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  1. 2025

  2. Metabolomic and gene networks approaches reveal the role of mitochondrial membrane proteins in response of human melanoma cells to THz radiation

    Butikova, E. A., Basov, N. V., Rogachev, A. D., Gaisler, E. V., Ivanisenko, V. A., Demenkov, P. S., Makarova, A. L. A., Ivanisenko, T. V., Razumov, I. A., Kolomeyets, D. A., Cheresiz, S. V., Solovieva, O. I., Larionov, K. P., Sotnikova, Y. S., Patrushev, Y. V., Kolchanov, N. A., Pokrovsky, A. G., Vinokurov, N. A., Kanygin, V. V., Popik, V. M., & 1 othersShevchenko, O. A., Mar 2025, In: Biochimica et Biophysica Acta - Molecular and Cell Biology of Lipids. 1870, 2, 159595.

    Research output: Contribution to journal › Article › peer-review

  3. Plant Detection in RGB Images from Unmanned Aerial Vehicles Using Segmentation by Deep Learning and an Impact of Model Accuracy on Downstream Analysis

    Kozhekin, M. V., Genaev, M. A., Komyshev, E. G., Zavyalov, Z. A. & Afonnikov, D. A., 20 Jan 2025, In: Journal of Imaging. 11, 1, 28.

    Research output: Contribution to journal › Article › peer-review

  4. The Role of Long Noncoding RNAs in Plants

    Pronozin, A. Y. & Afonnikov, D. A., 20 Jan 2025, In: Russian Journal of Genetics. 61, 1, p. 1-18 18 p.

    Research output: Contribution to journal › Article › peer-review

  5. Asymmetry of Motif Conservation Within Their Homotypic Pairs Distinguishes DNA-Binding Domains of Target Transcription Factors in ChIP-Seq Data

    Levitsky, V. G., Raditsa, V. V., Tsukanov, A. V., Mukhin, A. M., Zhimulev, I. F. & Merkulova, T. I., 4 Jan 2025, In: International Journal of Molecular Sciences. 26, 1, 386.

    Research output: Contribution to journal › Article › peer-review

  6. Pharmacological targeting of caspase-8/c-FLIPL heterodimer enhances complex II assembly and elimination of pancreatic cancer cells

    König, C., Ivanisenko, N. V., Ivanisenko, V. A., Kulms, D. & Lavrik, I. N., 3 Jan 2025, In: Communications Biology. 8, 1, 4.

    Research output: Contribution to journal › Article › peer-review

  7. The Effect of Codon Reassignment on the Properties and Structure of the Mitochondrial Proteins of the Baikal Amphipods

    Yudinceva, A. V., Romanova, E. V., Sherbakov, D. Y. & Bukin, Y. S., 2025, In: Mathematical Biology and Bioinformatics. 20, 1, p. 54-70 17 p.

    Research output: Contribution to journal › Article › peer-review

  8. 2024

  9. A software module to assess the metabolic potential of mutant strains of the bacterium Corynebacterium glutamicum

    Kazantsev, F. V., Trofimova, M. F., Khlebodarova, T. M., Matushkin, Y. G. & Lashin, S. A., Dec 2024, In: Vavilovskii Zhurnal Genetiki i Selektsii. 28, 8, p. 897-903 7 p.

    Research output: Contribution to journal › Article › peer-review

  10. Candidate SNP markers of changes in the expression levels of the human SCN9A gene as a hub gene for pain generation, perception, response and anesthesia

    Dotsenko, P. A., Zolotareva, K. A., Ivanov, R. A., Chadaeva, I. V., Podkolodnyy, N. L., Ivanisenko, V. A., Demenkov, P. S., Lashin, S. A. & Ponomarenko, M. P., Dec 2024, In: Vavilovskii Zhurnal Genetiki i Selektsii. 28, 8, p. 808-821 14 p.

