Featured Publications

Mikhail Karasikov, Harun Mustafa, Daniel Danciu, Oleksandr Kulkov, Marc Zimmermann, Christopher Barber, Gunnar Rätsch, André Kahles (2025). Efficient and accurate search in petabase-scale sequence repositories. In Nature.

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Mikhail Karasikov, Joost van Doorn, Nicolas Känzig, Melis Erdal Cesur, Hugo Mark Horlings, Robert Berke, Fei Tang, Sebastian Otálora (2025). Training state-of-the-art pathology foundation models with orders of magnitude less data. MICCAI 2025.

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kaiko.ai, Nanne Aben, Edwin D. de Jong, Ioannis Gatopoulos, Nicolas Känzig, Mikhail Karasikov, Axel Lagré, Roman Moser, Joost van Doorn, Fei Tang (2024). Towards large-scale training of pathology foundation models. In arXiv.

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Mikhail Karasikov (2023). Scalable Annotated Genome Graphs for Representing Sequence Data. In ETH Zurich Research Collection.

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Mikhail Karasikov, Harun Mustafa, Gunnar Rätsch, André Kahles (2021). Lossless Indexing with Counting de Bruijn Graphs. In RECOMB 2022.

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Daniel Danciu, Mikhail Karasikov, Harun Mustafa, André Kahles, Gunnar Rätsch (2021). Topology-based Sparsification of Graph Annotations. In ISMB/ECCB 2021.

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Mikhail Karasikov, Harun Mustafa, Daniel Danciu, Marc Zimmermann, Christopher Barber, Gunnar Rätsch, André Kahles (2020). MetaGraph: Indexing and Analysing Nucleotide Archives at Petabase-scale. In bioRxiv.

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Mikhail Karasikov, Guillaume Pagès, Sergei Grudinin (2018). Smooth Orientation-Dependent Scoring Function for Coarse-Grained Protein Quality Assessment. In Bioinformatics.

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Mikhail Karasikov, Harun Mustafa, Amir Joudaki, Sara Javadzadeh No, Gunnar Rätsch, André Kahles (2018). Sparse Binary Relation Representations for Genome Graph Annotation. In RECOMB 2019.

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