Pablo Mendieta
@pabster212.bsky.social
Genomics/Genetics/Bioinformatics
🌱Plant guy 🌱
All opinions my own
🌱Plant guy 🌱
All opinions my own
Reposted by Pablo Mendieta
Efficient creation of decorative double-flowered petunia through CRISPR/Cas9.
From: onlinelibrary.wiley.com/doi/full/10....
From: onlinelibrary.wiley.com/doi/full/10....
October 1, 2025 at 2:06 PM
Efficient creation of decorative double-flowered petunia through CRISPR/Cas9.
From: onlinelibrary.wiley.com/doi/full/10....
From: onlinelibrary.wiley.com/doi/full/10....
Reposted by Pablo Mendieta
Where do I get cheap plant tissue culture stuff? E.g., MS, agar, and plant hormones?
Also, CTAB?
Also, CTAB?
September 26, 2025 at 11:48 AM
Where do I get cheap plant tissue culture stuff? E.g., MS, agar, and plant hormones?
Also, CTAB?
Also, CTAB?
Reposted by Pablo Mendieta
Beyond supergenes: the diverse roles of inversions in trait evolution www.cell.com/trends/ecolo...
Beyond supergenes: the diverse roles of inversions in trait evolution
Chromosomal inversions are ubiquitous across the Tree of Life, with genome-wide studies
revealing a bias toward smaller inversions, yet research has disproportionately focused
on large, supergene-like...
www.cell.com
September 8, 2025 at 7:21 PM
Beyond supergenes: the diverse roles of inversions in trait evolution www.cell.com/trends/ecolo...
Reposted by Pablo Mendieta
Dear GenZ members of the #Drosophila community! You are needed to make cool fly research viral in your social media world! As a boomer I do not understand that sphere, but I can consult and contribute our enormous fund of outreach resources: droso4public.wordpress.com. Please, get in contact!
(no title)
droso4public is a central resource store supporting science communication and advocacy for Drosophila
droso4public.wordpress.com
August 25, 2025 at 10:02 AM
Dear GenZ members of the #Drosophila community! You are needed to make cool fly research viral in your social media world! As a boomer I do not understand that sphere, but I can consult and contribute our enormous fund of outreach resources: droso4public.wordpress.com. Please, get in contact!
Reposted by Pablo Mendieta
Hey Drosophilists: Might you maintain Fuyama's original gynogenetic "gyn-F9" (BDSC #5353) stock in your library?
The current stock from Bloomington is not producing progeny with ms(k81) males.
Thank you!!!
The current stock from Bloomington is not producing progeny with ms(k81) males.
Thank you!!!
August 24, 2025 at 11:36 AM
Hey Drosophilists: Might you maintain Fuyama's original gynogenetic "gyn-F9" (BDSC #5353) stock in your library?
The current stock from Bloomington is not producing progeny with ms(k81) males.
Thank you!!!
The current stock from Bloomington is not producing progeny with ms(k81) males.
Thank you!!!
Fields in science often lionize early researchers. Whether it’s McClintock in maize or Thomas Hunt in Drosophila land.
I think the plant single cell community should really work to highlight the work of Esau highlight her work as the basis of much of our understanding of
I think the plant single cell community should really work to highlight the work of Esau highlight her work as the basis of much of our understanding of
Katherine Esau on Plant Anatomy, Electron Microscopy, and Why Foundational Science Matters: The Botanist Who Wrote the Book on Plant Life
voxmeditantis.com/2025/08/19/k...
#WomenInSTEM #STEM #Botany #Phloem #Microscopy
voxmeditantis.com/2025/08/19/k...
#WomenInSTEM #STEM #Botany #Phloem #Microscopy
Katherine Esau on Plant Anatomy, Electron Microscopy, and Why Foundational Science Matters: The Botanist Who Wrote the Book on Plant Life
Katherine Esau, Ukrainian immigrant who revolutionised plant biology, discusses her journey from sugar beet fields to pioneering electron microscopy. The definitive plant anatomist explains how her…
voxmeditantis.com
August 20, 2025 at 1:31 PM
Fields in science often lionize early researchers. Whether it’s McClintock in maize or Thomas Hunt in Drosophila land.
I think the plant single cell community should really work to highlight the work of Esau highlight her work as the basis of much of our understanding of
I think the plant single cell community should really work to highlight the work of Esau highlight her work as the basis of much of our understanding of
Reposted by Pablo Mendieta
The fact that a paper from 1995 is still behind paywall is...what's the word I'm looking for...egregious. That was 30 years ago.
www.science.org/doi/abs/10.1...
www.science.org/doi/abs/10.1...
