Junyue @junyue_cao Twitter profile

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Junyue

@junyue_cao

4 months

What if 1 million scRNA-seq libraries can be prepared within $1k? Here we go 👉 21 million cells from 623 mouse tissues, spanning 5 life stages & 3 genotypes, all in a SINGLE study by ONE remarkable student Zehao @Tommyz626 from our lab @RockefellerUniv !

A Panoramic View of Cell Population Dynamics in Mammalian Aging

To elucidate the aging-associated cellular population dynamics throughout the body, here we present PanSci, a single-cell transcriptome atlas profiling over 20 million cells from 623 mouse tissue...

www.biorxiv.org

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Junyue

@junyue_cao

7 months

EasySci is now published! 🌟 A big congratulations to Andras, @ziyu__lu , and Jasper from our team at @RockefellerUniv . Planning to prepare a scRNA-seq library for 1 million cells on a budget of just $700?Discover our detailed protocol here:

A global view of aging and Alzheimer’s pathogenesis-associated cell population dynamics and...

Nature Genetics - Single-cell transcriptomes and single-cell chromatin accessibility profiles generated using EasySci provide a global view of aging and Alzheimer’s pathogenesis-associated...

www.nature.com

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Junyue

@junyue_cao

2 years

Hello World! Thrilled to share the first two preprints from Cao lab at @RockefellerUniv . Both focus on understanding cell population dynamics in aging/AD through new single-cell genomic techniques, led by our fantastic @ziyu and Andras!

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Junyue

@junyue_cao

9 months

PerturbSci-Kinetics for high-throughput functional characterization of RNA dynamic regulators is published today @NatureBiotech , led by fantastic @xu_zxu from our lab @RockefellerUniv !

Nature Biotechnology

@NatureBiotech

9 months

Dissecting key regulators of transcriptome kinetics through scalable single-cell RNA profiling of pooled CRISPR screens

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Junyue

@junyue_cao

4 years

I am deeply honored to receive this Grand Prize from @ScienceMagazine and @scilifelab ! This is not possible without the great support from my Ph.D. mentor @JShendure ! Also thanks to all friends and colleagues from @uwgenome and @RockefellerUniv .

Rockefeller University

@RockefellerUniv

4 years

Rockefeller's @junyue_cao has won the @ScienceMagazine & @scilifelab Grand Prize For Young Scientists! Cao is recognized for his work using single-cell genomic methods to enable developmental mapping of entire organisms. Read his essay here:

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Junyue

@junyue_cao

4 years

Our new work about visualizing cell state dynamics with sci-fate is out: ! Also, I am thrilled to announce that I will start my lab in @RockefellerUniv , August 2020 ()! So grateful to the support from my amazing mentor @JShendure and

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Junyue

@junyue_cao

1 year

Excited to share our latest preprint from Cao Lab - PerturbSci-Kinetics, led by brilliant @xu_zxu ! The technique captures single-cell transcriptome, nascent RNA, and sgRNA identity in pooled CRISPR screens, for identifying key regulators of RNA kinetics.

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Junyue

@junyue_cao

4 years

Please check our newest work! A human cell atlas of both gene expression and chromatin accessibility across 15 fetal tissues! All data are available on . The protocol is available on .

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Junyue

@junyue_cao

9 months

How does aging impact the proliferation and differentiation rates across diverse cell types in the brain? Explore this question with TrackerSci in @CellCellPress : . Kudos to the incredible @ziyu__lu and Melissa Zhang of our lab @RockefellerUniv !

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Junyue

@junyue_cao

3 years

Very excited to receive the NIH Director's New Innovator Award from @NIH_CommonFund for developing single-cell techniques to profile cell dynamics in vivo. Thanks to the enormous support from my PhD advisor @JShendure , our collaborators, and colleagues from @RockefellerUniv !

NIH Common Fund

@NIH_CommonFund

3 years

Find out what innovative, high-impact #biomedical or behavioral research projects early career investigators are pursuing with @NIHDirector ’s New Innovator awards: . #NIHHighRisk

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Junyue

@junyue_cao

4 years

Thanks, Jay! It is such an amazing experience with so many exciting moments in the last five years. Just feel so fortunate to have all the support from you and all friends in @JShendure lab and @uwgenome . Flying to NYC tomorrow and will miss you all and Seattle so much!!

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Junyue

@junyue_cao

2 years

Highlights of the first: 1. EasySci - 1M snRNA with library cost of ~$700 2. 1.5M snRNAseq + 400k snATAC of mouse brains across the adult lifespan and two AD models 3. >30 Age or AD-associated rare cell types 4. >100k snRNA-seq of human AD samples

A global view of aging and Alzheimer’s pathogenesis-associated cell population dynamics and...

