Nature research paper: Basal cell of origin resolves neuroendocrine–tuft lineage plasticity in cancer go.nature.com/3ViRTAP

Now online in Cancer Discovery @aacrjournals.bsky.social: Development and Prospective Validation of a Cell-free DNA-based Model for the Early Detection of Pancreatic Cancer - by Xiuchao Wang, Hongwei Wang, Meng Zhang, Jun Yu, Chuntao Gao, Yunfeng Cui, Jihui Hao, et al. doi.org/10.1158/2159...

🚨 New preprints from our lab!
First, we introduce Cryo-mtscATAC-seq, led by Maren (@ms-maren.bsky.social ), enabling high-throughput clonal tracing from frozen human samples by isolating nuclei with their mitochondria (“CryoCells”).
👉 www.biorxiv.org/content/10.1...

EPI-Clone is a transgene-free lineage tracing method that uses single-cell DNA methylation analysis to track hematopoietic stem cell clones over time #NBThighlight www.nature.com/articles/s41...

CRISPRai simultaneously activates and represses two genes in single cells go.nature.com/4apFU9q rdcu.be/efe0E

1/ Transposable elements are often called "jumping genes" because they mobilize within genomes. 🧬 But did you know they can also jump 𝘣𝘦𝘵𝘸𝘦𝘦𝘯 cells? 🤯 Our new study reveals how retrotransposons invade the germline directly from somatic cells. www.biorxiv.org/content/10.1... A short thread 🧵👇

Information storage across a microbial community using universal RNA barcoding - @lauren-stadler.bsky.social @joffsilberg.bsky.social go.nature.com/440gL5E

New paper out in @bloodjournal.bsky.social. In this study lead by Daria Karpova and Hector Encabo, we investigated the effect of frequent blood donations (FD) on clonal hematopoiesis (CH). Briefly, FD selects for DNMT3A mutations rendering HSC sensitive to stimulation by EPO. doi.org/10.1182/bloo...

🚀 Join the #ISCO2025 community at @mdc-berlin.bsky.social on May 12-13! 🚀 Don't miss this incredible opportunity to connect with top #singlecell & #spatial omics experts and participate in a special Workshop led by @itaiyanai.bsky.social. ⏳Abstract submissions: March 21) www.isco-conference.eu

New spatial method, Perturb-FISH, combines imaging-based spatial transcriptomic measurements with CRISPR screening to reveal effects within and between cells. #Science

Want to track clonality in organoids, cancer models, or in vivo transplants? Try our STRACK barcoding libraries from Addgene: www.addgene.org/233208/ www.addgene.org/233210/ www.addgene.org/233209/. If you need help establishing it, reach out—happy to collaborate and troubleshoot

Beyond excited to say my first PhD paper is out today in @CellStemCell 📷. Here, we explored the role of epigenetic heterogeneity on malignant expansion, using a new approach called STRACK www.cell.com/cell-stem-ce...

🧪New technique reveals how the same mutations give rise to very different types of #leukaemia. 📰 Cell Stem Cell, supported by #CRISContraelCáncer. ✍️ Indranil Singh, Daniel Fernández-Pérez, Pedro Sánchez Sánchez, @alejofraticelli.bsky.social. ➡️ bit.ly/3QyrAnJ 📌 doi.org/10.1016/j.st...

Here is a growing list of conferences and schools in gene regulation for 2025 generegulation.org/conferences-.... You can order/filter this list by the date, deadline, location. Please reply here to suggest new events* *should be specific to gene regulation

Epidemiological studies have linked dirty air to dementia and other brain disorders. Nature reports on how researchers are trying to determine how pollutants do their damage, and how much harm they cause. 🧪

Very interesting work - @alejofraticelli.bsky.social @shalinhnaik.bsky.social www.nature.com/articles/s41...

Excited to share James Jusuf's preprint: By integrating Micro-C with SuperRes Live-Imaging we can calibrate genomics&imaging to perform absolute quantification of looping (e.g. this loop is present 3%) We quantify mESC 36k loops: <loops> are generally rare (2.3%) www.biorxiv.org/content/10.1...

Sometimes, the exciting papers with more surprising findings have a harder time in the current scientific community. This is such an example. I think how cells remember past exposures and how this impacts their future fates is still poorly understood.

Chromatin-based memory as a self-stabilizing influence on cell identity | Genome Biology #Chromatin #CellFate #Review genomebiology.biomedcentral.com/articles/10....