    Research output: Contribution to journal › Article › peer-review

  11. Candidate SNP Markers Significantly Altering the Affinity of the TATA-Binding Protein for the Promoters of Human Genes Associated with Primary Open-Angle Glaucoma

    Zolotareva, K., Dotsenko, P. A., Podkolodnyy, N., Ivanov, R., Makarova, A. L., Chadaeva, I., Bogomolov, A., Demenkov, P. S., Ivanisenko, V., Oshchepkov, D. & Ponomarenko, M., Dec 2024, In: International Journal of Molecular Sciences. 25, 23, 12802.

    Research output: Contribution to journal › Article › peer-review

  12. Computer analysis shows differences between mitochondrial miRNAs and other miRNAs

    Vorozheykin, P. S. & Titov, I. I., Dec 2024, In: Вавиловский журнал генетики и селекции. 28, 8, p. 834-842 9 p.

    Research output: Contribution to journal › Article › peer-review

  13. MetArea: a software package for analysis of the mutually exclusive occurrence in pairs of motifs of transcription factor binding sites based on ChIP-seq data

    Levitsky, V. G., Tsukanov, A. V. & Merkulova, T. I., Dec 2024, In: Vavilovskii Zhurnal Genetiki i Selektsii. 28, 8, p. 822-833 12 p.

    Research output: Contribution to journal › Article › peer-review

  14. Nearly complete genome sequences of the first two identified Colorado potato beetle viruses

    Antonets, M., Bodnev, S., Rotskaya, U., Kosman, E., Tregubchak, T., Bauer, T., Azaev, M., Kryukov, V. & Antonets, D., Dec 2024, In: Scientific Reports. 14, 1, 9 p., 352.

    Research output: Contribution to journal › Article › peer-review

  15. Reconstruction and computational analysis of the microRNA regulation gene network in wheat drought response mechanisms

    Kleshchev, M. A., Maltseva, A. V., Antropova, E. A., Demenkov, P. S., Ivanisenko, T. V., Orlov, Y. L., Chao, H., Chen, M., Kolchanov, N. A. & Ivanisenko, V. A., Dec 2024, In: Vavilovskii Zhurnal Genetiki i Selektsii. 28, 8, p. 904-917 14 p.

    Research output: Contribution to journal › Article › peer-review

  16. Root cap border cells as regulators of rhizosphere microbiota

    Omelyanchuk, N. A., Cherenko, V. A. & Zemlyanskaya, E. V., Dec 2024, In: Vavilovskii Zhurnal Genetiki i Selektsii. 28, 8, p. 918-926 9 p.

    Research output: Contribution to journal › Article › peer-review

  17. Search for and functional annotation of multi-domain PLA2 family proteins in flatworms

    Bocharnikova, M. E., Turnaev, I. I. & Afonnikov, D. A., Dec 2024, In: Вавиловский журнал генетики и селекции. 28, 8, p. 854-863 10 p.

    Research output: Contribution to journal › Article › peer-review

  18. Программа для проведения филостратиграфического анализа генных сетей Homo sapiens, полученных с помощью ANDSystem (ЭНДФилострат) / A program for conducting phylostratigraphic analysis of Homo sapiens gene networks obtained using ANDSystem (ANDPhylostrat)

    Яцык, И. В., Иванисенко, Т. В., Деменков, П. С. & Иванисенко, В. А., 27 Nov 2024, Patent No. 2024688299, 24 Oct 2024, Priority date 24 Oct 2024, Priority No. 2024685094

    Research output: Patent › Software registration

  19. Targeting type I DED interactions at the DED filament serves as a sensitive switch for cell fate decisions

    König, C., Ivanisenko, N. V., Hillert-Richter, L. K., Namjoshi, D., Natu, K., Espe, J., Reinhold, D., Kolchanov, N. A., Ivanisenko, V. A., Kähne, T., Bose, K. & Lavrik, I. N., 21 Nov 2024, In: Cell Chemical Biology. 31, 11, p. 1969-1985.e6 24 p.

    Research output: Contribution to journal › Article › peer-review

  20. Design of Ctenophore Ca2+-Regulated Photoprotein Berovin Capable of Being Converted into Active Protein Under Physiological Conditions: Computational and Experimental Approaches

    Burakova, L. P., Ivanisenko, N. V., Rukosueva, N. V., Ivanisenko, V. A. & Vysotski, E. S., 19 Nov 2024, In: Life. 14, 11, 1508.

