| Yurkina A., Badaeva E., González Franco M., Sokolova V., Divashuk M. | Bioinformatic analysis of the repeatomes of Aegilops species with U and M genomes | [Sym 01] 1. Structural and functional organization of genomes | Aegilops; genome-wide sequencing, repeatome |
| Pavel Denisov, Natalya Mikhanoshina, Marina Krotova, Vera Muravieva, Roman Izyumov, Tatiana Priputnevich | Phage-mediated mechanism of genomic stability in healthy Lactobacillus iners lineages | [Sym 01] 1. Structural and functional organization of genomes | Lactobacillus iners, Bacterial vaginosis, Whole genome sequencing, prophage, operon |
| K.A. Deinichenko, P.A. Grebnev, A.M. Shaymardanov, A.A. Ivashechkin, K.S. Grammatikati, D.V. Svetlichnyy | Benchmark of the Oxford Nanopore, EM-seq, and HumanMethylationEPIC BeadChip for detection of the 5mC sites in cancer and normal samples | [Sym 01] 1. Structural and functional organization of genomes | DNA methylation, epigenetics,DNA modification, nanopore sequencing, DNA methylation detection, enzymatic methyl-sequencing |
| Semenova E., Fisunov G. | Prediction of promoter activity regions in Mycoplasmoides gallisepticum using machine learning and agent-based modeling | [Sym 01] 2. Regulatory genomics | minimal cell; machine learning; prediction of bacterial promoter activity; mycoplasmas; agent-based modeling (ABM) |
| Podkolodnaya O, Chadaeva I, Podkolodnyy N, Rasskazov D, Tverdokhleb N, Bogomolov A, Kondratyuk E, Oshchepkov D, Ponomarenko M | MiceDEGdb: a knowledge base on differentially expressed mouse genes as a model object in biomedical research | [Sym 01] 2. Regulatory genomics | knowledge base, differentially expressed gene, mouse, model object, biomedical research |
| Kudasheva E.R., Shmarin V.V., Guvatova Z.G. | Transcriptomic alterations induced by perlatolic acid are accompanied by modulation of SASP genes in human fibroblasts | [Sym 01] 4. Genome-wide transcriptomics (differential gene expression) | perlatolic acid, aging, RNA-seq, SASP, normal fibroblasts. |
| Chistyakov A., Korchagin V., Arakelyan M., Chrustaleva A., Martyrosyan I., Ryskov A. | Characterization of the gene expression profile in brain and ovarian tissues of parthenogenetic lizards of the genus Darevskia and their parental species | [Sym 01] 4. Genome-wide transcriptomics (differential gene expression) | Darevskia lizards; parthenogenesis; transcriptome; differential expression |
| Bezuglov V., Akhtyamov P., Favorov A., Kasianov, A., Stupnikov A. | Exploring efficiency of bulk RNA-sequencing differential expression signatures | [Sym 01] 4. Genome-wide transcriptomics (differential gene expression) | differential expression analysis; DE signatures; RNA-sequencing; Hobotnica score; |
| Grushina V., Pintus S. | Impact of Cold Stress on Immune Response in Chickens: Analysis of Transcriptomic Changes and Regulatory Enhancers | [Sym 01] 4. Genome-wide transcriptomics (differential gene expression) | cold stress, Gallus gallus, inflammatory response, RNA-seq, enhancers |
| Rasskazov D., Deryuzhenko M., Zolotareva K., Tverdokhleb N., Makovka Yu., Suslov V., Podkolodnyy N., Bogomolov A., Podkolodnaya O., Kondratyuk E., Chadaeva I., Fedoseeva L., Seryapina A., Oshchepkov D., Markel A., Redina O., Gruntenko N.1, Kolchanov N., Ponomarenko M. | FlyDEGdb: a knowledge base of differentially expressed genes in Drosophila melanogaster as a model animal for biomedicine | [Sym 01] 4. Genome-wide transcriptomics (differential gene expression) | human, disease, biomedicine, model animal, fruit fly Drosophila melanogaster, differentially expressed genes (DEGs), RNA-Seq, qPCR, microarray; knowledge base |
