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).

My Google scholar profile.

Selected articles
  1. (2019) What do neighbors tell about you: the local context of cis-regulatory modules complicates prediction of regulatory variants. Dmitry D Penzar, Arsenii O Zinkevich, Ilya E Vorontsov, Vasily V Sitnik, Alexander V Favorov, Vsevolod J Makeev, Ivan V Kulakovskiy.
    Frontiers in genetics, 31 October 2019. doi:10.3389/fgene.2019.01078
  2. (2017) HOCOMOCO: Towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis. Ivan V Kulakovskiy, Ilya E Vorontsov, Ivan S Yevshin, Ruslan N Sharipov, Alla D Fedorova, Eugene I Rumynskiy, Yulia A Medvedeva, Arturo Magana-Mora, Vladimir B Bajic, Dmitry A Papatsenko, Fedor A Kolpakov, Vsevolod J Makeev.
    Nucleic Acids Research, Volume 46, Issue D1, 4 January 2018, Pages D252–D259. doi:10.1093/nar/gkx1106
  3. (2016) Negative selection maintains transcription factor binding motifs in human cancer. Ilya E Vorontsov, Grigory Khimulya, Elena N Lukianova, Daria D Nikolaeva, Irina A Eliseeva, Ivan V Kulakovskiy and Vsevolod J Makeev.
    BMC Genomics 2016, 17(Suppl 2):395. doi:10.1186/s12864-016-2728-9
  4. (2016) HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models. Ivan V. Kulakovskiy , Ilya E. Vorontsov , Ivan S. Yevshin, Anastasiia V. Soboleva, Artem S. Kasianov, Haitham Ashoor, Wail Ba-alawi, Vladimir B. Bajic, Yulia A. Medvedeva, Fedor A. Kolpakov and Vsevolod J. Makeev.
    Nucleic acids research (2015). doi:10.1093/nar/gkv1249
  5. (2015) PERFECTOS-APE - Predicting Regulatory Functional Effect of SNPs by Approximate P-value Estimation. I.E. Vorontsov, I.V. Kulakovskiy, G.Khimulya, D.D. Nikolaeva and V.J. Makeev.
    Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOINFORMATICS-2015), pages 102-108.doi:10.5220/0005189301020108
  6. (2015) EpiFactors: a comprehensive database of human epigenetic factors and complexes. Yulia A Medvedeva, Andreas Lennartsson, Rezvan Ehsani, Ivan V Kulakovskiy, Ilya E Vorontsov, Pouda Panahandeh, Grigory Khimulya, Takeya Kasukawa, Finn Drabløs, FANTOM Consortium.
    Database (2015). doi:10.1093/database/bav067
  7. (2014) A promoter-level mammalian expression atlas. The FANTOM Consortium.
    Nature 507, 462–470 (27 March 2014). doi:10.1038/nature13182
  8. (2013) In silico motif analysis suggests an interplay of transcriptional and translational control in mTOR response. Eliseeva IA, Vorontsov IE, Babeyev KE, Buyanova SM, Sysoeva MA, Kondrashov FA, Kulakovskiy IV.
    Translation 2013; 1:e27469; doi:10.4161/trla.27469
  9. (2013) Jaccard index based similarity measure to compare transcription factor binding site models. Ilya E Vorontsov, Ivan V Kulakovskiy and Vsevolod J Makeev.
    Algorithms for Molecular Biology, 2013, 8:23; doi:10.1186/1748-7188-8-23
  10. (2013) From binding motifs in ChIP-Seq data to improved models of transcription factor binding sites. I. Kulakovskiy, V. Levitsky, D. Oshchepkov, L. Bryzgalov, I. Vorontsov, V. Makeev.
    Journal of Bioinformatics and Computational Biology (J Bioinform Comput Biol) , 11(1): 1340004; doi:10.1142/S0219720013400040
  11. (2013) Learning advanced TFBS models from chip-seq data diChIPMunk: Effective construction of dinucleotide positional weight matrices. Kulakovskiy, I.V., Levitsky, V.G., Oschepkov, D.G., Vorontsov, I.E., Makeev, V.J.
    BIOINFORMATICS 2013 - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms. doi:10.5220/0004238201460150
  12. (2013) HOCOMOCO: a comprehensive collection of human transcription factor binding sites models. I.V. Kulakovskiy, Y.A. Medvedeva, U. Schaefer, A.S. Kasianov, I.E. Vorontsov, V.B. Bajic, V.J. Makeev.
    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:

Teaching activities:

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:

Contacts: