Aleksey Doroshkov Department: Sector of Monogenic Forms of Common Diseases Pluralist: Laboratory of protist systems biology Room: 1317 Email: AD@bionet.nsc.ru

Publications

2024	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 Aleksandr V Bobrovskikh, Ulyana S Zubairova, Ludmila G Naumenko, Alexey V Doroshkov [Biology]
	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. [Plants]
	In Vitro vs. In Vivo Transcriptomic Approach Revealed Core Pathways of Nitrogen Deficiency Response in Tea Plant (Camellia sinensis (L.) Kuntze) Lidiia Samarina, Lyudmila Malyukova, Songbo Wang, Aleksandr Bobrovskikh, Alexey Doroshkov, Ruset Shkhalakhova, Karina Manakhova, Natalia Koninskaya, Alexandra Matskiv, Alexey Ryndin, Elena Khlestkina, Yuriy Orlov [INT J MOL SCI]
	Nitrogen deficiency differentially affects lignin biosynthesis genes and flavanols accumulation in tolerant and susceptible tea genotypes (Camellia sinensis (L.) Kuntze) Lidiia Samarina, Lyudmila Malyukova, Songbo Wang, Yang Li, Alexey Doroshkov, Aleksandr Bobrovskikh, Ruset Shkhalakhova, Natalia Koninskaya, Alexandra Matskiv, Andrey Velikiy, Alexey Ryndin, Elena Khlestkina [Plant Stress]
	Thraustochytrids: Evolution, Ultrastructure, Biotechnology, and Modeling Menzorov A.G., Iukhtanov D.A., Naumenko L.G., Bobrovskikh A.V., Zubairova U.S., Morozova K.N., Doroshkov A.V. [INT J MOL SCI]
2023	Fishing Innate Immune System Properties through the Transcriptomic Single-Cell Data of Teleostei Aleksandr V. Bobrovskikh, Ulyana S. Zubairova, Alexey V. Doroshkov [Biology]
2022	Isolation and transcriptome analysis of a biotechnologically promising Black Sea protist, Thraustochytrium aureum ssp. strugatskii Dmitrii K. Konstantinov, Aleksei Menzorov, Olga Krivenko, Alexey V. Doroshkov [PeerJ]
	Particle-Based Imaging Tools Revealing Water Flows in Maize Nodal Vascular Plexus Ulyana S. Zubairova, Aleksandra Yu. Kravtsova, Alexander V. Romashchenko, Anastasiia A. Pushkareva, Alexey V. Doroshkov [Plants]
	Transcriptomic Data Meta-Analysis Sheds Light on High Light Response in Arabidopsis thaliana L. Бобровских Александр Владимирович Зубаирова Ульяна Станиславовна Бондарь Евгения Ивановна Лавреха Виктория Вадимовна Дорошков Алексей Владимирович [INT J MOL SCI]
2021	A Sight on Single-Cell Transcriptomics in Plants Through the Prism of Cell-Based Computational Modeling Approaches: Benefits and Challenges for Data Analysis Aleksandr Bobrovskikh, Alexey Doroshkov, Stefano Mazzoleni, Fabrizio Cartenì, Francesco Giannino, Ulyana Zubairova [Frontiers in Genetics]
	Comparative transcriptome profiling of a resistant vs susceptible bread wheat (Triticum aestivum L.) cultivar in response to water deficit and cold stress Dmitrii K. Konstantinov​, Ulyana S. Zubairova, Anton A. Ermakov, Alexey V. Doroshkov [PeerJ]
2020	Comparative Expression Analysis of Stress-Inducible Candidate Genes in Response to Cold and Drought in Tea Plant Lidiia S. Samarina, Alexandr V. Bobrovskikh, Alexey V. Doroshkov,Lyudmila S. Malyukova, Alexandra O. Matskiv, Ruslan S. Rakhmangulov, Natalia G. Koninskaya, Valentina I. Malyarovskaya, Wei Tong, Enhua Xia, Karina A. Manakhova, Alexey V. Ryndin, Yuriy L. Orlov [Frontiers in Genetics]
	Subcellular compartmentalization of the plant antioxidant system: an integrated overview Aleksandr Bobrovskikh​, Ulyana Zubairova, Alexey Kolodkin, Alexey Doroshkov [PeerJ]
