Featured Publications

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. Accepted for MICCAI 2025.

Cite Project DOI Preprint Code Model

Mikhail Karasikov, Harun Mustafa, Daniel Danciu, Marc Zimmermann, Christopher Barber, Gunnar Rätsch, André Kahles (2024). Indexing All Life's Known Biological Sequences. In review.

Cite Project DOI Preprint Code

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.

Cite Project DOI Preprint Model

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

Cite DOI Thesis

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

Cite Project DOI Preprint Code

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

PDF Cite Project Slides DOI Code

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.

Cite Project DOI Preprint Code

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

PDF Cite Project DOI Code

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.

PDF Cite Project Slides DOI Code