Yotam Drier
@yotamd.bsky.social
Epigenomics and chromosome topology in cancer • Assistant Professor, Faculty of Medicine, Hebrew University of Jerusalem • yotamdrier.ekmd.huji.ac.il
Reposted by Yotam Drier
How embryos stay “on time” as they grow?
Happy to share our recent publication: Quantitative modeling of mRNA degradation reveals tempo-dependent mRNA clearance in early embryos
(1/7)
academic.oup.com/nar/article/...
Happy to share our recent publication: Quantitative modeling of mRNA degradation reveals tempo-dependent mRNA clearance in early embryos
(1/7)
academic.oup.com/nar/article/...
Quantitative modeling of mRNA degradation reveals tempo-dependent mRNA clearance in early embryos
Abstract. As embryos transition from maternal to zygotic control, precise clearance of pre-loaded maternal mRNAs is essential for initiating new zygotic ge
academic.oup.com
August 5, 2025 at 8:23 PM
How embryos stay “on time” as they grow?
Happy to share our recent publication: Quantitative modeling of mRNA degradation reveals tempo-dependent mRNA clearance in early embryos
(1/7)
academic.oup.com/nar/article/...
Happy to share our recent publication: Quantitative modeling of mRNA degradation reveals tempo-dependent mRNA clearance in early embryos
(1/7)
academic.oup.com/nar/article/...
Reposted by Yotam Drier
1. Today the NIH director issued a new directive slashing overhead rates to 15%.
I want to provide some context on what that means and why it matters.
grants.nih.gov/grants/guide...
I want to provide some context on what that means and why it matters.
grants.nih.gov/grants/guide...
NOT-OD-25-068: Supplemental Guidance to the 2024 NIH Grants Policy Statement: Indirect Cost Rates
NIH Funding Opportunities and Notices in the NIH Guide for Grants and Contracts: Supplemental Guidance to the 2024 NIH Grants Policy Statement: Indirect Cost Rates NOT-OD-25-068. OD
grants.nih.gov
February 8, 2025 at 12:18 AM
1. Today the NIH director issued a new directive slashing overhead rates to 15%.
I want to provide some context on what that means and why it matters.
grants.nih.gov/grants/guide...
I want to provide some context on what that means and why it matters.
grants.nih.gov/grants/guide...
Reposted by Yotam Drier
Why can a human tolerate a drug that globally inhibits transcription? Why do transcription inhibitors not cure cancer? Our first paper of 2025 may help explain (some) of this!
So incredibly proud of @tobiaswilliams.bsky.social & Ewa Michalak who led the work!
www.cell.com/molecular-ce...
So incredibly proud of @tobiaswilliams.bsky.social & Ewa Michalak who led the work!
www.cell.com/molecular-ce...
mRNA export factors store nascent transcripts within nuclear speckles as an adaptive response to transient global inhibition of transcription
Transcription inhibitors also disrupt nuclear export. Here, Williams et al. reveal that mRNA export factors sense transcription inhibition and adapt by storing mature export-competent mRNA in nuclear speckles. This enables rapid release when transcription resumes and ensures retention of cellular identity and viability during a transient global transcription insult.
www.cell.com
January 2, 2025 at 8:03 PM
Why can a human tolerate a drug that globally inhibits transcription? Why do transcription inhibitors not cure cancer? Our first paper of 2025 may help explain (some) of this!
So incredibly proud of @tobiaswilliams.bsky.social & Ewa Michalak who led the work!
www.cell.com/molecular-ce...
So incredibly proud of @tobiaswilliams.bsky.social & Ewa Michalak who led the work!
www.cell.com/molecular-ce...
Reposted by Yotam Drier
Ever wondered how transcription choreographs histone modifications? Our work reveals the basis of co-transcriptional H3K36me3 by SETD2. We visualize how a histone writer coordinates with the transcription machinery! This is the magnus opus of @jonmarkert.bsky.social!
tinyurl.com/setd2
tinyurl.com/setd2
December 12, 2024 at 7:16 PM
Ever wondered how transcription choreographs histone modifications? Our work reveals the basis of co-transcriptional H3K36me3 by SETD2. We visualize how a histone writer coordinates with the transcription machinery! This is the magnus opus of @jonmarkert.bsky.social!
tinyurl.com/setd2
tinyurl.com/setd2
Reposted by Yotam Drier
Have you been thinking hard about statistical modelling of scATAC-seq data? (No.)
Luckily for you, @aaronkwc.bsky.social has!
Aaron will help you grok:
What's going on?
What is TF-IDF?
Is there really single-cell level chromatin information?
Check it out 👇
www.biorxiv.org/content/10.1...
