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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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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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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 · 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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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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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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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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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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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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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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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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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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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
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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PlantEvolution 🌱🌾 @plantevolution.bsky.social · 02/08/2025
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...
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Mary Williams @PlantTeaching @plantteaching.bsky.social · 25/07/2025
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...
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Ari Pekka Mähönen @apmahonen.bsky.social · 02/07/2025
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...
nature.com
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.
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Vinay Shukla @vinayshukla.bsky.social · 02/07/2025
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
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Chongyuan Luo @chongyuanluo.bsky.social · 23/06/2025
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.
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Natanella Illouz-Eliaz @natanellae.bsky.social · 16/06/2025
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! 🙏🏻🌱📖📕
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Travis Lee @tralee-sci.bsky.social · 12/06/2025
Graphical abstract of the year award goes to www.sciencedirect.com/science/arti...
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Moi Expósito-Alonso (MOILAB) @mexpositoalonso.bsky.social · 30/05/2025
Super excited to release a huge evolution project on the works for many years: Evolution experiments synchronized across climates to understand rapid adaptation Preprint: doi.org/10.1101/2025... All data available: www.grene-net.org/data #MOILAB @ucberkeleyofficial.bsky.social @hhmi.org 🧵👇
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nikogeldner.bsky.social @nikogeldner.bsky.social · 30/05/2025
We have a unique opportunity for a junior researcher, PhD student or postdoc, to use a revolutionary technique for mineral nutrient imaging and tracing in plants. Please re-post! Interested candidates should apply through the portal at the link below: career5.successfactors.eu/career?compa...
career5.successfactors.eu
Career Opportunities: Postdoc or PhD student position in Plant Physiology (22260)
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Tatsuya Nobori @tatsuyanobori.bsky.social · 22/05/2025
Excited to share my new Tansley Review @newphyt.bsky.social on emerging single-cell and spatial omics technologies, many of which are just beginning to be applied in plant biology! Big opportunities lie ahead for the field. [1/n]  nph.onlinelibrary.wiley.com/doi/10.1111/...
nph.onlinelibrary.wiley.com
Exploring the untapped potential of single‐cell and spatial omics in plant biology
Advances in single-cell and spatial omics technologies have revolutionised biology by revealing the diverse molecular states of individual cells and their spatial organization within tissues. The fie...
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Rashmi Sasidharan @rsasidharan.bsky.social · 24/04/2025
Two publications this month showcasing our efforts to understand multi stress resilience in plants www.nature.com/articles/s42... academic.oup.com/plphys/artic...
nature.com
Mechanisms of plant acclimation to multiple abiotic stresses - Communications Biology
A review summarizes the current understanding of the complex molecular pathways mediating plant responses to multiple abiotic stresses, and discusses current and future challenges and unanswered quest...
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Alexandre Marand @marand-lab.bsky.social · 17/04/2025
Grateful to share that our study on "The genetic architecture of cell type–specific cis regulation in maize" is now published in @science.org! Huge thank you to all co-authors and the 4 tough, but fair, reviewers who all helped to improve the study 🌽🧬 www.science.org/doi/10.1126/...
science.org
The genetic architecture of cell type–specific cis regulation in maize
Gene expression and complex phenotypes are determined by the activity of cis-regulatory elements. However, an understanding of how extant genetic variants affect cis regulation remains limited. Here, ...
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jameswalker303.bsky.social @jameswalker303.bsky.social · 09/04/2025
I'm thrilled to share that our study is now published in Cell: Extensive N4 cytosine methylation is essential for Marchantia sperm function. www.cell.com/cell/fulltex... This paper confirms our 4mC discovery in Marchantia sperm and takes it much further. A thread: 0/13
cell.com
Extensive N4 cytosine methylation is essential for Marchantia sperm function
Global N4 cytosine methylation in Marchantia polymorpha sperm regulates gene expression and promotes sperm fertility.
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Margot Smit @likeyoda1.bsky.social · 03/04/2025
Our lab's first review article written with @yadhusankar.bsky.social and @vijayalakshmi.bsky.social is out now in The Plant Journal! 🎉🌱 We discuss temporal regulation of (plant) development. When and how do plants control organ and cell identity progression? onlinelibrary.wiley.com/doi/10.1111/...
onlinelibrary.wiley.com
A space for time. Exploring temporal regulation of plant development across spatial scales
Developmental timing in plants is tightly regulated at the whole-organism scale, from germination to flowering. Less is known about when and how local transitions are temporally regulated. Not every ...
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