Author

Julia Rühle

Universitat Pompeu FabraORCID 0000-0002-1479-3633Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Approach:experimental assay· 3 Organism:mouse· 3 Research Focus:cell type annotation· 2 Assay:DNA methylation· 2 Research Focus:gene regulatory network inference· 2 Approach:statistical model· 2 Research Focus:trajectory inference· 2 Research Focus:clustering· 1

Frequent Co-Authors

Chelsea Szu‐TuiD· 3 shared Lars VelteniD· 3 shared Robert FrömeliD· 3 shared Aina BernaliD· 2 shared Agostina BianchiiD· 1 shared Alejo Rodriguez-FraticelliiD· 1 shared Ansuman T. SatpathyiD· 1 shared Caleb A. LareauiD· 1 shared

Activity by Year

2025-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 35 mutual co-author links

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3 shared papersGenomics

Chelsea Szu‐TuORCID

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3 papers

Recent·Most cited

Lentiviral single-cell MPRA of synthetic enhancers reveals motif affinity-based encoding of cell type specificity

Julia Rühle, Robert Frömel, Aina Bernal, Chelsea Szu‐Tu, Joseph S. Bowness, Lars Velten

The paper develops sc-lentiMPRA to analyze enhancer activity and specificity in single cells during differentiation, finding motif affinity influences TF response patterns.

bioRxiv · Mar 2, 2026 · PreprintGenomics

Somatic epimutations enable single-cell lineage tracing in native hematopoiesis across the murine and human lifespan

Michael Scherer, Indranil Singh, Martina Maria Braun, Chelsea Szu‐Tu, Pedro Sánchez-Sánchez, Dominik Lindenhofer, Niels Asger Jakobsen, Verena Körber, Michael Kardorff, Lena Nitsch, Pauline Kautz, Julia Rühle, Agostina Bianchi, Luca Cozzuto, Robert Frömel, , Lars Velten

This paper introduces EPI-clone, a method using DNA methylation to trace clonal lineages in hematopoiesis without genetic engineering, showing clonal complexity declines with age in mice and expands in humans.

Nature · May 21, 2025Peer-reviewedGenomics

Synthetic enhancers reveal design principles of cell state specific regulatory elements in hematopoiesis

Robert Frömel, Julia Rühle, Aina Bernal, Chelsea Szu‐Tu, Felix Pacheco Pastor, Rosa Martinez-Corral, Lars Velten

The paper identifies design principles of cell-state specific enhancers by analyzing synthetic DNA sequences in hematopoietic differentiation.

Cell · May 8, 2025Peer-reviewedMolecular Biology