denard.bsky.social - Profile | ThreadSky | a Reddit-style client for Bluesky

A simple place to start changing things is to stop systematically distributing conference awards among students from big famous labs.

submitted 4 days ago • 0 comments

People always stop me in the street to ask: "Yoav, where are the disease-associated eQLTs? We found a lot in GTEx but we can't find anymore. Do you know where they are?" (For the record, no one has ever asked me this, but it is a really good question!) I think we know where they are.

submitted 6 days ago • 2 comments

This sounds incredibly important.

submitted 11 days ago • 0 comments

The preliminary program of ProbGen 2026, which will be held at UC Berkeley, is now up: probgen2026.github.io Sharing on behalf of Rasmus Nielsen who is not on this site. For more see his thread on that other site: x.com/ras_nielsen/...

submitted 11 days ago • 0 comments

The lab has started using CatBoost to predict selective constraint in mammalian coding sequences, and it is shocking how good it is. It could make it possible to test adaptation accounting for constraint as McDonald-Kreitman does, but without having to do a lot of resequencing to get PN/PS.

submitted 25 days ago • 0 comments

As I am preparing my MIRA renewal submission, I have been wondering, should I count in the progress report the publications that were not on the main topic of my initial proposal, but were made possible by the methods that we developed for the proposal?

submitted 47 days ago • 2 comments

Fun collaboration with Mélodie Bastian and Nicolas Lartillot. Pi_S and Pi_N/Pi_S extracted from genome assemblies follow nearly neutral predictions across 150 mammals. Getting closer to getting the constraint controls needed to detect ancient epidemics mammals-wide. www.biorxiv.org/content/10.1...

submitted 52 days ago • 1 comment

This excellent preprint makes me wonder how frequent reversion of adaptive substitutions is (that are deleterious when the selective pressure is gone), and how much of of the true extent of adaptation we might miss looking at divergence after the fact as result. www.biorxiv.org/content/10.1...

submitted 62 days ago • 0 comments

Our latest paper revisits Haldane 1957 on speed limits to adaptation, the paper that triggered neutral theory. We clarify and then significantly extend the theory, and apply the resulting model to @mexpositoalonso.bsky.social's data doi.org/10.1093/gene... 1/14

submitted 89 days ago • 8 comments

Shameless self promotion of an excellent article on #EvMed #PetosParadox by @vcallier.bsky.social heads up @ubuffalo.bsky.social 🧪 🐘 🦇🐋🧫🧬

submitted 92 days ago • 0 comments

The question of selection during the Black Death will likely require a Yersinia pestis-human-host interactome. Looking at selection at human YIPs (Yersinia-interacting proteins) should be more specific and powerful than immune genes in general. Population genetics in a silo can only go so far.

submitted 98 days ago • 0 comments

Following criticisms raised concerning our article www.nature.com/articles/s41..., we just confirmed our original conclusions, demonstrating that the rs2549794 variant near the ERAP2 locus displays a strong positive selection signal associated with the Black Death ☠️ www.nature.com/articles/s41...

submitted 112 days ago • 0 comments

I am a bit surprised to see many posts on the response to the selection during Black Death paper without also a link to the response to the response, as it has been out for a long while now: www.nature.com/articles/s41... www.biorxiv.org/content/10.1...

submitted 99 days ago • 0 comments

A few macro shots of flying bees I took recently in Tucson. Winter is a bit different here.

submitted 106 days ago • 0 comments

1/2) You cannot look for a general sweep signature in humans without carefully controlling for functional density and background selection, i.e. trying to make other things equal. The persistent lack of consideration for such as basic control has been a bizarre thing to witness.

submitted 107 days ago • 1 comment

Was just discussing evidence of positive natural selection in humans with a colleague who cited Hernandez 2011 paper for the lack of selective sweeps pubmed.ncbi.nlm.nih.gov/21330547/ and his firm belief that this showed that studies showing natural selection in humans are mostly false positives 1/n

submitted 107 days ago • 2 comments

C'est tres simple. Jayce et les Conquérants de la Lumiere ne sont pas venus, et les Monstroplantes ont gagné.