2019	LSM-W2: Laser Scanning Microscopy Worker for Wheat Leaf Surface Morphology Zubairova U.S., Verman P.Yu., Oshchepkova P.S., Elsukova A.S., Doroshkov A.V. [BMC SYST BIOL]
	Phylostratigraphic Analysis Shows the Earliest Origination of the Abiotic Stress Associated Genes in A. thaliana Zakhar S. Mustafin, Vladimir I. Zamyatin, Dmitrii K. Konstantinov, Aleksej V. Doroshkov, Sergey A. Lashin, Dmitry A. Afonnikov [Genes]
	Quantitative characteristics of pubescence in wheat (Triticum aestivum L.) are associated with photosynthetic parameters under conditions of normal and limited water supply Tatyana A. Pshenichnikova, Alexey V. Doroshkov, Svetlana V. Osipova, Alexey V. Permyakov, Marina D. Permyakova, Vadim M. Efimov, Dmitry A. Afonnikov [PLANTA]
	Stress-induced changes in the expression of antioxidant system genes for rice (Oryza sativa L.) and bread wheat (Triticum aestivum L.) Anton Ermakov, Aleksandr Bobrovskikh, Ulyana Zubairova, Dmitrii Konstantinov, Alexey Doroshkov [PeerJ]
	The evolution of gene regulatory networks controlling Arabidopsis thaliana L. trichome development. Doroshkov AV, Konstantinov DK, Afonnikov DA, Gunbin KV. [BMC PLANT BIOL]
2018	Опушение листа у картофеля Solanum tuberosum: морфология, функциональная роль и методы исследования. Дорошков А.В., Афонников Д.А. [Vavilov journal of genetics and breeding]
	Паттерн эпидермиса листа пшеницы как модель для изучения влияния стрессовых условий на морфогенез Зубаирова У. С., Дорошков А. В. [Vavilov journal of genetics and breeding]
	Предсказание методами системной биологии наиболее перспективных генов-мишеней для селекции на устойчивость к окислительному стрессу С3 и С4 культурных злаков А. В. Дорошков, А. В. Бобровских [Vavilov journal of genetics and breeding]
2017	Diversity of leaf pubescence in bread wheat and relative species Tatyana A. Pshenichnikova, Alexey V. Doroshkov, Alexander V. Simonov, Dmitry A. Afonnikov, Andreas Bo¨rner [Genetic Resources and Crop Evolution]
2016	Identification of nuclear genes controlling chlorophyll synthesis in barley by RNA-seq Shmakov N.A., Vasiliev G.V., Shatskaya N.V., Doroshkov A.V., Gordeeva E.I., Afonnikov D.A., Khlestkina E.K. [BMC PLANT BIOL]
	Interactions between leaf pubescence genes in bread wheat as assessed by high throughput phenotyping. Doroshkov A.V., Afonnikov D.A., Dobrovolskaya O.B., Pshenichnikova T.A. [EUPHYTICA]
	Methods of high-throughput plant phenotyping for large-scale breeding and genetic experiments D. A. Afonnikov, M. A. Genaev, A. V. Doroshkov, E. G. Komyshev, T. A. Pshenichnikova [RUSS J GENET+]
	Regions of the bread wheat D genome associated with variation in key photosynthesis traits and shoot biomass under both well watered and water deficient conditions Svetlana Osipova, Alexey Permyakov, Marina Permyakova, Tatyana Pshenichnikova, Vasiliy Verkhoturov, Alexandr Rudikovsky, Elena Rudikovskaya, Alexandr Shishparenok, Alexey Doroshkov, Andreas Börner [J APPL GENET]
	Оценка количественных характеристик опушения листьев картофеля с использованием анализа цифровых микроизображений А.В. Дорошков, А.В. Симонов, А.Д. Сафонова, Д.А. Афонников, И.Е. Лихенко, Н.А. Колчанов [Достижения науки и техники АПК]
	Протокол анализа количественных характеристик опушения листа картофеля А.В. Дорошков, М.А. Генаев, Д.А. Афонников [Vavilov journal of genetics and breeding]
