Travis Lee
@tralee-sci.bsky.social
Post doc in the Ecker lab @ The Salk Institute. PhD in the Bailey-Serres lab @ UCR. Posts include papers I'm reading and things that I 3D print
@TrALEE_Sci on Twitter
@TrALEE_Sci on Twitter
Pinned
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...
@natanellae.bsky.social @tatsuyanobori.bsky.social @joeecker.bsky.social
www.nature.com/articles/s41...
Reposted by Travis Lee
We like to introduce map3C, developed by Joseph Galasso, that drastically improves the mapping and contact calling performance of snm3C-seq and now enables accurate 3D genome modeling. map3C was developed in collaboration with
Jason Ernst and Frank Alber. www.biorxiv.org/content/10.1...
Jason Ernst and Frank Alber. www.biorxiv.org/content/10.1...
October 15, 2025 at 4:32 PM
We like to introduce map3C, developed by Joseph Galasso, that drastically improves the mapping and contact calling performance of snm3C-seq and now enables accurate 3D genome modeling. map3C was developed in collaboration with
Jason Ernst and Frank Alber. www.biorxiv.org/content/10.1...
Jason Ernst and Frank Alber. www.biorxiv.org/content/10.1...
Reposted by Travis Lee
New pre-print from the team!
The manuscript is @emma-raven.bsky.social's PhD work showing that whether a leaf is a carbon sink or a carbon source influences how they execute immune responses.
Have a read!
#PlantScience
@johninnescentre.bsky.social
The manuscript is @emma-raven.bsky.social's PhD work showing that whether a leaf is a carbon sink or a carbon source influences how they execute immune responses.
Have a read!
#PlantScience
@johninnescentre.bsky.social
Primary metabolism underpins the execution of immune responses in different tissues of the same plant https://www.biorxiv.org/content/10.1101/2025.10.11.681807v1
October 14, 2025 at 7:16 AM
New pre-print from the team!
The manuscript is @emma-raven.bsky.social's PhD work showing that whether a leaf is a carbon sink or a carbon source influences how they execute immune responses.
Have a read!
#PlantScience
@johninnescentre.bsky.social
The manuscript is @emma-raven.bsky.social's PhD work showing that whether a leaf is a carbon sink or a carbon source influences how they execute immune responses.
Have a read!
#PlantScience
@johninnescentre.bsky.social
Reposted by Travis Lee
Congrats, Joe Ecker @salkinstitute.bsky.social, to receiving the McClintock Prize! Joe has been a visionary leader of the field of genetics and genomics – not only for plants – for decades
www.salk.edu/news-release...
www.salk.edu/news-release...
October 10, 2025 at 5:34 PM
Congrats, Joe Ecker @salkinstitute.bsky.social, to receiving the McClintock Prize! Joe has been a visionary leader of the field of genetics and genomics – not only for plants – for decades
www.salk.edu/news-release...
www.salk.edu/news-release...
Reposted by Travis Lee
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...
www.biorxiv.org/content/10.1...
September 22, 2025 at 6:47 AM
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...
www.biorxiv.org/content/10.1...
Reposted by Travis Lee
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.
Chromatin accessibility in rice & related grasses: how regulatory DNA elements evolve across cell types & species; identifying potential silencers.
September 19, 2025 at 8:51 AM
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.
Chromatin accessibility in rice & related grasses: how regulatory DNA elements evolve across cell types & species; identifying potential silencers.
A timely article as several recent conference discussions have led to similar thoughts
www.nature.com/articles/s41...
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
September 3, 2025 at 8:53 PM
A timely article as several recent conference discussions have led to similar thoughts
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Travis Lee
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.
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
August 31, 2025 at 2:17 AM
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.
doi.org/10.1038/s414...
Read thread below 👇
Reposted by Travis Lee
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!
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!
August 28, 2025 at 2:06 PM
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!
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!
Reposted by Travis Lee
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
August 27, 2025 at 6:07 PM
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...
Reposted by Travis Lee
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...
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
August 25, 2025 at 4:55 PM
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...
www.sciencedirect.com/science/arti...
Reposted by Travis Lee
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...
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
August 20, 2025 at 9:29 PM
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...
doi.org/10.7554/eLif...
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!
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...
@natanellae.bsky.social @tatsuyanobori.bsky.social @joeecker.bsky.social
www.nature.com/articles/s41...
August 20, 2025 at 6:25 PM
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!
Reposted by Travis Lee
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
August 20, 2025 at 12:55 AM
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
Reposted by Travis Lee
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
August 20, 2025 at 12:42 AM
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
Reposted by Travis Lee
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...
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
August 19, 2025 at 7:20 PM
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...
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...
Reposted by Travis Lee
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.
An extensive single-nucleus and spatial transcriptomic atlas of the Arabidopsis life cycle that represents 10 developmental time points in 6 diverse organs.
August 19, 2025 at 10:36 AM
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.
An extensive single-nucleus and spatial transcriptomic atlas of the Arabidopsis life cycle that represents 10 developmental time points in 6 diverse organs.
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...
@natanellae.bsky.social @tatsuyanobori.bsky.social @joeecker.bsky.social
www.nature.com/articles/s41...
August 19, 2025 at 9:17 AM
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...
@natanellae.bsky.social @tatsuyanobori.bsky.social @joeecker.bsky.social
www.nature.com/articles/s41...
Reposted by Travis Lee
1/3 New preprint led by Shanshan Wang, in collaboration with the Timmermans lab.
Several groups have presented sc/snRNA-seq analyses of Arabidopsis leaves after bacterial infection before. Is there anything left to discover? Turns out: Yes.
