Bogdan Kirillov

Research advisor: Maxim Panov

Program entry year: 2019

Graduated from Skoltech in 2019 (Interpretable evaluation of Cas9-gRNA and Cpf1-gRNA specificity to correct and incorrect targets via Deep Learning.)

Research project: Uncertainty Quantification and Neural Network Interpretation for studying CRISPR mechanisms

Research interests: CRISPR/Cas systems, Deep Learning applied to Bioinformatics

Academic mobility:
During MSc: University: NCBI, Bethesda, USA

Laboratory: Evolutionary Genomics Research Group, https://www.ncbi.nlm.nih.gov/research/groups/koonin/

Dates: 03.12.2018 – 19.04.2019

Industry Immersion:
Company: Semantic Hub, http://semantic-hub.com/

Project: Extraction of biologically-relevant information from scientific texts

Papers

• Kirillov, B., & Panov, M. (2022). Measuring internal inequality in capsule networks for supervised anomaly detection. Scientific Reports, 12(1), 1-11.
• Kirillov, B., Savitskaya, E., Panov, M., Ogurtsov, A. Y., Shabalina, S. A., Koonin, E. V., & Severinov, K. V. (2022). Uncertainty-aware and interpretable evaluation of Cas9–gRNA and Cas12a–gRNA specificity for fully matched and partially mismatched targets with Deep Kernel Learning. Nucleic acids research, 50(2), e11-e11.
• Petrovskaya, A., Kirillov, B., Asmolova, A., Galli, G., Feurra, M., & Medvedeva, A. (2020). Examining the effects of transcranial direct current stimulation on human episodic memory with machine learning. PLOS ONE. https://doi.org/10.1371/journal.pone.0235179

Conference presentations:

• Capsule Networks: state of the art and applications. Kirillov B. Huawei Machine Learning Workshop, 2021 November 22-25. Oral presentation.
• Deterministic DNA embeddings with no predefined kmer length. Kirillov B., Panov M. MCCMB 2021, Moscow, Russian Federation, 2021 July 31-August 2. Poster presentation.
• Explainable Clostridium difficile variant classification based on CRISPR array contents. Kirillov B., Stepakov A., Muzyukina P., Severinov K. CRISPR 2021, online, 2021 June 1-10. Poster presentation.
• Siamese neural networks for metagenomics binning, Bioinformatics of Genome Regulation and Structure/Systems Biology (BGRS\SB-2018). Kirillov B. Novosibirsk, Russian Federation, 2018 August 20-25. Poster presentation.
• guideSim: Metric Learning for evaluation of CRISPR effector efficiency. Kirillov B., Savitskaya E., Severinov K. CRISPR 2018, Vilnius, Lithuania, 2018 June 20-23. Poster presentation.