Mikhail M.

Bioinformatician with 7+ years of experience in omics data analysis

I’m seeking short-term or consultancy-based remote opportunities in bioinformatics, ideally at the interface of gene regulation, chromatin organisation, and multiomics data analysis. With 7+ years of experience in academic research, I bring expertise in reproducible pipeline development, deep biological interpretation, and cross-disciplinary collaboration. I’m especially interested in roles that allow me to apply my skills to translational or data-driven discovery projects in academia, biotech, or clinical research.

Последнее обновление резюме 06.05.2025
Адрес Amsterdam, Netherlands
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Опыт

The Netherlands Cancer Institute (NKI), Amsterdam, Netherlands
Bioinformatics PhD Student
Апр 2021 - Текущий
◼ Led cross-disciplinary research projects on gene regulation and chromatin structure, advancing biological data analysis and leadership skills ◼ Developed scalable pipelines to process and integrate high-throughput sequencing data (ATAC-seq, RNA-seq, TT-seq, ChIP-seq, Hi-C, Micro-C, long-reads) ◼ Conducted large-scale analyses of over 100 public and in-house datasets to support multiple research projects ◼ Collaborated closely with wet-lab scientists to design validation experiments based on computational predictions, gaining a deep understanding of experimental design, data acquisition processes, and method limitations ◼ Disproved a long-standing model of ZNF143 as a chromatin looping factor, revealing its role as an essential transcriptional regulator of mitochondrial genes (published in Molecular Cell) ◼ Co-authored a pioneering study describing "fountains" as a novel 3D genome architecture feature, identifying their regulatory factors and their effects on gene expression ◼ Built a computational framework integrating allele-specific multiomics and deep learning to identify functional non-coding variants in personal genomes, with potential applications in clinical research and personalised medicine ◼ Supervised a Master's student on a major computational internship project for the thesis ◼ Published 4 first-author research papers (including 1 review) and co-authored 3 additional studies in high-impact journals ◼ Presented at 7 renowned international conferences (4 selected oral presentations)
Институт биологии гена Российской академии наук (ИБГ РАН), Москва, Россия
Research Assistant
Сен 2018 - Мар 2021
◼ Developed skills in high-throughput sequencing data processing (Hi-C, RNA-seq, ChIP-seq) and bioinformatics pipelines development ◼ Led omics data analysis for an international collaboration project on the role of SETDB1 in lung cancer (published in Nucleic Acids Research) ◼ Investigated the emerging concept of phase separation in 3D genome organisation, contributing to one of the early studies on the topic (published in Nucleic Acids Research) ◼ Benchmarked 29 software tools for prokaryotic chromatin domain annotation (published in Bioinformatics) ◼ Led the development of a novel 3D genome data visualisation tool in collaboration with a supervised Bachelor’s student (published in BMC Bioinformatics) ◼ Contributed to the development of a novel method for investigating RNA-DNA interactions ◼ Published 2 first-author research papers and co-authored 6 additional studies
The European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom
Internship Student
Янв 2018 - Июн 2018
◼ Applied structural bioinformatics to study how proteases work and how they evolved to perform various enzymatic reactions ◼ Developed a set of metrics to differentiate between promiscuous and specific proteases based on structural data, protein-peptide interactions, and substrate modeling ◼ Designed a proof-of-concept computational workflow that laid the groundwork for follow-up research, which was later continued by a postdoctoral researcher
Agency for Science, Technology and Research (A*STAR), Singapore
Internship Student
Июл 2017 - Дек 2017
◼ Applied phylogenetic methods to analyse the conservation of actin-binding proteins (actins, profilins, thymosins), providing evolutionary insights into protein function across species ◼ Performed phylogenetic and sequence analysis of the ParMRC system components in Clostridium perfringens

Образование

Московский физико-технический институт (МФТИ)
Факультет биологической и медицинской физики (ФБМФ)
Сен 2019 - Июн 2021
Магистр прикладной математики и физики, с отличием
Московский физико-технический институт (МФТИ)
Факультет биологической и медицинской физики (ФБМФ)
Сен 2014 - Июн 2019
Бакалавр прикладной математики и физики, с отличием

В чем вы сильны?

Skills: 

  • development and adaptation of bioinformatics pipelines
  • experience in analysis and integration of high-throughput sequencing data
  • solid understanding of bioinformatics software and tools
  • knowledge of molecular biology methods and experimental designs
  • comfortable working independently or collaboratively in a multidisciplinary mixed wet/dry lab environment
  • strong written and verbal communication skills.

Programming: proficiency in Python and bash, familiarity with R.

Data types: 

  • experienced in ATAC-seq, RNA-seq, nascent RNA-seq, ChIP-seq, Hi-C, Micro-C, and 4C-seq
  • familiar with PacBio HiFi, 10X linked-reads, WGS, GWAS/eQTL, mass-spectrometry, flow cytometry, and image analysis.

Расскажите о себе что-нибудь еще: публикации, конференции, хобби

KEY PUBLICATIONS:

  • Magnitov, Maresca et al. “ZNF143 is a transcriptional regulator of nuclear-encoded mitochondrial genes that acts independently of looping and CTCF”, Molecular Cell, 2025 (DOI: 10.1016/j.molcel.2024.11.031).
  • Zakharova, Magnitov et al. “SETDB1 fuels the lung cancer phenotype by modulating epigenome, 3D genome organization and chromatin mechanical properties”, Nucleic Acids Research, 2022 (DOI: 10.1093/nar/gkac234).
  • Magnitov, Garaev et al. “Pentad: a tool for distance‑dependent analysis of Hi‑C interactions within and between chromatin compartments”, BMC bioinformatics, 2022 (DOI: 10.1186/s12859-022-04654-6).
  • Liu, Magnitov et al. “Rapid depletion of CTCF and cohesin proteins reveals dynamic features of chromosome architecture”, bioRxiv, 2021 (DOI: 10.1101/2021.08.27.457977)
  • Magnitov et al. “Benchmark of software tools for prokaryotic chromosomal interaction domain identification”, Bioinformatics, 2020 (DOI: 10.1093/bioinformatics/btaa555).
  • Ochoa, Magnitov et al. “An automated protocol for modelling peptide substrates to proteases”, BMC Bioinformatics, 2020 (DOI: 10.1186/s12859-020-03931-6).

CONFERENCES:

  • EMBL Transcription & Chromatin 2022 (Heidelberg, Germany, poster presentation)
  • IFOM 4DGenomics 2023 (Milan, Italy, poster presentation)
  • NWO Life 2023 (Egmond aan Zee, The Netherlands, oral presentation)
  • EMBL Transcription & Chromatin 2024 (Heidelberg, Germany, poster presentation)
  • Genetics Retreat 2024 (Amsterdam, The Netherlands, oral presentation)
  • NVHG Annual Meeting 2024 (Amsterdam, The Netherlands, oral presentation)
  • NWO Life 2025 (Egmond aan Zee, The Netherlands, oral presentation)