Author

Yukiko Shimada

Friedrich Miescher Institute

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Bioinformatics· 1 Molecular Biology· 1

Signature Assays, Organisms & Methods

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Research Focus:benchmarking· 1 Approach:deep learning· 1 Assay:DNA methylation· 1 Approach:experimental assay· 1 Research Focus:gene regulatory network inference· 1 Organism:mouse· 1 Organism:yeast· 1

Frequent Co-Authors

Marc BühleriD· 2 shared Fabio MohniD· 1 shared Jakob SchnabliD· 1 shared Jennifer Steiner· 1 shared Josip AheliD· 1 shared Lea DuempelmanniD· 1 shared Michaela SchwaigeriD· 1 shared Sarah H. CarliD· 1 shared

Activity by Year

2020-2026 · peak 1/yr

Co-Author Collaboration Network

9 top collaborators · 24 mutual co-author links

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2 shared papersMolecular Biology

Marc BühlerORCID

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2 papers

Recent·Most cited

ChAHP Silences SINE Retrotransposons by Inhibiting TFIIIB Recruitment

Jakob Schnabl, Fabio Mohn, Michaela Schwaiger, Josip Ahel, Jennifer Steiner, Yukiko Shimada, Sirisha Aluri, Marc Bühler

The paper identifies ChAHP as a repressor of SINE B2 elements by inhibiting TFIIIB recruitment, revealing a novel mechanism for controlling POL III-dependent transcription.

Molecular Cell · Jul 1, 2026Peer-reviewedMolecular Biology

A fully automated deep learning pipeline for high-throughput colony segmentation and classification

Sarah H. Carl, Lea Duempelmann, Yukiko Shimada, Marc Bühler

The paper develops an automated deep learning pipeline to segment and classify yeast colonies, achieving 100x faster quantification than manual methods.

Biology Open · Jun 2, 2020Peer-reviewedBioinformatics