About
My name is Timofei Ryko and this is my Master CV, where you can find all the information about my education, work experience, projects, skills, and achievements. For easier navigation, you can use the table of contents below.
Contents
Programming, Data science, Bioinformatics
Bioinformatics and computational biology
Talks and Scientific popularization
Work experience
- Product Owner at Hawex Group LTD
- Oct 2022 — now (Jan 2023)
- My team and I are developing a startup in a bigger company, I have a 30% share
- We are creating a platform for professionals in biotechnology and bioinformatics
- We have the following sections: Job and study, Science news, People, Events
- I have implemented AI to create content and markup data
- We make biotechnology professionals happy and effective to move progress forward, connecting scientists to each other and with business
- Machine learning engineer at the University of Tartu, iCV Lab
- Jan 2022 — Oct 2022
- I worked on several industrial and research projects, related to computer vision
- The biggest and most interesting project was to develop an application for determining SpO2 by video
- Tutor of advanced biology for high school olympiads
- Sept 2021 — now (Jan 2023)
- During my work, I successfully trained 14 schoolchildren who became prize winners in the all-Russian school biology Olympiad (VOS)
- I have taught courses in the following subjects:
- Biochemistry
- Cell and molecular biology
- Genetics
- Plant physiology
- Botany
Education and Summer schools
High school
- Academic Lyceum "Physics and Technology School" named after Zh. I. Alferov
- Top physics school in Saint Petersburg
- 8th and 9th grades
- Sep 2017 - Jun 2019
- AESC MSU – Kolmogorov boarding school is a department (faculty) of Moscow State University (QS top 50)
- The highest-rated school in Russia
- 10th grade
- Sep 2019 - Sep 2020
- One of the top schools in Russia
- 11th grade
- Sep 2020 - Jun 2021
- Graduated with a gold medal
Undergraduate
- University of Tartu, Science and Technology program
- I got a fully funded scholarship at the University
- Gained a lot of practical experience in the lab
- Completed the first year with a 4.78 / 5 GPA
- School of Molecular and Theoretical Biology 2022
- I passed a highly competitive selection for the summer school
- I worked in a team on a real bioinformatics project
- We presented our findings in a poster session
- Data Science program at Turing College — online school
- I got a scholarship from the hiring partners, so I study for free
Social impact projects
- BioQuest website
- Programmer, admin, methodist
- I’ve created a website that makes preparation for biological olympiads more enjoyable and effective
- This is a collection of biological questions, which can be filtered by areas, topics, and more, automatic answers checking is also available
- Over 1000 active users
- Current version
- Version with the old design, but more functionality
- Potter’s Snap game
- CEO, HR, product manager, idea author
- We are developing a non-profit game based on the book «Harry Potter and the Methods of Rationality» by Eliezer Yudkowsky
- Team:
- 2 programmers
- 3 writers + 1 writing lead
- 1 illustrator
- The aim of the project is to popularize rationality and transhumanism as well as create a dream game for Yudkowsky’s book fans
Bioinformatics research
- Analysis of human diseases with exome sequence association data
- The project was performed during SMTB (School of Molecular and Theoretical Biology) under the supervision of Olga Bochkareva and Sofia Buyanova
- We participated in a poster session at the SMTB 2022 conference
- We created a first version of a pipeline, which helps find associations which are biologically interpretable. We used existing expression, protein interaction data, mice knockout data, and existing variation data to verify that we get meaningful results. During our research we found multiple ways to improve SNP prioritization and pipeline automation and are planning to implement these ways.
