Igor Fesenko, PhD

Summary

Ph.D. in Genetics with over a decade of extensive experience in proteomics, peptidomics, multi-omics data analysis, and visualization, as well as statistical analysis. My responsibilities include designing and coordinating research projects, preparing manuscripts, writing grant proposals, managing grant applications, and leading interdisciplinary research teams.

I am focused on understanding the function of peptides and microproteins encoded by small open reading frames (smORFs). I am particularly intrigued by the regulatory roles of peptides in immune response and in communication with the microbiota.

Skills

• Skilled in mass-spectrometry and data analysis of MS data: FragPipe, DIA-NN, MaxQuant, Mascot, X!Tandem, SearchGUI, PEAKS;
• Programming Languages: Python, R, Bash, SQL
• Good experience in data analysis and visualization: Pandas, NumPy, Matplotlib, Seaborn, Plotly, scikit-learn, stats, and more
• Skilled at Ribo-seq, RNA-seq и nanopore sequencing: Bowtie, Hisat2, Trimgalore, Trimmomatic, FeatureCounts, edgeR, Guppy 4, minimap, StringTie, scanpy
• Effective in alignment of DNA and protein sequences (MAFFT, Clustal, Muscle, T-coffee, etc.) and phylogenetic analysis (Phylip package, PhyML, MEGA, HyPhy, etc.)
• Skilled at protein structure prediction (ESMFold, AlphaFold2, foldseek, DALI)

Experience

Postdoctoral Associate (2025-present) Massachusetts Institute of Technology

• Postdoc in Feng Zhang Lab

Visiting Researcher (2023-2025) National Institutes of Health (NIH)

• Visiting researcher at Evolutionary Biology group (NCBI/NLM)

Head of the Laboratory of System Analysis of Proteins and Peptides (2022-2023)
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry

• Lead projects for analysis the role of peptides and microproteins in plant-microbe interactions

Group leader at the Laboratory of Functional genomics and Plant proteomics (2018-2022) Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry

• Designing and coordinating research projects in the field of the system plant biology

Senior Researcher at the Laboratory of Proteomics (2011-2018) Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry

• Designing and coordinating research projects in the field of the system plant biology

Lecturer at the Department of Genetics (2006-2015)
Russian State Agrarian University

• Developing and teaching undergraduate courses in “Genetics,” “Molecular Biology,” and “Molecular Genetics”

Projects

Uncovering the role of microproteins in bacterial genomes (link)

• I systematically examined their coding potential, structural features, evolutionary conservation, and selection regime of small genes in Enterobacteriaceae genomes.

Studying the roles of long non-coding RNAs in formation of plant cell proteome (link)

• New families of functional peptides that are coded by small ORFs in different groups of plants were found

Analysis of plant and animal peptidomes (link)

• Methods for the extraction and analysis of endogenous peptides were developed

Education

Dr.Sc. in Molecular Biology (Habilitation)

Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow

2022

Ph.D. in Genetics

Russian State Agrarian University, Russia, Moscow

2005

Publications

Book Chapter:

1. Fesenko I, Khazigaleeva R, Govorun V, Ivanov V. (2018). Analysis of Endogenous Peptide Pools of Physcomitrella patens Moss. Methods Mol Biol. 1719:395-405. doi: 10.1007/978-1-4939-7537-2_27. PMID: 29476527.
2. Lyapina, I., Fesenko, I. (2024). Intracellular and Extracellular Peptidomes of the Model Plant, Physcomitrium patens. In: Schrader, M., Fricker, L.D. (eds) Peptidomics. Methods in Molecular Biology, vol 2758. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3646-6_20

Journal publications:

