Karsten Rippe
@karsten-rippe.bsky.social
Happy to report that the Xenium system for spatial transcriptomics in the Single Cell Open Lab www.dkfz.de/en/single-ce... @dkfz.bsky.social was the first one worldwide to pass the mark of 100 runs according to @10xgenomics.bsky.social. And it keeps on running with another one, so stay tuned...
Single-cell Open Lab - German Cancer Research Center
www.dkfz.de
August 21, 2025 at 4:12 PM
Happy to report that the Xenium system for spatial transcriptomics in the Single Cell Open Lab www.dkfz.de/en/single-ce... @dkfz.bsky.social was the first one worldwide to pass the mark of 100 runs according to @10xgenomics.bsky.social. And it keeps on running with another one, so stay tuned...
"In our view, it [hexanediol] should thus be avoided and not be used as evidence for the formation of an assembly via phase separation or the fluid-like nature of a condensate in vitro or in vivo." doi.org/10.1038/s414...
Current practices in the study of biomolecular condensates: a community comment - Nature Communications
The realization that the cell is abundantly compartmentalized into biomolecular condensates has opened new opportunities for understanding the physics and chemistry underlying many cellular processes1...
doi.org
August 21, 2025 at 3:38 PM
"In our view, it [hexanediol] should thus be avoided and not be used as evidence for the formation of an assembly via phase separation or the fluid-like nature of a condensate in vitro or in vivo." doi.org/10.1038/s414...
Glad that the preprint on identifying and characterizing rare tumor-reactive T cells in multiple myeloma & AML patients is out now doi.org/10.1101/2025.... Single-cell TCR and transcriptome profiling & immunopeptidomics revealed conserved programs and shared non-canonical antigens.
August 13, 2025 at 12:58 PM
Glad that the preprint on identifying and characterizing rare tumor-reactive T cells in multiple myeloma & AML patients is out now doi.org/10.1101/2025.... Single-cell TCR and transcriptome profiling & immunopeptidomics revealed conserved programs and shared non-canonical antigens.
Liquid-liquid phase separation of HP1? Not in our mouse fibroblasts… This paper by the Fabian Erdel group offers a fresh perspective on how this can be reconciled with seemingly conflicting reports: The phase separation propensity of HP1 decreases from yeast → fly → mouse. doi.org/10.1038/s414...
July 11, 2025 at 5:35 AM
Liquid-liquid phase separation of HP1? Not in our mouse fibroblasts… This paper by the Fabian Erdel group offers a fresh perspective on how this can be reconciled with seemingly conflicting reports: The phase separation propensity of HP1 decreases from yeast → fly → mouse. doi.org/10.1038/s414...
1/ Spatial transcriptomics technologies are rapidly evolving. We compared five methods—Visium, RNAscope HiPlex, Molecular Cartography, Merscope, and Xenium—and developed technology-agnostic quality control metrics to guide their use: doi.org/10.1186/s130...
Comparison of spatial transcriptomics technologies using tumor cryosections - Genome Biology
Background Spatial transcriptomics technologies are revolutionizing our understanding of intra-tumor heterogeneity and the tumor microenvironment by revealing single-cell molecular profiles within the...
doi.org
June 20, 2025 at 7:32 PM
1/ Spatial transcriptomics technologies are rapidly evolving. We compared five methods—Visium, RNAscope HiPlex, Molecular Cartography, Merscope, and Xenium—and developed technology-agnostic quality control metrics to guide their use: doi.org/10.1186/s130...
How do transcription compartments form — and does phase separation drive gene expression? I enjoyed discussing these questions with @akispapantonis.bsky.social a lot, and we put our thoughts together for @naturerevgenet.bsky.social, now out at rdcu.be/erP1u
June 19, 2025 at 6:28 PM
How do transcription compartments form — and does phase separation drive gene expression? I enjoyed discussing these questions with @akispapantonis.bsky.social a lot, and we put our thoughts together for @naturerevgenet.bsky.social, now out at rdcu.be/erP1u
From enhancer hijacking to ecDNA and onco-condensates – we review how changes in nuclear architecture drive oncogenic gene expression by disrupting enhancer–promoter communication. doi.org/10.1002/ijc..... Kudos to Isabelle Seufert, @claire-vrgs.bsky.social and Sina Wille 👏
April 12, 2025 at 8:38 PM
From enhancer hijacking to ecDNA and onco-condensates – we review how changes in nuclear architecture drive oncogenic gene expression by disrupting enhancer–promoter communication. doi.org/10.1002/ijc..... Kudos to Isabelle Seufert, @claire-vrgs.bsky.social and Sina Wille 👏
Thanks to the Wissenschaftsrat @wissrat.bsky.social — the German Science and Humanities Council — for their clear statement expressing solidarity with US research institutions and scientists and defending academic freedom. www.wissenschaftsrat.de/SharedDocs/P...