| Deryuzhenko M., Zolotareva K., Rasskazov D., Podkolodnyy N., Tverdokhleb N., Sharypova E., Ponomarenko P., Chadaeva I., Bogomolov A., Kondratyuk E., Savinkova L., Podkolodnaya O., Gruntenko N., Kolchanov N., Ponomarenko M. | FlySNP_TATAdb: a knowledge base of SNP markers of Drosophila melanogaster gene promoters as a model animal for biomedicine that alter the affinity of TATA-binding protein (TBP) to these promoters and the expression of these genes | [Sym 01] 4. Genome-wide transcriptomics (differential gene expression) | Drosophila melanogaster, TATA-binding protein, TATA box, regulatory polymorphism, gene expression, estimates in silico; genome-wide analysis; verification ex vivo |
| Kulagin K.A., Bogdanova A.S., Gladys N.S., Kazakova E.M. | Proteome-Level Mechanisms of the Intracellular Response to Oxidative Stress in Candida glabrata with Deletion of the RPN4 Transcription Factor | [Sym 01] 4. Genome-wide transcriptomics (differential gene expression) | Candida glabrata; RPN4; oxidative stress; proteomics; proteasome; 4-NQO |
| Chadaeva I., Vishnevsky O., Kuzminykh K., Yatsyk I., Kondratyuk E. | Transcription Factors within the Human RAAS Associative Gene Network | [Sym 02] 1. Reconstruction, computational analysis and modeling of gene networks and metabolic pathways | Renin-angiotensin-aldosterone system, RAAS, Associative gene network, Computer program ANDSystem, Functional annotation, Gene Ontology, GO, Regulation of gene expression, Transcription factor |
| Oleg D. Fateev, Vasily E. Akimov, Olga V. Glushkova, Aleksandr V. Bolbat, Azat V. Abdullatypov, Olga A. Antonova, Vladimir V. Shiryagin, Nikolai A. Bugaev-Makarovsky, Vladimir S. Yudin, Anton A. Keskinov, Sergei M. Yudin, Dmitriy V. Svetlichny, and Veronika I. Skvortsova | Single-Cell RNA-Seq Profiling of Transposable Element Expression in Human Peripheral Blood Cells During Viral Infections | [Sym 02] 1. Reconstruction, computational analysis and modeling of gene networks and metabolic pathways | transposable elements; mobile genetic elements; LINE; SINE; SVA; viral infections; PBMC; scRNA-seq; COVID-19; HIV; influenza A |
| I. Chadaeva, V. Suslov, K. Kuzminykh, R. Ivanov, E. Kondratyuk, M. Ponomarenko | Phylogenetic characteristics of the gene network associated with the renin-angiotensin-aldosterone system | [Sym 02] 1. Reconstruction, computational analysis and modeling of gene networks and metabolic pathways | renin-angiotensin-aldosterone system (RAAS); evolutionary genetics; bioinformatics; phylostratigraphic analysis; endothelin; phospholipase; natural selection; neutral drift; index of evolutionary age of a gene; divergence index |
| I. Chadaeva, K. Kuzminykh, N. Levanova, P. Ponomarenko, P. Demenkov, E. Kondratyuk, V. Suslov, M. Ponomarenko | Reconstruction of the associative gene network of the renin-angiotensin-aldosterone system under pharmacological correction of its dysfunction | [Sym 02] 1. Reconstruction, computational analysis and modeling of gene networks and metabolic pathways | renin-angiotensin-aldosterone system (RAAS); human; SNP marker; therapeutic target; associative gene network; ANDSystem web service; protein-protein interactions; protein-drug interactions |
| Ilyina M., Borisevich S., Khamitov E., Shcherbakov D., Arkhipov S. | Conformational dynamics and species specificity of chymosin interaction with κ casein in cow and dolphin: a comparative analysis by molecular docking and molecular dynamics simulations | [Sym 03] 1. Structural biology of proteins, nucleic acids and membranes | molecular dynamics; molecular docking; chymosin; κ-casein |
