Mikhail Karasikov

Mikhail Karasikov

PhD Student

ETH Zurich

Biography

I am a PhD student at ETH Zurich supervised by André Kahles and Gunnar Rätsch.

My work is focused on designing algorithms and compressed data structures for indexing very large collections of sequences and developing methods scalable to the entire sequence read archive. These methods build graph representations that enable analysis and queries, which would otherwise be practically impossible using only the raw data.

Prior to ETH Zurich, I studied Math, Physics, and Optimal Control at the Moscow Institute of Physics and Technology (MIPT). Then, I did a double Master’s program studying Mathematics and Machine Learning at MIPT and Skoltech. At the same time, I completed a two-year CS program at the Yandex School of Data Analysis and then interned at Inria Grenoble-Rhône-Alpes working on various problems of computational structural biology.

Interests
  • Machine Learning
  • Bioinformatics
  • Computational Biology
  • Compressed Data Structures
Free time
Education
  • Ph.D. in Computer Science, present

    ETH Zurich, Zurich, Switzerland

  • M.Sc. in Math. and Computer Science, 2017

    Skolkovo Institute of Science and Technology (Skoltech), Moscow, Russia

  • M.Sc. in Applied Math. and Physics, 2017

    Moscow Institute of Physics and Technology (MIPT), Moscow, Russia

  • B.Sc. in Applied Math. and Physics, 2015

    Moscow Institute of Physics and Technology (MIPT), Moscow, Russia

Projects

Ocean Microbiomics Database
Collaboration with Sunagawa Lab. Provided k-mer based sequence search and Counting de Bruijn graph indexes for the Genome Collection of the Ocean Microbiomics Database. Other contributors: Lucas Paoli, Harun Mustafa, Andre Kahles. (Published in Nature).
MetaGraph
A C++ framework library for indexing very large collections of DNA/Protein sequences and a tool for sequence search, alignment, and assembly. Although the target use cases of MetaGraph overlap with BLAST, MetaGraph mainly focuses on the scalable indexing of raw sequencing data in annotated de Bruijn graphs with up to $\sim 10^{12}$ nodes and $\sim 10^{7}$ annotation labels. It also provides an online platform MetaGraph Online. Other contributors: Marc Zimmermann, Thomas Zhou, the MetaGraph team.
GeoDNA
A portal for sequence search and geographical positioning based on the metagenomic MetaSUB data. The initial prototype was set up on a weekend but it served well and was also used as a base for the MetaGraph Search platform. Other contributors: Marc Zimmermann, Jiayu Chen, André Kahles, Thomas Zhou. (Published in Cell).
De Bruijn Graph Visualizer
A small web app visualizing de Bruijn graphs and the BOSS table (Bowe et al.). Written for educational purposes to interactively illustrate the core data structure used for graph representation in MetaGraph.
Sentiment Analysis
A small demo for sentiment analysis of reviews on Russian banks (one of those quick hands-on projects I did when studied at YSDA).
After a night of “bombarding” banki.ru with random web scraping requests, our dorm network got banned by IP. Fortunately, the 5k successfully scraped reviews were enough to complete the project. However, my roommates and I had been reminded about this every time we had to use a VPN to check reviews on banks since then.

Featured Publications

(2021). Lossless Indexing with Counting de Bruijn Graphs. In RECOMB 2022.

Cite Project DOI Preprint Code

(2021). Topology-based Sparsification of Graph Annotations. In ISMB/ECCB 2021.

PDF Cite Project Slides DOI Code

(2020). MetaGraph: Indexing and Analysing Nucleotide Archives at Petabase-scale. In bioRxiv.

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(2018). Sparse Binary Relation Representations for Genome Graph Annotation. In RECOMB 2019.

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Teaching

Courses TAed at ETH Zürich, Institute for Machine Learning:

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