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
1/ Excited to share our new bioRxiv preprint! "4D spatial transcriptomics reveals nodule identity emerges through stacked parallel developmental programs" 📄 doi.org/10.64898/202... Using Xenium, we generated a 4D (3D space + time) atlas of nodule development in Medicago truncatula.
Thrilled to share that our paper is now online in @PlantPhys 🌱 🍅 doi.org/10.1093/plph... Many thanks to all co-authors and collaborators who made this work possible!!! Also, thanks to Hannah Rae Thomas for summarizing our work here: doi.org/10.1093/plph...
Phytochrome-interacting factors integrate environmental signals to regulate tomato growth and development
Light-responsive transcription factors mediate tomato responses to shade, shaping plant architecture and modulating fruit production and seed dormancy.
doi.org
How do cells break symmetry to generate new shape and form? Using the apical hook as a model, we @joeecker.bsky.social applied spatial and single-cell multiomics, and identify a regulatory hotspot in a transient cell niche that drives this U-shaped structure 1/8 bsky.app/profile/bior...
bioRxivpreprint@biorxivpreprint.bsky.social · 3mo agoTransient cell states encode positional information to direct asymmetric growth https://www.biorxiv.org/content/10.64898/2026.05.21.726925v1
Thrilled to announce our newest preprint on #dedifferentiation in Arabidopsis 🧬🌱. We used scRNA-seq and hormone treatments to track transcriptional reprogramming in diverse somatic cell types and found what we think is some pretty cool biology. Feedback welcome! www.biorxiv.org/content/10.6...
biorxiv.org
Now online at @natplants.nature.com ‼️ Led by Jierui Zhao, a former PhD student @gmivienna.bsky.social & together w/ @moritznowack.bsky.social lab, we uncover how #autophagy shapes salt stress tolerance and lifespan. www.nature.com/articles/s41... www.nature.com/articles/s41... A short 🧵👇
Cell-type-specific autophagy in root-hair-forming cells is essential for salt stress tolerance in Arabidopsis thaliana - Nature Plants
This study reveals that enhanced autophagy in root-hair-forming cells helps Arabidopsis store excess sodium, control oxidative stress and tolerate salt stress.
nature.com
Latest paper from the lab with several collaborators: We've built a four-dimensional spatial transcriptome atlas of barley grain development and germination, allowing detailed interrogation of where and when genes are expressed academic.oup.com/plcell/artic...
A four-dimensional spatial transcriptome atlas of barley caryopsis development and germination
A four-dimensional spatial gene expression transcriptome atlas of Hordeum vulgare (barley) grain development and germination revealed tissue, cell, cluster
academic.oup.com
Our new experimental evolution study across 30+ locations using the plant Arabidopsis thaliana —— we direct "see" adaptation and extinction to different climates at the genetic as it happens! Read it in Science dx.doi.org/10.1126/scie... @ucberkeleyofficial.bsky.social @hhmi-science.bsky.social
We recently published a first story on combining spatial and single cell transcriptomics in barley (see here: www.nature.com/articles/s41...) Lets go for the next level now, i.e. understanding gene networks and barley meristem development in 4D!
Imputation integrates single-cell and spatial gene expression data to resolve transcriptional networks in barley shoot meristem development - Nature Plants
Spatially resolved gene expression during barley development was done by integrating an scRNA-seq dataset from cells with unknown position with spatial transcriptomics. This dataset is publicly availa...
nature.com
New collaborative preprint out in which we use @10xgenomics.bsky.social Xenium to do some (a lot!) of plant spatial transcriptomics, led by Jim Whelan's team: "Mitochondrial Retrograde Signaling in Arabidopsis thaliana: heterogenous, spatial and polarised aspects" www.biorxiv.org/content/10.6...
biorxiv.org
New preprint! The same TFs can drive distinct regulatory programs depending on where they bind. TSS → rapid stress responses Intronic & upstream → cell-type programs Enhancer-like CRMs → embryo/meristem programs Coding-sequence binding → repression www.biorxiv.org/content/10.6...
Who lived in a pineapple under the sea? All of our ancestors www.science.org/doi/10.1126/...
Integrative phylogenomics positions sponges at the root of the animal tree
Determining whether sponges or ctenophores root the animal tree has important implications for understanding early animal evolution. Here, we examined support for these competing hypotheses by constru...
science.org
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...
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
bioRxiv Plant Bio@biorxiv-plants.bsky.social · 10mo agoPrimary 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
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...
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...
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.
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...
nature.com
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
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!
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...
biorxiv.org
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…
sciencedirect.com
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 · 12mo agoThrilled 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...
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
arabidopsisdevatlas.salk.edu
Natanella Illouz-Eliaz@natanellae.bsky.social · 12mo agoFrom 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...
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
arabidopsisdevatlas.salk.edu
Travis Lee@tralee-sci.bsky.social · 12mo agoThrilled 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...
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.
nature.com
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.