Pressemitteilungen - Solidarität mit Einrichtungen und Forschenden in den USA
Der Wissenschaftsrat (WR) und die Hochschulrektorenkonferenz (HRK) kritisieren Angriffe auf die Wissenschaftsfreiheit und erklären ihre Solidarität mit US-amerikanischen Einrichtungen, Wissenschaftlerinnen und Wissenschaftlern.
www.wissenschaftsrat.de
April 9, 2025 at 6:52 PM
Thanks to the Wissenschaftsrat @wissrat.bsky.social — the German Science and Humanities Council — for their clear statement expressing solidarity with US research institutions and scientists and defending academic freedom. www.wissenschaftsrat.de/SharedDocs/P...
“We all rely on science.” U.S. scientists are speaking out for scientific integrity and academic freedom. What they’re doing matters. We owe them our solidarity and a clear stand beside them.
www.nytimes.com/2025/03/31/s...
www.nytimes.com/2025/03/31/s...
Trump Administration Has Begun a War on Science, Researchers Say (Gift Article)
Nearly 2,000 scientists urged that Congress restore funding to federal agencies decimated by recent cuts.
www.nytimes.com
March 31, 2025 at 10:39 PM
“We all rely on science.” U.S. scientists are speaking out for scientific integrity and academic freedom. What they’re doing matters. We owe them our solidarity and a clear stand beside them.
www.nytimes.com/2025/03/31/s...
www.nytimes.com/2025/03/31/s...
A mechanism for maintaining and spreading H3K9me3 in heterochromatin from the Fejes Toth and Aravin labs that depends on the local H3K9me3 density: HP1 dimers recruit SetDB1 to chromatin by simultaneously binding H3K9me3 on histone H3 and auto-methylated SetDB1. www.biorxiv.org/content/10.1...
January 25, 2025 at 9:17 AM
A mechanism for maintaining and spreading H3K9me3 in heterochromatin from the Fejes Toth and Aravin labs that depends on the local H3K9me3 density: HP1 dimers recruit SetDB1 to chromatin by simultaneously binding H3K9me3 on histone H3 and auto-methylated SetDB1. www.biorxiv.org/content/10.1...
Fakten sind das Rückgrat unserer Demokratie
Facts are the backbone of our democracy
When facts are treated as opinions and replaced by rhetoric or propaganda, meaningful discourse suffers, threatening democracy and leaving it vulnerable to manipulation.
www.openpetition.de/!ychtb
Facts are the backbone of our democracy
When facts are treated as opinions and replaced by rhetoric or propaganda, meaningful discourse suffers, threatening democracy and leaving it vulnerable to manipulation.
www.openpetition.de/!ychtb
Fakten sind das Rückgrat unserer Demokratie - Online-Petition
Liebe Mitbürgerinnen und Mitbürger, als Wissenschaftlerinnen und Wissenschaftler arbeiten wir täglich daran, die Grundlagen für fundierte Entscheidungen und Innovationen zu schaffen – basierend auf üb...
www.openpetition.de
January 22, 2025 at 8:14 PM
Fakten sind das Rückgrat unserer Demokratie
Facts are the backbone of our democracy
When facts are treated as opinions and replaced by rhetoric or propaganda, meaningful discourse suffers, threatening democracy and leaving it vulnerable to manipulation.
www.openpetition.de/!ychtb
Facts are the backbone of our democracy
When facts are treated as opinions and replaced by rhetoric or propaganda, meaningful discourse suffers, threatening democracy and leaving it vulnerable to manipulation.
www.openpetition.de/!ychtb
🧬 1/ Heterochromatin protein 1 (HP1) still surprises us after all these years: It simply sticks to chromatin when pericentric heterochromatin domains – the chromocenters – are activated in mouse fibroblasts and acts as a local rather than global repressor. New preprint: doi.org/10.1101/2024...
December 13, 2024 at 1:47 PM
🧬 1/ Heterochromatin protein 1 (HP1) still surprises us after all these years: It simply sticks to chromatin when pericentric heterochromatin domains – the chromocenters – are activated in mouse fibroblasts and acts as a local rather than global repressor. New preprint: doi.org/10.1101/2024...
