Teaching
In general, I do not enjoy teaching, especially routinely. However, the academic career is inseparable from teaching. Thus, when I agree to give any workshop or lecture or hackathon and I am free to choose the topic (happens in approximately half of the situations), I normally propose not the topic I am very proficient in, but instead a topic which I know in general, but want to refresh or improve my knowledge of it. Here I describe my teaching experience, starting with the most recent ones and ending with the oldest examples.
Speaker (Spring-Summer 2024, online, organised by Institute of Bioinformatics Research and Education, Serbia)
This experience was not teaching in its classical understanding, more like 1.5 hour long “podcast” session with me and other experts in the following fields: “Germline short variant discovery for medical genomics”, “Calling complex variants (CNVs and SVs)”, “Somatic variant analysis” and finally “The art of solving undiagnosed cases”. The videos are available on youtube and are in English. The text summaries are available here.
Organiser and speaker at the Solve-RD online Solvathon for short read genome sequencing data (November 2023, based in Barcelona, Spain)
We prepared a two day workshop for the analysis of the NGS-sequenced whole genomes of unsolved rare disease patients and presented it to the corresponding clinicians (one of four Solvathons organised by the Solve-RD consortium). Our goal was to analyse almost 3000 GS datasets, filter and annotate the results and share it with the corresponding clinicians so they could diagnose their patients, and around 10 of the patients were solved or likely solved during our Solvathon (partially reported in e.g. this publication).
Together with collaborators with delivered tens of online explanatory sessions to different European Research Network representatives (20-40 participants per seminar) on the interpretation of structural variants calls of different nature.
Speaker at the NGSchool 2022 (Warsaw, Poland)
Workshop on “Cross-validation and model evaluation” (video in English) and a workshop on “Survival analysis” (video in English).
Lectures and hackathon mentor at the Summer school in bioinformatics, (Bioinformatics Institute, St Petersburg, Russia, 2021)
Lecture “Pan Cancer Analysis of Whole Genomes” (video in Russian) and “Genetics for healthy people” (video in Russian), hackathon “Methods of statistical modelling for risk prediction using genomic data”.
Hackathon co-mentor at the NGSchool 2019 (Warsaw, Poland)
Was a co-organiser of the school and a co-mentor of a team of 8 scientists working on the hackathon “Cell-of-origin chromatin organization shapes the mutational landscape of cancer” (based on this paper) with Maja Kuzman.
Lectures and hackathon mentor at the Summer school in bioinformatics, (Bioinformatics Institute, St Petersburg, Russia, 2018)
Lecture “The Pan-Cancer Atlas” (video in Russian), hackathon “Detection for CNV/CNA in germline/somatic contexts using several tools as an example” for 5 days and a team of 8 biologists and bioinformaticians.
Workshop on statistics, NGSchool 2017 (Warsaw, Poland)
I was one of the organisers of that school and it was the most strange place I ever gave a workshop.
Lectures and workshop at the Summer school in bioinformatics, (Bioinformatics Institute, Dolgoprudny, Moscow Oblast, Russia, 2017)
Two 2-hour workshops “Introduction into Statistics and R”, lecture “Standing on the Shoulders of Giants, or Why Consortia Are Needed” (video in Russian), lecture “DNA methylation and epigenetic clock” (video in Russian).
Lecture and workshop on methylation changes in aging in humans, System biology workshop 2017, St Petersburg, Russia.
Workshop on CNV detection and surprising intro into statistics, NGSchool 2016 (Vysoké Tatry, Slovakia)
Initially I applied to the school as a participant, but instead was invited as a speaker. I covered theoretical introduction into copy-number variants and conducted a workshop. I was also asked to provide a workshop on statistics, absolutely surprisingly for me - it was a challenge but also a lot of fun!
CRG Introduction to Statistics and R (CRG, Barcelona, 2016 and 2017)
Designed and conducted two three hours practicums on statistical inference and regression modelling. Materials are available here: 2016, 2017.
First hackathon mentorship (Summer school in bioinformatics, Bioinformatics Institute, St Petersburg, Russia, 2014)
Led a team of 9 biologists and programmers for a 5 days hackathon about polar bear population inference based on the 2014 Cell paper. We summarized our experience in organisation these hackathons in a blog post (in Russian).
First project leading experience (Bioinformatics Institute, St Petersburg, Russia, 2014)
I tried semester long student project leading in 2014, simultaneously two of them. Both projects were devoted to the prediction of the number of particles after rounds of multiplex PCR (with a practical meaning of detection of copy-number changes), one from the point of view of stochastic modelling, another - more classical machine learning. It was a very rewarding experience mostly because both students were smart and hard working.