| Elena T. Aliper, Roman G. Efremov | SARS-CoV-2 spike protein’s HR2 domain: the molecular determinant for membrane activity and possible role during membrane fusion | [Sym 03] 1. Structural biology of proteins, nucleic acids and membranes | molecular hydrophobicity potential; molecular dynamics simulation; Monte Carlo conformational search; viral fusion proteins; membrane-active peptides; heptad repeat domains |
| Vlasenkova R.A., Bogdanov M.V., Kiyamova R.G., Akberova N.I. | Integrative structural and topological analysis of the NaPi2b transporter in the tumor microenvironment: discrepancy in sensitivity between traditional Molecular Dynamics metrics and Network Centrality Analysis | [Sym 03] 1. Structural biology of proteins, nucleic acids and membranes | NaPi2b; molecular dynamics; ovarian cancer |
| Paston S.V., Kotb O.M., Murzakova I.F., Ivanova D.N. | Study of damage in the DNA structure under the influence of ionizing radiation of various natures | [Sym 03] 1. Structural biology of proteins, nucleic acids and membranes | hERG; peptide modulators; molecular modelling; COPII; |
| Krylova T.V., Kshondzer T.A., Nikitina T.V., Sotnichenko E.D., Karpova L.A., Anashkina A.A. | Development of Inhibitors for the LpxC Protein E. coli | [Sym 3] 2. Pharmacology, cheminformatics and chemical biology | antibiotic resistance; LpxC; E. coli; lipid A; inhibitors; virtual screening |
| Malyugin E., Afonnikov D. | OrthoML2GO: a hybrid approach for protein function annotation based on homology, orthogroups and machine learning | [Sym 04] Big biological data analysis, ontologies and artificial intelligence | protein function prediction; gene ontology; homology; orthogroup; machine learning; gradient boosting |
| Bezuglov V., Rudnev S., Ashapkin V., Shtratnikova V., Sergeyev O. | Somatotype AI prediction models based on bioimpedance data in the prospective male cohort of the Russian Children's Study | [Sym 04] Big biological data analysis, ontologies and artificial intelligence | Russian Children's Study; machine learning; somatotype; bioimpedance; anthropometry |
| Sufyanova Z.R., Ekomasova N.V., Dzhaubermezov M.A., Akhmetshin A.A., Gabidullina L.R., Khidiyatova I.M., D.S. Prokofyeva, Karunas A.S., Chekanov N.N., E.K. Khusnutdinova | Immunogenetic features of adaptation of the Turkic peoples of the Volga-Ural region: analysis of the genes of the HLA complex | [Sym 05] Medical, population, and evolutionary genomics/genetics of humans | HLA gene complex; Bashkirs; Tatars; iSAFE; evolution |
| Marusin A.V., Swarovskaja M.G., Kornetov A.N., Bocharova A.V., Stepanov V.A. | Association analysis of the rs6119285 polymorphic variant in the DNMT3B gene with schizophrenia in the Siberian population of Russians | [Sym 5] Population, evolutionary and medical human genomics/genetics | genetic polymorphism, susceptibility, schizophrenia, DNA methylation |
| Koreneenkov A., Vyazemskaya E., Medvedeva A. | Clinical Re-analysis of Whole Exomes Outside Specialized Genetic Laboratories: Isolated Software Solutions for Clinical, Educational, and Research Applications | [Sym 5] Population, evolutionary and medical human genomics/genetics | bioinformatics; containerization; whole exome; clinical interpretation; medical education |
| Kozitskaya Irina, Zhdanova Oksana | Assessment of phytoplankton productivity in Peter the Great Bay based on satellite data | [Sym 6] Fundamental questions in evolutionary systems biology: from genes and gene networks to populations and ecosystems | mathematical model, chlorophyll, phytoplankton, diffusion. |
