PhD in Biology

Scientific supervisor

Georgiy Arapidi

Main place of work:

Federal Scientific and Clinical Center for Physical and Chemical Medicine of the Federal Medical and Biological Agency

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Professional interests/research projects:

Students are invited to the laboratory of systems biology of the Federal Scientific and Practical Center "Physical-Chemical Medicine" to carry out bachelor's / master's work and participate in grants. The proposed work can be carried out on the basis of the Institute of Bioorganic Chemistry of the Russian Academy of Sciences and the Federal Scientific and Research Center of the FCM of the FMBA. All studies are carried out using modern mass spectrometers and sequencers. The main vector of work will be directed to the field of systems biology, devoted to the comparison of transcriptomic, genomic, proteomic and metabolomic data.
In case of active participation in the work of the laboratory - material support.

We offer the following work topics:
- Study of intercellular communication between cancer cells after exposure to chemotherapy (bioinformatic analysis of RNA-seq data, proteomic and metabolomic analysis)
- Investigation of the effect of proteins involved in alternative splicing of transcripts on the chemoresistance of patients with ovarian cancer (meta-analysis of shRNA-seq and RIP-seq data)
- Search for epigenetic and transcriptional signatures of the epithelial-mesenchymal transition in the development of various types of cancer (meta-analysis of data from The Cancer Genome Atlas portal and other resources)
- Search for epigenetic and transcriptional drivers of genomic instability in the development of prostate cancer (meta-analysis of data from The Cancer Genome Atlas portal and other resources)
- Identification of functional relationships between potential peptide biomarkers of socially significant human diseases identified in blood serum and plasma (experimental work on the isolation of proteins and peptides and their further analysis by mass spectrometry)
- Search and identification in serum and plasma of peptide fragments that are not related to known human proteins (lncRNA and sORF translation products, food peptides and intestinal microbiota)
Of particular interest to our laboratory are oncological, autoimmune and neurodegenerative diseases.
Main publications:
1) Kuznetsov A, Voronina A, Govorun V, Arapidi. Critical Review of Existing MHC I Immunopeptidome Isolation Methods. G. Molecules. 2020 Nov 19;25(22):5409. doi: 10.3390/molecules25225409. PMID: 33228004
2) Anufrieva KS, Shender VО, Arapidi GP, Pavlyukov MS, Shakhparonov MI, Shnaider PV, Butenko IO, Lagarkova MA, Govorun VM. Therapy-induced stress response is associated with downregulation of pre-mRNA splicing in cancer cells. Genome Med. 2018 Jun 27;10(1):49. doi: 10.1186/s13073-018-0557-y. PMID: 29950180
3) Babalyan K, Sultanov R, Generozov E, Sharova E, Kostryukova E, Larin A, Kanygina A, Govorun V, Arapidi G. LogLoss-BERAF: An ensemble-based machine learning model for constructing highly accurate diagnostic sets of methylation sites accounting for heterogeneity in prostate cancer. PLoS One. 2018 Nov 2;13(11):e0204371. doi: 10.1371/journal.pone.0204371. eCollection 2018. PMID: 30388122
4) Sultanov RI, Arapidi GP, Vinogradova SV, Govorun VM, Luster DG, Ignatov AN. BMC Genomics. Comprehensive analysis of draft genomes of two closely related pseudomonas syringae phylogroup 2b strains infecting mono- and dicotyledon host plants. 2016 Dec 28;17(Suppl 14):1010. doi: 10.1186/s12864-016-3358-y. PMID: 28105943
5) Lomakin Y, Arapidi GP, Chernov A, Ziganshin R, Tcyganov E, Lyadova I, Butenko IO, Osetrova M, Ponomarenko N, Telegin G, Govorun VM, Gabibov A, Belogurov A. Exposure to the Epstein-Barr Viral Antigen Latent Membrane Protein 1 Induces Myelin-Reactive Antibodies In Vivo. Jr. Front Immunol. 2017 Jul 6;8:777. doi: 10.3389/fimmu.2017.00777. eCollection 2017. PMID: 28729867
6) Shender VO, Pavlyukov MS, Ziganshin RH, Arapidi GP, Kovalchuk SI, Anikanov NA, Altukhov IA, Alexeev DG, Butenko IO, Shavarda AL, Khomyakova EB, Evtushenko E, Ashrafyan LA, Antonova IB, Kuznetcov IN, Gorbachev AY, Shakhparonov MI, Govorun VM. Proteome-metabolome profiling of ovarian cancer ascites reveals novel components involved in intercellular communication. Mol Cell Proteomics. 2014 Dec;13(12):3558-71. doi: 10.1074/mcp.M114.041194. Epub 2014 Sep 30. PMID: 25271300
7) Pavlyukov MS, Yu H, Bastola S, Minata M, Shender VO, Lee Y, Zhang S, Wang J, Komarova S, Wang J, Yamaguchi S, Alsheikh HA, Shi J, Chen D, Mohyeldin A, Kim SH, Shin YJ, Anufrieva K, Evtushenko EG, Antipova NV, Arapidi GP, Govorun V, Pestov NB, Shakhparonov MI, Lee LJ, Nam DH, Nakano I. Apoptotic Cell-Derived Extracellular Vesicles Promote Malignancy of Glioblastoma Via Intercellular Transfer of Splicing Factors. Cancer Cell. 2018 Jul 9;34(1):119-135.e10. doi: 10.1016/j.ccell.2018.05.012. Epub 2018 Jun 21. PMID: 29937354
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