Trans2express – de novo transcriptome assembly pipeline optimized for gene expression analysis.

Authors: Kasianova, Aleksandra M.^1,2 (AUTHOR), Penin, Aleksey A.¹ (AUTHOR), Schelkunov, Mikhail I.^1,2 (AUTHOR), Kasianov, Artem S.¹ (AUTHOR), Logacheva, Maria D.^1,2 (AUTHOR), Klepikova, Anna V.¹ (AUTHOR) annklepikova@gmail.com

Source: Plant Methods. 8/16/2024, Vol. 20, p1-11. 11p.

Subject Terms: *GENE expression, *BOTANISTS, *EUKARYOTIC genomes, *ARABIDOPSIS thaliana, *PLANT species

Origin and diversity of Capsella bursa-pastoris from the genomic point of view.

Authors: Penin, Aleksey A.¹ (AUTHOR) alekseypenin@gmail.com, Kasianov, Artem S.¹ (AUTHOR), Klepikova, Anna V.¹ (AUTHOR), Omelchenko, Denis O.¹ (AUTHOR), Makarenko, Maksim S.¹ (AUTHOR), Logacheva, Maria D.^1,2 (AUTHOR)

Source: BMC Biology. 3/5/2024, Vol. 22 Issue 1, p1-15. 15p.

Subject Terms: *BIOLOGICAL evolution, *INTROGRESSION (Genetics), *CHROMOSOMES, *RUBELLA, *POLYPLOIDY, *ARABIDOPSIS thaliana

Genomic analysis reveals cryptic diversity in aphelids and sheds light on the emergence of Fungi

Authors: Mikhailov, Kirill V., Karpov, Sergey A., Letcher, Peter M., Lee, Philip A., Logacheva, Maria D., Penin, Aleksey A., Nesterenko, Maksim A., Pozdnyakov, Igor R., Potapenko, Evgenii V., Sherbakov, Dmitry Y., Panchin, Yuri V., Aleoshin, Vladimir V.

Source: In Current Biology 7 November 2022 32(21):4607-4619

Chromosome-Scale Assembly of Capsella orientalis, Maternal Progenitor of Cosmopolitan Allotetraploid C. bursa-pastoris.

Authors: Kasianova, Alexandra M^1,2, Mityukov, Vladislav D³, German, Dmitry A⁴, Kasianov, Artem S⁵, Penin, Aleksey A^2,6, Logacheva, Maria D^1,2

Source: Genome Biology & Evolution; Jan2025, Vol. 17 Issue 1, p1-6, 6p

An update to database TraVA: organ-specific cold stress response in Arabidopsis thaliana

Authors: Klepikova, Anna, Kulakovskiy, Ivan, Kasianov, Artem, Logacheva, Maria, Penin, Aleksey

Source: BMC plant biology. 19(1):29-40

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100185658598.0x000001&indx=1&recIds=ETOCvdc_100185658598.0x000001

Cooption of heat shock regulatory system for anhydrobiosis in the sleeping chironomid Polypedilum vanderplanki

Authors: Mazin, Pavel V., Shagimardanova, Elena, Kozlova, Olga, Cherkasov, Alexander, Sutormin, Roman, Stepanova, Vita V., Stupnikov, Alexey, Logacheva, Maria, Penin, Aleksey, Sogame, Yoichiro, Cornette, Richard, Tokumoto, Shoko, Miyata, Yugo, Kikawada, Takahiro, Gelfand, Mikhail S., Gusev, Oleg

Source: Proceedings of the National Academy of Sciences of the United States of America, 2018 Mar 01. 115(10), E2477-E2486.

