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Li Zhao

@lizhao.bsky.social
583 followers 438 following 41 posts

Associate Professor at the Rockefeller University. We study gene origination, molecular evolution, and the genetic basis of adaptive traits.

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Reposted by Li Zhao
ching-hochang.bsky.social @ching-hochang.bsky.social · 08/10/2026
Thrilled to share that our paper is finally out in Science Advances! 🔗 www.science.org/doi/10.1126/... TL;DR: A Drosophila protamine acts as shields resolving conflict between X and Y chromosomes. Disruption unleashes meiotic drive that kills X-bearing sperm and skews progeny sex ratios. 🪰🧬ᯡ
science.org
Rapid protamine evolution suppresses meiotic drive in Drosophila
Many animal species replace histones with protamines during spermatogenesis. Although essential for sperm function, protamines evolve rapidly for reasons that remain unknown. Using in vivo gene replac...
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Reposted by Li Zhao
ching-hochang.bsky.social @ching-hochang.bsky.social · 11/07/2025
We’re actively recruiting at all levels: RAs, MS students, PhD students, and postdocs. If you’re passionate about evolutionary biology and excited to explore how lives are shaped by genetic conflicts, we’d love to hear from you! sites.google.com/view/ecg-lab...
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Reposted by Li Zhao
ching-hochang.bsky.social @ching-hochang.bsky.social · 08/10/2026
Research is full of uncertainty, but every once in a while, nature works out exactly as you hypothesized. In 2019, while finishing my PhD, I pitched a bold idea in an email to @harmitmalik.bsky.social (below). Seven years later, it feels surreal to see that hypothesis become empirical reality. 🧵👇
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Graham Coop @gcbias.bsky.social · 10/09/2026
I’m looking to hire an NIH funded postdoc to join our lab here at Davis (please RT). Ongoing areas of interest include: 1) polygenic signals of selection from time series, ARGs, GWAS, etc 2) The interpretation of GWAS, polygenic scores, & sources of confounding
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Li Zhao @lizhao.bsky.social · 11/09/2026
As I recall, the predictions from most of the five models converged, but we did not focus on that question and used the best-scoring prediction for downstream study. You can check the FlyPredictome website; I believe it lists results from all five models, not just the best-performing one.
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Li Zhao @lizhao.bsky.social · 11/09/2026
To be clear, they are not more likely to form direct interactions than other evidence, not the null expectation. The FlyPredictome bioRxiv manuscript found a similar pattern. Whether this reflects the dynamic nature of PPIs or AF2 prediction is unclear to us, perhaps both.
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Reposted by Li Zhao
Dan Schrider @samurscicop.bsky.social · 28/04/2026
Please circulate: I will have a postdoc opening soon, ideally with a start date sometime this summer or fall. If you're interested in empirical population genetics, computational methods development, and/or evolutionary modeling via simulation, don't hesitate to reach out. For more info on the lab:
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Li Zhao @lizhao.bsky.social · 27/03/2026
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
academic.oup.com
The Origin and Evolution of Sex Peptide and Sex Peptide Receptor Interactions
Abstract. Post-mating responses play a vital role in successful reproduction across diverse species. In fruit flies, sex peptide binds to the sex peptide r
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Li Zhao @lizhao.bsky.social · 27/03/2026
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.
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Li Zhao @lizhao.bsky.social · 27/03/2026
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.
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Li Zhao @lizhao.bsky.social · 27/03/2026
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.
melppi.github.io
DmelPPI Project
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Li Zhao @lizhao.bsky.social · 27/03/2026
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...
journals.plos.org
A predicted structural interactome reveals binding interference from intrinsically disordered regions
Author summary Understanding which proteins interact with each other and how they interact is essential for uncovering fundamental biology and for identifying new pathways involved in health and disea...
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Li Zhao @lizhao.bsky.social · 24/03/2026
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
sciencedirect.com
Machine learning for evolutionary genetics and molecular evolution
Over the past decade, the rapid expansion of large-scale data and advances in computational power have allowed machine learning (ML), especially deep …
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Reposted by Li Zhao
Jun Ishigohoka @junishigohoka.bsky.social · 27/02/2026
www.sciencedirect.com/science/arti...
sciencedirect.com
Strain variation identifies a neural substrate for behavioral evolution in Drosophila
Sexual selection acts on heritable differences within species, driving the parallel diversification of signal production in one sex and behavioral res…
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Reposted by Li Zhao
Nature Reviews Genetics @natrevgenet.nature.com · 29/01/2026
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!