| Medvedeva S., Cherepanova O., Sattarov D., Teptina A. | New data on ploidy and variability of the ITS 1-2 region of Betula tianschanica Rupr. | [Sym 6] Fundamental questions in evolutionary systems biology: from genes and gene networks to populations and ecosystems | flow cytometry, DNA content, Tianshan birch, genetic polymorphism, nuclear rDNA |
| Turnaev I.I., Ivanov R.A., Lashin S.A., Afonnikov D.A. | Evolutionary characteristics of the gene network of the cell cycle | [Sym 6] Fundamental questions in evolutionary systems biology: from genes and gene networks to populations and ecosystems | gene network; cell cycle; genes age index; gene divergence index |
| Kaznina N., Repkina N., Titov A. | Transcriptional activity of transport protein genes in Brassicajuncea leaves under increasing zinc content in the environment | [Sym 7] Plant genomics, genetics and systems biology | BjYSL5, BjNRAMP3, Sarepta mustard, zinc excess, number of gene transcripts |
| Napalkova V.V., Filippov E.G. | ITS-RIBOTYPING AS A TOOL FOR PHYLOGENETIC ANALYSIS AND CERTIFICATION OF PAEONIA L. SPECIES IN THE COLLECTION OF THE BOTANICAL GARDEN OF THE URAL BRANCH OF RAS | [Sym 7] Plant genomics, genetics and systems biology | Paeonia; ITS sequencing; phylogenetic analysis; genetic diversity |
| Khavpacheva D.Kh., Shchennikova A.V., Kochieva E.Z. | The adaptive response of maize plants to cold stress is associated with differential expression of carotenoid and ABA synthesis genes | [Sym 07] Plant genomics, genetics and systems biology | Zea mays; cold stress; transcriptome; carotenoid biosynthesis genes |
| Filyushin M., Shchennikova A., Kochieva E. | Anthocyanin biosynthesis in garlic (Allium sativum L.) organs: comparative expression analysis data | [Sym 07] Plant genomics, genetics and systems biology | garlic; anthocyanin biosynthesis; anthocyanin coloration; flavonoid pathway |
| Chikina E., Tsybko A., Voronina T., Starinnov Z., Melnikova V., Sabirov M., Bimpisidis Z., Nesmelov A., Kaminskaya Y., Gainullina A., Shagimardanova E., Naumenko V., Gusev O., and Romanov R. | Molecular mechanisms of impaired emotional learning in an idiopathic model of autism | [Sym 08] 1. Genomics, genetics, and systems biology of laboratory animals and genetic models of human diseases | autism spectrum disorder; amygdala; fear conditioning; BTBR; single-cell sequencing |
| Motsar E., Sheveleva A., Sharko F., Chirkov S. | Virome analysis of symptomatic phlox plants (Phlox paniculata) revealed three new viruses of this crop | [Sym 09] 1. Microbial communities of natural and anthropogenic habitats, biocollections, creation of producer strains | ornamentals; phlox; nepovirus; ilarvirus; satellite RNA; virome; high-throughput sequencing |
| Selezneva Al.D.*, Selezneva An.D., Burdennyy A.M., Loginov V.I., Braga E.A. | Bioinformatic construction of lncRNA–microRNA–mRNA axes involved in ferroptosis regulation in lung adenocarcinoma | [Sym 10] 1. Molecular medicine: gene expression and human diseases | lncRNA, microRNA, mRNA, lung adenocarcinoma, ferroptosis, competing endogenous RNA |
| Selezneva An.D., Selezneva Al.D., Loginov V.I., Burdennyy A.M., Braga E.A. | Construction of a ceRNA network potentially involved in the regulation of DNA methylation and demethylation processes in clear cell renal cell carcinoma using bioinformatics tools | [Sym 10] 1. Molecular medicine: gene expression and human diseases | clear cell renal cell carcinoma; competing endogenous RNAs; long non-coding RNAs; microRNAs; mRNAs; bioinformatics analysis |
| Utkina O.V., Burdennyy A.M., Loginov V.I., Pronina I.V. | Competing Endogenous RNAs as Markers for the Detection of High-Grade Serous Ovarian Cancer | [Sym 10] 1. Molecular medicine: gene expression and human diseases | ovarian serous carcinoma, long non-coding RNA, oncomarkers |
