Epigenetics Update - Dissecting gene regulatory networks governing human cortical cell fate go.nature.com/4b9X4w7
Alex A. Pollen (University of California San Francisco) reporting in Nature
#Epigenetics #GRNs #Chromatin
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Gain deeper insights into gene regulation; epigenometech.com
#ForestryRes
Hybrid CNNs + ML decode plant GRNs with 95% precision, spotlighting MYB46, MYB83 🌱 Transfer learning scales to crops.🧬
Details: www.maxapress.com/article/doi/10.48130/for...
#grns #transferlearning #plants
There is an echo here of the situation in #gastruloids where it is possible to see un uncoupling between #GRNs and #CRNs (cell regulatory networks) www.sciencedirect.com/science/arti...
#CellsRUs
It is also of interest that it not that straightforward to map the AP heterochrony to GRNs and that we need to expand our horizons. Emergent properties of cell ensembles can govern gene activity and can do more than #GRNs #NotInTheGenes
Among the new #GRNs that we identified, #GABA signalling emerges as a previously unrecognised player in #glioblastoma.
Now we applied #MOBILE, a #ML based method, to integrate #multiomics data from #GB and uncovered new #GRNs and #TFs relevant for #glioblastoma pathogenesis.
📝 doi.org/10.1101/2025...
📣 New pre-print from the lab:
👉 “Gene regulatory networks linked to GABA signalling emerge as relevant for glioblastoma pathogenesis” #Glioblastoma #GB #GRNs #multiomics #GABA #CancerNeuroscience #ML #GBM
📝 Read the #BioRxiv here:
doi.org/10.1101/2025...
14/ We believe this approach can be applied to other cancers to uncover—and exploit—plasticity brakes. Get in touch if interested! #GBM #MultiOmics #CancerResearch #deeplearning #cancerneuroscience #GRNs #Cancer #singlecell
youtu.be/o3sH8cQ485c. Jim Santelle’s , former Federal Attorney for the Eastern District of Wisconser He informed us about the legal battles being wages to save democracy from the admin's illegal actions He is ultimately inspiring. #guardrail #savedemocracy #grassrootsnorthshore #GRNS #grnsaction
Great visit/talks from F. Corson on his work with @jeromegros.bsky.social
#Mechanobiology and #GRNs in avian #gastrulation www.nature.com/articles/s41... The output is clearly the product of an interaction between both but one has to start and rule; there is much that is #NotInTheGenes
Overview of HCNetlas. Top: Schematic representation of the workflow from single-cell transcriptomic data collection to the construction of the HCNetlas. Single-cell RNA sequencing data preannotated for cell type were used to build CGNs using the scHumanNet framework. HCNetlas is comprised of a comprehensive collection of these gene networks, representing various human tissues and cell types. Bottom left: UMAP visualization of CGNs based on gene profiles, highlighting the major cell lineages, with node size representing the number of genes in each network. Bottom right: UMAP plot displaying the interrelationship among the CGNs based on network gene profiles for major organs or tissue types. Each point represents a gene network associated with a specific organ or tissue type colored distinctly.
Alterations of gene regulatory networks (GRNs) in specific #CellTypes can cause disease. This study presents HCNetlas, a compilation of cell-type-specific #GRNs across healthy human tissues that can be used to uncover associations between #DiseaseGenes & cell types 🧪 @plosbiology.org plos.io/4jIwg7P
Overview of HCNetlas. Top: Schematic representation of the workflow from single-cell transcriptomic data collection to the construction of the HCNetlas. Single-cell RNA sequencing data preannotated for cell type were used to build CGNs using the scHumanNet framework. HCNetlas is comprised of a comprehensive collection of these gene networks, representing various human tissues and cell types. Bottom left: UMAP visualization of CGNs based on gene profiles, highlighting the major cell lineages, with node size representing the number of genes in each network. Bottom right: UMAP plot displaying the interrelationship among the CGNs based on network gene profiles for major organs or tissue types. Each point represents a gene network associated with a specific organ or tissue type colored distinctly.
