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  1. 2026

  2. Diversity of lncRNAs in the pan-transcriptome of maize inbred lines

    Pronozin, A. Y., Shmakov, N. A. & Afonnikov, D. A., 3 Jan 2026, In: BMC Genomics. 27, 1, 15 p.

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

  3. AIMarkerFinder: AI-Assisted Marker Discovery Based on an Integrated Approach of Autoencoders and Kolmogorov–Arnold Networks

    Demenkov, P. S., Ivanisenko, T. V. & Ivanisenko, V. A., 2026, In: Informatics. 13, 1, 13 p., 2.

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

  4. 2025

  5. Epigenetic Signatures of Social Defeat Stress Varying Duration

    Bondar, N., Reshetnikov, V., Ritter, P., Ershov, N., Zhukova, N., Kolmykov, S. & Merkulova, T., 19 Dec 2025, In: International Journal of Molecular Sciences. 27, 1, 21 p., 18.

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

  6. Программа для определения взаимного влияния лекарств «Безопасные лекарства»

    Иванисенко, В. А., Иванисенко, Т. В., Яцык, И. В. & Деменков, П. С., 17 Dec 2025, Роспатент - Федеральная служба по интеллектуальной собственности, Patent No. 2025696239, 4 Dec 2025, Priority date 4 Dec 2025, Priority No. 2025695254

    Research output: Patent › Software registration

  7. База данных влияния факторов повышенной утомляемости, характерных для городской среды, на молекулярно-генетические и фенотипические характеристики организма человека

    Иванисенко, В. А., Иванисенко, Т. В., Яцык, И. В. & Деменков, П. С., 19 Nov 2025, Роспатент - Федеральная служба по интеллектуальной собственности, Patent No. 2025625300, 29 Oct 2025, Priority date 29 Oct 2025, Priority No. 2025624676

    Research output: Patent › Database registration

  8. База данных влияния бессонницы, характерной для городской среды, на молекулярно- генетические и фенотипические характеристики организма человека

    Иванисенко, В. А., Иванисенко, Т. В., Яцык, И. В. & Деменков, П. С., 11 Nov 2025, Роспатент - Федеральная служба по интеллектуальной собственности, Patent No. 2025625017, 29 Oct 2025, Priority date 29 Oct 2025, Priority No. 2025624647

    Research output: Patent › Database registration

  9. База данных влияния гипоксии, связанной с условиями жизни в городской среде, на молекулярно-генетические, физиологические и фенотипические характеристики организма человека

    Иванисенко, В. А., Иванисенко, Т. В., Яцык, И. В. & Деменков, П. С., 6 Nov 2025, Роспатент - Федеральная служба по интеллектуальной собственности, Patent No. 2025624919, 29 Oct 2025, Priority date 29 Oct 2025, Priority No. 2025624660

    Research output: Patent › Database registration

  10. Genetic and Pathogenic Overlaps Between Autism Spectrum Disorder and Alzheimer’s Disease: Evolutionary Features and Opportunities for Drug Repurposing

    Trifonova, E. A., Pashchenko, A. A., Ivanov, R. A., Kochetov, A. V. & Lashin, S. A., 16 Oct 2025, In: International Journal of Molecular Sciences. 26, 20, p. 10066

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

  11. Analysis of coat texture characteristics of bread wheat grains obtained from digital images

    Avzalov, D. R., Arif, M. A. R., Komyshev, E. G., Koval, V. S., Börner, A. & Afonnikov, D. A., 30 Sept 2025, In: Frontiers in Plant Science. 16, p. 1659548

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

  12. EBSn, a Robust Synthetic Reporter for Monitoring Ethylene Responses in Plants

    Fernandez‐moreno, J., Fenech, M., Yaschenko, A. E., Zhao, C., Neubauer, M., Davis, H. N., Marchi, A. J., Concannon, R., Keren‐keiserman, A., Reuveni, M., Levitsky, V., Oshchepkov, D., Dolgikh, V., Goldshmidt, A., Ascencio‐ibáñez, J. T., Zemlyanskaya, E., Alonso, J. M. & Stepanova, A. N., 21 Sept 2025, In: Plant Biotechnology Journal.

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

  13. New Sights into Bioinformatics of Gene Regulations and Structure

    Anashkina, A. A., Orlova, N. G., Kolchanov, N. A. & Orlov, Y. L., 4 Jul 2025, In: International Journal of Molecular Sciences. 26, 13

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

  14. Special Issue “25 Anniversary of Bioinformatics of Genome Regulation and Structure Conference Series”

    Orlov, Y. L., Orlova, N. G., Chen, M. & Kolchanov, N. A., 4 Jul 2025, In: International Journal of Molecular Sciences. 26, 13, 7 p., 6447.

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

  15. Counting touching wheat grains in images based on elliptical approximation

    Avzalov, D. R., Komyshev, E. G. & Afonnikov, D. A., Jul 2025, In: Вавиловский журнал генетики и селекции. 29, 4, p. 608-614 7 p., 13.

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

  16. Deep learning approach to the estimation of the ratio of reproductive modes in a partially clonal population

    Nikolaeva, T. A., Poroshina, A. A. & Sherbakov, D. Y., Jun 2025, In: Vavilovskii Zhurnal Genetiki i Selektsii. 29, 3, p. 467-473 7 p., 14.