2015	Computer high-throughput approaches to wheat phenotyping: application to leaf pubescence analysis Afonnikov D.A., Genaev M.A., Doroshkov A.V., Komyshev E.G., Pshenichnikova T.A. Simonov A.V. [The 3rd Intern. Conference “Plant Genetics, Genomics, Bioinformatics and Biotechnology”, Abstract book]
	Genetic dissection of earliness by analysis of a recombinant chromosome substitution double haploid mapping population of bread wheat (Triticum aestivum L.) in different geographic regions Tatyana A. Pshenichnikova, Elena K. Khlestkina, Svetlana Landjeva, Alexey V. Doroshkov, Tanya Kartseva, Andreas Bo¨rner, Alexander V. Simonov, Ludmila V. Shchukina, Evgeniya V. Morozova [EUPHYTICA]
	The effect of plant hormones on the manifestation of leaf pubescence genes in bread wheat. Doroshkov A.V., Simonov A.V., Afonnikov D.A., Kasyanov N.S., Pshenichnikova T.A. [The 3rd Intern. Conference “Plant Genetics, Genomics, Bioinformatics and Biotechnology”, Abstract book]
2013	Генетический контроль опушения листа у изогенных линий мягкой пшеницы сорта Новосибирская 67 Дорошков А.В., Афонников Д.А., Пшеничникова Т.А. [RUSS J GENET+]
2012	Combined in silico/in vivo analysis of mechanisms providing for root apical meristem self-organization and maintenance Mironova VV, Omelyanchuk NA, Novoselova ES, Doroshkov AV, Kazantsev FV, Kochetov AV, Kolchanov NA, Mjolsness E, Likhoshvai VA. [ANN BOT-LONDON]
	Computer approaches to wheat high-throughput phenotyping Afonnikov D., Genaev M., Doroshkov A., Denisyuk V., Morozova E., Simonov A., Pshenichnikova T. [Journal of Stress Physiology & Biochemistry]
	Extraction of quantitative characteristics describing wheat leaf pubescence with a novel image processing technique Mikhail A. Genaev, Alexey V. Doroshkov, Tatyana A. Pshenichnikova, Nikolay A. Kolchanov, Dmitry A. Afonnikov [PLANTA]
	WheatPGE: A system for analysis of relationships among the phenotype, genotype, and environment in wheat M. A. Genaev, A. V. Doroshkov, E. V. Morozova, T. A. Pshenichnikova and D. A. Afonnikov [Russian Journal of Genetics: Applied Research]
	Информационная поддержка селекционно-генетического эксперимента у пшеницы в системе WheatPGE Генаев М.А., Дорошков А.В., Пшеничникова Т.А., Морозова Е.В., Симонов А.В., Афонников Д.А. [Mathematical Biology & Bioinformatics]
	Информационный портал "Биотехнология растений" - Интернет ресурс для поддержки экспериментов в области генной инженерии растений, генетики и селекции пшеницы. Кочетов А.В., Смирнова О.Г., Ибрагимова С.С., Рассказов Д.А., Афонников Д.А., Генаев М.А., Дорошков А.В., Пшеничникова Т.А., Симонов А.В., Морозова Е.В. [Vavilov journal of genetics and breeding]
2011	Анализ особенностей морфологии и наследования опушения листа пшеницы Triticum aestivum L. с помощью компьютерных методов фенотипирования. Дорошков А.В., Пшеничникова Т.А., Афонников Д.А. [RUSS J GENET+]
	КОМПЬЮТЕРНАЯ СИСТЕМА WheatPGE ДЛЯ АНАЛИЗА ВЗАИМОСВЯЗИ ФЕНОТИП-ГЕНОТИП-ОКРУЖАЮЩАЯ СРЕДА У ПШЕНИЦЫ М.А. Генаев, A.В. Дорошков, Е.В. Морозова, Т.А. Пшеничникова, Д.А. Афонников [Vavilov journal of genetics and breeding]
2009	Применение компьютерного анализа микроизображений листа для оценки характеристик опушения листа пшеницы Triticum Aestivum L Дорошков А.В., Арсенина С.И., Пшеничникова Т.А., Афонников Д.А. [Информационный вестник ВОГИС]