    Research output: Contribution to journal › Article › peer-review

  21. Cytokinins regulate spatially specific ethylene production to control root growth in Arabidopsis

    Yamoune, A., Zdarska, M., Depaepe, T., Rudolfova, A., Skalak, J., Berendzen, K. W., Mira-Rodado, V., Fitz, M., Pekarova, B., Nicolas Mala, K. L., Tarr, P., Spackova, E., Tomovicova, L., Parizkova, B., Franczyk, A., Kovacova, I., Dolgikh, V., Zemlyanskaya, E., Pernisova, M., Novak, O., & 4 othersMeyerowitz, E., Harter, K., Van Der Straeten, D. & Hejatko, J., 11 Nov 2024, In: Plant Communications. 5, 11, 17 p., 101013.

    Research output: Contribution to journal › Article › peer-review

  22. An Accurate and Efficient Approach to Knowledge Extraction from Scientific Publications Using Structured Ontology Models, Graph Neural Networks, and Large Language Models

    Ivanisenko, T. V., Demenkov, P. S. & Ivanisenko, V. A., 3 Nov 2024, In: International Journal of Molecular Sciences. 25, 21, 11811.

    Research output: Contribution to journal › Article › peer-review

  23. Image-Based Quantitative Analysis of Epidermal Morphology in Wild Potato Leaves

    Zubairova, U. S., Fomin, I. N., Koloshina, K. A., Barchuk, A. I., Erst, T. V., Chalaya, N. A., Gerasimova, S. V. & Doroshkov, A. V., 1 Nov 2024, In: Plants. 13, 21, 14 p., 3084.

    Research output: Contribution to journal › Article › peer-review

  24. AI-Assisted Identification of Primary and Secondary Metabolomic Markers for Postoperative Delirium

    Ivanisenko, V. A., Rogachev, A. D., Makarova, A-L. A., Basov, N. V., Gaisler, E. V., Kuzmicheva, I. N., Demenkov, P. S., Venzel, A. S., Ivanisenko, T. V., Antropova, E. A., Kolchanov, N. A., Plesko, V. V., Moroz, G. B., Lomivorotov, V. V. & Pokrovsky, A. G., Nov 2024, In: International Journal of Molecular Sciences. 25, 21, 11847.

    Research output: Contribution to journal › Article › peer-review

  25. Primary multistep phosphorelay activation comprises both cytokinin and abiotic stress responses: insights from comparative analysis of Brassica type-A response regulators

    Nicolas Mala, K. L., Skalak, J., Zemlyanskaya, E., Dolgikh, V., Jedlickova, V., Robert, H. S., Havlickova, L., Panzarova, K., Trtilek, M., Bancroft, I. & Hejatko, J., 1 Oct 2024, In: Journal of Experimental Botany. 75, 20, p. 6346-6368 23 p.

    Research output: Contribution to journal › Article › peer-review

  26. Catching the Big Fish in Big Data: A Meta-Analysis of Zebrafish Kidney scRNA-Seq Datasets Highlights Conserved Molecular Profiles of Macrophages and Neutrophils in Vertebrates

    Bobrovskikh, A. V., Zubairova, U. S., Naumenko, L. G. & Doroshkov, A. V., Oct 2024, In: Biology. 13, 10, 773.

    Research output: Contribution to journal › Article › peer-review

  27. Evaluation of the Spike Diversity of Seven Hexaploid Wheat Species and an Artificial Amphidiploid Using a Quadrangle Model Obtained from 2D Images

    Komyshev, E. G., Genaev, M. A., Kruchinina, Y. V., Koval, V. S., Goncharov, N. P. & Afonnikov, D. A., Oct 2024, In: Plants. 13, 19, 2736.

    Research output: Contribution to journal › Article › peer-review

  28. Genomic background sequences systematically outperform synthetic ones in de novo motif discovery for ChIP-seq data

    Raditsa, V. V., Tsukanov, A. V., Bogomolov, A. G. & Levitsky, V. G., 1 Sept 2024, In: NAR Genomics and Bioinformatics. 6, 3, 15 p., qae090.