Although several studies have applied single-cell approaches to explore gene expression changes in aged brains, they were limited by the relatively shallow sampling of brain cell populations, and...

www.biorxiv.org

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Junyue

@junyue_cao

2 months

🎉 Congratulations to Dr. Andras Sziraki, our first graduate student, for an outstanding PhD dissertation!! 🎓 Please check out his featured work here: .

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Junyue

@junyue_cao

5 years

Recover past, current and future transcriptome dynamics at single cell level in real time - please check our latest preprint!

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Junyue

@junyue_cao

4 years

Excited to see the official announcement from Rockefeller! Please check our website: We are recruiting!

Rockefeller University

@RockefellerUniv

4 years

Excited that @junyue_cao will be joining Rockefeller this summer! Cao examines patterns of gene expression to better understand how cells differentiate into distinct types and how the body’s organs maintain stable populations of cells throughout life.

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Junyue

@junyue_cao

5 years

Thanks so much to the support from our lab @JShendure , MCB program @MCBSeattle , and all friends in our department @uwgenome !

UW Graduate School

@UWGradSchool

5 years

We’re announcing the winners of 3MT! People’s choice AND the second place award goes to Junyue Cao, @MCBSeattle #3mt #uw #uwgradsuccess

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Junyue

@junyue_cao

9 months

Congratulations, Zihan! A fantastic start to your 3rd year in graduate school 🎉

Zihan Xu

@xu_zxu

9 months

Thrilled to see the first chapter of my phd work published online at @NatureBiotech 📄 Grateful for every incredible member of the @junyue_cao Lab that made this possible!

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Junyue

@junyue_cao

2 years

Highlights of the second: 1. Trackersci -profiling ATAC/RNA dynamics of progenitor cells in vivo 2. Cellular proliferation/differentiation potential quantified across ages 3. ~800k snRNAseq of the aged human brain 4. Regional-specific progenitor cells

A comprehensive view of cell-type-specific temporal dynamics in human and mouse brains

Progenitor cells play fundamental roles in preserving optimal organismal functions under normal, aging, and disease conditions. However, progenitor cells are incompletely characterized, especially in...

www.biorxiv.org

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Junyue

@junyue_cao

5 years

So excited to share our research! Great collaboration with @malte_spielmann with enormous support from @JShendure and @coletrapnell ! sci-RNA-seq3 for profiling the cell-ome of whole embryo comprising five development stages, 61 individuals, 2 million cells in a single experiment!

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Junyue

@junyue_cao

3 years

Congratulations to my previous baymate @bethkarenmartin in @JShendure lab for this fantastic work! sci-RNA-seq is now much easier, cheaper, and compatible with more tissues!!

Jay Shendure

@JShendure

3 years

Our latest preprint, from the ingenious @bethkarenmartin , is an optimized, streamlined version of the three-level combinatorial indexing (split/pool) protocol for single cell RNA-seq (sci-RNA-seq3), originally developed by @junyue_cao . 1/4

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Junyue

@junyue_cao

6 years

Our latest paper sci-CAR in Science!

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Junyue

@junyue_cao

1 year

Fantastic work delineating how life is generated by 12 million single-cell transcriptomes in a single study (from E8 to P0)! Congratulations to my former colleagues at @JShendure lab, especially @CXchengxiangQIU and @bethkarenmartin !

Jay Shendure

@JShendure

1 year

Excited to share our lab's latest preprint, led by @CXchengxiangQIU , @bethkarenmartin & Ian Welsh of @jacksonlab . We set out to build a single cell roadmap for all of mouse prenatal development, from single cell zygote to free-living pup. Preprint: 1/n

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Junyue

@junyue_cao

7 months

Single-cell characterization of many genetic mutants at the scale of the entire organism! A great collaboration with @malte_spielmann lab and my fantastic colleagues in @JShendure lab!

Malte Spielmann

@malte_spielmann

7 months

So happy to share the final version of our single cell whole embryo paper out today @Nature ! Such a great collaboration with @junyue_cao & @JShendure labs @UKSH_KI_HL @UniLuebeck @MPI_MolGen @kieluni Check out the summary by @HenckJana :

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Junyue

@junyue_cao

4 years

friends in @uwgenome and @MCBSeattle , special thanks to @coletrapnell , Robert Waterston, David Beier, @vram142 @cusanovich @malte_spielmann @jspacker @jaydencaomom and my awesome labmates. Excited to start and we are recruiting! Please check the website if you are interested!

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Junyue

@junyue_cao

2 years

Also, If you are interested in genomics technique development or aging biology, we have two postdoc positions open immediately!

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Junyue

@junyue_cao

2 years

Really appreciate the support from all authors, our great collaborators (Nelson lab, Gan lab, and Ge lab), @cegs_ica , and great suggestions from @JShendure and @satijalab !!

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Junyue

@junyue_cao

4 months

Exciting insights: 👉 Identified >200 cell states with significant changes in aging. 👉 Aging progresses in distinct waves, not linearly. 👉 Revealed organ-specific change in immune cells during aging. 👉 Decoded lymphocyte interactions with other cells using 'cell-knockdown'.

