Michael Scherer

Michael Scherer

@scherermich.bsky.social

Group leader in Computational Biology working on (single-cell) epigenomics and cancer @dkfz.bsky.social genomic.social/@scherermichael https://orcid.org/0000-0001-7990-6179 https://www.linkedin.com/in/michael-scherer-34780a134/

492 followers529 following27 posts

Michael Scherer
@scherermich.bsky.social

Out in Bioinformatics: tinyurl.com/pbvhrsft. Patient-derived xenograft (PDX) models are increasingly used to study the response to cancer therapy over time. Molecular profiling of PDX tumors is challenging due to the contamination with mouse DNA, which may hide the true biological signal.

tinyurl.comXenoMix: Estimating mouse content from DNA methylation data of Patient-Derived Xenograft modelsAbstractSummary. DNA methylation microarrays enable cost-effective, high-throughput profiling of human and mouse samples and are widely used to study epige
Michael Scherer
@scherermich.bsky.social

To address this issue, Nima developed XenoMix, a light-weight tools that estimates mouse contamination from DNA methylation microarray data. We validated XenoMix in artificially generated human-mouse mixtures and found that it almost perfectly predicts the mouse fraction.

Michael Scherer reposted

Mick Milsom
@milsommick.bsky.social

New publication from the groups of Duncan Odom, Marieke Essers and myself: Concentrating cell-type-specific transcriptional signatures in bone marrow from interspecies comparisons: Cell Genomics www.cell.com/cell-genomic... @dkfz.bsky.social

cell.comConcentrating cell-type-specific transcriptional signatures in bone marrow from interspecies comparisonsThe authors present a framework to isolate condensed marker gene signatures by requiring both conserved cell-type specificity and conserved expression across multi-species scRNA-seq datasets. Bone mar...

Michael Scherer reposted

Ann-Kristin Reimann (née Dicke)
@akdicke.bsky.social

Check out our newest preprint! Happy to be part of this team and proud of our work @smialkovska.bsky.social & @angelikafeldmann.bsky.social ⬇️

Angelika Feldmann@angelikafeldmann.bsky.social

1\ 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/10.64898/202..., focusing on the massive loss of promoter interactions during neuronal differentiation.

doi.orgDevelopmentally programmed loss of long-range Polycomb interactions is regulated by cohesinDistal regulatory elements (DREs), such as enhancers, can regulate genes across megabase-long distances, presumably via coming into close spatial proximity. The establishment of new transcriptional programmes during cell type transitions is associated with widespread rewiring of the spatial organisation of the genome, including gain and loss of chromatin interactions. Extensive effort has been invested into understanding how chromatin interactions are formed during development, yet the mechanisms underlying their developmental loss remain largely unclear. By leveraging chromatin accessibility-assisted footprinting, acute protein degradation and chromatin conformation capture, we show that loss of promoter interactions cannot be explained by reduced binding of sequence-specific transcription factors (TFs). Instead, we identify a subset of interactions that depend on cohesin for programmed developmental disruption. These sites are characterized by high Polycomb enrichment and TF occupancy and engage in strong long-range interactions that undergo extensive differentiation-dependent rewiring. Preventing interaction loss by acute cohesin degradation results in the preferential downregulation of associated genes. Together, these results suggest that cohesin indirectly regulates developmental loss of Polycomb interactions by enabling the acquisition of other potentially regulatory contacts in a process that may shape transcriptional programs during cell type transitions. ### Competing Interest Statement The authors have declared no competing interest. European Research Council Helmholtz Society, VH-NG-1604

Michael Scherer reposted

Deutsches Krebsforschungszentrum (DKFZ)
@dkfz.bsky.social

Dr. Clarissa Gerhäuser (DKFZ), co-author of the study: "A large part of what makes a tumor dangerous lies not in the genes themselves, but in the regulatory regions of the genome that control when and to what extent a gene is expressed. Only whole-genome analysis makes these levels visible ."