#plantscience
www.biorxiv.org/content/10.1...
Several groups have presented sc/snRNA-seq analyses of Arabidopsis leaves after bacterial infection before. Is there anything left to discover? Turns out: Yes.
#plantscience
www.biorxiv.org/content/10.1...
August 2, 2025 at 2:46 PM
1/3 New preprint led by Shanshan Wang, in collaboration with the Timmermans lab.
Several groups have presented sc/snRNA-seq analyses of Arabidopsis leaves after bacterial infection before. Is there anything left to discover? Turns out: Yes.
#plantscience
www.biorxiv.org/content/10.1...
Several groups have presented sc/snRNA-seq analyses of Arabidopsis leaves after bacterial infection before. Is there anything left to discover? Turns out: Yes.
#plantscience
www.biorxiv.org/content/10.1...
Reposted by Travis Lee
Next up, a satellite meeting of #PlantBio2025, a celebration of the late great scientist, Joanne Chory share.google/xfOr0g8QkZ4A...
Led off by Joe Ecker, and a list of her awards.
She also trained a lot of people, see
academictree.org/plantbio/tre...
Led off by Joe Ecker, and a list of her awards.
She also trained a lot of people, see
academictree.org/plantbio/tre...
July 25, 2025 at 6:24 PM
Next up, a satellite meeting of #PlantBio2025, a celebration of the late great scientist, Joanne Chory share.google/xfOr0g8QkZ4A...
Led off by Joe Ecker, and a list of her awards.
She also trained a lot of people, see
academictree.org/plantbio/tre...
Led off by Joe Ecker, and a list of her awards.
She also trained a lot of people, see
academictree.org/plantbio/tre...
Reposted by Travis Lee
How plants sense injury in their barrier tissue, periderm? Painstakingly detailed and amazing work by post doc Hiroyuki Iida shows that wounding is sensed by the diffusion of two gases: ethylene and oxygen. @treebiocoe.bsky.social @erc.europa.eu 1/x 🧵 www.nature.com/articles/s41...
Plants monitor the integrity of their barrier by sensing gas diffusion - Nature
A study using Arabidopsis shows that plants can monitor the integrity of their outer barriers by sensing gas diffusion, enabling them to initiate wound repair to prevent water loss and pathogen entry.
www.nature.com
July 2, 2025 at 4:20 PM
How plants sense injury in their barrier tissue, periderm? Painstakingly detailed and amazing work by post doc Hiroyuki Iida shows that wounding is sensed by the diffusion of two gases: ethylene and oxygen. @treebiocoe.bsky.social @erc.europa.eu 1/x 🧵 www.nature.com/articles/s41...
Reposted by Travis Lee
Plants "bleed" too, but through gases!
When wounded, ethylene leaks out and oxygen seeps in. This gas shift acts as an alarm, triggering self-repair to seal the breach. Excited to share our new collaborative work uncovering this clever plant mechanism! Excellent summary here, indulge!
#plantscience
When wounded, ethylene leaks out and oxygen seeps in. This gas shift acts as an alarm, triggering self-repair to seal the breach. Excited to share our new collaborative work uncovering this clever plant mechanism! Excellent summary here, indulge!
#plantscience
July 2, 2025 at 5:26 PM
Plants "bleed" too, but through gases!
When wounded, ethylene leaks out and oxygen seeps in. This gas shift acts as an alarm, triggering self-repair to seal the breach. Excited to share our new collaborative work uncovering this clever plant mechanism! Excellent summary here, indulge!
#plantscience
When wounded, ethylene leaks out and oxygen seeps in. This gas shift acts as an alarm, triggering self-repair to seal the breach. Excited to share our new collaborative work uncovering this clever plant mechanism! Excellent summary here, indulge!
#plantscience
Reposted by Travis Lee
Preprint alert: single-cell methylation signature of autism in collaboration with Dan Geschwind. Autism-mC signal is enriched in promoters and cell-type enhancers but uncorrelated with gene expression. Led by @GeschwindLab Postdoc Katie Eyring and grad student Cuining Liu.
A Single-Cell Atlas of DNA Methylation in Autism Spectrum Disorder Reveals Distinct Regulatory and Aging Signatures https://www.biorxiv.org/content/10.1101/2025.06.17.660162v1
June 23, 2025 at 3:06 PM
Preprint alert: single-cell methylation signature of autism in collaboration with Dan Geschwind. Autism-mC signal is enriched in promoters and cell-type enhancers but uncorrelated with gene expression. Led by @GeschwindLab Postdoc Katie Eyring and grad student Cuining Liu.
Reposted by Travis Lee
I am humbled and honored to receive the Arabidopsis dissemination award. Thank you @naascarabidopsis.bsky.social for this recognition and I wish I could be there with you all! #ICAR2025
Thank you @joeecker.bsky.social for welcoming me into the Arabidopsis world!
🙏🏻🌱📖📕
Thank you @joeecker.bsky.social for welcoming me into the Arabidopsis world!
🙏🏻🌱📖📕
Natanella Elouz-Elias at Salk is honored for her work to disseminate Arabidopsis knowledge! #ICAR2025
June 16, 2025 at 7:07 PM
I am humbled and honored to receive the Arabidopsis dissemination award. Thank you @naascarabidopsis.bsky.social for this recognition and I wish I could be there with you all! #ICAR2025
Thank you @joeecker.bsky.social for welcoming me into the Arabidopsis world!
🙏🏻🌱📖📕
Thank you @joeecker.bsky.social for welcoming me into the Arabidopsis world!
🙏🏻🌱📖📕
June 12, 2025 at 10:23 PM