Access URL: https://www.jstor.org/stable/26507913

RNA-seq highlights parallel and contrasting patterns in the evolution of the nuclear genome of fully mycoheterotrophic plants

Authors: Schelkunov, Mikhail, Penin, Aleksey, Logacheva, Maria

Source: BMC genomics. 19(1):1-16

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100174878758.0x000001&indx=1&recIds=ETOCvdc_100174878758.0x000001

Whole transcriptome profiling of adult and infective stages of the trematode Opisthorchis felineus

Authors: Pomaznoy, Mikhail Yu, Logacheva, Maria D., Young, Neil D., Penin, Aleksey A., Ershov, Nikita I., Katokhin, Alexey V., Mordvinov, Viatcheslav A.

Source: In Parasitology International February 2016 65(1):12-19

The genome of the toxic invasive species Heracleum sosnowskyi carries an increased number of genes despite absence of recent whole‐genome duplications.

Authors: Schelkunov, Mikhail I., Shtratnikova, Viktoria Yu., Klepikova, Anna V., Makarenko, Maksim S., Omelchenko, Denis O., Novikova, Lyudmila A., Obukhova, Ekaterina N., Bogdanov, Viktor P., Penin, Aleksey A., Logacheva, Maria D.

Source: Plant Journal; Jan2024, Vol. 117 Issue 2, p449-463, 15p

Subject Terms: CARROTS, INTRODUCED species, GENOMICS, GENES, PLANT genes, PLANT spacing

A high resolution map of the Arabidopsis thaliana developmental transcriptome based on RNA‐seq profiling

Authors: Klepikova, Anna V., Kasianov, Artem S., Gerasimov, Evgeny S., Logacheva, Maria D., Penin, Aleksey A.

Source: Plant journal. 88(6):1058-1070

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100085842780.0x000001&indx=1&recIds=ETOCvdc_100085842780.0x000001

The Genome of Intoshia linei Affirms Orthonectids as Highly Simplified Spiralians

Authors: Mikhailov, Kirill V., Slyusarev, Georgy S., Nikitin, Mikhail A., Logacheva, Maria D., Penin, Aleksey A., Aleoshin, Vladimir V., Panchin, Yuri V.

Source: Current biology. 26(13):1768-1774

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100035342988.0x000001&indx=1&recIds=ETOCvdc_100035342988.0x000001

Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains

Authors: Ulianov, Sergey V., Khrameeva, Ekaterina E., Gavrilov, Alexey A., Flyamer, Ilya M., Kos, Pavel, Mikhaleva, Elena A., Penin, Aleksey A., Logacheva, Maria D., Imakaev, Maxim V., Chertovich, Alexander

Source: Genome research. 26(1):70-84

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN604491239&indx=1&recIds=ETOCRN604491239

Population Genomics of Two Closely Related Anhydrobiotic Midges Reveals Differences in Adaptation to Extreme Desiccation.

Authors: Shaikhutdinov, Nurislam M¹, nurislam.shaikhutdinov@gmail.com, Klink, Galya V², Garushyants, Sofya K², Kozlova, Olga S¹, Cherkasov, Alexander V¹, Kikawada, Takahiro³, Okuda, Takashi⁴, Pemba, Dylo⁵, Shagimardanova, Elena I¹, Penin, Aleksey A², Deviatiiarov, Ruslan M¹, Gazizova, Guzel R¹, Cornette, Richard³, nurislam.shaikhutdinov@gmail.com, Gusev, Oleg A^1,6,7, nurislam.shaikhutdinov@gmail.com, Bazykin, Georgii A², nurislam.shaikhutdinov@gmail.com

Source: Genome Biology & Evolution; Oct2023, Vol. 15 Issue 10, p1-15, 15p

Correlation between number and position of floral organs in Arabidopsis

Authors: Penin, Aleksey A., Logacheva, Maria D.

Source: Annals of Botany, 2011 Jul 01. 108(1), 123-131.