Happy to share the latest work from Preeti Sahu, with Adriana Sanchez-Danes on the biomechanics of cell fate choices during tumor initiation! We implement/test a 3D vertex model with proliferation and fate choices for multilayered tissues! See 🧵 below (1/n) bit.ly/3ZXxJzk

The big 4 of grant writing: 1. Credibility: The topic fits your expertise 2. Narrative: It's clear what is the problem, the solution, and why you’re the right person for it 3. Juicy details: Flex your mastery of the topic 4. The concept: You connect every part to the big question

Extremely cool system for in vitro culture! Synthetic organizer cells, engineered to spatially self-assemble around stem cells, can be used to create specific morphogen gradients and systematically guide in vitro development Congrats to everyone involved! www.cell.com/cell/abstrac...

This is so cool

This is a really amazing study!

www.biorxiv.org/content/10.1... Our study published today on #bioRxiv describe the identification of a deaminase that converts 5mC to T, enabling direct sequencing of the human methylome and genome. This achievement was made possible through a collaborative effort across all departments at #NEB.

Just in time for thanksgiving our paper is out ☄️ using fluctuating methylation clocks as barcodes we show that the variation in the hematopoietic stem cell pool that (in most of us) leads to clonal hematopoiesis in later life is likely present *before birth* 👉🏼 www.nature.com/articles/s41...

🔺🔺🔺RED TRIANGLE ALERT 🔺🔺🔺 Ever wonder how #TADs compare across the tree of life?Look no further & read our Review!!! Find out what genes & 3D chromatin can & can't do in Bacteria! Archeae! Yeast! Plants! Animals! SMCs & RNA-Pol are the only thing they have in common www.nature.com/articles/s41...

New on BioRxiv: We report a new, endogenous molecular clock in unmodified human cells and tissues. It is ticking away right now in almost every cell in your body. Paper here: www.biorxiv.org/content/10.1... 1/

Cell division is NOT a must for differentiation during early zebrafish embryogenesis. www.nature.com/articles/s41...

In this review @gracebower.bsky.social & I discuss recent evidence showing that, unlike canonical enhancers, long-range enhancers located hundreds of kb from their targets rely on additional mechanisms to ensure robust gene activation during mammal development. www.sciencedirect.com/science/arti...

A multi-omic atlas of human embryonic skeletal development, from Sarah Teichmann’s group; introducing the interesting SNP2Cell tool to link cell-type-specific regulatory networks to polygenic traits www.nature.com/articles/s41...

Interesting new method to map nucleosomes in 3D, "Proximity Copy Paste (PCP)". www.biorxiv.org/content/10.1... ▶️ mapped connectivity of nucleosomes in S. cerevisiae ▶️ chromatin is predominantly organized into regularly spaced nucleosome arrays ▶️ metaphase chromosomes packed by arrayed cohesin hubs

Want to make beautiful scientific figures? Easy! The NIH released a library of 2000+ free scientific illustrations called *BioArt*. Check it out! bioart.niaid.nih.gov #AcademicSky #PsychSciSky 🧠🟦 🧪

CpGPT: a Foundation Model for DNA Methylation www.biorxiv.org/content/10.1... MethylGPT: a foundation model for the DNA methylome www.biorxiv.org/content/10.1... Exciting self supervised models trained on massive cross-platform methylation data by @bowang87.bsky.social lab. 1/

Professors: we must start teaching creativity in science! Interested in teaching the creative scientific process at your university? Here's our materials to help: Workshops: www.night-science.org/teaching_mat... Editorials: www.biomedcentral.com/collections/... Podcast: nightscience.buzzsprout.com

Official website for EMBO meiosis 2025 is live now! Looking forward to seeing you in Switzerland next June! #meiosis4eva meetings.embo.org/event/25-mei...

A stimulating workshop on the subject of Waddington Landscapes in Lyon last week, prompted me to compose some thoughts on dynamical landscapes, gene regulatory networks, and single cell transcriptomics briscoelab.org/morphogenalia/

NEW paper 🚨 Have you ever wondered how the RNA degradosome picks its targets for mRNA decay? Can we predict how quickly a mRNA will decay inside cells? Drs. Cetnar, Hossain, & Vezeau characterized 50000+ synthetic mRNAs to provide quantitative answers! 🧵 begins www.nature.com/articles/s41...

Preprint describing the systematic identification of TF binding motifs and of TFs which preferentially bind methylated DNA. #epigenomics

I've been meaning to write a lengthy thread about our experiences with DNA methylation editing in mouse ESCs if that would be useful (or interesting?) for a niche audience here. tl;dr: it was frustrating but we learned a lot, and it ended with our shiny new pub (1/17) www.nature.com/articles/s41...