Nature@nature.com

Nature research paper: Integrated signatures define mutational processes in prostate cancer go.nature.com/4xLwBNN

go.nature.comIntegrated signatures define mutational processes in prostate cancer - NatureEight integrated mutational footprints collectively explain the mutational processes in 85% of primary prostate cancer genomes.

Michael Scherer reposted

Deutsches Krebsforschungszentrum (DKFZ)
@dkfz.bsky.social

With funding from the German Research Foundation’s @dfg.de Heisenberg Program, DKFZ researcher Aurélie Ernst aims to investigate how massive changes in the genome contribute to the development of cancer. Her research focuses on a phenomenon known as chromothripsis. t1p.de/wai9l

t1p.deHeisenberg Professorship for Aurélie ErnstWith funding from the German Research Foundation’s (DFG) Heisenberg Program, DKFZ researcher Aurélie Ernst aims to investigate how massive changes in the genome contribute to the development of cancer...

Michael Scherer reposted

NEJM.org
@nejm.org

In a phase 2, randomized trial, azacitidine–venetoclax therapy led to significantly longer event-free survival than induction chemotherapy among induction-eligible patients with AML. Full PARADIGM Research Summary: https://nej.md/4zJr1wV

Michael Scherer reposted

Lena Kutscher
@lenakutscher.bsky.social

Excited to be awarded an ERC STG to continue our work on sex differences in medulloblastoma. Also happy that the ERC was also awarded to two other great people at DKFZ and my grad school roommate Kimberly Siletti at the UMCU!

Deutsches Krebsforschungszentrum (DKFZ)@dkfz.bsky.social

Three DKFZ-researchers have each been awarded a Starting Grant from the @erc.europa.eu this year. Daniel Kirschenbaum, Lena Kutscher and Michael Scherer impressed the ERC with their innovative research approaches to fundamental questions in cancer medicine. Congratulations! 👏 #ERCStG t1p.de/tk12d

t1p.deTriple ERC Success at the German Cancer Research CenterThree researchers at the German Cancer Research Center (DKFZ) have each been awarded a Starting Grant from the European Research Council (ERC) this year. Daniel Kirschenbaum, Lena Kutscher, and Michael Scherer impressed the ERC with their innovative research approaches to fundamental questions in cancer medicine. With the funding, they plan to investigate why certain brain tumors occur more frequently in boys than in girls, how brain tumors suppress the immune system, and which epigenetic characteristics make cancer cells resistant to drugs.

Michael Scherer reposted

Deutsches Krebsforschungszentrum (DKFZ)
@dkfz.bsky.social

Three DKFZ-researchers have each been awarded a Starting Grant from the @erc.europa.eu this year. Daniel Kirschenbaum, Lena Kutscher and Michael Scherer impressed the ERC with their innovative research approaches to fundamental questions in cancer medicine. Congratulations! 👏 #ERCStG t1p.de/tk12d

t1p.deTriple ERC Success at the German Cancer Research CenterThree researchers at the German Cancer Research Center (DKFZ) have each been awarded a Starting Grant from the European Research Council (ERC) this year. Daniel Kirschenbaum, Lena Kutscher, and Michael Scherer impressed the ERC with their innovative research approaches to fundamental questions in cancer medicine. With the funding, they plan to investigate why certain brain tumors occur more frequently in boys than in girls, how brain tumors suppress the immune system, and which epigenetic characteristics make cancer cells resistant to drugs.

Michael Scherer reposted

Deutsches Krebsforschungszentrum (DKFZ)
@dkfz.bsky.social

Gleich drei Forschende am DKFZ erhalten dieses Jahr einen Starting Grant des Europäischen Forschungsrats (ERC). Daniel Kirschenbaum, Lena Kutscher und Michael Scherer überzeugten mit innovativen Forschungsansätzen zu grundlegenden Fragen der Krebsmedizin. 👏 #ERCStG @erc.europa.eu t1p.de/nctvv