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Li Zhao @lizhao.bsky.social · 29/01/2026
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.
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Li Zhao @lizhao.bsky.social · 29/01/2026
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.
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Li Zhao @lizhao.bsky.social · 29/01/2026
Interestingly, D. suzukii and D. subpulchrella showed stronger firing, but behaviorally, they showed indifference to CO2, suggesting another layer of central brain innovation.
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Li Zhao @lizhao.bsky.social · 29/01/2026
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.
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Li Zhao @lizhao.bsky.social · 29/01/2026
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...
journals.plos.org
Molecular evolution of CO2-sensing ab1C neurons underlies divergent sensory responses in the Drosophila suzukii species group
Author summary Animals rely on their senses to locate food sources and identify suitable reproductive sites in their environment. Closely related species can evolve strikingly different preferences as...
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Molly Przeworski @mollyprz.bsky.social · 14/01/2026
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*.
events.simonsfoundation.org
Home - NY Population Genetics meeting
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Mark Peifer (He, him) @peiferlabunc.bsky.social · 12/12/2025
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...
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.
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Li Zhao @lizhao.bsky.social · 14/11/2025
Please help spread the words @cedricfeschotte.bsky.social @anthonygeneva.bsky.social @danielbolnick.bsky.social @levine-lab.bsky.social @itaiyanai.bsky.social @lucksmith.bsky.social
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Li Zhao @lizhao.bsky.social · 14/11/2025
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.
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Li Zhao @lizhao.bsky.social · 08/09/2025
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?
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The Rockefeller University @rockefeller.edu · 18/08/2025
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.
rockefeller.edu
A. James Hudspeth, neuroscientist who unlocked secrets of hearing, has died - News
A. James Hudspeth, a Rockefeller neuroscientist who discovered how sound waves are converted into electrical signals in the ear's cochlea, died Saturday at his home in Manhattan. A pioneering scientist and dedicated mentor, he was the university's F.M. ...
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Ben Hopkins @brhopkins92.bsky.social · 18/06/2025
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 🪰🧬
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Li Zhao @lizhao.bsky.social · 16/07/2025
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.
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Li Zhao @lizhao.bsky.social · 16/07/2025
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)
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Li Zhao @lizhao.bsky.social · 16/07/2025
Thank you for your kind words. Look forward to seeing more of your work in this subfield too.
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Li Zhao @lizhao.bsky.social · 15/07/2025
Here is the Rockefeller press release: www.rockefeller.edu/news/38025-h.... Thank you for promoting our science.
rockefeller.edu
How new genes get switched on - News
Scientists discovered an identical neural circuit that operates differently in male and female mice.
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Li Zhao @lizhao.bsky.social · 15/07/2025
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.
rdcu.be
Gene regulatory networks and essential transcription factors for de novo-originated genes
Nature Ecology & Evolution - A combination of computational methods applied to single-cell RNA sequencing data and genetic experiments shows that a small number of transcription factors are...
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Jae Young Choi @jychoi.bsky.social · 15/07/2025
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...
biorxiv.org
Topsicle: a method for estimating telomere length from whole genome long-read sequencing data
Telomeres protect chromosome ends and its length varies significantly between organisms. Because telomere length variation is associated with various biomedical and eco-evolutionary phenotypes, many b...
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Reposted by Li Zhao
The Rockefeller University @rockefeller.edu · 14/07/2025
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.
rockefeller.edu
How new genes get switched on - News
Scientists discovered an identical neural circuit that operates differently in male and female mice.
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Li Zhao @lizhao.bsky.social · 20/06/2025
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!
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Casey Dunn @caseywdunn.bsky.social · 11/06/2025
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
dunnlab.org
The Dunn Lab
Casey Dunn's laboratory in the Department of Ecology and Evolutionary Biology at Yale University.