    Research output: Contribution to journal › Article › peer-review

  29. SmartCrop cognitive platform: modules for automatic knowledge extraction from scientific publications, patents and factual databases for reconstruction and analysis of gene networks of stress response in rice and wheat

    Иванисенко, В. А., Деменков, П. С., Иванисенко, Т. В., Антропова, Е. А., Волянская, А. Р., Зубаирова, У. С., Макарова, А-Л. А., Орлов, Ю. Л. & Chen, M., Aug 2024, Bioinformatics of Genome Regulation and Structure Systems Biology (BGRS/SB-2024): The 14th International Multiconference (05-10 August 2024, Novosibirsk, Russia). Новосибирск: Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, p. 2188-2190 3 p.

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › Research › peer-review

  30. Assembly and Genome Annotation of Different Strains of Apple Fruit Moth Virus (Cydia pomonella granulovirus)

    Лахова, Т. Н., Цыгичко, А., Клименко, А. И., Исмаилов, В., Васильев, Г., Асатурова, А. & Лашин, С. А., Jul 2024, In: International Journal of Molecular Sciences. 25, 13, 7146.

    Research output: Contribution to journal › Article › peer-review

  31. Computational Reconstruction of the Transcription Factor Regulatory Network Induced by Auxin in Arabidopsis thaliana L.

    Omelyanchuk, N. A., Lavrekha, V. V., Bogomolov, A. G., Dolgikh, V. A., Sidorenko, A. D. & Zemlyanskaya, E. V., Jul 2024, In: Plants. 13, 14, 1905.

    Research output: Contribution to journal › Article › peer-review

  32. Конвейер обработки гиперспектральных изображений на примере исследования зерен ячменя, содержащих меланин

    Busov, I. D., Genaev, M. A., Komyshev, E. G., Koval, V. S., Zykova, T. E., Glagoleva, A. Y. & Afonnikov, D. A., Jul 2024, In: Vavilovskii Zhurnal Genetiki i Selektsii. 28, 4, p. 443-455 13 p., 9.

    Research output: Contribution to journal › Article › peer-review

  33. A bird's-eye overview of molecular mechanisms regulating feed intake in chickens—with mammalian comparisons

    Volyanskaya, A. R., Akberdin, I. R., Kulyashov, M. A., Yevshin, I. S., Romanov, M. N., Shagimardanova, E. I., Gusev, O. A. & Kolpakov, F. A., Jun 2024, In: Animal Nutrition. 17, p. 61-74 14 p.

    Research output: Contribution to journal › Review article › peer-review

  34. Enrichment of Grain Anthocyanin Content through Marker-Assisted Breeding for Ant1, Ant2 or HvMyc2 Genes in Barley (Hordeum vulgare L.)

    Kukoeva, T. V., Molobekova, C. A., Totsky, I. V., Vasiliev, G. V., Pronozin, A. Y., Afonnikov, D. A., Khlestkina, E. K. & Shoeva, O. Y., Jun 2024, In: Agronomy. 14, 6, 1231.

    Research output: Contribution to journal › Article › peer-review

  35. Lake Baikal amphipods and their genomes, great and small

    Drozdova, P. B., Madyarova, E. V., Gurkov, A. N., Saranchina, A. E., Romanova, E. V., Petunina, J. V., Peretolchina, T. E., Sherbakov, D. Y. & Timofeyev, M. A., Jun 2024, In: Vavilovskii Zhurnal Genetiki i Selektsii. 28, 3, p. 317-325 9 p., 6.

    Research output: Contribution to journal › Article › peer-review

  36. Physiologically based pharmacokinetic model for predicting the biodistribution of albumin nanoparticles after induction and recovery from acute lung injury

    Кутумова, Е. О., Акбердин, И. Р., Egorova, V. S., Kolesova, E. P., Parodi, A., Pokrovsky, V. S., Zamyatnin Jr., A. A. & Колпаков, Ф. А., 30 May 2024, In: Heliyon. 10, 10, 16 p., e30962.

