This project actually took a long time. One of the first questions we studied using this idea was this paper, which used structural modeling and ancestral sequence reconstruction to examine ligand-receptor (sex peptide, SPR) evolution. academic.oup.com/mbe/article/... @official-smbe.bsky.social
If we trust AlphaFold, it means either the experimental data are very noisy, or the interactions inferred from them are primarily indirect. Either way, we need to think more deeply about what it means for protein-protein interactions in the cellular context.
A “concerning” observation is that protein interactions inferred from experimental data are not more likely to show direct interactions in AlphaFold models than what we normally consider weak evidence, e.g., coexpression or text mining.
Most predicted dimers involve binding through disordered regions, not just ordered regions. We generated a DmelPPI website melppi.github.io, so you may download publishable data for your pairs of interest.
In our recent paper in PLoS Computational Biology, we used AlphaFold2 Multimer to predict the structural details of ~28,000 protein-protein interactions from high-confidence STRING pairs in Drosophila, and identified interesting patterns in disordered regions. journals.plos.org/ploscompbiol...
We wrote a review on using machine learning to study evolutionary genetics and molecular evolution in Trends in Genetics. It is open access—please take a look if you are interested in this topic www.sciencedirect.com/science/arti... @cp-trendsgenetics.bsky.social
De novo genes arise from previously non-coding sequences. This evolutionary path — when randomly expressed sequences become folded and active proteins — challenges our understanding of genetic innovation. New Review by @bornberglab.bsky.social and @lacholt.bsky.social out now!
For me, this is a neat example of evolution's flexibility: similar ecological traits can evolve through distinct genetic mechanisms yet converge on the same physiology, even in closely related species.
We recreated this CO₂ sensitivity in D. melanogaster by generating transgenic lines that swap regulatory or protein-coding sequences from D. suzukii and D. subpulchrella and found that enhancers and proteins in each species play different roles in this convergent trait.
Interestingly, D. suzukii and D. subpulchrella showed stronger firing, but behaviorally, they showed indifference to CO2, suggesting another layer of central brain innovation.
What’s wild: D. suzukii and its sister species show an early burst of neural firing when they smell CO₂, a timing feature missing in D. melanogaster. Same cue, different neural code.
Very excited to share the work by Alice Gadau. We found that D. suzukii (the invasive pest that loves ripe fruit) doesn’t hate CO₂, while classic lab flies avoid it. That tiny sensory shift helps explain a big ecological transition.
journals.plos.org/plosgenetics...
Registration for the 2026 NY Area Population Genetics meeting is now open, at events.simonsfoundation.org/e0mEoL?rt=8k.... Registration is free but required; if you are submitting an abstract, note that the deadline is *January 30th*.
Dear Mark, Only three days left to nominate for the Larry Sandler Award! The award recognizes excellent recent graduates who have completed a PhD in Drosophila research. The awardee will receive a fantastic opportunity to present the Larry Sandler Memorial Lecture at the 67th Annual Drosophila Research Conference in Chicago, IL! The deadline to nominate is Monday, December 15, 2025. Nominate Here For more information visit the website.
Fly Friends: The Larry Sandler Award recognizes the PhD student with the most amazing these using Drosophila as a model. Just three days left to nominate someone. For more info on the process and the link to nominations, see:
genetics-gsa.org/drosophila-2...
Please help spread the words @cedricfeschotte.bsky.social @anthonygeneva.bsky.social @danielbolnick.bsky.social @levine-lab.bsky.social @itaiyanai.bsky.social @lucksmith.bsky.social
Our NY area population genetics meeting is back and "upgraded", as Simons Foundation @simonsfoundation.org generously agreed to host. Please save the date: March 9, 2026. Look forward to seeing many of you from NY and beyond.
Wow. You truly transformed the house into a great one. How did you mange to have a garden and make sure deers don't eat everything?
We are deeply saddened to share that our friend and colleague Jim Hudspeth passed away on Saturday. We will remember and continue to be inspired by Jim’s integrity, his humility, and his unwavering commitment to discovery.
I am delighted to be starting as an assistant professor in the Department of Molecular Genetics & Microbiology at the University of Florida in January 2026. The lab is broadly interested in the functional, developmental, and evolutionary genetics of cell types and organs across flies and beyond 🪰🧬
as one would wonder if it's the tMAC effect or Achi/Vis effect. For the transgenic+RNAseq analysis we see 5 genes (aly, come, tomb, p55 and wuc) showed positive exp. correlations with vis expression, whereas topi and mip40 did not. The 5 genes may play a partial role although we are not sure yet.
Thanks for the kind words, Jongmin. This work was the work I briefly mentioned in the Q&A (but not the talk) related to your question in my seminar visit at Cornell last fall. We checked the tMAC complex and the pattern observed by large-scale computation is specific to Achi/Vis... ( next thread)
Thank you for your kind words. Look forward to seeing more of your work in this subfield too.
Here is the Rockefeller press release: www.rockefeller.edu/news/38025-h.... Thank you for promoting our science.
Our latest paper is out: rdcu.be/ev6Ym — one of my favorite projects. It began about 8 years ago when Nobel laureate Torsten Wiesel asked me: what transcription factors regulate new genes? I had no idea then. Now we have some answers.
I'm very excited to share a new method my grad student @linhngk.bsky.social and I have developed. Here's Topsicle a new computational method for analyzing long read sequencing data and estimate telomere length. Please see our preprint or this thread for detail!
www.biorxiv.org/content/10.1...
Rockefeller's @lizhao.bsky.social has spent nearly a decade cataloguing evolutionarily young genes. Now, complementary studies in @pnas.org and @natecoevo.nature.com are the first to demonstrate how these new genes are regulated and expressed.
If you are an SMBE member and received the election email (it may have gone to your junk folder), I would be honored if you would consider voting for me for councilor. You may also choose to vote for other scientists, and I encourage you to participate in the election. Thank you!
I hope to take a PhD student in the coming application cycle. Please reach out if you are interested in joining our lab in EEB at Yale, especially if interested in working on the natural history/ phylogenetics/ morphology/ population biology/ development/ genomics of siphonophores. dunnlab.org
Postdoc job opportunity! We're looking for ECR in evolutionary genomics to study the relation between intra-specific gene expression variability, polymorphism, and macro-evolutionary rates. We have the data in 3 fishes & amphioxus, just waiting for your expertise and enthusiasm!
tinyurl.com/3aewk286
