Author

Katja Eschbach

ETH Zurich

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· 2 Systems Biology· 2 Neuroscience· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 5 Research Focus:differential expression· 3 Organism:human· 3 Assay:scRNA-seq· 3 Assay:bulk RNA-seq· 2 Research Focus:cell type annotation· 2 Organism:mouse· 2 Research Focus:batch correction / integration· 1

Frequent Co-Authors

Christian BeiseliD· 5 shared Erik van NimwegeniD· 3 shared Abdullah KahramaniD· 2 shared Alice GrisoniD· 2 shared Alva Rani JamesiD· 2 shared André Fedier· 2 shared André KahlesiD· 2 shared Andrea Jacobs· 2 shared

Activity by Year

2015-2022 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 31 mutual co-author links

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5 shared papersSystems Biology

Christian BeiselORCID

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Author profile →

5 papers

Recent·Most cited

The protooncogene Ski regulates the neuron-glia switch during development of the mammalian cerebral cortex

Alice Grison, Zahra Karimaddini, Jérémie Breda, Tanzila Mukhtar, Marcelo Boareto, Katja Eschbach, Christian Beisel, Dagmar Iber, Erik van Nimwegen, Verdon Taylor, Suzana Atanasoski

The paper investigates the role of the protooncogene Ski in regulating the neuron-glia switch during mammalian cerebral cortex development and identifies its interaction with the BMP signaling pathway.

bioRxiv · Dec 16, 2022 · PreprintSystems Biology

Temporal and sequential transcriptional dynamics define lineage shifts in corticogenesis

Tanzila Mukhtar, Jérémie Breda, Manal A. Adam, Marcelo Boareto, Pascal Grobecker, Zahra Karimaddini, Alice Grison, Katja Eschbach, Chandrasekhar Ramakrishnan, Swen Vermeul, Michal J. Okoniewski, Mikhail V. Pachkov, Corey C. Harwell, Suzana Atanasoski, Christian Beisel, , Verdon Taylor

The paper maps transcriptional dynamics in murine cortical development, identifying lineage shifts and gene regulatory networks in neural stem cells, basal progenitors, and newborn neurons.

The EMBO Journal · Nov 8, 2022Peer-reviewedNeuroscience

scROSHI - robust supervised hierarchical identification of single cells

Michael Prummer, Anne Bertolini, Lars Bosshard, Florian Barkmann, Josephine Yates, Valentina Boeva, Ruedi H. Aebersold, Melike Ak, Faisal Alquaddoomi, Jonas B. Albinus, Ilaria Alborelli, Sonali Andani, Per-Olof Attinger, Marina Bacac, Daniel Baumhoer, , Berend Snijder

scROSHI identifies cell types without training data by using pre-existing gene sets and hierarchical relationships, outperforming methods in low-data and high-diversity scenarios.

NAR Genomics and Bioinformatics · Jun 1, 2022Peer-reviewedBioinformatics

SCIM: Universal Single-Cell Matching with Unpaired Feature Sets

Stefan G. Stark, Joanna Ficek, Francesco Locatello, Ximena Bonilla, Stéphane Chevrier, Franziska Singer, Ruedi H. Aebersold, Faisal Alquaddoomi, Jonas B. Albinus, Ilaria Alborelli, Sonali Andani, Per-Olof Attinger, Marina Bacac, Daniel Baumhoer, Beatrice Beck‐Schimmer, , Vipin T. Sreedharan

SCIM matches single-cell measurements across technologies by learning a technology-invariant latent space and applying bipartite matching, achieving high accuracy in real-world datasets.

Bioinformatics · Sep 14, 2020Peer-reviewedBioinformatics

Exploiting variability of single cells to uncover the in vivo hierarchy of miRNA targets

Andrzej Jerzy Rzepiela, Arnau Vina-Vilaseca, Jeremie Breda, Souvik Ghosh, Afzal P Syed, Andreas J Gruber, William A Grandy, Katja Eschbach, Christian Beisel, Erik van Nimwegen, Mihaela Zavolan

The paper uses single-cell sequencing and mathematical modeling to estimate miRNA target parameters and uncover their in vivo hierarchy.

bioRxiv · Dec 23, 2015 · PreprintSystems Biology