submitted 118 days ago • 0 comments

New paper with @lucievirevolte.bsky.social and @psudmant.bsky.social, led by Lucie Etienne and Amandine Le Corf. The sub-cellular localization of important innate antiviral factor GBP5 has evolved multiple times during bat evolution, with consequences for activity. www.biorxiv.org/content/10.1...

submitted 118 days ago • 0 comments

👀Our latest work, led by Amandine Le Corf fantastic PhD student alumni @biorxivpreprint.bsky.social . Great collab @denard.bsky.social @psudmant.bsky.social Genomic and functional #adaptations in #GBP5 highlight specificities of #bat antiviral innate #immunity 🦇🦠 www.biorxiv.org/content/10.1...

submitted 119 days ago • 1 comment

Macro shot of bees mid-flight around poppies at the Tucson Botanical Gardens.

submitted 123 days ago • 0 comments

#a7rv macro shots with a cheap Tamron travel zoom lens. Can't wait to see what comes out of a proper macro lens.

submitted 153 days ago • 0 comments

A crop of ~8% of the original raw, not even with a prime lens. The new camera is a beast.

submitted 167 days ago • 1 comment

An excellent article by B. Charlesworth. I would add a potential "exctinction bias" (those populations we are seeing have higher diversity given their),hybridization processes homogenizing diversity, and epistasis at very large population sizes. academic.oup.com/gbe/article/...

submitted 180 days ago • 0 comments

What do GWAS and rare variant burden tests discover, and why? Do these studies find the most IMPORTANT genes? If not, how DO they rank genes? Here we present a surprising result: these studies actually test for SPECIFICITY! A 🧵on what this means... (🧪🧬) www.biorxiv.org/content/10.1...

submitted 182 days ago • 4 comments

Based on struggles with specific CNN training sets, we have started considering the idea of finding a limit recombination rate below which it becomes very hard to distinguish real sweeps from false +. Demography-dependent, and there may be regions of the genome where the issue just cannot be solved.

submitted 181 days ago • 0 comments

A very interesting preprint. The same is likely true for closely related bat species with great phenotypic differences maintained in the presence of massive gene flow. www.biorxiv.org/content/10.1...

submitted 185 days ago • 1 comment

Photography has become a lot easier than it used to. Shot this today without a tripod, no macro lens, and windy conditions. Unthinkable without insane pro skills with good gear even from just 15 years ago.

submitted 186 days ago • 0 comments

We identified protein domains in LUCA (Last Universal Common Ancestor). Their distinctive amino acid usage reveals the order amino acids were added to the genetic code, based mostly on size. Older proteins hint at earlier alternative codes. 1/15 @seekingluca.bsky.social www.pnas.org/doi/10.1073/...

submitted 186 days ago • 12 comments

An interesting question that came up going over a comps proposal: do sweeps without introgression bias ABBA-BABA based D or F statistics?

submitted 188 days ago • 1 comment

Check it out - PhD student @maggiesteiner.bsky.social's nice thread and link to our new preprint on how sample design, in terms of how geographically narrow vs broad a sample is, impacts the discovery/SFS of deleterious variants.

submitted 194 days ago • 1 comment

Your SNPs aren't where you think they are. ~10% of SNPs in maize aren't where the vcf says they are. Work by Edwin Solares when he was a pdoc in the lab. With a doi as a couple folks have asked for something they could cite (hopefully a paper someday). 🖥️🧬 figshare.com/articles/fig...

submitted 194 days ago • 1 comment

As we approach mid-winter, an illustration of cave art showing two Reindeer; from Font de Gaume cave, France. One is licking or smelling the other who appears to be sleeping? giving birth? dead or dying?. Originally rendered by someone of the Magdalenian culture, 16,000 years ago. #AncientSky 🦣🏺

submitted 196 days ago • 19 comments

🧪 Join us in Tucson! We will begin reviewing applications on December 9 for our tenure track faculty position on the genomics of resilience @uofa-eeb.bsky.social! Apply here: arizona.csod.com/ux/ats/caree...

submitted 196 days ago • 0 comments

Germany has been a head scratcher for me. It is persisting with irrational energy policies driven by science-denying ideology, that they have the audacity to still try to force on the rest of Europe. The inability of the country to get in order and be a leader is telling.

submitted 198 days ago • 1 comment