Emil Valeeva (Viesná)^they/them

Bioinformatician ⋅ Python Developer

Email: snowboard_refinery@proton.me
WhatsApp: +374 55 758884
Codeberg: https://codeberg.org/screwery
ORCiD: https://orcid.org/0000-0003-3480-3963
Address: Yerevan, Armenia

About

Bioinformatician and Python developer with 4+ years of experience building production-grade bioinformatics workflows for research and clinical genetics projects. Skilled in Python, R/Bioconductor, C/C++, and CI/CD tools. Deep expertise in processing and interpreting NGS data (WGS, WES, Hi‑C, Exo‑C, RNA‑seq, ChIP‑seq), variant prioritization, and detecting chromosomal rearrangements via Hi‑C. Proven ability to develop reproducible pipelines and analytical tools, maintain secure lab servers, and deliver full‑stack solutions (FastAPI, Flask, SQLAlchemy, HTML5/CSS3). Experienced in QA practices (Unittest, Pylint, GTest, Codacy), and open‑source distribution. Co‑author on multiple peer‑reviewed genomics papers, an active open‑source contributor, and a strong collaborator in multidisciplinary teams.

Skills

Programming: Python (pandas, NumPy, scikit-learn), R (Bioconductor), C/C++, Bash, async, OOP.
Omics Processing: WGS, WES, Hi‑C, Exo‑C, RNA‑seq, ChIP‑seq.
Bioinformatics: BLAST, Bowtie, BWA, GATK, Juicer, SAMtools, Picard, ChIPseeker, DEseq2.
Clinical Genetics: SNP prioritization, detection of chromosomal rearrangements via Hi-C, OMIM.
Visualization: Matplotlib, Seaborn, Plotly, ggplot2, Juicebox.
CI/CD: Git, Docker, Conda, PyPI.
QA: Unittest, Pylint, Cppcheck, GTest, Codacy, bug reporting.
Fullstack: HTML5/CSS3, jQuery, Bootstrap, FastAPI, Flask, SQLAlchemy.
Design & Layout: TeX/LaTeX, Inkscape, book layout, mathematical formulae render, scientific presentations, vector illustration creation, raster-to-vector conversion.

Experience

Institute of Cytology & Genetics, SB RAS 2019—23

Ontogenesis Genomic Mechanisms Sector

Bioinformatics technician

Research in genetics, molecular biology, and bioinformatics (Homo sapiens, Aedes sp., Gallus gallus)
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)

Institute of Gene Biology RAS 2024—25

Laboratory of Regulation of Gene Expression in Development

Invited specialist-bioinformatician

Research in genetics of D. melanogaster
Processing, quality control, and interpretation of new generation sequencing data (ChIP-seq, RNA-seq)
Bioinformatics tools development (Python, R)

Freelance 2016—26

Various Projects

Developer, Designer, Copywriter

Backend development using FastAPI and SQLAlchemy
Site parsing script development
Joomla! and Wordpress website administration
Document format conversion, TeX (XeTeX) development
Vector illustration creation, raster-to-vector conversion
Copywriting on Russian (including SEO) on various topics
Editing and correction of texts on Russian

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

Pet 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

Reports

Valeev, E., Belokopytova, P., Fishman, V. (2020) “Web-3DPredictor: a web interface for high-resolution prediction of genome architecture”. Bioinformatics of Genome Regulation and Structure/Systems Biology (BGRS/SB-2020). The Twelfth International Multiconference Abstracts. ICG SB RAS : Novosibirsk, Russia. Pp. 130. ISBN 978-5-91291-051-7. Link: https://www.spsl.nsc.ru/FullText/konfe/BGRSSB-2020.pdf (Abstracts PDF)
Иванощук, Д. Е., Шахтшнейдер, Е. В., Валеев, Э. С., Овсянникова, А. К., Михайлова, С. В., Рымар, О. Д., Воевода, М. И. (2021) “Молекулярно-генетическая диагностика моногенных форм сахарного диабета”. Сахарный диабет — 2021: от мониторинга к управлению. Материалы IV российской междисциплинарной научно-практической конференции с международным участием. НИИКЭЛ — филиал ИЦиГ СО РАН : Новосибирск, Россия. Стр. 54-55. Ссылка: https://www.elibrary.ru/item.asp?id=45843731 (eLibrary: 45843731)
Иванощук, Д. Е., Овсянникова, А. К., Валеев, Э. С., Михайлова, С. В., Рымар, О. Д., Шахтшнейдер, Е. В. (2020) “Новый вариант делеции в гене GCK у пациента с диабетом MODY типа 2”. Фундаментальные исследования в эндокринологии: современная стратегия развития и технологии персонализированной медицины. Материалы конференции с международным участием. Издательство СО РАН : Новосибирск, Россия. Стр. 11. Ссылка: https://www.elibrary.ru/item.asp?id=44383983 (eLibrary: 44383983)
Иванощук, Д. Е., Валеев, Э. С., Белокопытова, П. С., Фенькова, О. В., Михайлова, С. В., Шахтшнейдер, Е. В., Фишман, В. С., Фурсова, А. Ж., Воевода, М. И. (2019) “Поиск потенциально патогенных генетических вариантов у пациентов с врожденной глаукомой: первичные данные интерпретации двух клинических случаев”. VI международная конференция молодых ученых: биофизиков, биотехнологов, молекулярных биологов и вирусологов. Сборник тезисов. Новосибирский национальный исследовательский государственный университет : Новосибирск, Россия. Стр. 510-514. Ссылка: https://elibrary.ru/item.asp?id=41449757 (eLibrary: 41449757)
Фишман, В. С., Валеев, Э. С., Белокопытова, П. С., Фенькова, О. В., Михайлова, С. В., Фурсова, А. Ж., Воевода, М. И., Иванощук, Д. Е. (2019) “Скрининг редких замен в генах, вовлечённых в дисгенез угла передней камеры глаза у пациентов с врождённой глаукомой”. Генетика — фундаментальная основа инноваций в медицине и селекции. Материалы VIII научно-практической конференции с международным участием. Издательство Южного федерального университета : Ростов-на-Дону — Таганрог, Россия. Стр. 57-58. ISBN 978-5-9275-3236-0. Ссылка: https://www.elibrary.ru/item.asp?id=42976647 (eLibrary: 42976647)

Emil Valeeva (Viesná)they/them