Programming, Data science, Bioinformatics
Programming languages
- Python — advanced level
- R — medium level
- MATLAB — medium level
- Rust — basic knowledge
- Java — basic knowledge
Markup and frontend
- HTML — medium level
- Bootstrap — medium level
- CSS — basic knowledge
- JavaScript — basic knowledge
- Markdown
- LaTex
Skills
Coding
- Python Asyncio — basic knowledge
- Web development
- Django — medium
- FastAPI — basic
- SQLAclhemy — medium
- AIOGram — advanced (telegram bots)
- Web scraping and API
- Working with RESP API, JSON /LXML
- Beautiful Soup
- Selenium — medium
- Bash and Unix
- Git and GitHub
Data Science
- Explorational Data Analysis (EDA) and statistics
- Pandas — advanced
- Seaborn and matplotlib — advanced
- Statsmodels, SciPy
- SQL — medium level
- Machine learning
- Scikit-learn — advanced (custom transformers, encoders, etc)
- Boosting algorithms (XGBoost, CatBoost, LightGBM)
- TensorFlow and Keras — basic
- Automation with featuretools and auto-sklearn
- Bayesian hyperparameter tuning with Optuna
- Simple NLP with SpaCy, tokens clusterization techniques
- Computer Vision (application to histopathology)
Bioinformatics and computational biology
- Single-cell analysis with Scanpy
- Working with Entrez APIs using biopython utilities
- ODE modeling with MATLAB
- Ensembl Variant Effect Predictor with plugins configuration
- Genes annotation with biomart, Ensembl REST API and other tools
- Analyzing sequence association data
Portfolio
- BioQuest — website on Django
- Django 4
- Bootstrap 5
- OOP principles
- EDAwesome — my Python library for quick and nice explorational data analysis
- EDA: pandas, seaborn, matplotlib
- Packaging with poetry
- Home credit dataset analysis and loan repayment prediction — capstone project from the Turing College
- EDA: pandas, seaborn, matplotlib
- Scikit-learn — advanced (custom transformers, encoders, etc)
- Automation with featuretools and auto-sklearn
- Bayesian hyperparameter tuning with Optuna
- Simple NLP with SpaCy, tokens clusterization techniques
- I got 93/100 on code review at Turing College
- Podcast analysis — data analysis project from the Turing College
- SQL
- EDA: pandas, seaborn, matplotlib
- SQLAclhemy
- AIOGram
- Python Asyncio
- Working with RESP API, JSON /LXML
- Beautiful Soup
- Selenium
- Working with Entrez APIs using biopython utilities
- Tgscraper — Python package for telegram scraping
- Modeling for the iGEM competition
- ODE modeling with MATLAB
- Analyzing sequence association data
- EDA: pandas, seaborn, matplotlib
- Beautiful Soup
- Ensembl Variant Effect Predictor with plugins configuration
- EDA: pandas, seaborn, matplotlib
- TensorFlow and Keras
- It was the final project for the course «Machine Learning in Synthetic Biology» at the University and I got an A for it
- Single-cell analysis with Scanpy
- Genes annotation with biomart, Ensembl REST API and other tools
- Outlook emails parser (the source code is unavailable for legal reasons)
- Machine learning system for determining SpO2 by video (the source code is unavailable for legal reasons)
Talks and Scientific popularization
- Talk on SciBerloga bioinformatics community meetup
- Prof. O. Kalinina (Helmholtz Institute) and A. Zalevsky (IBH RAS) and other scientists gave a talk on these meetups
- Article about medicines against COVID-19 and their biological mechanisms on the leading Russian portal for doctors and med students medach.pro
- BioLogic and BioNews — scientific popular telegram channels
- Creator, writer, chief editor
Undergraduate achievements
- Got a fully funded scholarship at the University of Tartu
- Medalist of the iGEM 2022 (student synthetic biology team projects competition)
High school achievements
- Winner of the all-Russian school biology Olympiad (VOS), top 20 in the country
- 1st place in Russia at the School Biology Olympiad (SHBO)
- Graduated from one of the best schools in Moscow, the CPM school with a gold medal
- Numerous successes in biological tournaments
(competitions where teams solve and present solutions to non-standard biological problems and oppose each other)
- Two-time winner of the All-Russian tournament young biologists
(team classification)
- Winner of the All-Russian tournament of young biologists
(individual)
- Three-time winner of the Tournament of young biologists of St. Petersburg
(team classification)
- Two-time winner of the Tournament of young biologists of St. Petersburg
(individual)
- The regional stage of the all-Russian school biology Olympiad winner
- Two-time winner in Moscow
- Winner in St. Petersburg
- Three-time absolute winner at the City Olympiad in Biology in St. Petersburg
- Diploma of the 1st degree at the City Olympiad in Biology in St. Petersburg