Gene Trap Tagging of PROLIFERA, an Essential MCM2-3-5-Like Gene in Arabidopsis
Gene trap transposon mutagenesis can identify essential genes whose functions in later development are obscured by an early lethal phenotype. In higher plants, many genes are required for haploid game...
www.science.org
August 5, 2025 at 4:28 AM
The fact that a paper from 1995 is still behind paywall is...what's the word I'm looking for...egregious. That was 30 years ago.
www.science.org/doi/abs/10.1...
www.science.org/doi/abs/10.1...
Reposted by Pablo Mendieta
#PlantBio2025
I’ll be speaking in the final plenary—sharing the story behind this paper and some new, unpublished work from my lab at TSL. Hope people stick around till the end (though a few already warned me they’re leaving early 😅)!
I’ll be speaking in the final plenary—sharing the story behind this paper and some new, unpublished work from my lab at TSL. Hope people stick around till the end (though a few already warned me they’re leaving early 😅)!
New year, new paper! Now published in @nature.com. We identified and characterised diverse immune cell states in plants under pathogen attack. My postdoc work in the Ecker lab at @salkinstitute.bsky.social. A thread (0/n)
#PlantScience
www.nature.com/articles/s41...
#PlantScience
www.nature.com/articles/s41...
July 26, 2025 at 5:09 PM
#PlantBio2025
I’ll be speaking in the final plenary—sharing the story behind this paper and some new, unpublished work from my lab at TSL. Hope people stick around till the end (though a few already warned me they’re leaving early 😅)!
I’ll be speaking in the final plenary—sharing the story behind this paper and some new, unpublished work from my lab at TSL. Hope people stick around till the end (though a few already warned me they’re leaving early 😅)!
Reposted by Pablo Mendieta
Up next at the Presidential Plenary Seminar: Bob Schmitz takes the stage to discuss “Leveraging Plant Epigenomics to Decode the Complexity of Non-Coding Regulation.” 🌱🧬 #PlantBio2025
July 26, 2025 at 10:40 PM
Up next at the Presidential Plenary Seminar: Bob Schmitz takes the stage to discuss “Leveraging Plant Epigenomics to Decode the Complexity of Non-Coding Regulation.” 🌱🧬 #PlantBio2025
Reposted by Pablo Mendieta
Can anyone point me to full resolution versions of these classic images from NHGRI that show the growth of GWAS from ~2006--2015? I'm looking for the timelapse versions.
(I know many of you are waiting for the GWAS chapters of my free online textbook on human genetics--they are coming, but slowly!)
(I know many of you are waiting for the GWAS chapters of my free online textbook on human genetics--they are coming, but slowly!)
July 26, 2025 at 1:45 PM
Can anyone point me to full resolution versions of these classic images from NHGRI that show the growth of GWAS from ~2006--2015? I'm looking for the timelapse versions.
(I know many of you are waiting for the GWAS chapters of my free online textbook on human genetics--they are coming, but slowly!)
(I know many of you are waiting for the GWAS chapters of my free online textbook on human genetics--they are coming, but slowly!)
Reposted by Pablo Mendieta
Very excited that our work on directional symplastic transport in differentiated root is now published!A developmental switch controls cell-to-cell transport in roots via pectin-linked plasmodesmata changes: Molecular Plant www.cell.com/molecular-pl...
July 22, 2025 at 9:52 AM
Very excited that our work on directional symplastic transport in differentiated root is now published!A developmental switch controls cell-to-cell transport in roots via pectin-linked plasmodesmata changes: Molecular Plant www.cell.com/molecular-pl...
Reposted by Pablo Mendieta
"We found that TF orthologues from distant species retain
nearly identical binding preferences, while on the same timescales the gain and loss of TFBSs are widespread."
From: www.nature.com/articles/s41...
nearly identical binding preferences, while on the same timescales the gain and loss of TFBSs are widespread."
From: www.nature.com/articles/s41...
Recruitment, rewiring and deep conservation in flowering plant gene regulation - Nature Plants
A highly scalable approach is used to generate 3,000 genome-wide maps of transcription factor binding in ten flowering plants, along with multi-species single-nucleus RNA-seq atlases. Together, the re...
www.nature.com
July 21, 2025 at 12:09 PM
"We found that TF orthologues from distant species retain
nearly identical binding preferences, while on the same timescales the gain and loss of TFBSs are widespread."
From: www.nature.com/articles/s41...
nearly identical binding preferences, while on the same timescales the gain and loss of TFBSs are widespread."
From: www.nature.com/articles/s41...
