bartdeplancke.bsky.social - Profile | ThreadSky | a Reddit-style client for Bluesky

Really cool method 'Trace-n-seq' that allows for the molecular characterization of single neurons that innervate the pancreas and how this is altered in a cancer context at high resolution. www.nature.com/articles/s41...

submitted 2 days ago • 0 comments

wow 🚀! Need to look into the details, but sounds really exciting: Seq-Scope-X --> new spatial transcriptomics & proteomics technology that achieves sub-200 nm super-resolution, surpassing the diffraction limit of optical microscopy by physically enlarging tissues. www.biorxiv.org/content/bior...

submitted 13 days ago • 0 comments

👍

submitted 29 days ago • 0 comments

A new mechanism for cancer-induced immune evasion. We knew about cancer cells hijacking mitochondria. Now we learn about how their mitochondrial transfer to T cells impairs the tumor immune response. www.nature.com/articles/s41... www.nature.com/articles/d41...

submitted 35 days ago • 8 comments

Interesting study showing how a heart disease-linked TF, TBX5, regulates 3D chromatin independently of transcription, via structural and cohesin-regulating roles in a dose-dependent fashion www.biorxiv.org/content/10.1...

submitted 40 days ago • 0 comments

Cool new method (PERFF-seq) for profiling rare cell states via #scRNAseq, allowing for the isolation of rare cell populations by fluorescently labeling specific transcripts after which the respective cells are sorted, thus uncovering more phenotypic heterogeneity. www.nature.com/articles/s41...

submitted 46 days ago • 0 comments

Fantastic opportunity: 🚀 Calling early-career scientists! Apply for the 2025 ELISIR Scholar at EPFL. From outstanding PhD straight to group leader. Join an interdisciplinary research community to conduct independent research in any area of #lifesciences in Lausanne, CH 👉 go.epfl.ch/ELISIR

submitted 47 days ago • 0 comments

Interesting study showing that Bicoid clusters in fly embryos preserve nuclear concentration info, guiding gene expression despite non-linear LLPS models. These clusters also act as high-fidelity sensors, key for fast, precise transcriptional regulation. www.science.org/doi/10.1126/...

submitted 51 days ago • 0 comments

Superb work by Wouter @Zouters & @OlgaPushkarev developing ChromatinHD, two scale-adaptive #machinelearning models & interpretation tools that use #scRNAseq + #scATACseq data to better understand how chromatin accessibility relates to gene expression doi.org/10.1038/s414... Happy 2025 everyone 🎆 !

submitted 51 days ago • 1 comment

Cool framework to systematically compare & evaluate methods that integrate scRNA+ATAC-seq data to infer GRNs, highlighting limitations & variability in performance across different tasks and clear challenge to capture causal relationships from perturbation assays www.biorxiv.org/content/bior...

submitted 64 days ago • 0 comments

Interesting study on the use of #scRNA-seq data for protein level prediction. It highlights the limitations of mRNA as a predictor of protein expression and the effectiveness of #machine-learning models in improving protein abundance estimations. www.biorxiv.org/content/10.1...

submitted 68 days ago • 0 comments

Judith's magnum opus from her postdoc in our lab: a genome-integrated massively parallel reporter assay for quantitative insights into enhancer-promoter communication, AI benchmarking, variant dissection, & promoter motif characterization. It will be the foundation of her new lab @USC, Jan 2025! 🚀

submitted 71 days ago • 0 comments

📣 Please share: We’re hiring a tenure-track Group Leader in Multicellular Systems to explore the molecular and cellular mechanisms driving the formation, maintenance, or destabilization of tissues, organs and organisms. Apply at: www.fmi.ch/education-ca...

submitted 72 days ago • 4 comments

1/7 Planning to build a single-cell atlas? Or wondering how atlases can be useful to your research? Read our guide on single-cell atlases www.nature.com/articles/s41... published in Nature Methods, by @lisasikkema.bsky.social, @khrovatin.bsky.social, Malte Luecken, @fabiantheis.bsky.social et al.

submitted 75 days ago • 1 comment

Major milestone: Tabula Sapiens 2.0 maps tissue composition & TF expression in 175 cell types, identifying 745 ubiquitous & 890 cell type-specific TFs (many still uncharacterized -> #Codebook) w/ roles in tissue homeostasis, stress response & metabolism. #SingleCell www.biorxiv.org/content/10.1...

submitted 80 days ago • 0 comments

A grand milestone in single cell drug screening!

submitted 83 days ago • 0 comments

A deep learning-based image analysis algorithm, MouseMapper, to enable comprehensive analysis of disease-associated changes at the whole-body scale, and applied to study nervous and immune systems in high-fat diet induced obesity. One word: wow!

