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Reposted by Travis Lee

Daan Weits @daanweits.bsky.social · 16d

Coming to you live from #ISPLORE2025JP Fresh preprint from my lab showing that leaves progressively oxygenate and how this is important for their morphogenesis.Thanks to our collaborators from @Fra_LicO2si lab. #plantscience
www.biorxiv.org/content/10.1...

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Reposted by Travis Lee

Nature Plants @natplants.nature.com · 19d

New OA Article: "A single-cell rice atlas integrates multi-species data to reveal cis-regulatory evolution" rdcu.be/eHce3

Chromatin accessibility in rice & related grasses: how regulatory DNA elements evolve across cell types & species; identifying potential silencers.

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Travis Lee @tralee-sci.bsky.social · Sep 3

A timely article as several recent conference discussions have led to similar thoughts

www.nature.com/articles/s41...

Multiple overlapping binding sites determine transcription factor occupancy - Nature

A new method enables comprehensive screening and identification of low-affinity DNA binding sites for transcription factors, and reveals that nucleotides flanking high-affinity binding sites create ov...

www.nature.com

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Travis Lee @tralee-sci.bsky.social · Sep 1

Thank you Rashmi!

Reposted by Travis Lee

Natanella Illouz-Eliaz @natanellae.bsky.social · Aug 31

Our #research on #drought #recovery, now published with @springernature.com in @natcomms.nature.com:
Drought recovery in plants triggers a cell-state-specific immune activation.
doi.org/10.1038/s414...

Read thread below 👇

Drought recovery in plants triggers a cell-state-specific immune activation - Nature Communications

Post-drought rehydration triggers a preventive immune response in plants, revealing targets to enhance crop resilience by linking drought stress recovery with improved pathogen resistance.

doi.org

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Reposted by Travis Lee

Ronan @omalley-regulome.bsky.social · Aug 28

Our new Nature Plants paper is out (and we’re on the cover 😁)!👉 bit.ly/4lS8sOB
By combining scRNA-seq with conserved TF binding (multiDAP) we define gene regulatory networks for 65 cell types across 4 tissues in a wide range of flowering plants!

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Reposted by Travis Lee

Charlotte Kirchhelle @ckirchhelle.bsky.social · Aug 27

Thrilled to share our latest work: how plants control growth through activation of a surface-specific growth programme. Thanks @zoenv.bsky.social, @nathan-german.bsky.social and the other coauthors for all the hard work! www.biorxiv.org/content/10.1...

Plant cells at the organ surface use mechanical cues to activate a specific growth control programme

During morphogenesis of multicellular organs, cells acquire distinct identities that meet specific functional requirements. Epidermal identity is widely considered essential for plant morphogenesis du...

www.biorxiv.org

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Reposted by Travis Lee

Sjon Hartman @hartman-plantlab.com · Aug 25

Happy to see our latest #plantscience review by @aidamaric.bsky.social, @advaitagashe.bsky.social and Johanna onlinr! We describe how epigenetic mechanisms control ethylene signal generation and progression, and how ethylene in turn modulates chromatin.

www.sciencedirect.com/science/arti...

Ethylene signal integration through epigenetic mechanisms in plants

Ethylene is an essential phytohormone that controls a plethora of plant developmental and stress responses. Accordingly, ethylene signal generation an…

www.sciencedirect.com

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Travis Lee @tralee-sci.bsky.social · Aug 22

#Kpopdemonhuntersquad

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Reposted by Travis Lee

North American Arabidopsis Steering Committee @naascarabidopsis.bsky.social · Aug 20

Plz share! (I am a co-author from NAASC) “An unwelcoming climate & culture at scientific conferences is an obstacle to retaining scientists w/marginalized identities. Here we describe..a professional plant science societies..collaboration to make conferences more inclusive.”
doi.org/10.7554/eLif...