    Research output: Contribution to journal › Article › peer-review

  37. Identification of Novel Loci Precisely Modulating Pre-Harvest Sprouting Resistance and Red Color Components of the Seed Coat in T. aestivum L.

    Afonnikova, S. D., Kiseleva, A. A., Fedyaeva, A. V., Komyshev, E. G., Koval, V. S., Afonnikov, D. A. & Salina, E. A., 9 May 2024, In: Plants. 13, 10, 21 p., 1309.

    Research output: Contribution to journal › Article › peer-review

  38. Biochemical, Genetic, and Grain Digital Evaluation of Soft Winter Wheat Varieties with Different Germination Index

    Fedyaeva, A. V., Afonnikova, S. D., Afonnikov, D. A., Smirnova, O. G., Deeva, V. N., Pryanishnikov, A. I. & Salina, E. A., Apr 2024, In: Russian Journal of Plant Physiology. 71, 2, 10 p., 56.

    Research output: Contribution to journal › Article › peer-review

  39. Genetic Mechanisms Regulating Root Cap Cell Renewal in Arabidopsis thaliana L.

    Cherenko, V. A., Omelyanchuk, N. A. & Zemlyanskaya, E. V., Apr 2024, In: Russian Journal of Plant Physiology. 71, 2, 12 p., 51.

    Research output: Contribution to journal › Article › peer-review

  40. AtSNP_TATAdb: Candidate Molecular Markers of Plant Advantages Related to Single Nucleotide Polymorphisms within Proximal Promoters of Arabidopsis thaliana L.

    Bogomolov, A., Zolotareva, K., Filonov, S., Chadaeva, I., Rasskazov, D., Sharypova, E., Podkolodnyy, N., Ponomarenko, P., Savinkova, L., Tverdokhleb, N., Khandaev, B., Kondratyuk, E., Podkolodnaya, O., Zemlyanskaya, E., Kolchanov, N. A. & Ponomarenko, M., Jan 2024, In: International Journal of Molecular Sciences. 25, 1, 607.

    Research output: Contribution to journal › Article › peer-review

  41. Hormone-regulated expansins: expression, localization, and cell wall biomechanics in Arabidopsis root growth

    Samalova, M., Melnikava, A., Elsayad, K., Peaucelle, A., Gahurova, E., Gumulec, J., Spyroglou, I., Zemlyanskaya, E. V., Ubogoeva, E. V., Balkova, D., Demko, M., Blavet, N., Alexiou, P., Benes, V., Mouille, G. & Hejatko, J., Jan 2024, In: Plant Physiology. 194, 1, p. 209-228 20 p.

    Research output: Contribution to journal › Article › peer-review

  42. Peak Scores Significantly Depend on the Relationships between Contextual Signals in ChIP-Seq Peaks

    Vishnevsky, O. V., Bocharnikov, A. V. & Ignatieva, E. V., Jan 2024, In: International Journal of Molecular Sciences. 25, 2, 1011.

    Research output: Contribution to journal › Article › peer-review

  43. Computational identification of promising genetic markers associated with molecular mechanisms of reduced rice resistance to Rhizoctonia solani under excess nitrogen fertilization using gene network reconstruction and analysis methods

    Antropova, E. A., Volyanskaya, A. R., Adamovskaya, A. V., Demenkov, P. S., Yatsyk, I. V., Ivanisenko, T. V., Orlov, Y. L., Haoyu, C., Chen, M. & Ivanisenko, V. A., 2024, In: Vavilovskii Zhurnal Genetiki i Selektsii. 28, 8, p. 960-973 14 p.

    Research output: Contribution to journal › Article › peer-review

  44. Gene networks and metabolomic screening analysis revealed specific pathways of amino acid and acylcarnitine profile alterations in blood plasma of patients with Parkinson’s disease and vascular parkinsonism

    Makarova, A. A., Melnikova, P. M., Rogachev, A. D., Demenkov, P. S., Ivanisenko, T. V., Predtechenskaya, E. V., Karmanov, S. Y., Koval, V. V., Pokrovsky, A. G., Lavrik, I. N., Kolchanov, N. A. & Ivanisenko, V. A., 2024, In: Вавиловский журнал генетики и селекции. 28, 8, p. 927-939 13 p.