submitted 83 days ago • 0 comments

Really cool 'synthetic' approach to better understand the molecular mechanisms underlying endogenous (!) gene regulation, something that the field has so far been lacking!

submitted 84 days ago • 1 comment

Massive study to identify functional relationships between genes and understand how genetic background influences gene perturbation effects. www.biorxiv.org/content/10.1...

submitted 85 days ago • 0 comments

Huge effort resulting in improved TF binding site models. Congrats to the winners but also all participants for pushing analytical borders and finally also to Vanja Kulakovskiy @halfacrocodile.bsky.social‬ & team for organizing it all!

submitted 87 days ago • 0 comments

Interesting study showing that the incorporation of Med15 into Gcn4 condensates and the formation of soluble complexes with Med15 are better predictors of transcriptional activity than homotypic phase separation www.biorxiv.org/content/10.1...

submitted 92 days ago • 0 comments

Please share broadly! We (Molecular Genetics, University of Toronto) are looking for a new faculty member! Deadline Dec 19. Those working on model organisms and using genomics, computational and systems approaches are strongly encouraged to apply! Reach out w/ Qs! jobs.utoronto.ca/job/Toronto-...

submitted 120 days ago • 0 comments

How do cells remember transient signals? New work reveals that a transient pulse of histone deacetylase inhibition leaves a lasting mark on 3D genome architecture in mESCs, linking chromatin dynamics to cellular memory and gene expression robustness. www.biorxiv.org/content/10.1...

submitted 93 days ago • 2 comments

I think we all do & those who claim otherwise I don't believe ;). As PIs, it's simply hard to keep up with many rapidly evolving fields at the same time, making us feel superficial. But it's also the beauty of being a scholar: we can learn from our own lab members and colleagues around us!

submitted 94 days ago • 1 comment

Amazing 💪

submitted 94 days ago • 0 comments

The Institute for Integrative Biology of the Cell #I2BCParisSaclay is seeking to recruit new group leaders in cell biology #UnivParisSaclay #CNRSbiologie #CEAParisSaclay The application dealine is February 28, 2025

submitted 96 days ago • 0 comments

Interesting outlook on the anticipated impact of single-molecule temporal omics to track RNA, proteins and metabolites in real-time to capture dynamic molecular heterogeneity doi.org/10.1038/s415...

submitted 97 days ago • 0 comments

Really nice new paper using transfer learning with precise TF dose modulation to predict how chromatin accessibility at REs responds to changes in TF levels, also showing how TF dose perturbations can induce distinct phenotypes, even within shared cellular contexts, but lots of questions remain!

submitted 100 days ago • 0 comments

This huge effort started >6 yrs ago, using 5 TF-DNA binding assays (ChIP-seq, genomic & conv. HT-SELEX, PBM & SMilE-seq) to probe the uncharacterized TF space, likely reaching the limit of 'human DNA binding capacity'. Great collab. w/ ‪@halfacrocodile.bsky.social‬, @timhughesto.bsky.social & teams

submitted 100 days ago • 0 comments

Incredible resource for DNA binding protein specificity from the Codebook consortium. www.biorxiv.org/content/10.1... www.biorxiv.org/content/10.1... www.biorxiv.org/content/10.1... www.biorxiv.org/content/10.1... Am reading these in detail & will have a lot to say. Stay tuned for thoughts.

submitted 105 days ago • 3 comments

Excited to contribute a final Codebook paper. Great work by @antonigralak.bsky.social & team using a new methylation-sensitive SMiLE-seq method to explore the methylation-specific DNA binding preferences of (uncharacterized) human #TranscriptionFactors #Epigenetics www.biorxiv.org/content/10.1...

submitted 104 days ago • 0 comments

(1/12) Excited to present the results of the large-scale benchmarking of DNA motif discovery tools using the Codebook data compendium on poorly studied human transcription factors and the Codebook Motif Explorer: dx.doi.org/10.1101/2024..., mex.autosome.org ⬇️.

submitted 104 days ago • 1 comment

Very happy w/ our new work, excellently conceived & led by Judith Kribelbauer (new Faculty at USC starting Jan 2025!), uncovering a 'new' TF class: 'context TFs' that boost local enhancer activity and mediate enhancer-enhancer communication, forming ‘chromatin modules’. For details, t.co/Nk6DBD4CGk

submitted 105 days ago • 0 comments

👉Great opportunity for those stemming from computer science, physics, engineering, applied mathematics, or other relevant AI fields, aiming e.g. to use their expertise to advance biology/medicine: epfl.ch/research/fun.... Feel free to reach out!

submitted 105 days ago • 0 comments