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

  17. Evolutionary Transcriptomics of Cancer Development

    Ivanov, R., Afonnikov, D., Matushkin, Y. & Lashin, S., 23 May 2025, In: International Journal of Molecular Sciences. 26, 11, 15 p., 5041.

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

  18. 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, 17 p., 159595.

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

  19. 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

  20. 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

  21. 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

  22. 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

  23. Frame-based mathematical models – a tool for the study of molecular genetic systems

    Kazantsev, F. V., Lashin, S. A. & Matushkin, Y. G., 2025, In: Vavilovskii Zhurnal Genetiki i Selektsii. 29, 8, p. 1288-1294 7 p., 14.

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

  24. Hedgehog signaling in humans: the HH_Signal_pathway_db knowledge base

    Bukharina, T. A., Bondarenko, A. M. & Furman, D. P., 2025, In: Вавиловский журнал генетики и селекции. 29, 7, p. 978-989 12 p., 6.

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

  25. Влияние переназначения кодонов на свойства и структуру митохондриальных белков байкальских амфипод

    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

  26. Генная сеть и база знаний по терморегуляции организма человека

    Ignatieva, E. V., Demenkov, P. S., Bogomolov, A. G., Ivanov, R. A., Lashin, S. A., Mikhailova, A. D., Alekseeva, A. E. & Yudin, N. S., 2025, In: Vavilovskii Zhurnal Genetiki i Selektsii. 29, 7, p. 1009-1019 11 p., 9.

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

  27. Исследование инсектицидного и фунгицидного потенциала бактерий эндофитов пшеницы, сои и рапса методами биоинформатического анализа

    Lakhova, T. N., Klimenko, A. I., Vasiliev, G. V., Gyrnets, E. Y., Asaturova, A. M. & Lashin, S. A., 2025, In: Vavilovskii Zhurnal Genetiki i Selektsii. 29, 8, p. 1304-1317 14 p., 16.

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

  28. Компьютерное предсказание сети взаимодействий длинных некодирующих РНК и микроРНК кукурузы на основе транскриптома мутантной линии fuzzy tassel

    Yan, J., Pronozin, A. Y. & Afonnikov, D. A., 2025, In: Vavilovskii Zhurnal Genetiki i Selektsii. 29, 8, p. 1295-1303 9 p., 15.

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

  29. Математические модели метаболизма железа: структура и функции

    Melchenko, N. I. & Akberdin, I. R., 2025, In: Vavilovskii Zhurnal Genetiki i Selektsii. 29, 7, p. 1031-1040 10 p., 11.

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

  30. Применение программно-информационной системы ANDSystem для поиска мишеней таргетной терапии ревматоидного артрита на основе анализа биологических процессов

    Mishchenko, E. L., Yatsyk, I. V., Demenkov, P. S., Adamovskaya, A. V., Ivanisenko, T. V., Kleshchev, M. A. & Ivanisenko, V. A., 2025, In: Vavilovskii Zhurnal Genetiki i Selektsii. 29, 7, p. 1020-1030 11 p., 10.

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

  31. Программа PlantReg 1.1: анализ взаимного расположения сайтов связывания транскрипционных факторов в промоторах генов-мишеней для уточнения молекулярных механизмов их активности в регуляторных сетях

    Lavrekha, V. V., Omelyanchuk, N. A., Bogomolov, A. G., Ryabov, Y. A., Mukebenova, P. K. & Zemlyanskaya, E. V., 2025, In: Vavilovskii Zhurnal Genetiki i Selektsii. 29, 7, p. 940-951 12 p., 3.

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

  32. Реконструкция и анализ генной сети регуляции апоптоза при гепатоцеллюлярной карциноме на основе данных scRNA-seq и базы знаний ANDSystem

    Adamovskaya, A. V., Yatsyk, I. V., Kleshchev, M. A., Demenkov, P. S., Ivanisenko, T. V. & Ivanisenko, V. A., 2025, In: Vavilovskii Zhurnal Genetiki i Selektsii. 29, 7, p. 963-977 15 p., 5.

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

  33. Роль длинных некодирующих РНК в растениях

    Пронозин, А. Ю. & Афонников, Д. А., 2025, In: Генетика. 61, 1, p. 3-23

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

  34. 2024

  35. 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

  36. 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

  37. 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

  38. 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., Dec 2024, In: Vavilovskii Zhurnal Genetiki i Selektsii. 28, 8, p. 960-973 14 p.

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

  39. 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

  40. 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., Dec 2024, In: Вавиловский журнал генетики и селекции. 28, 8, p. 927-939 13 p.

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

  41. 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., Dec 2024, In: Вавиловский журнал генетики и селекции. 28, 8, p. 882-896 15 p.

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

  42. 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

  43. 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

  44. 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., Dec 2024, In: Вавиловский журнал генетики и селекции. 28, 8, p. 874-881 8 p.

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

  45. 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., Dec 2024, In: Vavilovskii Zhurnal Genetiki i Selektsii. 28, 8, p. 950-959 10 p.

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

  46. 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

  47. 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., Dec 2024, In: Вавиловский журнал генетики и селекции. 28, 8, p. 864-873 10 p.

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

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

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

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

  49. 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

  50. 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

  51. 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

  52. 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

  53. 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

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