Reposted by Pablo Mendieta
Cool story! Congratulations to everyone involved.
#plantscience
#plantscience
An exciting day! Our latest work is now out; we ask the question, are there any differences between plant mitochondria with and without mtDNA? 🌱
onlinelibrary.wiley.com/doi/10.1111/... (1/9)
onlinelibrary.wiley.com/doi/10.1111/... (1/9)
(ID‐ICPMB05) Running on Empty: Mitochondria Without DNA Exhibit Differential Motility and Connectivity
Plant mitochondria are in continuous motion. While providing ATP to other cellular processes, they also constantly consume ATP to move rapidly within the cell. This movement is in part related to tak....
onlinelibrary.wiley.com
July 14, 2025 at 5:20 PM
Cool story! Congratulations to everyone involved.
#plantscience
#plantscience
Reposted by Pablo Mendieta
I'll be joining the Department of Plant Biology at Michigan State University in Mid August as an Assistant Professor.
cxli233.github.io/cxLi_lab/
cxli233.github.io/cxLi_lab/
June 21, 2025 at 2:34 PM
I'll be joining the Department of Plant Biology at Michigan State University in Mid August as an Assistant Professor.
cxli233.github.io/cxLi_lab/
cxli233.github.io/cxLi_lab/
Reposted by Pablo Mendieta
Textbooks: “Enhancers are just a bunch of TFBSs”
But how do they REALLY work?
New paper with many contributors here @berkeleylab.lbl.gov, @anshulkundaje.bsky.social, @anusri.bsky.social
A 🧵 (1/n)
Free access link: rdcu.be/erD22
But how do they REALLY work?
New paper with many contributors here @berkeleylab.lbl.gov, @anshulkundaje.bsky.social, @anusri.bsky.social
A 🧵 (1/n)
Free access link: rdcu.be/erD22
June 18, 2025 at 5:56 PM
Textbooks: “Enhancers are just a bunch of TFBSs”
But how do they REALLY work?
New paper with many contributors here @berkeleylab.lbl.gov, @anshulkundaje.bsky.social, @anusri.bsky.social
A 🧵 (1/n)
Free access link: rdcu.be/erD22
But how do they REALLY work?
New paper with many contributors here @berkeleylab.lbl.gov, @anshulkundaje.bsky.social, @anusri.bsky.social
A 🧵 (1/n)
Free access link: rdcu.be/erD22
Reposted by Pablo Mendieta
Much more important things going on in the world, but wanted to share this new work on parent-of-origin effects & “non-canonical” genomic imprinting in developmental plasticity of honey bees, out now in Genome Biology 🧪🧬🔄 link.springer.com/article/10.1...
Intragenomic conflict associated with extreme phenotypic plasticity in queen-worker caste determination in honey bees (Apis mellifera) - Genome Biology
Background Caste determination of honey bees (Apis mellifera) exemplifies developmental plasticity, where differences in larval diet result in identical genotypes yielding either long-lived, reproduct...
link.springer.com
June 18, 2025 at 3:30 PM
Much more important things going on in the world, but wanted to share this new work on parent-of-origin effects & “non-canonical” genomic imprinting in developmental plasticity of honey bees, out now in Genome Biology 🧪🧬🔄 link.springer.com/article/10.1...
Reposted by Pablo Mendieta
EPIGENETIC HULK READY TO SMASH AGAIN! GET IN LOSERS!
June 13, 2025 at 4:30 AM
EPIGENETIC HULK READY TO SMASH AGAIN! GET IN LOSERS!
Reposted by Pablo Mendieta
Excited to share my first PhD paper in the @sbmontgom.bsky.social lab with @tamigj.bsky.social (www.biorxiv.org/content/10.1...)! Standard QTL methods treat each gene independently. But what if a single variant regulates multiple nearby genes at once - what we call “allelic proxitropy”? 🧵 ⬇️
June 8, 2025 at 5:39 PM
Excited to share my first PhD paper in the @sbmontgom.bsky.social lab with @tamigj.bsky.social (www.biorxiv.org/content/10.1...)! Standard QTL methods treat each gene independently. But what if a single variant regulates multiple nearby genes at once - what we call “allelic proxitropy”? 🧵 ⬇️
Reposted by Pablo Mendieta
CREsted: modeling genomic and synthetic cell type-specific enhancers across tissues and species www.biorxiv.org/content/10.1... 🧬🖥️🧪 github.com/aertslab/CRE...
May 14, 2025 at 8:02 PM
CREsted: modeling genomic and synthetic cell type-specific enhancers across tissues and species www.biorxiv.org/content/10.1... 🧬🖥️🧪 github.com/aertslab/CRE...