t1p.deDreifacher ERC-Erfolg am Deutschen KrebsforschungszentrumGleich drei Forschende am Deutschen Krebsforschungszentrum (DKFZ) erhalten dieses Jahr einen Starting Grant des Europäischen Forschungsrats (ERC). Daniel Kirschenbaum, Lena Kutscher und Michael Scherer überzeugten mit innovativen Forschungsansätzen zu grundlegenden Fragen der Krebsmedizin. Mit den Fördermitteln wollen sie untersuchen, warum bestimmte Hirntumoren bei Jungen häufiger auftreten als bei Mädchen, wie Hirntumoren die Immunabwehr ausbremsen und welche epigenetischen Eigenschaften Krebszellen resistent gegen Medikamente machen.

Michael Scherer reposted

Lars Velten
@larsplus.bsky.social

@juruehle.bsky.social's PhD work is now out in Genome Biology 📚🧬 : Lentiviral single-cell MPRA of synthetic enhancers reveals motif affinity-based encoding of cell state specificity link.springer.com/article/10.1186/s13059-026-04186-9 Julia achieved three cool things with this work...🧵

link.springer.comLentiviral single-cell MPRA of synthetic enhancers reveals motif affinity-based encoding of cell state specificity - Genome BiologyBackground Cell state-specific gene expression programs emerge from the interplay between cis-regulatory elements (CREs), such as enhancers, and transcription factors (TFs). Massively parallel reporte...

Michael Scherer reposted

Deutsches Krebsforschungszentrum (DKFZ)
@dkfz.bsky.social

Ein Team von Forschenden aus dem DKFZ und HI-STEM hat einen vielversprechenden neuen Ansatz zur Behandlung von fortgeschrittenem Darmkrebs entdeckt. Sie identifizierten einen Marker für metastasierten Darmkrebs, der die Achillesferse besonders aggressiver Tumorzellen ist. t1p.de/wzspb

t1p.deNeu entdeckter Marker für metastasierten Darmkrebs ist die Achillesferse besonders aggressiver TumorzellenEin Team unter Leitung von Forschenden aus dem Deutschen Krebsforschungszentrum (DKFZ) und dem Stammzell-Institut HI-STEM* hat einen vielversprechenden neuen Ansatz zur Behandlung von fortgeschrittene...

Michael Scherer reposted

Simon Haas
@simonhaas.bsky.social

In our new study, we identify stem cell kinetics and cellular competition as key principles underlying hematopoietic stem cell diversity. Fun collab@milsommick.bsky.social Florian Grünschläger@estherrodriguezc.bsky.social, Tamar Nizharadze, T. Höfer, D. Hübschmann(1/6) www.nature.com/articles/s41...

Michael Scherer reposted

Deutsches Krebsforschungszentrum (DKFZ)
@dkfz.bsky.social

Dreaming of a career in cancer research? Join the International PhD Program at DKFZ - Germany’s largest biomedical research center. Explore #cancerresearch including #cancerbiology, #bioinformatics, #epidemiology & #medicalphysics. The Summer Selection is open now 👉 apply here: t1p.de/hl56b

Michael Scherer reposted

Mick Milsom
@milsommick.bsky.social

Join us this summer in Frankfurt for outstanding science and a great community…….so easy to travel to, and Heidelberg is only a short train ride away if you want to visit our historic old town located on the Neckar river.

ISEH - International Society for Experimental Hematology@isehsociety.bsky.social

Registration is open for #ISEH2026! Register now to secure the lowest rate. We look forward to welcoming you to Germany - willkommen! 👉️ iseh.org/Annual-Meeti...

Michael Scherer reposted

Lars Velten
@larsplus.bsky.social

Proud of @juruehle.bsky.social for getting her PhD paper on biorxiv! In it, we take synthetic enhancer screens to the single cell level, offering new insight into how transcription factors and enhancers interact 👀

Julia Rühle@juruehle.bsky.social

The main project of my PhD 🧬🔬 is out: we developed single-cell lentiMPRA, a lentivirus-based method to measure enhancer activity and transcriptomes at single-cell resolution. We then applied sc-lentiMPRA to fully synthetic enhancers 🧩... 🔗 doi.org/10.64898/202...

doi.orgdoi.org

Michael Scherer reposted

Lars Velten
@larsplus.bsky.social

Early bird registration is closing Feb 28! We will have an AMAZING party!