| Tychinin D.I., Kobyzeva P.A., Vladimirov I.S., Mukhin V.E., Svetlichny D.V. | Transcriptome of T-Regulatory Cells in T1D: The Role of BACH2 in Maintaining Immune Tolerance | [Sym 10] 1. Molecular medicine: gene expression and human diseases | Type 1 diabetes (T1D), peripheral blood mononuclear cells (PBMC), T-regulatory cells (Tregs), gene networks, BACH2 |
| Rippinen D., Solovieva A. | Fibroblast-like synoviocytes as a basis for an in vitro model for primary screening of targeted therapy in rheumatoid arthritis | [Sym 10] 1. Molecular medicine: gene expression and human diseases | rheumatoid arthritis; fibroblast-like synoviocytes; in vitro model |
| Dyagileva A., Rybalkina O., Chernyaev I., Kisakov D., Kisakova L., Sharabin S., Krasnikova S. | Study of the effect of erythropoietin-encoding mRNA on the development of anemia induced by cytostatic therapy | [Sym 10] 1. Molecular medicine: gene expression and human diseases | mRNA technology; erythropoietin; anemia; chemotherapy |
| Dotsenko P., Zolotareva K., Podkolodnyy N., Ivanov R., Makarova A.-L.,Chadaeva I., Bogomolov A., Demenkov P., Ivanisenko V., Oshchepkov D., Ponomarenko M. | Identification of potential single nucleotide polymorphism (SNP) markers of significant changes in the affinity of TATA-binding protein to promoters of human genes associated with primary open-angle glaucoma (POAG) | [Sym 10] 1. Molecular medicine: gene expression and human diseases | human; primary open-angle glaucoma (POAG); gene; promoter; TATA-binding protein (TBP);TATA box; single nucleotide polymorphism (SNP); SNP marker; gene expression change;phylostratigraphic age; in silico test |
| Dolgalev E., Lykov A. | The effect of the cyanobacteria Leptolyngbya cf. ectocarpi on the severity of inflammatory bowel disease in mice | [Sym 10] 2. Molecular pathology, diagnostics, and therapy | cyanobacteria, sodium dextran sulfate, inflammatory bowel disease, blood biochemistry, cytokines |
| Lykov A., Uvarov I., Dolgalev E. | Impact of the marine cyanobacteria Leptolyngbya cf. ectocarpi on somatic cell function in mice suffering from inflammatory bowel disease and toxic hepatitis | [Sym 10] 2. Molecular pathology, diagnostics, and therapy | cyanobacteria, somatic cells, oxidase, apoptosis, cytokines |
| Uvarov I.P., Lykov A.P. | Anti-inflammatory, antioxidant, and hepatoprotective effects of cyanobacteria Leptolyngbya cf. ectocarpi in mice with toxic hepatitis | [Sym 10] 2. Molecular pathology, diagnostics, and therapy | cyanobacteria, toxic hepatitis, blood biochemistry profile, cytokines |
| Kazakov O., Kabakov A., Poveshchenko A., Cherkas V., Bodrova N., Sultanova L. | The influence of photodynamic therapy and a combination of photodynamic therapy and surgical treatment of breast cancer on the relationship between pro-oncogenic and antioncogenic microRNAs in the thymus with thymus structure | [Sym 10] 2. Molecular pathology, diagnostics, and therapy | thymus gland; breast cancer; therapeutic measures; surgical treatment |
| Kabakov A., Kazakov O., Poveshchenko A., Cherkas V., Kononchuk V., Kalinina T., Bodrova N., Sultanova L. | Quantity of pro-oncogenic miRNAs and tumor-suppressive miRNAs in lymph in experimental breast cancer | [Sym 10] 2. Molecular pathology, diagnostics, and therapy | breast cancer, lymph, chemotherapy |
| Bodrova N., Kabakov A., Poveschenko A., Kazakov O.1, Cherkas V. | Changes Ki-67 after chemotherapy for experimental breast cancer | [Sym 10] 2. Molecular pathology, diagnostics, and therapy | Ki-67, breast cancer, rats, chemotherapy. |
