Danil D. Kotelnikov

CV

Bioinformatics, structural and molecular biology, molecular genetic diagnostics.

Details

Availability
Open to relocation, EU and US
Languages
English, C1
E-mail
danil.kotelnikov.02@gmail.com
Telegram
@yourlilygarden
ORCID
0009-0003-5159-5796

Experience

  • 2023 – Research assistant Laboratory of protein biochemistry and chemical pathology, biomedical research institute
    • Computational design of single-domain antibodies against poliovirus type 1 antigens, Sabin strain, since 2025.
    • Structure prediction and docking: protein–ligand, protein–protein, antigen–antibody, protein–nucleic acid.
    • Molecular dynamics of supramolecular complexes; ligand and metal-site parameterisation; binding free energy.
    • Primer design for isothermal amplification of potato pathogens, 2023–2024.
    • In-house semi-automated computational pipelines for structural biology.
  • 2025 – 2026 Bioinformatician Laboratory of molecular genetic studies of plants, agricultural university
    • Primer design for PCR and isothermal methods; multiple genome alignment; SSR and SNP marker discovery.
    • Species identification of Fusarium: ITS, TEF-1α and calmodulin amplification, cycle sequencing, capillary electrophoresis.
    • Commissioning and metrological verification of a capillary genetic analyser.
    • Sequencing data processing in Python with Biopython; marker sets for cereal breeding; training of two specialists.
  • 2024 – 2026 Researcher Laboratory of biotechnology, crop research institute
    • Full laboratory cycle: nucleic acid extraction, PCR in all formats, electrophoresis, Sanger sequencing.
    • Short-read library preparation on a DNB-based sequencing platform.
    • Plant genome assembly from short and long reads and against a reference; annotation, read QC, genome profiling.
    • Sequencing and assembly of the genome of wild soybean accession KBL-107.

Competencies

Structural biology and protein design

  • Structure prediction: AlphaFold2, AlphaFold-Multimer, AlphaFold3, tFold-Ab, Chai-1, Boltz-1, Protenix.
  • Docking: AutoDock, AutoDock Vina, VinaGPU, MOE, Glide; Rosetta3, ClusPro 2.0, ReplicaDock 2.0; HDOCK, ZDOCK.
  • Molecular dynamics: GROMACS; CHARMM36, AMBER14/19, OPLS4, OPLS-AA; CHARMM-GUI; CGenFF, OpenFF, GAFF, MCPB.py.
  • Binding free energy: Uni-GBSA, gmx_MMPBSA. Trajectory analysis: RMSD, RMSF, hydrogen bonds, PLIP.
  • Antibody developability: ProtParam, NanoMelt, CamSol, AlgPred2.

Genomics and sequence bioinformatics

  • Assembly: ABySS2, SPAdes, MaSuRCA, SOAPdenovo, MEGAHIT, RagTag; gap closing with TGSGapCloser.
  • QC and mapping: FastQC, MultiQC, BWA-MEM2, Bowtie2. Annotation: Augustus, Liftoff.
  • Genome profiling and heterozygosity: KMC, Jellyfish, GenomeScope, smudgeplot, kmergenie. Alignment: progressiveMauve.
  • Transcription factor binding site prediction; SSR and SNP marker validation.
  • Primer design: Primer3, Unipro UGENE, LAMPrimersIQ, NEB Primer Design.

Molecular diagnostics and marker-assisted selection

  • Complete molecular identification workflow: marker gene choice, primer design, species attribution.
  • Species-specific diagnostic systems for plant pathogens; isothermal amplification with lateral flow detection.
  • Marker-assisted selection: touchdown protocols for polyploid genomes, KASP competitive allele-specific assay.
  • Product separation: agarose and capillary electrophoresis, CAPS and dCAPS restriction analysis.

Experimental laboratory work

  • Nucleic acid extraction: precipitation, magnetic beads, spin columns; spectrophotometry and fluorimetry.
  • PCR: quantitative, reverse-transcription, real-time; LAMP; RPA/MIRA.
  • Cycle sequencing, Sanger sequencing, capillary electrophoresis, fragment analysis.
  • Short-read library preparation; MinION nanopore sequencing.
  • Capillary genetic analyser: commissioning, metrological verification, maintenance.

Computing

  • Linux; Python with Biopython: chromatogram processing, base calling, consensus assembly, analytical graphics.
  • In-house computational pipelines for structural biology.
  • Own compute node: Intel Xeon Platinum 8368, 512 GB RAM.

Education

  • 2026 – MSc, Applied Mathematics and Informatics Programme “Bioinformatics in Agriculture”. In progress.
  • 2024 – 2026 BSc with honours, Animal Science Agricultural university. Grade point average 4.90 of 5.00. Thesis: zoohygienic analysis of Fusarium moulds in feed by molecular genetic diagnostics.
  • 2020 – 2024 General Medicine Medical academy. Studied to the winter examination session of 2023/24; 35 credits transferred.
  • 2026 Molecular genetic methods: PCR, fragment analysis, Sanger sequencing Agricultural university. 36 hours.
  • 2024 Bioinformatic and experimental approaches using the MinION sequencer Biomedical research institute. Internship.

Grants

  • 2025 – National science foundation project Structural and functional characterisation of poliovirus pseudoviral particles after inactivation by chemical means and by accelerated electrons. Executor.
  • 2026 National academic leadership programme Identification of plant pathogens and marker support for cereal breeding. Executor.
  • 2023 – 2024 National genetic technologies programme Microbiomes of agrocenoses: screening, monitoring and management of microbial consortia for regenerative agriculture. Co-executor on three subprojects.

Recognition

  • 2026 National competition for the best research work, final stage Laureate diploma, eighth place; winner of the additional category “Digitalisation in animal husbandry” for Felex, open-source software for diet formulation with a local intelligent agent.
  • 2025 National competition for the best research work, Animal Science First place at stage I; first-degree diploma at stage II; laureate diploma at the final stage, sixth place. Work: molecular biological tools for the identification of zearalenone and the diagnosis of Fusarium fungi in feed by in silico methods.
  • 2026 Letters of appreciation from the university Rector For research achievements and for academic excellence.
  • 2025 Letter of recommendation From the Head of the Centre for Practical Education, biomedical research institute.

Talks

  • 2025 Inside the northernmost soybean: sequencing and assembly of the genome of wild soybean accession KBL-107 Conference “Young scientists for science”. Diploma for the presentation.
  • 2024 3rd Annual School of Young Researchers in Genetic Technologies Abstract published in the proceedings.
  • 2023 Youth of the 21st century: a step into the future Regional research and practice conference.