• Fesenko I, Shabalina S., Storz G., Koonin E.V. De novo origin of numerous microproteins in enterobacteria. Nucleic Acids Res. 2025 (Accepted)
• Fesenko I, Sahakyan,H., Dhyani,R., Shabalina,S.A., Storz,G. and Koonin,E.V. (2025) The hidden bacterial microproteome. Mol. Cell, 10.1016/j.molcel.2025.01.025.
• Lyapina, I., Ganaeva, D., … Fesenko I. (2025) Comparative analysis of small secreted peptide signaling during defense response: insights from vascular and non-vascular plants. Physiologia Plantarum, 177(2), e70147.
• Azarkina R., Makeeva A., … Fesenko I. (2025) The Proteomic and Peptidomic Response of Wheat (Triticum aestivum L.) to Drought Stress. Plants 14 (14), 2168
• Mamaeva A, Lyapina I, Knyazev A, Golub N, Mollaev T, Chudinova E, Elansky S, Babenko VV, Veselovsky VA, Klimina KM, Gribova T, Kharlampieva D, Lazarev V, Fesenko I. RALF peptides modulate immune response in the moss Physcomitrium patens. Front. Plant Sci. 2023 Jan 27;14:1077301.
• Sedlov IA, Fesenko I. Methods for Analysis of Interactome of Microproteins Encoded by Short Open Reading Frames. Russ. J. Bioorganic Chem. Springer; 2023;49(4):717–30.
• Glushkevich A, Spechenkova N, Fesenko I, Knyazev A, Samarskaya V, Kalinina NO, Taliansky M, Love AJ. Transcriptomic Reprogramming, Alternative Splicing and RNA Methylation in Potato (Solanum tuberosum L.) Plants in Response to Potato Virus Y Infection. Plants. 2022 Feb 25;11(5).
• Lyapina I, Ivanov V, Fesenko I. Peptidome: Chaos or Inevitability. Int. J. Mol. Sci. 2021 Dec 4;22(23).
• Fesenko I, Shabalina SA, Mamaeva A, Knyazev A, Glushkevich A, Lyapina I, Ziganshin R, Kovalchuk S, Kharlampieva D, Lazarev V, Taliansky M, Koonin EV. A vast pool of lineage-specific microproteins encoded by long non-coding RNAs in plants. Nucleic Acids Res. 2021 Oct 11;49(18):10328–46.
• Breygina M, Klimenko E, Shilov E, Podolyan A, Mamaeva A, Zgoda V, Fesenko I. Hydrogen peroxide in tobacco stigma exudate affects pollen proteome and membrane potential in pollen tubes. Plant Biol. 2021 Jul;23(4):592–602.
• Spechenkova N, Fesenko I, Mamaeva A, Suprunova TP, Kalinina NO, Love AJ, Taliansky M. The Resistance Responses of Potato Plants to Potato Virus Y Are Associated with an Increased Cellular Methionine Content and an Altered SAM:SAH Methylation Index. Viruses. 2021 May 21;13(6).
• Lyapina I, Filippova A, Kovalchuk S, Ziganshin R, Mamaeva A, Lazarev V, Latsis I, Mikhalchik E, Panasenko O, Ivanov O, Ivanov V, Fesenko I. Possible role of small secreted peptides (SSPs) in immune signaling in bryophytes. Plant Mol. Biol. 2021 May;106(1-2):123–43.
• Kartashov AV, Zlobin IE, Pashkovskiy PP, Pojidaeva ES, Ivanov YV, Mamaeva AS, Fesenko I, Kuznetsov VV. Quantitative analysis of differential dehydrin regulation in pine and spruce seedlings under water deficit. Plant Physiol. Biochem. 2021 May;162:237–46.
• Taliansky M, Samarskaya V, Zavriev SK, Fesenko I, Kalinina NO, Love AJ. RNA-Based Technologies for Engineering Plant Virus Resistance. Plants. 2021 Jan 2;10(1).
• Mamaeva A, Taliansky M, Filippova A, Love AJ, Golub N, Fesenko I. The role of chloroplast protein remodeling in stress responses and shaping of the plant peptidome. New Phytol. 2020 Sep;227(5):1326–34.
• Fesenko I, Spechenkova N, Mamaeva A, Makhotenko AV, Love AJ, Kalinina NO, Taliansky M. Role of the methionine cycle in the temperature-sensitive responses of potato plants to potato virus Y. Mol. Plant Pathol. 2021 Jan;22(1):77–91.
• Lyapina I, Filippova A, Fesenko I. The Role of Peptide Signals Hidden in the Structure of Functional Proteins in Plant Immune Responses. Int. J. Mol. Sci. 2019 Sep 5;20(18).
