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Li Zhao

@lizhao.bsky.social

490 followers 400 following 26 posts

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

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Li Zhao @lizhao.bsky.social · Jul 15

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.

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...

rdcu.be

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Li Zhao @lizhao.bsky.social · Sep 8

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?

Reposted by Li Zhao

The Rockefeller University @handle.invalid · Aug 18

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.

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. ...

www.rockefeller.edu

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Reposted by Li Zhao

Ben Hopkins @brhopkins92.bsky.social · Jun 18

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 · Jul 16

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.

Li Zhao @lizhao.bsky.social · Jul 16

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)

Li Zhao @lizhao.bsky.social · Jul 16

Thank you for your kind words. Look forward to seeing more of your work in this subfield too.

Li Zhao @lizhao.bsky.social · Jul 15

Here is the Rockefeller press release: www.rockefeller.edu/news/38025-h.... Thank you for promoting our science.

How new genes get switched on - News

Scientists discovered an identical neural circuit that operates differently in male and female mice.

www.rockefeller.edu

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Li Zhao @lizhao.bsky.social · Jul 15

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...

rdcu.be

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Reposted by Li Zhao

Jae Young Choi @jychoi.bsky.social · Jul 15

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...

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...

www.biorxiv.org

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Reposted by Li Zhao

The Rockefeller University @handle.invalid · Jul 14

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.

How new genes get switched on - News

Scientists discovered an identical neural circuit that operates differently in male and female mice.

www.rockefeller.edu

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Li Zhao @lizhao.bsky.social · Jun 20

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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Reposted by Li Zhao

Casey Dunn @caseywdunn.bsky.social · Jun 11

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

The Dunn Lab

Casey Dunn's laboratory in the Department of Ecology and Evolutionary Biology at Yale University.

dunnlab.org

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Reposted by Li Zhao

Marc Robinson-Rechavi @marcrr.bsky.social · May 13

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

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…

tinyurl.com

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Reposted by Li Zhao

The Vallee Foundation @valleefoundation.bsky.social · May 13

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...

Duke to Award Three Honorary Degrees at 2025 Commencement Ceremony | Duke Today

today.duke.edu

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Li Zhao @lizhao.bsky.social · May 8

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/...

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

academic.oup.com

Li Zhao @lizhao.bsky.social · May 8

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 · May 8

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

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 ...

pnas.org

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Reposted by Li Zhao

The Guardian @theguardian.com · Apr 9

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

www.theguardian.com

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Reposted by Li Zhao

Matthew Herron @matthewherron.bsky.social · Feb 19

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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Reposted by Li Zhao

Genetics Society of America @genetics-gsa.bsky.social · Feb 17

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 · Feb 6

Such a simple and efficient way to make a small quantity of specific fly food media👍

Reposted by Li Zhao

Wanhe Li @xseedling.bsky.social · Feb 6

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 · Jan 31

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 · Jan 31

So sad to hear the news.

Reposted by Li Zhao

Yoav Gilad @ygilad.bsky.social · Jan 17

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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