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Travis Lee

@tralee-sci.bsky.social
315 followers 320 following 47 posts

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 Personal website: travislee.science @TrALEE_Sci on Twitter

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Reposted by Travis Lee
Bas Bargmann @bas-bargmann.bsky.social · 25/09/2026
I am very pleased to present the lab’s first #bluetorial! This concerns our recent publication in Development @dev-journal.bsky.social doi.org/10.1242/dev.... This work, led by postdoc (and former grad student) Kelsey Reed, is the result of many years of hard work by a wonderful team. (1/n)
doi.org
A protoplast-based method to visualize early cell biological events in plant cellular reprogramming and regeneration
Summary: This study presents a live-imaging platform for tracking individual plant protoplasts in culture, enabling analysis of cellular processes, signaling dynamics and developmental transitions.
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Reposted by Travis Lee
Nicholas Provart @bar-plantbio.bsky.social · 24/09/2026
Check out the BAR's Single Cell Data Portal at bar.utoronto.ca/single_cell_..., in beta. There's a curated list of scRNA-seq datasets with viewer links, our own CellxGene instance for exploring 14 datasets from 6 papers, and a new tool, SUPeR Viewer! Thanks to PCA and C-SPIRIT for input.
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N End Rules @n-end-rules.bsky.social · 16/09/2026
We introduce a new transducer of oxygen sensing: Cys2-HYT1 @isamanrique.bsky.social @charlene-kunaka.bsky.social Susanna Ubeda Tomas & @gunjansharma88.bsky.social ma88.bsky.social lead work defining HYT1 contribution to root hypoxia tolerance. @natcomms.nature.com www.nature.com/articles/s41...
nature.com
Hierarchical regulation of oxygen-sensing through coupled transducers in Arabidopsis thaliana - Nature Communications
The PLANT CYSTEINE OXIDASE (PCO) N-degron pathway contributes to oxygen sensing in plants. Here the authors identify HYPOXIA TRANSDUCER1 (HYT1) as a substrate of PCO and show it forms a coherent feed-...
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Mary Williams @PlantTeaching @plantteaching.bsky.social · 16/09/2026
Many of you may have heard the terrible news of Dr. Meng Chen's sudden death. I just found this tribute from UC Riverside cnas.ucr.edu/news/2026/09... and a beautiful review article he contributed to @plantphys.bsky.social earlier this year, "25 years of photobodies" doi.org/10.1093/plph... 💔
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Travis Lee @tralee-sci.bsky.social · 15/09/2026
A nice collaboration that questioned if we can gain further insights into heterogeneous and lowly expressed transcripts from mixed cell population bulk transcriptome datasets. I'm looking forward to finding additional insights from reanalysis of some of our published datasets!
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Reposted by Travis Lee
Min-Yao Jhu @minyaojhu.bsky.social · 24/06/2026
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.
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Reposted by Travis Lee
yogevborko.bsky.social @yogevborko.bsky.social · 17/06/2026
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...
doi.org
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.
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Travis Lee @tralee-sci.bsky.social · 23/05/2026
Thanks Mat!
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Travis Lee @tralee-sci.bsky.social · 22/05/2026
Lastly, I would like to thank all authors for their contributions, who have made all of this work possible! 8/8
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Travis Lee @tralee-sci.bsky.social · 22/05/2026
We also provide interactive access to at our web portal to explore expression data and TF motif activity within our single-cell and multi-modal datasets. 7/8 arabidopsisdevatlas.salk.edu
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Travis Lee @tralee-sci.bsky.social · 22/05/2026
This results in a model where positionally defined cell states bifurcate to asymmetrically regulate cell elongation to form the apical hook arch. We hypothesize that these divergent regulatory networks may be utilized broadly to regulate plant morphogenesis and bending 6/8
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Travis Lee @tralee-sci.bsky.social · 22/05/2026
Zooming in on these cells, GRN construction reveals bifurcating regulatory networks that asymmetrically drive cell elongation through hormonal regulation. As predicted by our GRN, we also rescue our mutant phenotype with exogenous GA hormone treatment 5/8
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Travis Lee @tralee-sci.bsky.social · 22/05/2026
We identify a transient cell niche below the shoot meristematic region that functions as a regulatory 'hub,' and find that mutation of TFs specifically expressed and with binding activity in these cells leads to defects in apical hook form 4/8
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Travis Lee @tralee-sci.bsky.social · 22/05/2026
Using genetic mutants and manual dissection, we find vast heterogeneity within cell types in the apical hook attributed to intersecting developmental and hormonal regulation. Our spatial datasets enable the identification of the (developmental) time and place of this regulation 3/8
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Travis Lee @tralee-sci.bsky.social · 22/05/2026
How do organisms grow an arch? In the apical hook, counter hormone gradients drive cell elongation asymmetrically; but as a standing wave cells transiently enter and exit the apical hook over a span of hours, which complicates our understanding of this structure 2/8
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Travis Lee @tralee-sci.bsky.social · 22/05/2026
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...