    Research output: Contribution to journal › Article › peer-review

  45. Investigation of metabolic features of glioblastoma tissue and the peritumoral environment using targeted metabolomics screening by LC-MS/MS and gene network analysis

    Basov, N. V., Adamovskaya, A. V., Rogachev, A. D., Gaisler, E. V., Demenkov, P. S., Ivanisenko, T. V., Venzel, A. S., Mishinov, S. V., Stupak, V. V., Cheresiz, S. V., Oleshko, O. S., Butikova, E. A., Osechkova, A. E., Sotnikova, Y. S., Patrushev, Y. V., Pozdnyakov, A. S., Lavrik, I. N., Ivanisenko, V. A. & Pokrovsky, A. G., 2024, In: Вавиловский журнал генетики и селекции. 28, 8, p. 882-896 15 p.

    Research output: Contribution to journal › Article › peer-review

  46. Orthoweb: a software package for evolutionary analysis of gene networks

    Ivanov, R. A., Mukhin, A. M., Kazantsev, F. V., Mustafin, Z. S., Afonnikov, D. A., Matushkin, Y. G. & Lashin, S. A., 2024, In: Вавиловский журнал генетики и селекции. 28, 8, p. 874-881 8 p.

    Research output: Contribution to journal › Article › peer-review

  47. PlantReg: the reconstruction of links between transcription factor regulatory networks and biological processes under their control

    Lavrekha, V. V., Omelyanchuk, N. A., Bogomolov, A. G. & Zemlyanskaya, E. V., 2024, In: Vavilovskii Zhurnal Genetiki i Selektsii. 28, 8, p. 950-959 10 p.

    Research output: Contribution to journal › Article › peer-review

  48. Reconstruction and computer analysis of the structural and functional organization of the gene network regulating cholesterol biosynthesis in humans and the evolutionary characteristics of the genes involved in the network

    Mikhailova, A. D., Lashin, S. A., Ivanisenko, V. A., Demenkov, P. S. & Игнатьева, Е. В., 2024, In: Вавиловский журнал генетики и селекции. 28, 8, p. 864-873 10 p.

    Research output: Contribution to journal › Article › peer-review

  49. Reconstruction of gene regulatory networks from single cell transcriptomic data

    Rybakov, M. A., Omelyanchuk, N. A. & Zemlyanskaya, E. V., 2024, In: Vavilovskii Zhurnal Genetiki i Selektsii. 28, 8, p. 974-981 8 p.

    Research output: Contribution to journal › Article › peer-review

  50. 2023

  51. State-of the-Art Constraint-Based Modeling of Microbial Metabolism: From Basics to Context-Specific Models with a Focus on Methanotrophs

    Куляшов, М. А., Колмыков, С. К., Хлебодарова, Т. М. & Акбердин, И. Р., 14 Dec 2023, In: Microorganisms. 11, 12, 22 p., 2987.

    Research output: Contribution to journal › Review article › peer-review

  52. Fishing Innate Immune System Properties through the Transcriptomic Single-Cell Data of Teleostei

    Bobrovskikh, A. V., Zubairova, U. S. & Doroshkov, A. V., 12 Dec 2023, In: Biology. 12, 12, 1516.

    Research output: Contribution to journal › Review article › peer-review

  53. Программа расшифровки аббревиатур сущностей в рефератах научных публикаций на основе их контекста (ЭНДДекрипт) / Program for decoding entity abbreviations in abstracts of scientific publications based on their context (ANDDecrypt)

    Иванисенко, Т. В., Деменков, П. С. & Иванисенко, В. А., 8 Dec 2023, Роспатент - Федеральная служба по интеллектуальной собственности, Patent No. 2023686851, 16 Nov 2023, Priority date 16 Nov 2023, Priority No. 2023684403

    Research output: Patent › Software registration

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