| Voropaeva E., Kuznetsova I., Orlov P., Minnikh S., Nesterets A., Maximov V., Pospelova T. | Concentration and safety of freely circulating DNA in acute myeloid leukemia | [Sym 10] 2. Molecular pathology, diagnostics, and therapy | circulating cell-free DNA; acute myeloid leukemias; minimal residual disease; integrity index |
| Volodina O.V., Smirnikhina S.A. | Evaluation of Genome Editing Outcomes: From CRISPResso2 Automation to Statistical Correction of Background Variants | [Sym 10] 2. Molecular pathology, diagnostics, and therapy | gene editing, CRISPResso2, deep targeted sequencing |
| Poveshchenko A., Cherkas V., Kabakov A., Kazakov O., Shipova A., Kondratyuk E., Bodrova N., Vasiliev G. | Composition of the intestinal microbiota of female Wistar rats with experimental breast cancer and different therapeutic methods | [Sym 10] 2. Molecular pathology, diagnostics, and therapy | breast cancer (BC), intestinal microbiota, induction |
| Bondarenko N., Baidina V., Surovtseva M., Kim I., Ostapets S., Naumov A., Baigonakova G., Marchenko E., Poveshchenko O. | Functional state of mesenchymal stem cells from Bichat fat pad on nitinol mesh implants | [Sym 10] 2. Molecular pathology, diagnostics, and therapy | mesh implant, mesenchymal stem cells, Biсhat fat pads, viability |
| Epimakhova Е., Vetlugina T., ,Prokopieva V., Kisel N., Bokhan N. | Levels of lipopolysaccharide (LPS), lipopolysaccharide-binding protein (LBP) and high-mobility group B1 protein (HMGB1) in the blood serum of patients with alcohol dependence at different stages of the disease. | [Sym 10] 2. Molecular pathology, diagnostics, and therapy | lipopolysaccharide; lipopolysaccharide-binding protein; protein HMGB1, alcohol dependence |
| Ovchinnikov V.S., Rachkovskaya L.N., Shvetsova A.M., Korolev M.A., Letyagin A.Yu. | Manganese-modified sorbent: in vitro study of its effect on blood leukocytes | [Sym 10] 2. Molecular pathology, diagnostics, and therapy | sorbent; manganese; leukocytes; hemosorption |
| Obanina N., Bgatova N. | Chloroquine Modulates AQP4 Expression and Glymphatic Function in Melanoma B16 | [Sym 10] 3. Interstitial space and extravascular drainage/transport pathways | AQP4; Melanoma B16; Glymphatic System; Chloroquine |
| Petoukhov Sergey Valentinovich | Algebraic grammar of bioinformatics and the evolutionary paradigm of algebraic-operator Darwinism | [Sym 11] Cognitive science, neurogenetics, neuroinformatics, and systems computational biology | algebraic bioinformatics, alphabets, inheritance, algorithms, matrices |
| Kladova O., Bakman A., Tyugashev T., Kuznetsova A. | Study of the enzymatic properties of natural polymorphic variants of human alkyladenine DNA glycosylase AAG | [Sym 12] 1. Processes of maintaining genome stability and reproduction of genetic information | DNA repair; Alkyladenine DNA Glycosylase; AAG, single nucleotide polymorphism; enzymatic activity, SNP. |
| Avdonina S.А., Surovtseva M.A., Poveshchenko О.V. | The effect of conditioned media from MSCs obtained from bone marrow, limbus, and Bichat fat pads on the proliferative and migratory activity of induced and mature corneal myofibroblasts | [Sym 12] 2. Apoptosis and other fundamental cellular processes regulating cell fate | myofibroblasts; conditioned medium; proliferative activity; migratory activity; MSC |
| Kozeneva V., Chekashov I., Rozhkova I., Chulkova S., Brusentsev E., Rakhmanova T., Solovyeva S., Amstislavsky S. | Effects of Assisted Reproductive Technologies on Postnatal Ontogenesis in 5xFAD Mice, a Model of Alzheimer’s Disease | [Sym 13] 4. Heterogeneity of the aging process and age-related diseases | Alzheimer’s disease; transgenic model; embryo transfer, in vitro embryo culture, long-term effects |