Alterations of gene regulatory networks (GRNs) in specific #CellTypes can cause disease. This study presents HCNetlas, a compilation of cell-type-specific #GRNs across healthy human tissues that can be used to uncover associations between #DiseaseGenes & cell types 🧪 @plosbiology.org plos.io/4jIwg7P
Overview of HCNetlas. Top: Schematic representation of the workflow from single-cell transcriptomic data collection to the construction of the HCNetlas. Single-cell RNA sequencing data preannotated for cell type were used to build CGNs using the scHumanNet framework. HCNetlas is comprised of a comprehensive collection of these gene networks, representing various human tissues and cell types. Bottom left: UMAP visualization of CGNs based on gene profiles, highlighting the major cell lineages, with node size representing the number of genes in each network. Bottom right: UMAP plot displaying the interrelationship among the CGNs based on network gene profiles for major organs or tissue types. Each point represents a gene network associated with a specific organ or tissue type colored distinctly.
Alterations of gene regulatory networks (GRNs) in specific #CellTypes can cause disease. This study presents HCNetlas, a compilation of cell-type-specific #GRNs across healthy human tissues that can be used to uncover associations between #DiseaseGenes & cell types 🧪 @plosbiology.org plos.io/4jIwg7P
Does learning create agency? 🤔 New study shows Pavlovian conditioning in gene regulatory networks increases causal emergence—making the system greater than its parts. This suggests learning can build agency! #AI #biology #emergence #learning #GRNs #causality osf.io/preprints/os...
GRETA graphical abstract
We present Gene Regulatory nETwork Analsyis (GRETA), a framework to infer, compare and evaluate gene regulatory networks #GRNs. With it, we have benchmarked multimodal and unimodal GRN inference methods. Check the results here 👇
Paper: doi.org/10.1101/2024.12.20.629764
Code: github.com/saezlab/greta
📣 Heads up for new followers (welcome! 🫶). I work in #RNAbiology (3' UTRs) and now #hematopoiesis #grns. I’m always eager to help make #bioinfo workflows more reproducible, so if you ever need #conda #condaforge #bioconda help please reach out! 🚀
github.com/mfansler
Advertisement for the Gene Regulatory Networks for Development course at the Marine Biological Laboratory in Woods Hole, MA. Text reads: "Gene Regulatory Networks (GRN) are the key to genomic control of development in animals and plants! Get Hands-On Training at the Gene Regulatory Networks for Development Course in Woods Hole, MA. Course Dates: Oct. 6-29, 2024. Applications due July 18, 2024. go.mbl.edu/GRN"
⏰Just TWO DAYS LEFT to apply to the Gene Regulatory Networks Advanced Research Training Course at the MBL!
Get hands on training on gene regulatory networks #GRNs with some of the best scientists in the field.
Applications due July 18, 2024! go.mbl.edu/GRN
Ready to talk about #GRNs in #EvoDevo with Kerstin Kaufmann (@HumboldtUni), @mfagny (@INRAE_France), @MarketaKau (@MPI_EvolBio) & @ArnauSebe (@CRGenomica)? Join us for S04 during @EED2024. Organized by @nturetz.bsky.social and me.
🌿 🧬 Introducing a new algorithm that revolutionizes the inference of #GRNs from time series data. It identifies communities of like-behaving genes in transcriptomic datasets.
https://buff.ly/3R5T587 from Maleana Khoury, Kenneth Berenhaut, Katherine Moore, et al.
Very proud of @BiolIntegrativa student Alexander Ramos-Diaz who just presented his poster on comparative analysis of development #GRNs at the @SocMexBioDes #SMBD18. #science #Mexico
Check out our perspective on inference of #developmental #GRNs in non-classical model systems just published @ICB_tweets. Thanks Felipe Aguilera (@faguilgen) and Alex Ramos for your contributions. #EvoDevo #Genomics...
Great first #RegulatoryGenomicsSeminar with groups from @LIIGH_UNAM, @CinvestavIra and our own #RegRNALab from @langebiomx. Lively discussion on inferring #GRNs and #lncRNA conservation followed by delicious 🍔. Thanks for hosting @AlexielMedyna!