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Marc Robinson-Rechavi @marcrr.bsky.social · 13/05/2025
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
tinyurl.com
Opportunités de carrière : Postdoctoral position in evolutionary genomics (22280)
Saisissez une liste de termes, que nous allons rechercher dans le titre du poste et sa description. \nAstuces\xa0:\n\nNous rechercherons tous les mots figurant dans la recherche.\nLes r\xe9sultats…
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The Vallee Foundation @valleefoundation.bsky.social · 13/05/2025
Congratulations to Feng Zhang (Vallee Scholar 2013) (Broad Inst, MIT, HHMI Investigator) who received an honorary doctorate from Duke University on Sunday! today.duke.edu/2025/04/duke...
today.duke.edu
Duke to Award Three Honorary Degrees at 2025 Commencement Ceremony | Duke Today
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Li Zhao @lizhao.bsky.social · 08/05/2025
4) he provided evidence supporting the cultivator model of de novo gene origination, a model he proposed to explore the link between novel genes/lncRNAs and nearby functionally important genes academic.oup.com/gbe/article/...
academic.oup.com
A Synergistic, Cultivator Model of De Novo Gene Origination
Abstract. The origin and fixation of evolutionarily young genes is a fundamental question in evolutionary biology. However, understanding the origins of ne
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Li Zhao @lizhao.bsky.social · 08/05/2025
2) he used single cell cluster and RNA FISH to confirm that many important "maker genes" show rapid changes of gene expression among specie, 3) he also find some interesting patterns of transcriptional busting size/frequency in spermatogenesis,
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Li Zhao @lizhao.bsky.social · 08/05/2025
I’m very glad to share our recent publication @pnas.org , led by UnJin Lee from our lab at @rockefelleruniv.bsky.social : pnas.org/doi/10.1073/.... In this work, he 1) developed a method to efficiently compare single-cell RNA-seq data from rapidly evolving tissues across multiple species, and
pnas.org
Comparative single-cell analysis of transcriptional bursting reveals the role of genome organization in de novo transcript origination | PNAS
Spermatogenesis is a key developmental process underlying the origination of newly evolved genes. However, rapid cell type–specific transcriptomic ...
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The Guardian @theguardian.com · 09/04/2025
We are witnessing the destruction of science in America | Paul Darren Bieniasz
theguardian.com
We are witnessing the destruction of science in America | Paul Darren Bieniasz
If we stay on this administration’s course, future life-saving medicines may never be invented
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Matthew Herron @matthewherron.bsky.social · 19/02/2025
I lost my job at the National Science Foundation yesterday, along with 167 of my colleagues, including some dear friends. This was the best job I've ever had, and I thought it would be my last. The PI community has been sympathetic and supportive, without exception. I will miss working for you.
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Genetics Society of America @genetics-gsa.bsky.social · 17/02/2025
We're excited to announce the 2025 Larry Sandler Award recipient, @peiwei-chen.bsky.social 🎉 This award recognizes students completing a PhD in Drosophila research. Dr. Chen will present the Larry Sandler Memorial Lecture on evolutionary innovation in genome defense at #Dros25 in March. 1/3🧵
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Li Zhao @lizhao.bsky.social · 06/02/2025
Such a simple and efficient way to make a small quantity of specific fly food media👍
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Wanhe Li @xseedling.bsky.social · 06/02/2025
Dear All, I believe that this thread will become one of my most important contributions to the fly field (I hope I will make other contributions)! Here, I introduce the Soy Milk Machine Fly Food Method, a.k.a., DeepCook!#Drosophila#NewPI
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Li Zhao @lizhao.bsky.social · 31/01/2025
So sad to hear of the passing of Scott Hawley. In 2008, Michael Ashburner, Scott Hawley, and Casey Bergman held a Drosophila genetics and genomics course in China. This course was instrumental in shaping me as a junior researcher, and I am forever grateful about this eye-opening experience.
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Li Zhao @lizhao.bsky.social · 31/01/2025
So sad to hear the news.
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Yoav Gilad @ygilad.bsky.social · 17/01/2025
My book, An Intuitive Primer on Effective Functional Genomics Study Design, is published! I’d really appreciate it if you could help spread the word, and I’d love to hear your thoughts and feedback. I hope people will find it useful. It’s available on Amazon: tinyurl.com/mx2hewen
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Matt Rockman @wormsrock.bsky.social · 23/01/2025
Undergrads: apply to NYU's Summer Undergraduate Research Program in Biology! 10 weeks of research in a structured setting, featuring terrific mentors, exciting biology, housing in New York, and a stipend. as.nyu.edu/biology/outr...
as.nyu.edu
Simons Foundation-NYU Biology Summer Undergraduate Research Program (SURP)
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