Arnaud Martin

Arnaud Martin

@evolvwing.bsky.social

Associate Professor of Biology at the George Washington University Interested in Pattern Formation, Evolutionary Tinkering, Genetics, #lociofevolution #dnacrobatics #evodevo #lepidoptera dnacrobatics.com pubs: https://rb.gy/nfg8p

2.4K followers1.6K following341 posts

Arnaud Martin reposted

Love Dalén
@lovedalen.bsky.social

🚨 Ancient DNA Alert 🚨 Do you depend on BWA aln, and worry that the world’s HPC clusters are pivoting towards GPUs? Fear no more! We here present G-ALN, a GPU implementation that is >6 times faster and produces byte-identical outputs to BWA aln! www.biorxiv.org/content/10.6...

Arnaud Martin
@evolvwing.bsky.social

For the love of god please use this and disyntangle synteny plots, folks!

Joe Hanly@hanliconius.bsky.social

I've made this so it can just take the output of Genespace and reorient the graph to having minimized tangling, and have a less tested version that can take other inputs including minimap2 alignments. This is very much in beta, hit me up if things aren't working. Here's a more complex untangling.

Arnaud Martin
@evolvwing.bsky.social

I mean, look at these plots. So many papers have an equivalent of the left version. bsky.app/profile/hanl...

Joe Hanly@hanliconius.bsky.social

It has a few basic rules (allow whole chr moves, whole chr flips, no connection dropping for prettier pictures, etc), and it generally does quite well. Here's some tangled data with 55 crossings, and the untangled version with 9 crossings, which in this case is the empirically solved min. 4/

Arnaud Martin reposted

Anyi Mazo-Vargas
@anyimv.bsky.social

🎉 First work from my lab at Duke University 🦋 Led by @tianshenbio.bsky.social Shen Tian, whose in situs are 😚🤌, with key contributions from @yf-joye-zhou.bsky.social Joye Zhou. Exploring the evolution of the WntA regulatory network in butterfly wing patterning. www.biorxiv.org/content/10.6...

biorxiv.orgGenetic circuit rewiring underlies a lineage-specific patterning machinery on butterfly wingsPhenotypes evolve through changes in gene regulatory networks (GRNs), but how changes in network topology contribute to phenotypic evolution is still poorly understood. Butterfly wing color patterns p...
Arnaud Martin
@evolvwing.bsky.social

Incredible post-doc opportunity here. Vinod's previous findings on bird structural coloration really knocked me off my feet (www.pnas.org/doi/full/10....). Getting into the omics seems very promising. Also Tours is a beautiful, vibrant city with tons of stuff to do all year.

Vinod Saranathan, The Evolutionary Photonics Lab@evolphotonics.bsky.social

Do you love birds? Have you ever wondered what makes them so colorful? Are you a PhD with expertise in -omics? If yes😃, we are offering a postdoc position at IRBI (CNRS/UTours). Come join us! Apply here: tinyurl.com/phas3sep by 28 October 2026 #ColSci #Birds #omics #HFSP-funded @hfspo.bsky.social

Arnaud Martin reposted

Antoine Molaro
@antoinemolaro.bsky.social

Hello World ! Its pre-print time ! Awesome collaboration led by Michel Cohen-Tannoudji (not on Bsky) and the one and only @deborahbourchis.bsky.social. #BFF We solved the molecular mechanism underlying a mysterious hybrid incompatibility in mice: the DDK syndrome. 🧵🍿 www.biorxiv.org/content/10.6...

biorxiv.orgTransposable Element insertions Repurpose Immune Endonucleases as Drivers of Reproductive Isolation in MiceThe emergence of reproductive barriers between closely related populations is a fundamental step in speciation, yet the underlying genetic mechanisms remain poorly understood in mammals. Here we resol...

Arnaud Martin reposted

Erik van Nimwegen
@erikvannimwegen.bsky.social

Hey, I heard about Bonsai, but now I heard there is another method called MILK that also visualizes scRNA-seq on trees. And it is much faster! Should I just use that then? A tree is a tree, right? TLDR: No. #methodsmatter Not even close. On realistic synthetic data MILK performs worse than UMAP.

Arnaud Martin
@evolvwing.bsky.social

How do people feel about "colon titles" for science articles? I find them increasingly gimmicky and often vacuous. I recommend against them to students and mentees but maybe I am too old-school?

Arnaud Martin
@evolvwing.bsky.social

Cell Press giving a rather biased, pro-eugenics platform to self-proclaimed "Biotech Barbie", former a Thiel Fellow who briefly married He Jiankui, and fails to properly frame the debate on germline editing. Partly bonkers, partly important, check out this thread 🤯

Joe Hanly@hanliconius.bsky.social

@cellpress.bsky.social has just released an.... interesting new 'short review' on pre-implantation gene editing, in which author Cathy Tie argues for the ethical imperative of pushing for this technology. www.sciencedirect.com/science/arti... There are, to put it mildly, a few issues here. 1/

Arnaud Martin reposted

Joe Hanly
@hanliconius.bsky.social

Replying to @hanliconius.bsky.social

I'm sorry, but there's no way to describe this but as a pro-eugenics Op-Ed disguised as a scientific review, and is a complete failure of editorial and ethical standards at @cellpress.bsky.social . This article should be retracted. 5/5

Arnaud Martin reposted

Tessa Montague
@tessamontague.bsky.social

I'm excited to share our new preprint: Generation of a transgenic cephalopod tinyurl.com/pc86jxz8 Cephalopods (cuttlefish, octopus & squid) are crazy critters that dynamically camouflage to their surroundings by changing the color, pattern, & texture of their skin, which they control w their brain.

Arnaud Martin reposted

Joe Hanly
@hanliconius.bsky.social

Very pleased to share that we just released a new ref genome for Colias eurytheme and added the first genome for C philodice to NCBI. Both chrom-level, made with pacbio hi-fi and ci-fi (=pac bio chromatin reads). Both from MD. Please use and share widely, I’ll have a citable source preprinted soon.

Arnaud Martin reposted

Joe Hanly
@hanliconius.bsky.social

I hate to do this with real data, but this is a persistent data vis issue in chromosome synteny riparian plots that we Need to get better at. Left, a synteny plot published today. Right, a rearranged version with exactly the same gross arrangement but with reordered chromosomes:

Arnaud Martin
@evolvwing.bsky.social

Great quote. In a recent piece Morizot also reminds us that "environment" is a derivative of "environ" : french / old french for "surroundings". Our language tends to make nature a foreign entity, at the skirts of civilization, when it actually permeates us.

Arnaud Martin
@evolvwing.bsky.social

for example, a slight clockwise rotation results in a palette that has significantly more chromatic contrast for "green-blind" (deuteranopia/nomaly) readers. There is red and yellow, but VARYING BRIGHTNESS IS KEY

Arnaud Martin reposted

napari
@napari.org

Sizzling Summer Series 4 - global 🌍️ napari 0.9.0 is about ready to fly out the door! ✈️ We would be grateful if you tried out the pre-release: Install into an environment with `pip install "napari[all]>=0.9.0rc1"` or try with uv in a temp environment with `uvx "napari[all]>=0.9.0rc1"`.

Arnaud Martin reposted

Rebekah Rogers
@evolscientist.bsky.social

We will be hosting DC Area research talks on Evolutionary Genetics at GW starting this Fall. First Tuesday of the Month at 3pm, Science and Engineering Hall. Co-founded with Manus Patten at Georgetown University. Please help spread the word.