Access URL: https://www.jstor.org/stable/43578372

The clustering of CpG islands may constitute an important determinant of the 3D organization of interphase chromosomes

Authors: Gushchanskaya, Ekaterina S, Artemov, Artem V, Ulyanov, Sergey V, Logacheva, Maria D, Penin, Aleksey A, Kotova, Elena S, Akopov, Sergey B, Nikolaev, Lev G, Iarovaia, Olga V, Sverdlov, Eugene D, Gavrilov, Alexey A, Razin, Sergey V

Source: Epigenetics. 9(7):951-963

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100050750637.0x000001&indx=1&recIds=ETOCvdc_100050750637.0x000001

Chromosome-Length Assembly of the Baikal Seal (Pusa sibirica) Genome Reveals a Historically Large Population Prior to Isolation in Lake Baikal.

Authors: Yakupova, Aliya, Tomarovsky, Andrey, Totikov, Azamat, Beklemisheva, Violetta, Logacheva, Maria, Perelman, Polina L., Komissarov, Aleksey, Dobrynin, Pavel, Krasheninnikova, Ksenia, Tamazian, Gaik, Serdyukova, Natalia A., Rayko, Mike, Bulyonkova, Tatiana, Cherkasov, Nikolay, Pylev, Vladimir, Peterfeld, Vladimir, Penin, Aleksey, Balanovska, Elena, Lapidus, Alla, OBrien, Stephen J.

Source: Genes; Mar2023, Vol. 14 Issue 3, p619, 22p

Subject Terms: KARYOTYPES, GENOMES, GENETIC variation, CHROMOSOME inversions, ICE sheets, SPECIES diversity, LAKES, HETEROZYGOSITY

Interspecific comparison of gene expression profiles using machine learning.

Authors: Kasianov, Artem S., Klepikova, Anna V., Mayorov, Alexey V., Buzanov, Gleb S., Logacheva, Maria D., Penin, Aleksey A.

Source: PLoS Computational Biology; 1/10/2023, Vol. 19 Issue 1, p1-20, 20p, 3 Graphs, 1 Map

Subject Terms: GENE expression profiling, BUCKWHEAT, MACHINE learning, GENE expression, CORN, FLOWERING of plants

Ectopic expression of HIV-1 Tat modifies gene expression in cultured B cells: implications for the development of B-cell lymphomas in HIV-1-infected patients.

Authors: Valyaeva, Anna A., Tikhomirova, Maria A., Potashnikova, Daria M., Bogomazova, Alexandra N., Snigiryova, Galina P., Penin, Aleksey A., Logacheva, Maria D., Arifulin, Eugene A., Shmakova, Anna A., Germini, Diego, Kachalova, Anastasia I., Saidova, Aleena A., Zharikova, Anastasia A., Musinova, Yana R., Mironov, Andrey A., Vassetzky, Yegor S., Sheval, Eugene V.

Source: PeerJ; Oct2022, p1-28, 28p

Subject Terms: GENE expression, LYMPHOBLASTOID cell lines, HIV, TAT protein, LYMPHOMAS, B cells

Transcriptome atlas of Phalaenopsis equestris.

Authors: Klepikova, Anna V., Kasianov, Artem S., Ezhova, Margarita A., Penin, Aleksey A., Logacheva, Maria D.

Source: PeerJ; Dec2021, p1-13, 13p

Subject Terms: PHALAENOPSIS, TRANSCRIPTOMES, GENE expression profiling, PLANT genes, GENE expression, GENE mapping

lepidium-like , a Naturally Occurring Mutant of Capsella bursa-pastoris , and Its Implications on the Evolution of Petal Loss in Cruciferae.

Authors: Klepikova, Anna V., Shnayder, Elina D., Kasianov, Artem S., Remizowa, Margarita V., Sokoloff, Dmitry D., Penin, Aleksey A.

Source: Frontiers in Plant Science; 11/25/2021, Vol. 12, p1-11, 11p

Subject Terms: HEREDITY, FLOWER development, BRASSICACEAE, PHENOTYPIC plasticity, FLOOR plans, PHENOTYPES, POLLINATORS, POLLINATION