Emil Viesná

Python Developer ⋅ QA Specialist ⋅ Bioinformatician

Email: snowboard_refinery@proton.me
Codeberg: https://codeberg.org/screwery
ORCiD: https://orcid.org/0000-0003-3480-3963

Skills

Python3: FastAPI, Flask, Selenium, website parsing, text data parsing.
TeX: Book layout, mathematical formulae render, scientific presentations.
Bioinformatics: NGS data QC, NGS data processing, NGS data clinical interpretation, bioinformatics software development.
Linux: Bash scripting, SSH configuration, Apache, Nginx, Lighttpd.
C / C++: Boost, Qt 6+, QML, OpenGL, GLM, cURL.
Cryptography: Tor, I2P, EFS, GnuPG, GPGME, Libgcrypt, Libassuan, Sodium.
Frontend: HTML5, CSS3, jQuery, AJAX, PureCSS, Bootstrap.
Blender: MakeHuman, SaplingTree, A.N.T. Landscape, asset generation, asset preparation for Godot.
Reengineering: Radare2, assembly development, disassembling.
QA: Unittest, Selenium, Pylint, Cppcheck, GTest, Codacy, bug reporting.
Vector design: Inkscape, vectorization of raster images, logo and icon design.
Nursing: Nursing care, management of medical records, laboratory tests.

Experience

Institute of Cytology & Genetics, SB RAS 2019—23

Ontogenesis Genomic Mechanisms Sector

Bioinformatics technician

Research in genetics, molecular biology, and bioinformatics
Processing, quality control, and interpretation of new generation sequencing data (WGS, WES, ChIP-seq, Hi-C, Exo-C)
Administration and security control of laboratory servers
Fullstack development, as part of research projects
Bioinformatics tools development (Python, R, C, C++, Golang)

Freelance 2016—25

Various Projects

Developer

Site parsing script development
Writing term papers and dissertations on mathematical linguistics
Document format conversion, TeX development

Cosmodent 2024—25

Department of Therapy

Assistant Dentist

Assisting the dentist during appointments: therapy, orthopedics, pediatric dentistry
Preparing the operation area, cleaning of premises
Maintenance of the dental tools, configuration of the medical devices
Stock accounting, restocking
Dental computed tomography, RVG single tooth images

Projects

Pawpyrus

Pawpyrus is a minimalist FOSS paper data storage based on QR codes and ArUco. It generates a PDF from any small-sized binary file. Further the paper storage can be scanned and decoded. The script is pure Python and a part of PyPI, so can be installed via pip.

Codeberg: https://codeberg.org/screwery/pawpyrus

Muppy

Muppy stands for MarkUp Preprocessor for Python, a simple exec() script which execute instructions inside comments. For now, Muppy can recognize C-styled, Python-styled, XML-styled and TeX-styled comments. The script is pure Python and a part of PyPI, so can be installed via pip.

Codeberg: https://codeberg.org/screwery/muppy

Listvennica's Mod

Listvennica's Mod is a decorative mod for Minecraft based on Fabric. It adds some blocks inspired with Siberian architecture. The mod is a part of Modrinth.