Reposted by Karsten Rippe
Please RS/RT. #GordonConference on "Histone and DNA Modifications" #epigenetics #chromatin 20-25. July 2025. Il Ciocco, Italy. Great speaker lineup.
➡️Register now www.grc.org/histone-and-...
➡️Register now www.grc.org/histone-and-...
December 8, 2024 at 11:38 AM
Please RS/RT. #GordonConference on "Histone and DNA Modifications" #epigenetics #chromatin 20-25. July 2025. Il Ciocco, Italy. Great speaker lineup.
➡️Register now www.grc.org/histone-and-...
➡️Register now www.grc.org/histone-and-...
Reposted by Karsten Rippe
By definition, enhancers can activate from a distance. But with increased distance between enhancer and promoter, the activation drops. To study this systematically, we build a synthetic locus: www.cell.com/molecular-ce... 1/12
Redirecting
doi.org
December 2, 2024 at 4:44 PM
By definition, enhancers can activate from a distance. But with increased distance between enhancer and promoter, the activation drops. To study this systematically, we build a synthetic locus: www.cell.com/molecular-ce... 1/12
Like ‘old Twitter’: The scientific community finds a new home on Bluesky | Science www.science.org/content/arti...
Like ‘old Twitter’: The scientific community finds a new home on Bluesky
After recent changes to Elon Musk’s X, a gradual migration turns into a stampede
www.science.org
December 3, 2024 at 6:11 AM
Like ‘old Twitter’: The scientific community finds a new home on Bluesky | Science www.science.org/content/arti...
Single-cell and molecular analyses show that long-term multiple myeloma survivors experience persistent immune alterations decades after therapy. Residual myeloma cells may fuel inflammatory immune circuits: Nature Communications doi.org/10.1038/s414... #MultipleMyeloma #CancerResearch #Immunology
Multiple myeloma long-term survivors exhibit sustained immune alterations decades after first-line therapy - Nature Communications
Understanding the immunological underpinnings of long-term survival in cancer is of high interest. Here, authors dissect the immune parameters of multiple myeloma long-term survivors following a singl...
doi.org
December 3, 2024 at 12:01 AM
Single-cell and molecular analyses show that long-term multiple myeloma survivors experience persistent immune alterations decades after therapy. Residual myeloma cells may fuel inflammatory immune circuits: Nature Communications doi.org/10.1038/s414... #MultipleMyeloma #CancerResearch #Immunology
Reposted by Karsten Rippe
📣 Preprint alert! We have studied the formation of pair-wise and multi-way enhancer-promoter interactions in the #3Dgenome in a lymphoid-to-myeloid transdifferentiation system and learned interesting new things about their function in #GeneRegulation. 1/10
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
www.biorxiv.org
November 22, 2024 at 11:58 AM
📣 Preprint alert! We have studied the formation of pair-wise and multi-way enhancer-promoter interactions in the #3Dgenome in a lymphoid-to-myeloid transdifferentiation system and learned interesting new things about their function in #GeneRegulation. 1/10
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
📢 Join us for the 26th Single Cell Center Heidelberg Workshop!
📍 EMBL, Large Operon
📅 Thursday, December 5, 2024
🌟 Register: indico.dkfz.de/event/871/
organized by @karsten-rippe.bsky.social,
@eileen-furlong.bsky.social, Josephine Bageritz, Charles Girardot & Natalia Gabrielli
📍 EMBL, Large Operon
📅 Thursday, December 5, 2024
🌟 Register: indico.dkfz.de/event/871/
organized by @karsten-rippe.bsky.social,
@eileen-furlong.bsky.social, Josephine Bageritz, Charles Girardot & Natalia Gabrielli
December 2, 2024 at 6:34 PM
📢 Join us for the 26th Single Cell Center Heidelberg Workshop!
📍 EMBL, Large Operon
📅 Thursday, December 5, 2024
🌟 Register: indico.dkfz.de/event/871/
organized by @karsten-rippe.bsky.social,
@eileen-furlong.bsky.social, Josephine Bageritz, Charles Girardot & Natalia Gabrielli
📍 EMBL, Large Operon
📅 Thursday, December 5, 2024
🌟 Register: indico.dkfz.de/event/871/
organized by @karsten-rippe.bsky.social,
@eileen-furlong.bsky.social, Josephine Bageritz, Charles Girardot & Natalia Gabrielli