Reposted by Pablo Mendieta
How do enhancers drive cell specificity? 🤔 Fascinating study used 64k+ synthetic sequences in blood cell differentiation & found activating TF sites often show negative synergy, converting TF gradients into sharp gene patterns! #Bioinformatics
www.cell.com/cell/fulltex...
www.cell.com/cell/fulltex...
Design principles of cell-state-specific enhancers in hematopoiesis
Screen of minimalistic enhancers in blood progenitor cells demonstrates widespread
dual activator-repressor function of transcription factors (TFs) and enables the model-guided
design of cell-state-sp...
www.cell.com
May 12, 2025 at 12:42 PM
How do enhancers drive cell specificity? 🤔 Fascinating study used 64k+ synthetic sequences in blood cell differentiation & found activating TF sites often show negative synergy, converting TF gradients into sharp gene patterns! #Bioinformatics
www.cell.com/cell/fulltex...
www.cell.com/cell/fulltex...
Reposted by Pablo Mendieta
Delighted to share our latest work deciphering the landscape of chromatin accessibility and modeling the DNA sequence syntax rules underlying gene regulation during human fetal development! www.biorxiv.org/content/10.1... Read on for more: 🧵 1/16 #GeneReg 🧬🖥️
Dissecting regulatory syntax in human development with scalable multiomics and deep learning
Transcription factors (TFs) establish cell identity during development by binding regulatory DNA in a sequence-specific manner, often promoting local chromatin accessibility, and regulating gene expre...
www.biorxiv.org
May 3, 2025 at 6:27 PM
Delighted to share our latest work deciphering the landscape of chromatin accessibility and modeling the DNA sequence syntax rules underlying gene regulation during human fetal development! www.biorxiv.org/content/10.1... Read on for more: 🧵 1/16 #GeneReg 🧬🖥️
Reposted by Pablo Mendieta
our work on the molecular differences between transcription factor isoforms is out now in Molecular Cell!
key point: 2/3rds of TF isos differ in properties like DNA binding & transcriptional activity
many are "negative regulators" & misexpressed in cancer
www.sciencedirect.com/science/arti...
key point: 2/3rds of TF isos differ in properties like DNA binding & transcriptional activity
many are "negative regulators" & misexpressed in cancer
www.sciencedirect.com/science/arti...
March 26, 2025 at 5:11 PM
our work on the molecular differences between transcription factor isoforms is out now in Molecular Cell!
key point: 2/3rds of TF isos differ in properties like DNA binding & transcriptional activity
many are "negative regulators" & misexpressed in cancer
www.sciencedirect.com/science/arti...
key point: 2/3rds of TF isos differ in properties like DNA binding & transcriptional activity
many are "negative regulators" & misexpressed in cancer
www.sciencedirect.com/science/arti...
Reposted by Pablo Mendieta
Reposted by Pablo Mendieta
genomebiology.biomedcentral.com/articles/10....
Quite an indictment of some of the current single cell "virtual cell" foundation models. Even for the relatively mundane applications, cell labeling, batch correction etc, they are poor compared to much simpler & cheaper methods.
Quite an indictment of some of the current single cell "virtual cell" foundation models. Even for the relatively mundane applications, cell labeling, batch correction etc, they are poor compared to much simpler & cheaper methods.
Zero-shot evaluation reveals limitations of single-cell foundation models - Genome Biology
Foundation models such as scGPT and Geneformer have not been rigorously evaluated in a setting where they are used without any further training (i.e., zero-shot). Understanding the performance of mode...
genomebiology.biomedcentral.com
April 20, 2025 at 4:14 PM
genomebiology.biomedcentral.com/articles/10....
Quite an indictment of some of the current single cell "virtual cell" foundation models. Even for the relatively mundane applications, cell labeling, batch correction etc, they are poor compared to much simpler & cheaper methods.
Quite an indictment of some of the current single cell "virtual cell" foundation models. Even for the relatively mundane applications, cell labeling, batch correction etc, they are poor compared to much simpler & cheaper methods.
Reposted by Pablo Mendieta
New preprint! We used single cell sequencing & metabolomics to look at cell type specificity of specialized metabolism in Camptotheca, the source of chemotherapeutic agent camptothecin, as well as comparative analyses w/ Catharanthus, which we previously worked on. 🧵
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
April 24, 2025 at 5:00 PM
New preprint! We used single cell sequencing & metabolomics to look at cell type specificity of specialized metabolism in Camptotheca, the source of chemotherapeutic agent camptothecin, as well as comparative analyses w/ Catharanthus, which we previously worked on. 🧵
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...