Pavel Kravchenko

Pavel Kravchenko

PhD Student · Max Planck Institute of Biochemistry, Munich

ORCID LinkedIn GitHub

About

I am a PhD student in the Totipotency department of Prof. Dr. Kikuë Tachibana, working to disentangle chromatin architecture and transcription regulation during zygotic genome activation. To do this, I develop direct multi-omics single-cell technologies and computational tools. I hold a Specialist degree (with Honors) from the Faculty of Bioengineering and Bioinformatics at Lomonosov Moscow State University. Outside the lab, I enjoy writing poetry and hiking.

Research Interests

Zygotic genome activation & totipotencyChromatin architectureTranscription regulationSingle-cell multi-omicsEnhancer–promoter contactsMachine learning for genomics

Skills

Programming

Python, R, Bash, Git, Slurm

Bioinformatics

ChIP-Seq, ATAC-Seq, RNA-Seq, Hi-C; evolution simulation (SLiM, Plink); biopolymer modeling (RNA/DNA/protein docking, folding, GROMACS); phylogenetics, SNP calling, LD & recombination detection, database parsing.

Molecular biology

Custom library design & sequencing, method development; embryo isolation, zygote microinjection, cell culture; protein expression & purification, WB, PAGE, EMSA; CUT&Tag, Hi-TrAC, TIP-Seq, RNA FISH, Y1H; immunofluorescence, expansion microscopy.

Languages

English (fluent), German (basic), French (reading knowledge).

Selected Publications

Vorontsov, I. et al. Cross-platform motif discovery and benchmarking to explore binding specificities of poorly studied human transcription factors. Communications Biology (2025).
Kravchenko, P. & Tachibana, K. Rise and SINE: roles of transcription factors and retrotransposable elements in zygotic genome activation. Nature Reviews Molecular Cell Biology (2024).
Gassler, J. et al. Zygotic genome activation by the totipotency pioneer factor Nr5a2. Science (2022).

Full list on ORCID.

Research Experience

Enhancer–promoter contacts and transcriptional regulation during early embryonic development

Jul 2020 – present · IMBA (Vienna), MPIB (Munich) · Supervisor: Prof. Dr. Kikuë Tachibana

Full-cycle method development, ML, MD, ATAC-Seq, TIP-Seq, RNA-Seq, CUT&Tag, Hi-C, mouse embryo cultures.

Bioinformatics services (sole proprietorship, B2Academy model)

2020 – 2021 · Client: IMBA (Vienna)

Founded two sole proprietorship businesses providing bioinformatics services.

Molecular basis of defective Polycomb regulation in Asx and Calypso mutants

Jun, Sep 2021 · MPIB · Supervisor: Dr. Jürg Müller

Machine learning for prediction of transcription factor binding sites

Sep 2018 – Jul 2020 · Vavilov Institute of General Genetics · Supervisor: Dr. Ivan Kulakovskiy

Evolution of mitochondrial DNA inheritance patterns

Sep 2017 – Jul 2022 · A.N. Belozersky Institute · Supervisor: Dr. Dmitry Knorre

Education

PhD, Totipotency Department

Jul 2022 – present · Max Planck Institute of Biochemistry & LMU, Munich · Supervisor: Prof. Dr. Kikuë Tachibana

GeneNovate — Nationwide entrepreneurship program

Jan – Jul 2025 · Munich / Berlin, Germany

Specialist (with Honors), Bioengineering & Bioinformatics

Sep 2016 – Jul 2022 · Lomonosov Moscow State University · GPA 4.94 / 5.00

Relevant courses: mathematical analysis, linear algebra, machine learning, molecular biology, statistics, genetic engineering, computer science, applied bioinformatics.

Talks, Conferences & Schools

Organizing & committees

  • NGSchool2026 — Head of content team (Warsaw, Nov 2026)
  • InPharma — content team (Munich, Apr 2026)
  • Interact — marketing team (Munich, Apr 2025)
  • Program committee, BIOSTEC 2023 (Lisbon, Feb 2023)

Oral presentations

  • Curious2024 — pioneer transcription factors and zygotic genome activation (Mainz, 2024)
  • SMILES @ Skoltech — decision trees on individual motifs for TFBS recognition (2020)
  • ITaSb — integrating position weight matrices in decision trees for TFBS prediction (Moscow, 2020)

Poster presentations

  • EMBL PhD Symposium — Rise and SINE (Heidelberg, 2024)
  • GenAI-School — survey of mtDNA recombination in Opisthokonta (Paris, 2024)
  • SMBE 2023 — survey of mtDNA recombination in Opisthokonta (Ferrara, 2023)

Selected schools attended

  • OxML — Oxford, 2025
  • GenAI-School — Paris, 2024
  • LMU & MPG Open Science Summer School — Munich, 2024
  • NGSchool2023 — Warsaw, 2023
  • GREEKC COST Action hackathon — Marseille, 2019
  • Future Biotech Winter Retreat — St. Petersburg, 2019
  • Summer MIPT School of Bioinformatics — Moscow, 2017

Teaching & Mentoring

Awards