I am moving. See you at 👋 #GoodbyeX 🌞 #HelloBluesky

9/ 🤘 It's a long way to the top if you wanna rock 'n' roll. but @IsabelleSeufert rocked it with help of great PhD/Master's students @DKFZ & BioQuant, and valuable contributions from @AkisPapantonis, @jpmallm1, @s_anders_m & Petros Kolovos labs & funding by @spp2202_dfg. #ACDC.

8/ 🔥 We reconcile findings from previous sequencing and microscopy studies into the genome-wide AC/DC model of #transcription regulation, revealing two co-existing chromatin compartment architectures. For the full story, check out our bioRxiv preprint at

7/ 🌟 Our approach is applicable across other cellular systems and perturbations like interferon signaling of TF knock-out. Results improve with deeper #scATAC-seq coverage. We pushed that to 150k unique fragments/cell, but RWireX works well with 20-30k fragments/cell.

6/ 📊 ACs have a stronger impact on transcriptional burst frequency, whereas DCs act more by modulating burst size. These findings put a new perspective on how cells achieve rapid and precise gene expression responses at different transcription output levels during inflammation.

5/ ⛰️ DCs (domains of contiguous co-accessibility) are regions of simultaneously accessible chromatin sites. These domains have a locally increased transcription factor binding activity and could represent the genomic footprint of TF hubs/condensates.

4/ 🧬 ACs (autonomous links of co-accessibility) denote long-range interactions between separated regulatory sites at ATAC peaks. We observed differences between rare and frequently occurring ACs, suggesting distinct roles of stochastic vs. architectural links.

3/ 💻 With our new software package RWireX available at #GitHub (, we computed co-accessibility in #scATAC-seq data. Our analysis revealed two distinct regulatory chromatin modules: ACs and DCs.

2/ 🔍 We investigated the proinflammatory response to TNFα in primary human cells using #scRNA and #scATAC sequencing and fluorescence microscopy. We identified ~1,500 TNFα-regulated genes (TRGs) that often clustered in the genome and exhibited induced co-expression.

1/ 🤔 Do #chromatinlooping-mediated promoter-#enhancer interactions drive gene expression? Or is the local enrichment of transcription factors into hubs/#condensates the key factor? Our AC/DC model of gene regulation at bioRxiv provides a new view on this.

Great joint effort with @jpmallm1 from the Single Cell Open Lab @DKFZ and driven by Anne Rademacher, @alik_huseyn0v and Michele Bortolomeazzi with valuable contributions from our collaborators @KiTZ_HD and crucial funding from the MULTI-SPACE program of @ResearchLifesci.

We demonstrate how reimaging of slides after the ST analysis can markedly improve cell segmentation accuracy and integrate additional transcript and antibody-based protein readouts on the same tissue section to expand the analysis.

Sensitivity and specificity of the ST technologies were compared with different approaches. To distinguish random unspecific binding from signal that originates from rare cell types, we assessed differences in the spatial distribution pattern of target and control probes.

We studied cryosections of medulloblastoma with extensive nodularity, a tumor chosen for its distinct microanatomy. The automated imaging-based ST methods (MC, Merscope, Xenium) resolved its tissue structure and cell-type-specific transcriptome profiles very well.

Which of the different spatial transcriptomics (ST) technologies should you use for your research? The lessons we have learnt from comparing RNAscope, Molecular Cartography (MC), Merscope, Xenium and Visium are now on bioRxiv 🧵

RT @crc_1064: Registration is open! Join us in October for our quadrennial international #chromatin symposium in Munich. Hear and meet amaz….

RT @DKFZ: Do you want to do excellent #postdoc research supported by one of the most prestigious fellowships in 🇪🇺? Do you want to work at….

Enjoying the work with @IsabelleSeufert and @jpmallm1 to increase the coverage of scATAC-seq for co-accessibility analysis and other applications Our latest data are at 150k unique fragments/cell. Stay tuned.

Our single cell analysis of MLL/KMT2A fusions in AML with Michael Lübbert's group @Uniklinik_Fr is now out in @BloodAdvances. It shows a progenitor-like phenotype of the novel MLL-EDC4 fusion. Free download link: Thanks to DFG FOR2674 for support.

RT @TeifLab: Our paper on nucleosome repositioning in CLL is now published in @genomeresearch! Led by @krissyvalp in our lab, collab with @….