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Junyue

@junyue_cao

2 years

Congratulations to @CXchengxiangQIU for the fantastic work!

Jay Shendure

@JShendure

2 years

Short thread on our latest work, from the incredible @CXchengxiangQIU (CX Qiu), entitled "Systematic reconstruction of cellular trajectories across mouse embryogenesis", which is out today in @NatureGenet . Link to accessible version: 1/n

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Junyue

@junyue_cao

1 year

Congrats Kathleen @kathleenabadie and @Kueh_Lab ! Great to see the preprint is out!

kathleenabadie

@kathleenabadie

1 year

Do you ever question prior decisions as you gain new information? Do you wonder if immune cells do too? Check out our @Kueh_Lab preprint about a flexible T cell decision-making strategy that enables robust and scalable control of immunological memory (1/n)

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Junyue

@junyue_cao

1 year

See the detailed highlight of PerturbSci-kinetics from the lead author Zihan @xu_zxu !

Zihan Xu

@xu_zxu

1 year

I am thrilled to share our latest research, PerturbSci-Kinetics, a novel low-cost and scalable combinatorial-indexing single-cell technique enabling the co-capture of transcriptomes, nascent transcriptomes, and genetic perturbations. (1/5)

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Junyue

@junyue_cao

3 years

So excited to try this out!

Rahul Satija

@satijalab

3 years

We're excited to release an Azimuth reference of human fetal development. Leverages an incredible sci-RNA-seq3 dataset of 15 organs from @coletrapnell @jshendure and @junyue_cao . You can map and annotate your own data onto this reference at

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Junyue

@junyue_cao

4 months

Thanks for the great support from all co-authors and our collaborators from @satijalab lab, UCSC @cellbrowser , and @cegs_ica ! The full dataset is available at: 👉 GEO 👉 UCSC cell browser () 👉 Azimuth ()

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Junyue

@junyue_cao

7 months

Thanks to every member of our team, our fantastic collaborators from @LiGanLab and Nelson lab, and my previous colleagues from @JShendure lab! We deeply appreciate the support from @RockefellerUniv and @cegs_ica , and the valuable suggestions from all reviewers and editors!

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Junyue

@junyue_cao

7 years

Worm atlas profiles gene readouts in every cell type in the animal

The roundworm stars in the first-ever compilation of gene readouts in every kind of cell in an animal. The readouts, which were taken at a particular stage in the worm's life, reveal, for example,...

phys.org

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Junyue

@junyue_cao

9 months

@NatureBiotech @xu_zxu @RockefellerUniv Thanks for the constructive feedback from the editors and all reviewers. We gratefully acknowledge our funders, including NIH, the Mathers Foundation, and @cegs_ica , and the great support from @JShendure and @satijalab !

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Junyue

@junyue_cao

2 years

@science_wallet @RockefellerUniv @ziyu With 5000 raw reads/cell, the sequencing cost (5 billion reads) for 1M cells ranges from $2k to $9k depending on the sequencing platform

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Junyue

@junyue_cao

2 years

A correction: this the real Twitter account of our Ziyu Lu: @Ziyu_0401

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Junyue

@junyue_cao

4 months

@ElliotHershberg Thanks Elliot! It still feels like yesterday for my dissertation : )

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Junyue

@junyue_cao

2 years

Congratulations on the Mendel award, Jay!!

Jay Shendure

@JShendure

2 years

Honored to have been the Mendel Lecturer at #ESHG2022 on the 200th anniversary of his birth, and for this very fun artwork by Alicia Bergsten and Christin Bjork 🧬😀🖼

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Junyue

@junyue_cao

1 year

@Xiaojie_Qiu Congratulations Xiaojie!!

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Junyue

@junyue_cao

5 years

@AnjaOllodart Thanks! - the timing is not in our plan but happy they are born together :)

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Junyue

@junyue_cao

5 years

It made my day😂

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Junyue

@junyue_cao

2 years

@HumphreysLab @Cell_Metabolism @HaikuoLi @EzrinRadixin @HaojiaWu Congratulations! Really great to see all these optimizations!

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Junyue

@junyue_cao

9 months

Thanks for the great support from our collaborators in Shaoyu Ge Lab, Peter Nelson Lab, and @cegs_ica ! Our work has been vastly improved from the preprint version thanks to constructive feedback from editors and all reviewers!

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Junyue

@junyue_cao

4 years

@jcjray Thanks for your support Christian!

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Junyue

@junyue_cao

2 years

@lpachter Hi Lior, we are currently uploading the data and will update the preprint once ready. Of course, if you are interested in the raw data, we are happy to share them upon request.

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Junyue

@junyue_cao

2 years

@SStevenWang @psscra Congratulations!

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Junyue

@junyue_cao

2 years

@MartinBJensen @RockefellerUniv @ziyu Thanks, Martin! Excited to explore more aging biology!