🧪🧬💻
Luckily for you, @aaronkwc.bsky.social has!
Aaron will help you grok:
What's going on?
What is TF-IDF?
Is there really single-cell level chromatin information?
Check it out 👇
www.biorxiv.org/content/10.1...
🧪🧬💻
Going beyond cell clustering and feature aggregation: Is there single cell level information in single-cell ATAC-seq data?
Single-cell Assay for Transposase Accessible Chromatin with sequencing (scATAC-seq) has become a widely used method for investigating chromatin accessibility at single-cell resolution. However, the re...
www.biorxiv.org
December 10, 2024 at 6:37 AM
Have you been thinking hard about statistical modelling of scATAC-seq data? (No.)
Luckily for you, @aaronkwc.bsky.social has!
Aaron will help you grok:
What's going on?
What is TF-IDF?
Is there really single-cell level chromatin information?
Check it out 👇
www.biorxiv.org/content/10.1...
🧪🧬💻
Luckily for you, @aaronkwc.bsky.social has!
Aaron will help you grok:
What's going on?
What is TF-IDF?
Is there really single-cell level chromatin information?
Check it out 👇
www.biorxiv.org/content/10.1...
🧪🧬💻
Reposted by Yotam Drier
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.
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.
December 9, 2024 at 2:12 PM
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.
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.
Reposted by Yotam Drier
Not checking nuclear markers like MALAT1 or intronic reads in your scRNA-seq data?🚨
We show their power to flag low-quality cells—even in top public datasets. It’s time to prioritize better QC for cleaner, more reliable genomics research!
Read more: bmcgenomics.biomedcentral.com/articles/10....
1/8
High content of nuclei-free low-quality cells in reference single-cell atlases: a call for more stringent quality control using nuclear fraction - BMC Genomics
The advent of droplet-based single-cell RNA-sequencing (scRNA-seq) has dramatically increased data throughput, enabling the release of a diverse array of tissue cell atlases to the public. However, we...
bmcgenomics.biomedcentral.com
December 3, 2024 at 8:38 AM
Not checking nuclear markers like MALAT1 or intronic reads in your scRNA-seq data?🚨
We show their power to flag low-quality cells—even in top public datasets. It’s time to prioritize better QC for cleaner, more reliable genomics research!
Read more: bmcgenomics.biomedcentral.com/articles/10....
1/8
Reposted by Yotam Drier
There's been some interest in this PLOS announcement, so despite it being light on details, here's why it's big. In our recent study 'The strain on scientific publishing' we showed how certain groups took off in total articles published.
Why? And why now?
direct.mit.edu/qss/article/...
1/n 🧵
Why? And why now?
direct.mit.edu/qss/article/...
1/n 🧵
December 2, 2024 at 9:14 PM
There's been some interest in this PLOS announcement, so despite it being light on details, here's why it's big. In our recent study 'The strain on scientific publishing' we showed how certain groups took off in total articles published.
Why? And why now?
direct.mit.edu/qss/article/...
1/n 🧵
Why? And why now?
direct.mit.edu/qss/article/...
1/n 🧵
Reposted by Yotam Drier
🧬🔍There are 50 petabases of freely-available DNA sequencing data. We introducing Logan Search which allows you to search for any DNA sequence in minutes, bringing Earth’s largest genomic resource to your fingertips.
🏔️ logan-search.org 🏔️
#Genomics #Bioinformatics #OpenScience
🏔️ logan-search.org 🏔️
#Genomics #Bioinformatics #OpenScience
November 11, 2024 at 7:29 PM
🧬🔍There are 50 petabases of freely-available DNA sequencing data. We introducing Logan Search which allows you to search for any DNA sequence in minutes, bringing Earth’s largest genomic resource to your fingertips.
🏔️ logan-search.org 🏔️
#Genomics #Bioinformatics #OpenScience
🏔️ logan-search.org 🏔️
#Genomics #Bioinformatics #OpenScience
Reposted by Yotam Drier
Today in Molecular Cell the work of one of my favorite (ex)PhD students in the Wysocka Lab: Dr. Christina Jensen. I saw this project develop throughout the years and it has kept me engaged in hypothesizing scenarios in every lab meeting. Congratulations to the authors!
www.cell.com/molecular-ce...
www.cell.com/molecular-ce...
Long-range regulation of transcription scales with genomic distance in a gene-specific manner
Jensen et al. show that targeting dCas9-VPR using a multiplexed array of RNA guides
results in effective activator recruitment to promoter-distal, previously inaccessible
genomic sites, allowing for l...
www.cell.com
December 3, 2024 at 2:51 AM
Today in Molecular Cell the work of one of my favorite (ex)PhD students in the Wysocka Lab: Dr. Christina Jensen. I saw this project develop throughout the years and it has kept me engaged in hypothesizing scenarios in every lab meeting. Congratulations to the authors!
www.cell.com/molecular-ce...
www.cell.com/molecular-ce...
