tracman
1/3
🔬🧬🔍 If you're interested in spatial omics and miRNAs, don’t miss our latest review!
We explore where the early field of spatial miRNomics stands, what’s missing, and why incorporating miRNAs matters for building richer spatial transcriptomic maps.
#SpatialOmics #miRNA #GeneRegulation
We're looking for a PhD student!
Join the team to develop new technologies for targeted spatial omics.
More info and instruction on how to apply at the following link:
su.varbi.com/what:job/job...
We've just been awarded a grant to study the cellular basis of regeneration – to track the progenitors of sensory organs in the context of leg regeneration, in our favourite crustacean tinyurl.com/parhyale, based on live imaging and cell tracking. The project involves some cool collaborations... 1/3
