Gene regulation community. #chromatin #nucleosome #TFbinding #CTCF #cancer #epigenetics. Personal views do not represent @TeifLab. Mostly moved to 🦋 and 🐘
London, UK
Joined January 2013
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Gene Regulation retweeted
MACS 3.1.0 is released with a jaw-dropping 40-60x improvement in speed, thanks to @jmschreiber91's auto-optimize work! AI achieved in one weekend what I've been hoping for years! Now peak calling that once took minutes can be completed in seconds! github.com/macs3-project/MAC… 1/2
Gene Regulation retweeted
How open is “open” chromatin? Our new Nature Genetics paper uses nucleosome-resolution modeling to reveal condensed euchromatin domains with short, accessible regulatory regions at the surface. nature.com/articles/s41588-0…
Gene Regulation retweeted
Excited to share our new preprint! ChromE-seq reads 3D chromatin and gene expression in one cell. Across ~400,000 human primary cells, B lineage has the fewest chromatin loops and is most perturbed in trisomy 21, driving the B-cell block in Down syndrome.
biorxiv.org/content/10.64898…
Gene Regulation retweeted
Are weak TF motifs important? @ZeitlingerLab use deep learning to systematically map low-affinity pioneer binding sites in mESCs and show that they cooperate with strong motifs to open chromatin. Preview w/ @gracecbower: cell.com/cell-genomics/fullt… Paper: cell.com/cell-genomics/fullt…
Gene Regulation retweeted
Excited to share a preprint on the structural mechanism of transcriptional activation by human Mediator, studied using integrative structural modeling.
Many thanks to Lacra Bintu @BintuLacra for helpful discussions!
biorxiv.org/content/10.64898…
@generegulation @MED_COMPLEX
Gene Regulation retweeted
After a long wait, tangermeme is out @naturemethods!
tangermeme implements the primitives of genomic sequence-to-function modeling with efficient, tested, and composable functions.
I use it every day in my work, and I hope you find it useful too.
nature.com/articles/s41592-0…
Gene Regulation retweeted
1/13
The human body runs on one genome—but every cell reads it differently. How?
To find out, we need to know both gene expression and chromatin accessibility in the same nucleus.
So we did, across 21 adult tissues and nearly half a million nuclei. 🧵
🔗 biorxiv.org/content/10.64898…
Gene Regulation retweeted
Our @Nature Research Briefing is now out 📝
Chromatin accessibility reveals disease risk that gene expression misses, because constrained genes buffer effects before they reach it 🛡
📝 Briefing: nature.com/articles/d41586-0…
📄 Paper: nature.com/articles/s41586-0…
xitter.cf/masakanai/status/21053…
Our single-nucleus immune multiome atlas is now out in @Nature! 🧬
10M PBMCs from 1,108 @FinnGen_FI donors recruited by @FRCBSresearch, profiled at @broadinstitute KCO with chromatin accessibility and gene expression in the same nuclei, to trace how disease variants act 🧵👇
Gene Regulation retweeted
🧬 Highly related @NatureGenet paper from @binzmit group, using nucleosome-resolution chromatin modeling: Euchromatin forms condensed domains with short active regions on the surface
nature.com/articles/s41588-0…
Congratulations! 🎉
Is euchromatin really “open”? 🧬 Using super-resolution imaging🔬 our new study @NatureGenet reveals: Euchromatin forms condensed domains in live cells. Cohesin constrains them and prevents domain mixing for proper transcriptional insulation🚧 🔗nature.com/articles/s41588-0… (1/2)
Gene Regulation retweeted
🧵 Excited to share our new preprint on how evolution may coordinate TF–TF interactions with the genomic arrangement of their binding sites.
This project was also heavily agentic from beginning to end.
Preprint:
biorxiv.org/content/10.64898…
Zheng et al, 2026. Transcription factors read a second regulatory code in chromatin. biorxiv.org/content/10.64898…
"TFs interpret two complementary layers of genomic information: the primary DNA sequence and a second code written into the nucleosome architecture"
Gene Regulation retweeted
Grateful to @CellReports for featuring our article tinyurl.com/n3uyuns8 Emergent #3Dgenome reorganization and graded #gene control through the stepwise assembly of #transcriptional #condensates on their cover tinyurl.com/3nvws23p @Pha_Tran_Papers @4DNucleome @generegulation
Gene Regulation retweeted
Oriented binding of transcription factors to nucleosomes remodels chromatin at human promoters dlvr.it/TVXnmw
Gene Regulation retweeted
We know a bit about how 3D chromatin interactions are formed, but what do we know about how they are disrupted? We asked this question in our latest preprint: doi.org/10.64898/2026.09.15.…, focusing on the massive loss of promoter interactions during neuronal differentiation.
Gene Regulation retweeted
🧬 How do cells remember?
Join us in Baeza 🇪🇸 for Transcriptional Memory in Health and Disease, 20–22 October.
💥 Young scientists: €250, including meals!
📢 Deadline extended to 27 Sept — you can do this!
unia.es/estudios-y-acceso/of…
#Epigenetics #Chromatin #SystemsBiology
Gene Regulation retweeted
🚨New preprint🚨 from super postdoc, @FabioGomezCano1, on modeling and removing ambient contamination (i.e. nuclei-free chromatin 🧬) in single-cell scifi-ATAC-seq experiments using his new tool, AmbientMapper.
biorxiv.org/content/10.64898…
Gene Regulation retweeted
Maintenance of nucleosome organization through replication and transcription counteracts aberrant coalescence of active chromatin dlvr.it/TVX6ZC
Gene Regulation retweeted
Inflammation can leave a structural mark on the genome. Using base-pair resolution chromatin conformation data, @BenceDaniel2, Andy Chen, and @SandorDanielne show that immune memory to inflammation can be stored in the 3D genome. @PNASNews @4DNucleome
pnas.org/doi/10.1073/pnas.26…
Gene Regulation retweeted
Review🚨
Ciriello, Oricchio&Co discuss how remodelling the 3D #chromatin structure in cancer is both a cause & consequence of genetic and epigenetic alterations and highlight how chromatin 3D conformation might be exploited for diagnosis and therapy.
📖⬇️
dlvr.it/TVVCLN