Reposted by Yotam Drier
Enhancer cooperativity can compensate for loss of activity over large genomic distances | Molecular Cell
#chromatin #enhancers
www.cell.com/molecular-ce...
#chromatin #enhancers
www.cell.com/molecular-ce...
Enhancer cooperativity can compensate for loss of activity over large genomic distances
Thomas, Feng, et al. introduce a synthetic platform that allows the building of complex
regulatory landscapes. Integrating the same enhancer at different distances from a
promoter uncovered that activ...
www.cell.com
December 3, 2024 at 5:43 AM
Enhancer cooperativity can compensate for loss of activity over large genomic distances | Molecular Cell
#chromatin #enhancers
www.cell.com/molecular-ce...
#chromatin #enhancers
www.cell.com/molecular-ce...
Reposted by Yotam Drier
Gene regulation involves thousands of proteins that bind DNA, yet comprehensively mapping these is challenging. Our paper in Nature Genetics describes ChIP-DIP, a method for genome-wide mapping of hundreds of DNA-protein interactions in a single experiment.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
ChIP-DIP maps binding of hundreds of proteins to DNA simultaneously and identifies diverse gene regulatory elements - Nature Genetics
ChIP-DIP (ChIP done in parallel) is a highly multiplex assay for protein–DNA binding, scalable to hundreds of proteins including modified histones, chromatin regulators and transcription factors, offe...
www.nature.com
November 27, 2024 at 4:13 AM
Gene regulation involves thousands of proteins that bind DNA, yet comprehensively mapping these is challenging. Our paper in Nature Genetics describes ChIP-DIP, a method for genome-wide mapping of hundreds of DNA-protein interactions in a single experiment.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Yotam Drier
Here’s the updated Computational Biology Starter Pack! Let me know if you'd like to be included.
go.bsky.app/QVPoZXp
go.bsky.app/QVPoZXp
November 24, 2024 at 4:33 PM
Here’s the updated Computational Biology Starter Pack! Let me know if you'd like to be included.
go.bsky.app/QVPoZXp
go.bsky.app/QVPoZXp
Reposted by Yotam Drier
Evolving cell states and oncogenic drivers during the progression of IDH-mutant gliomas - Nature Cancer 🧪
www.nature.com/articles/s43...
www.nature.com/articles/s43...
Evolving cell states and oncogenic drivers during the progression of IDH-mutant gliomas - Nature Cancer
Wu et al. perform single-cell analyses to explore the switch from low-grade to high-grade isocitrate-dehydrogenase-mutant glioma and show that it is characterized by oligodendrocyte progenitor cell-li...
www.nature.com
November 24, 2024 at 6:57 AM
Evolving cell states and oncogenic drivers during the progression of IDH-mutant gliomas - Nature Cancer 🧪
www.nature.com/articles/s43...
www.nature.com/articles/s43...
Reposted by Yotam Drier
It's my great pleasure to present the next big preprint from SheqLab! An exciting application of our O-MAP platform that I hope will transform the study of nuclear architecture.
If you've ever wanted to dissect the subnuclear "neighborhood" around an individual locus, read on! (1/30)
If you've ever wanted to dissect the subnuclear "neighborhood" around an individual locus, read on! (1/30)
November 21, 2024 at 1:27 AM
It's my great pleasure to present the next big preprint from SheqLab! An exciting application of our O-MAP platform that I hope will transform the study of nuclear architecture.
If you've ever wanted to dissect the subnuclear "neighborhood" around an individual locus, read on! (1/30)
If you've ever wanted to dissect the subnuclear "neighborhood" around an individual locus, read on! (1/30)
Reposted by Yotam Drier
November 21, 2024 at 5:13 PM
Reposted by Yotam Drier
Our paper with Carmel lab, the work of PhD student Yoav Mathov was just published in Nat Ecol Evol. www.nature.com/articles/s41....
Inferring DNA methylation in non-skeletal tissues of ancient specimens. A major challenge in studying DNA methylation in ancient samples is that it is tissue-specific.
Inferring DNA methylation in non-skeletal tissues of ancient specimens. A major challenge in studying DNA methylation in ancient samples is that it is tissue-specific.
www.nature.com
November 20, 2024 at 10:56 AM
Our paper with Carmel lab, the work of PhD student Yoav Mathov was just published in Nat Ecol Evol. www.nature.com/articles/s41....