Lars Velten@larsplus.bsky.social

ISCO (Innovations in Single-Cell OMICS) will be back in beautiful Barcelona! 🗓️ 28th/29th of May 2026 📍Barcelona Biomedical Research Park @prbb.org (beachfront!) Keynotes: @bartdeplancke.bsky.social and @bocklab.bsky.social Submit your abstract and present your research! www.isco-conference.eu

Michael Scherer reposted

Centre de Regulació Genòmica (CRG)
@crg.eu

Una buena noticia para empezar el año 😊 El trabajo liderado por @larsplus.bsky.social, investigador del CRG, ha sido reconocido por la Asociación Española contra el Cáncer como uno de los avances de investigación más destacados de 2025.

blog.contraelcancer.esLa investigación del cáncer en 2025 | Contra el CáncerDescubre los proyectos y avances clave en investigación contra el cáncer que cuentan con el apoyo de la Asociación Española Contra el Cáncer en 2025
Michael Scherer
@scherermich.bsky.social

Do not miss this conference!

Lars Velten@larsplus.bsky.social

ISCO (Innovations in Single-Cell OMICS) will be back in beautiful Barcelona! 🗓️ 28th/29th of May 2026 📍Barcelona Biomedical Research Park @prbb.org (beachfront!) Keynotes: @bartdeplancke.bsky.social and @bocklab.bsky.social Submit your abstract and present your research! www.isco-conference.eu

Michael Scherer
@scherermich.bsky.social

If you are thinking where to do your Postdoc, I can only give my highest recommendations to join Lars and his team!

Lars Velten@larsplus.bsky.social

We are looking for a postdoc to join our team! If you're interested in translating a cutting edge genomics technology (www.nature.com/articles/s41...) to real-life applications in hematology, this is for you. We offer a unique working environment ON THE BEACH: recruitment.crg.eu/content/jobs...

Michael Scherer reposted

Deutsches Krebsforschungszentrum (DKFZ)
@dkfz.bsky.social

🚀 Thinking about your next big career step in science? The Int'l PhD Program at DKFZ could be a perfect fit for you. 🌍 Work in an international environment, with 500+ doctoral researchers 🔬 Do cutting-edge cancer research Curious? Join our online info session on 20 Nov. Register here: t1p.de/ws7q3

Michael Scherer
@scherermich.bsky.social

DNA-methylation-based deconvolution can be a powerful tool for identifying novel disease subgroups. In our paper in Acta Neuropathologica, we show how this can be leveraged in IDH-mutant gliomas - specifically in oligodendrogliomas. doi.org/10.1007/s004...

doi.orgDNA methylation analysis reveals an epigenetic signature distinctive of high-grade oligodendroglioma - Acta NeuropathologicaIDH-mutant gliomas represent a subtype of diffuse gliomas that primarily affect patients in early to mid-adolescence. These tumors are classified into three distinct CNS WHO grades of malignancy. Accu...

Michael Scherer reposted

Deutsches Krebsforschungszentrum (DKFZ)
@dkfz.bsky.social

Ein Team aus Forschenden vom BIH, @mdc-berlin.bsky.social, DKFZ, HI-STEM und @qmul.bsky.social hat eine Technologie zur Entschlüsselung der Immunzell-Kommunikation entwickelt. Damit lässt sich unter anderem ablesen, warum Immuntherapien bei manchen Menschen wirken bei anderen nicht. t1p.de/w3v16

t1p.deWie Immunzellen kommunizieren, um Krankheiten und Krebs zu bekämpfenEin interdisziplinäres Team aus Wissenschaftlerinnen und Wissenschaftlern vom Berlin Institute of Health in der Charité (BIH), vom Max Delbrück Center, dem Deutschen Krebsforschungszentrum (DKFZ), dem...