Codeberg: https://codeberg.org/desertear/listvennica_mod

Education

Novosibirsk State University '22

Vladimir Zelman Institute for Medicine and Psychology

Qualification: General practitioner

Advanced Training Courses

MGNGS School '21

Bochkov's Research Centre for Medical Genetics

Clinical analysis and interpretation of NGS data

Publications

Salnikov, P., Belokopytova, P., Yan, A., Viesná, E., Korablev, A., Serova, I., Lukyanchikova, V., Stepanchuk, Ya., Torgunakov, N., Tikhomirov, S., Fishman, V. (2025) “Direction and modality of transcription changes caused by TAD boundary disruption in Slc29a3/Unc5b locus depends on tissue-specific epigenetic context”. Epigenetics & Chromatin. DOI: https://doi.org/10.1186/s13072-025-00618-1
Gridina, M., Lagunov, T., Belokopytova, P., Torgunakov, N., Nuriddinov, M., Nurislamov, A., Nazarenko, L. P., Kashevarova, A. A., Lopatkina, M. E., Vasilyev, S., Zuev, A., Belyaeva, E. O., Salyukova, O. A., Cheremnykh, A. D., Suhanova, N. N., Minzhenkova, M. E., Markova, Zh. G., Demina, N. A., Stepanchuk, Ya., Khabarova, A., Yan, A., Valeev, E., Koksharova, G., Grigor’eva, E. V., Kokh, N., Lukjanova, T., Maximova, Yu., Musatova, E., Shabanova, E., Kechin, A., Khrapov, E., Boyarskih, U., Ryzhkova, O., Suntsova, M., Matrosova, A., Karoli, M., Manakhov, A., Filipenko, M., Rogaev, E., Shilova, N. V., Lebedev, I. N., Fishman, V. (2025) “Combining chromosome conformation capture and exome sequencing for simultaneous detection of structural and single-nucleotide variants”. Genome Medicine. DOI: https://doi.org/10.1186/s13073-025-01471-3
Smirnov, A. V., Korablev, A. N., Serova, I. A., Yunusova, A. M., Muravyova, A. A., Valeev, E. S., Battulin, N. R. (2025) “Studying concatenation of the Cas9-cleaved transgenes using barcodes”. Vavilov Journal of Genetics and Breeding. DOI: https://doi.org/10.18699/vjgb-25-04
Kurochkina, Yu. D., Korolev, M. A., Letyagina, E. A., Fishman, V. S., Gridina, M. M., Valeeva, E. S. (2023) “A family case of a rare autoinflammatory disease associated with mutations in the NLRP3 and TNFRSF1A genes in the practice of a rheumatologist”. Bulletin of Siberian Medicine. DOI: https://doi.org/10.20538/1682-0363-2023-2-170-175
Gridina, M. M., Vesna, E., Minzhenkova, M. E., Shilova, N. V., Ryzhkova, O. P., Nazarenko, L. P., Belyaeva, E. O., Lebedev, I. N., Fishman, V. S. (2023) “Influence of human peripheral blood samples preprocessing on the quality of Hi-C libraries”. Vavilov Journal of Genetics and Breeding. DOI: https://doi.org/10.18699/vjgb-23-11
Ivanoshchuk, D., Shakhtshneider, E., Mikhailova, S., Ovsyannikova, A., Rymar, O., Valeeva, E., Orlov, P., Voevoda, M. (2023) “The Mutation Spectrum of Rare Variants in the Gene of Adenosine Triphosphate (ATP)-Binding Cassette Subfamily C Member 8 in Patients with a MODY Phenotype in Western Siberia”. Journal of Personalized Medicine. DOI: https://doi.org/10.3390/jpm13020172
Viesná, E., Fishman, V. (2023) “FastContext: A tool for identification of adapters and other sequence patterns in next generation sequencing (NGS) data”. Vavilov Journal of Genetics and Breeding. DOI: https://doi.org/10.18699/vjgb-22-97
Belokopytova, P., Viesná, E., Chiliński, M., Qi, Y., Salari, H., Di Stefano, M., Esposito, A., Conte, M., Chiariello, A. M., Teif, V. B., Plewczynski, D., Zhang, B., Jost, D., Fishman, V. (2022) “3DGenBench: a web-server to benchmark computational models for 3D Genomics”. Nucleic Acids Research. DOI: https://doi.org/10.1093/nar/gkac396
Ivanoshchuk, D. E., Ovsyannikova, A. K., Mikhailova, S. V., Shakhtshneider, E. V., Valeev, E. S., Rymar, O. D., Orlov, P. S., Voevoda, M. I. (2022) “Variants of the HNF4A and HNF1A genes in patients with impaired glucose metabolism and dyslipidemia”. Atherosclerosis. DOI: https://doi.org/10.52727/2078-256x-2021-17-4-11-19
Gridina, M., Mozheiko, E., Valeev, E., Nazarenko, L. P., Lopatkina, M. E., Markova, Z. G., Yablonskaya, M. I., Voinova, V. Y., Shilova, N. V., Lebedev, I. N., Fishman, V. (2021) “A cookbook for DNase Hi-C”. Epigenetics & Chromatin. DOI: https://doi.org/10.1186/s13072-021-00389-5
Shakhtshneider, E., Ivanoshchuk, D., Timoshchenko, O., Orlov, P., Semaev, S., Valeev, E., Goonko, A., Ladygina, N., Voevoda, M. (2021) “Analysis of Rare Variants in Genes Related to Lipid Metabolism in Patients with Familial Hypercholesterolemia in Western Siberia (Russia)”. Journal of Personalized Medicine. DOI: https://doi.org/10.3390/jpm11111232
Шахтшнейдер, Е. В., Иванощук, Д. Е., Рагино, Ю. И., Валеев, Э. С., Полонская, Я. В., Каштанова, Е. В., Чернявский, А. М., Мурашов, И. С., Воевода, М. И. (2021) “Высокопроизводительные молекулярно-генетические технологии для поиска новых этиопатогенетических факторов развития атеросклероза”. Атеросклероз. DOI: https://doi.org/10.52727/2078-256x-2021-17-3-83-84
Смирнов, А. В., Юнусова, А. М., Муравьева, А. А., Валеев, Э. С., Фишман, В. С., Баттулин, Н. Р. (2021) “Создание библиотек баркодированных плазмид с помощью метода клонирования по Гибсону”. Письма в Вавиловский журнал генетики и селекции. DOI: https://doi.org/10.18699/lettersvj2021-7-05
Striukova, E. S., Shakhtshneider, E. V., Ivanoshchuk, D. E., Ragino, Yu. I., Polonskaya, Ya. V., Murashov, I. S., Volkov, A. M., Kurguzov, A. V., Chernyavsky, A. M., Valeev, E. S., Maksimov, V. N., Kashtanova, E. V. (2021) “Analysis of f5 gene polymorphism in men with coronary atherosclerosis using whole exome sequencing”. Atherosclerosis. DOI: https://doi.org/10.52727/2078-256x-2021-17-29-37
Ivanoshchuk, D. E., Shakhtshneider, E. V., Rymar, O. D., Ovsyannikova, A. K., Mikhailova, S. V., Fishman, V. S., Valeev, E. S., Orlov, P. S., Voevoda, M. I. (2021) “The Mutation Spectrum of Maturity Onset Diabetes of the Young (MODY)-Associated Genes among Western Siberia Patients”. Journal of Personalized Medicine. DOI: https://doi.org/10.3390/jpm11010057