• Fesenko I, Kirov I, Kniazev A, Khazigaleeva R, Lazarev V, Kharlampieva D, Grafskaia E, Zgoda V, Butenko I, Arapidi G, Mamaeva A, Ivanov V, Govorun V. Distinct types of short open reading frames are translated in plant cells. Genome Res. 2019 Sep;29(9):1464–77.
• Fesenko I, Kirov IV, Filippova AA. Impact of noncoding part of the genome on the proteome plasticity of the eukaryotic cell. Russ. J. Bioorganic Chem. Pleiades Publishing Ltd; 2018 Jul;44(4):397–402.
• Fesenko I, Azarkina R, Kirov I, Kniazev A, Filippova A, Grafskaia E, Lazarev V, Zgoda V, Butenko I, Bukato O, Lyapina I, Nazarenko D, Elansky S, Mamaeva A, Ivanov V, Govorun V. Phytohormone treatment induces generation of cryptic peptides with antimicrobial activity in the Moss Physcomitrella patens. BMC Plant Biol. 2019 Jan 7;19(1):9.
• Filippova A, Lyapina I, Kirov I, Zgoda V, Belogurov A, Kudriaeva A, Ivanov V, Fesenko I. Salicylic acid influences the protease activity and posttranslation modifications of the secreted peptides in the moss Physcomitrella patens. J. Pept. Sci. 2019 Feb;25(2):e3138.
• Kirov I, Gilyok M, Knyazev A, Fesenko I. Pilot satellitome analysis of the model plant, Physcomitrella patens, revealed a transcribed and high-copy IGS related tandem repeat. Comp. Cytogenet. 2018 Dec 13;12(4):493–513.
• Kirov I, Khrustaleva L, Van Laere K, Soloviev A, Sofie Meeus, Romanov D, Fesenko I. DRAWID: user-friendly java software for chromosome measurements and idiogram drawing. Comp. Cytogenet. 2017 Nov 21;11(4):747–57.
• Fesenko I, Khazigaleeva R, Kirov I, Kniazev A, Glushenko O, Babalyan K, Arapidi G, Shashkova T, Butenko I, Zgoda V, Anufrieva K, Seredina A, Filippova A, Govorun V. Alternative splicing shapes transcriptome but not proteome diversity in Physcomitrella patens. Sci. Rep. 2017 Jun 2;7(1):2698.
• Fesenko I, Seredina A, Arapidi G, Ptushenko V, Urban A, Butenko I, Kovalchuk S, Babalyan K, Knyazev A, Khazigaleeva R, Pushkova E, Anikanov N, Ivanov V, Govorun VM. The Physcomitrella patens Chloroplast Proteome Changes in Response to Protoplastation. Front. Plant Sci. 2016 Nov 4;7:1661.
• Fesenko I, Arapidi GP, Skripnikov A, Alexeev DG, Kostryukova ES, Manolov AI, Altukhov IA, Khazigaleeva RA, Seredina AV, Kovalchuk SI, Ziganshin RH, Zgoda VG, Novikova SE, Semashko TA, Slizhikova DK, Ptushenko VV, Gorbachev AY, Govorun VM, Ivanov VT. Specific pools of endogenous peptides are present in gametophore, protonema, and protoplast cells of the moss Physcomitrella patens [Internet]. BMC Plant Biology. 2015. p. 87. Available from: http://dx.doi.org/10.1186/s12870-015-0468-7
• Divashuk MG, Bespalova LA, Vasilyev AV, Fesenko I, Puzyrnaya OY, Karlov GI. Reduced height genes and their importance in winter wheat cultivars grown in southern Russia. Euphytica. 2013 Mar 1;190(1):137–44.
• Fesenko I, Kuklev MY, Karlov GI. Development of a breeder-friendly functional codominant DNA marker for the I2 locus covering resistance to Fusarium oxysporum f. sp. lycopersici. Mol. Breed. Springer Science and Business Media LLC; 2013 Feb;31(2):495–9.
• Khrustaleva L, Kirov I, Romanov D, Budylin M, Lapitskaya I, Kiseleva A, Fesenko I, Karlov G. The chromosome organization of genes and some types of extragenic DNA in Allium. Acta Hortic. International Society for Horticultural Science (ISHS); 2012 Dec;(969):43–51.
• Karlov GI, Fesenko I, Andreeva GN, Khrustaleva LI. Chromosome organization of Ty1-copia-like retrotransposons in the tomato genome. Russ. J. Genet. Pleiades Publishing Ltd; 2010 Jun;46(6):677–81.
• Kuklev MY, Fesenko I, Karlov GI. Development of a CAPS marker for the verticillium wilt resistance in tomatoes. Russ. J. Genet. Pleiades Publishing Ltd; 2009 May;45(5):575–9.
• Fesenko I, Khrustaleva LI, Karlov GI. Organization of the 378-bp satellite repeat in terminal heterochromatin of Allium fistulosum. Russ. J. Genet. Springer Nature; 2002;38(7):745–53.