About me
Hi, I am Ilya Vorontsov (Илья Воронцов), researcher and developer from Moscow, Russia.
I study gene regulation in Vavilov Institute of General Genetics using bioinformatician data analysis (since 2012).
Selected articles
- (2019) What do neighbors tell about you: the local context of cis-regulatory modules complicates prediction of regulatory variants.
Frontiers in genetics, 31 October 2019. doi:10.3389/fgene.2019.01078 - (2017) HOCOMOCO: Towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis.
Nucleic Acids Research, Volume 46, Issue D1, 4 January 2018, Pages D252–D259. doi:10.1093/nar/gkx1106 - (2016) Negative selection maintains transcription factor binding motifs in human cancer.
BMC Genomics 2016, 17(Suppl 2):395. doi:10.1186/s12864-016-2728-9 - (2016) HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models.
Nucleic acids research (2015). doi:10.1093/nar/gkv1249 - (2015) PERFECTOS-APE - Predicting Regulatory Functional Effect of SNPs by Approximate P-value Estimation.
Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOINFORMATICS-2015), pages 102-108.doi:10.5220/0005189301020108 - (2015) EpiFactors: a comprehensive database of human epigenetic factors and complexes.
Database (2015). doi:10.1093/database/bav067 - (2014) A promoter-level mammalian expression atlas.
Nature 507, 462–470 (27 March 2014). doi:10.1038/nature13182 - (2013) In silico motif analysis suggests an interplay of transcriptional and translational control in mTOR response.
Translation 2013; 1:e27469; doi:10.4161/trla.27469 - (2013) Jaccard index based similarity measure to compare transcription factor binding site models.
Algorithms for Molecular Biology, 2013, 8:23; doi:10.1186/1748-7188-8-23 - (2013) From binding motifs in ChIP-Seq data to improved models of transcription factor binding sites.
Journal of Bioinformatics and Computational Biology (J Bioinform Comput Biol) , 11(1): 1340004; doi:10.1142/S0219720013400040 - (2013) Learning advanced TFBS models from chip-seq data diChIPMunk: Effective construction of dinucleotide positional weight matrices.
BIOINFORMATICS 2013 - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms. doi:10.5220/0004238201460150 - (2013) HOCOMOCO: a comprehensive collection of human transcription factor binding sites models.
Nucleic Acids Research, 41(D1): D195-D202, doi:10.1093/nar/gks1089
My repositories: github, bitbucket, lab’s github.
Here are some toolkits and services, I’ve developed at work.
Databases:
- HOCOMOCO - collection of transcription factor binding sites models. Developed web-interface and backend. Performed substantial part of data analysis.
- Epifactors - collection of epigenetic factors, corresponding genes and products. Developed web-interface and backend.
Web services:
- Web panel to access several command line tools developed in our lab via web interface. Developed web-interface, contributed to development of backend.
Toolkits:
- PerfectosAPE - java package to analyse effect of single nucleotide variant on transcription factor binding affinity
- MacroAPE - java package to perform comparison of transcription factor binding motifs (represented as PWM-s) and P-value estimation for PWM score/
- papolarity - python toolkit to analyze ribosome distribution along transcripts from Ribo-seq data.
- pasio - python/cython tool to perform segmentation/denoise of coverage profile into regions of constant Poisson parameter λ (given prior distribution λ ~ Γ(α,β)). Tool originally developed by Andrey Lando, my part was in performance optimization and packaging.
Some of my side projects:
- Analysis of draft dynamics in USSR during World War II (in Russian).
- Analysis of sci-hub daily activity patterns in different countries (in Russian).
- Automatic Identification of the Repressed Families and further integration of collected data into wiki-based project “Open List”.
- Interactive historical atlas based on parsing wikipedia, created by school students under my (and my colleague) supervision.
Teaching activities:
- I’m one of the teachers and organisers of Slon summer school of applied programming.
- Currated several projects in bioinformatics at the School of Molecular and Theoretical Biology.
- Wrote part of training material for Python course in Yandex.Lyceum.
- Curate projects at LearnPython courses.
- Teach 10-th and 11-th grade students in Intellectual school.
Technologies:
- Languages I speak: Russian (native), English (good enough to speak and write).
- Languages I write: Ruby (expert), Python (advanced), Cython(intermediate), Java (intermediate), C++ (intermediate), Javascript (intermediate), bash (advanced).
- Other experience: Data analysis and visualization, Machine Learning, full-stack web-development (most experience with Ruby on Rails), docker, git, scraping, basic SQL, Linked Data with RDF and SPARQL, LaTeX.
Education: Graduated Moscow Institute of Physics and Technology:
- Department of General and Applied Physics – Institute of Theoretical and Experimental Physics (Math and Physics, bachelor’s degree, 2011)
- Department of Innovation and High Technology – Yandex School of Data Analysis (Math and Computer Science, master’s degree, 2013)
- Vavilov Institute of General Genetics (Genetics, postgraduate study, 2017)
Career:
- 2012: development of marketplace for designers
- 2012 - now: Vavilov institute of General Genetics. Department of computational systems biology, research fellow
Here is my CV.
Other stuff:
- My articles for habrahabr.
- My general-purpose telegram channel «Шутки Шрёдингера» (Schrödinger Jokes).
- My telegram channel about open science.
Contacts:
- telegram: @VorontsovIE
- e-mail: vorontsov.i.e@gmail.com
- phone: +7(926)616-0892