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Alexandre Marand @marand-lab.bsky.social · 22/05/2026
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
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Travis Lee @tralee-sci.bsky.social · 16/05/2026
I eagerly await the reciprocal experiment www.nature.com/articles/d41...
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Reposted by Travis Lee
Yasin Dagdas @plantophagy.bsky.social · 06/05/2026
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 🧵👇
nature.com
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.
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Lewsey Lab @lewseylab.bsky.social · 24/04/2026
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...
academic.oup.com
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
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Reposted by Travis Lee
Moi Expósito-Alonso (MOILAB) @mexpositoalonso.bsky.social · 26/03/2026
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
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Rüdiger Simon @simonrdg.bsky.social · 18/02/2026
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!
nature.com
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...
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Reposted by Travis Lee
beckybart.bsky.social @beckybart.bsky.social · 17/02/2026
The Bart Lab at UC Berkeley is looking for a postdoc. Please share!
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Travis Lee @tralee-sci.bsky.social · 11/02/2026
Congrats Mat! 174(!) sections are truly impressive, excited to look into the data!
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Reposted by Travis Lee
Lewsey Lab @lewseylab.bsky.social · 11/02/2026
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
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Ronan @omalley-regulome.bsky.social · 10/02/2026
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...
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Travis Lee @tralee-sci.bsky.social · 13/11/2025
Who lived in a pineapple under the sea? All of our ancestors www.science.org/doi/10.1126/...
science.org
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...
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Reposted by Travis Lee
Chongyuan Luo @chongyuanluo.bsky.social · 15/10/2025
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...
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Reposted by Travis Lee
Christine Faulkner @pdchristine.bsky.social · 14/10/2025
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
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PlantEvolution 🌱🌾 @plantevolution.bsky.social · 10/10/2025
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...
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Daan Weits @daanweits.bsky.social · 22/09/2025
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 · 19/09/2025
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 · 03/09/2025
A timely article as several recent conference discussions have led to similar thoughts www.nature.com/articles/s41...
nature.com
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...
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Travis Lee @tralee-sci.bsky.social · 01/09/2025
Thank you Rashmi!
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Reposted by Travis Lee
Natanella Illouz-Eliaz @natanellae.bsky.social · 31/08/2025
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 👇
doi.org
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.
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Ronan @omalley-regulome.bsky.social · 28/08/2025
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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Charlotte Kirchhelle @ckirchhelle.bsky.social · 27/08/2025
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...
biorxiv.org
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...
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Sjon Hartman @hartman-plantlab.com · 25/08/2025
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...
sciencedirect.com
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…
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Travis Lee @tralee-sci.bsky.social · 22/08/2025
#Kpopdemonhuntersquad
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North American Arabidopsis Steering Committee @naascarabidopsis.bsky.social · 20/08/2025
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
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...
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Travis Lee @tralee-sci.bsky.social · 20/08/2025
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!
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Travis Lee @tralee-sci.bsky.social · 20/08/2025
It may arrive sooner than you think, the resources and equipment are there!
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joeecker.bsky.social @joeecker.bsky.social · 20/08/2025
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
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joeecker.bsky.social @joeecker.bsky.social · 20/08/2025
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
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Natanella Illouz-Eliaz @natanellae.bsky.social · 19/08/2025
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...
nature.com
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.
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Travis Lee @tralee-sci.bsky.social · 19/08/2025
All datasets should be back online as we experienced a surge of traffic, thank you for your patience!
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Travis Lee @tralee-sci.bsky.social · 19/08/2025
Thanks Alex!
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Nature Plants @natplants.nature.com · 19/08/2025
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 · 19/08/2025
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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