Inferring DNA methylation in non-skeletal tissues of ancient specimens. A major challenge in studying DNA methylation in ancient samples is that it is tissue-specific.
Inferring DNA methylation in non-skeletal tissues of ancient specimens. A major challenge in studying DNA methylation in ancient samples is that it is tissue-specific.
Reposted by Yotam Drier
Leonid Mirny and I wrote this for all interested in chromosomes: "The chromosome folding problem and how cells solve it"
www.cell.com/action/showP...
www.cell.com/action/showP...
www.cell.com
November 14, 2024 at 4:02 PM
Leonid Mirny and I wrote this for all interested in chromosomes: "The chromosome folding problem and how cells solve it"
www.cell.com/action/showP...
www.cell.com/action/showP...
Reposted by Yotam Drier
I’ve started making a starter pack for computational #cancer! Let me know if you’d like to be added or know someone who should be go.bsky.app/N6moBmG
November 12, 2024 at 8:58 PM
I’ve started making a starter pack for computational #cancer! Let me know if you’d like to be added or know someone who should be go.bsky.app/N6moBmG
Importing some of our recent updates from Twitter to facilitate the great migration. Happy to report our results on the role of SMCHD1 in facioscapulohumeral muscular dystrophy (FSHD). A very close and fun collaboration with Prof. Salton, this work was led by our amazing joint student, Eden Engal.
November 17, 2024 at 3:40 PM
Importing some of our recent updates from Twitter to facilitate the great migration. Happy to report our results on the role of SMCHD1 in facioscapulohumeral muscular dystrophy (FSHD). A very close and fun collaboration with Prof. Salton, this work was led by our amazing joint student, Eden Engal.
Importing some of our recent updates from Twitter to facilitate the great migration. Interested in inferring pathway activity in the single cell level from #SingleCell RNAseq data? check out SiPSiC. Details at: t.co/zeLafAiMHg
Available on bioconductor: t.co/CyK0YVokV9 and github: t.co/EzSWAUFeel
Available on bioconductor: t.co/CyK0YVokV9 and github: t.co/EzSWAUFeel
https://www.genome.org/cgi/doi/10.1101/gr.278431.123
t.co
November 17, 2024 at 3:26 PM
Importing some of our recent updates from Twitter to facilitate the great migration. Interested in inferring pathway activity in the single cell level from #SingleCell RNAseq data? check out SiPSiC. Details at: t.co/zeLafAiMHg
Available on bioconductor: t.co/CyK0YVokV9 and github: t.co/EzSWAUFeel
Available on bioconductor: t.co/CyK0YVokV9 and github: t.co/EzSWAUFeel
Reposted by Yotam Drier
Reposted by Yotam Drier
(1/8) 🚀 Excited to share our findings on a large-scale ChIP-seq assay for 166 previously uncharacterized human transcription factors (TFs) and their roles in both regulatory regions, and more strikingly, the “dark matter” genome. 🌌 doi.org/10.1101/2024....
Extensive binding of uncharacterized human transcription factors to genomic dark matter
Most of the human genome is thought to be non-functional, and includes large segments often referred to as “dark matter” DNA. The genome also encodes hundreds of putative and poorly characterized tran...
doi.org
November 15, 2024 at 7:02 PM
(1/8) 🚀 Excited to share our findings on a large-scale ChIP-seq assay for 166 previously uncharacterized human transcription factors (TFs) and their roles in both regulatory regions, and more strikingly, the “dark matter” genome. 🌌 doi.org/10.1101/2024....
Reposted by Yotam Drier
Pleasure to continue our collaboration with Marcus Wilson and group and play a small part in this study which is now out in the paper version. Read on to learn more about DNMT3A's interaction with H3K36me2 and H2AK119Ub modified nucleosomes:
www.embopress.org/doi/full/10....
#epigenetics
www.embopress.org/doi/full/10....
#epigenetics
The N-terminal region of DNMT3A engages the nucleosome surface to aid chromatin recruitment | EMBO reports
imageimageA UDR motif in DNMT3A acts in concert with other chromatin reading regions to promote
chromatin recruitment. A cryo-EM structure reveals that DNMT3A1 binds to H2AK119ub-marked
nucleosomes th...
www.embopress.org
November 13, 2024 at 4:53 PM
Pleasure to continue our collaboration with Marcus Wilson and group and play a small part in this study which is now out in the paper version. Read on to learn more about DNMT3A's interaction with H3K36me2 and H2AK119Ub modified nucleosomes:
www.embopress.org/doi/full/10....
#epigenetics
www.embopress.org/doi/full/10....
#epigenetics