Ivan Berest

📣 I hereby make my Bluesky debut to announce that our work linking DNA binding affinities and kinetics 𝘪𝘯 𝘷𝘪𝘵𝘳𝘰 and 𝘪𝘯 𝘷𝘪𝘷𝘰 for the human transcription factor KLF1 just got published in Cell! @cp-cell.bsky.social

www.cell.com/cell/fulltex...

Key findings in a thread (1/6):

Single-cell ultra-high-throughput multiplexed chromatin and RNA profiling reveals gene regulatory dynamics - Nature Methods This work presents SUM-seq, an ultra-high-throughput method for co-profiling chromatin accessibility and gene expression in single nuclei across multiplexed samples, advancing the study of gene regula...

SUM-seq out @natmethods.nature.com !


🚀 Ultra-high-throughput Multiplexed snATAC+RNA

Used to:
⏳ link temporal macrophage GRNs to immune disease genetics
🩸 map T cell regulatory landscapes
🧬✂️ dissect TF function in hiPSC differentiation via CRISPRi/a screens
doi.org/10.1038/s41592-025-02700-8
🧵

Tuft cell IL-17RB restrains IL-25 bioavailability and reveals context-dependent ILC2 hypoproliferation - Nature Immunology Tuft cells constitutively express IL-25 to sustain ILC2 homeostasis in the intestine, but mechanisms driving IL-25 secretion have been unclear. Here, Feng et al. find that tuft cells express IL-17RB, ...

Thrilled that the polished version of our tuft cell story published is now available online + open access in Nature Immunology @natureportfolio.nature.com
www.nature.com/articles/s41...

#CellPlasticity—the ability of cells to change their identity—is vital for tissue growth and repair. But when it goes unchecked, it can fuel #cancer. Our latest study examines how to block #LiverCancer by actively suppressing plasticity. www.nature.com/articles/s41... #CancerBiology

There has been a couple of manuscripts released regarding transcription factor footprinting - or digital genomic footprinting (DGF) as we call it. I would like to put some of the claims, results and conclusions in context, since I have worked and published on this for ~15 years. 1/n

Science is not really happening when the goal is a paper, a presentation, a grant, or any product. It only really happens when the goal is a process of discovery.

Right before the end of the year the Zaugg and Noh teams at EMBL shared SUM-seq: a scalable single cell ATAC+RNA method.

Perfect if you want to scale up time course, drug/CRISPR screen or atlas projects! 🖥️ 🧬
www.biorxiv.org/content/10.1...

Bash One-Liners for LLMs Tutorial on how llamafile makes LLMs shell scriptable.

This is so cool! Using LLM models as one-liners for specific small tasks, just as "awk" or "less". Cannot wait how this can change bioinformatics in future!

Dictionary of immune responses to cytokines at single-cell resolution - Nature An extensive global transcriptomics analysis of in vivo responses to 86 cytokines across more than 17 immune cell types reveals enormous complexity of cellular responses to cytokines, providing the ba...

Amazing paper investigating cellular responses to 86 cytokines on different immune cells by scRNA-seq. Great and powerful resource!