Ivan Berest
@berest.bsky.social
Hello ☁️💙✨ community!
Bioinformatician 👨💻🧬 Zaugg lab
Former member Kopf lab @ ETH Zurich
Previously PhD @EMBL Zaugg group
Passionate about chromatin, TFs and multiomics data analysis!
Favourite celltype: macrophages 👻
R/Bioconductor + Snakemake
Bioinformatician 👨💻🧬 Zaugg lab
Former member Kopf lab @ ETH Zurich
Previously PhD @EMBL Zaugg group
Passionate about chromatin, TFs and multiomics data analysis!
Favourite celltype: macrophages 👻
R/Bioconductor + Snakemake
Reposted by Ivan Berest
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
🧵
🚀 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
🧵
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...
doi.org
May 26, 2025 at 9:33 AM
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
🧵
🚀 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
🧵
Reposted by Ivan Berest
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...
www.nature.com/articles/s41...
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, ...
www.nature.com
March 12, 2025 at 1:32 PM
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...
www.nature.com/articles/s41...
Reposted by Ivan Berest
#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
February 13, 2025 at 12:16 PM
#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
Reposted by Ivan Berest
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
January 24, 2025 at 10:54 PM
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
Reposted by Ivan Berest
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.
December 14, 2024 at 6:00 PM
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.
Reposted by Ivan Berest
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...
Perfect if you want to scale up time course, drug/CRISPR screen or atlas projects! 🖥️ 🧬
www.biorxiv.org/content/10.1...
January 2, 2024 at 8:51 AM
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...
Perfect if you want to scale up time course, drug/CRISPR screen or atlas projects! 🖥️ 🧬
www.biorxiv.org/content/10.1...
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!
Bash One-Liners for LLMs
Tutorial on how llamafile makes LLMs shell scriptable.
s3.eu-central-1.wasabisys.com
December 14, 2023 at 8:34 AM
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!
Amazing paper investigating cellular responses to 86 cytokines on different immune cells by scRNA-seq. Great and powerful resource!
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...
www.nature.com
December 11, 2023 at 8:29 AM
Amazing paper investigating cellular responses to 86 cytokines on different immune cells by scRNA-seq. Great and powerful resource!