Equity, Diversity and Inclusion: Making conferences in the plant sciences more inclusive through community recommendations

The ROOT & SHOOT project in the plant sciences has produced guidelines to help scientific societies organize conferences that are more inclusive and offer more supportive environments to all attendees...

doi.org

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Travis Lee @tralee-sci.bsky.social · Aug 20

Thanks for the enthusiasm in using our online web browser! Due to the high traffic, we have allocated additional resources for user access, so if anyone encountered a bug with accessing the data, please give it a try again and reach out if additional errors are encountered!

Travis Lee @tralee-sci.bsky.social · Aug 19

Thrilled to have our spatial single-cell atlas of the Arabidopsis lifecycle in @NaturePlants. Turns out that its easy to make nice images when spatial expression of 1,000 genes is available! 1/n
@natanellae.bsky.social @tatsuyanobori.bsky.social @joeecker.bsky.social

www.nature.com/articles/s41...

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Travis Lee @tralee-sci.bsky.social · Aug 20

It may arrive sooner than you think, the resources and equipment are there!

Reposted by Travis Lee

joeecker.bsky.social @joeecker.bsky.social · Aug 20

a little secret- the actual amount of data produced and filtered using the Drosophila cell atlas standards was >800k but we more stringently filtered it to ~430k for all downstream analyses. We plan to make this additional 400k data availability in NCBI GEO and here arabidopsisdevatlas.salk.edu

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Reposted by Travis Lee

joeecker.bsky.social @joeecker.bsky.social · Aug 20

Tremendous work by the extremely talented postdocs @TrALEE_Sci @NatanellaE @nobolly .Thank you for putting in a major effort on this “side project” to develop a powerful community resource arabidopsisdevatlas.salk.edu

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Reposted by Travis Lee

Natanella Illouz-Eliaz @natanellae.bsky.social · Aug 19

From a gene’s single cell expression–through spatial localization–to novel function, and beyond!
Now out @natplants.nature.com
We built a comprehensive spatial-transcriptomic atlas of Arabidopsis, revealing cell-type identities across organs in unprecedented detail
www.nature.com/articles/s41...

A single-cell, spatial transcriptomic atlas of the Arabidopsis life cycle - Nature Plants

This study presents an extensive single-nucleus and spatial transcriptomic atlas of the Arabidopsis life cycle that represents ten distinct developmental time points inclusive of six diverse organs.

www.nature.com

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Travis Lee @tralee-sci.bsky.social · Aug 19

All datasets should be back online as we experienced a surge of traffic, thank you for your patience!

Travis Lee @tralee-sci.bsky.social · Aug 19

Thanks Alex!

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Reposted by Travis Lee

Nature Plants @natplants.nature.com · Aug 19

New OA Resource: "A single-cell, spatial transcriptomic atlas of the Arabidopsis life cycle" rdcu.be/eBmkU

An extensive single-nucleus and spatial transcriptomic atlas of the Arabidopsis life cycle that represents 10 developmental time points in 6 diverse organs.

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Travis Lee @tralee-sci.bsky.social · Aug 19

Thank you Laurence!
It looks like our server may have been overloaded with activity, I will ensure that all of the starts are up and running shortly. One challenge with our manuscript releasing at 2am local time!

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Travis Lee @tralee-sci.bsky.social · Aug 19

Thanks Sagar!

Travis Lee @tralee-sci.bsky.social · Aug 19

Thanks Kevin!

Travis Lee @tralee-sci.bsky.social · Aug 19

Thanks Dan!

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Travis Lee @tralee-sci.bsky.social · Aug 19

Thanks Sjon! Sad that I will miss out on isplore this year!

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Travis Lee @tralee-sci.bsky.social · Aug 19

We hope that this 'initial draft' of a spatially-resolved cell atlas of the Arabidopsis lifecycle will enable further biological discovery and function as a framework for future focused studies. 6/end

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Travis Lee @tralee-sci.bsky.social · Aug 19

We have made all datasets browsable with our web resource arabidopsisdevatlas.salk.edu that empowers anyone to ask where their favorite gene is expressed at single-cell resolution without the need for computational resources or bioinformatic background. 5/n

arabidopsisdevatlas.salk.edu

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