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2020

3D Analysis of Mitosis Distribution Pattern in the Plant Root Tip with iRoCS Toolbox

Lavrekha, V. V., Pasternak, T., Palme, K. & Mironova, V. V., 1 Jan 2020, In : Methods in molecular biology (Clifton, N.J.). 2094, p. 119-125 7 p.

Research output: Contribution to journalArticle

Faint gray bands in Drosophila melanogaster polytene chromosomes are formed by coding sequences of housekeeping genes

Demakova, O. V., Demakov, S. A., Boldyreva, L. V., Zykova, T. Y., Levitsky, V. G., Semeshin, V. F., Pokholkova, G. V., Sidorenko, D. S., Goncharov, F. P., Belyaeva, E. S. & Zhimulev, I. F., 1 Mar 2020, In : Chromosoma. 129, 1, p. 25-44 20 p.

Research output: Contribution to journalArticle

1 Citation (Scopus)

Fold-change-specific enrichment analysis (FSEA): Quantification of transcriptional response magnitude for functional gene groups

Wiebe, D. S., Omelyanchuk, N. A., Mukhin, A. M., Grosse, I., Lashin, S. A., Zemlyanskaya, E. V. & Mironova, V. V., 17 Apr 2020, In : Genes. 11, 4, 14 p., 434.

Research output: Contribution to journalArticle

Open Access

Genes containing long introns occupy series of bands and interbands in drosophila melanogaster polytene chromosomes

Khoroshko, V. A., Pokholkova, G. V., Levitsky, V. G., Zykova, T. Y., Antonenko, O. V., Belyaeva, E. S. & Zhimulev, I. F., Apr 2020, In : Genes. 11, 4, 32 p., 417.

Research output: Contribution to journalArticle

Open Access

Identification of Antimicrobial Peptides from Novel Lactobacillus fermentum Strain

Pavlova, A. S., Ozhegov, G. D., Arapidi, G. P., Butenko, I. O., Fomin, E. S., Alemasov, N. A., Afonnikov, D. A., Yarullina, D. R., Ivanov, V. T., Govorun, V. M. & Kayumov, A. R., 1 Feb 2020, In : Protein Journal. 39, 1, p. 73-84 12 p.

Research output: Contribution to journalArticle

metaRE R package for meta-analysis of transcriptome data to identify the cis-regulatory code behind the transcriptional reprogramming

Novikova, D. D., Cherenkov, P. A., Sizentsova, Y. G. & Mironova, V. V., 1 Jun 2020, In : Genes. 11, 6, p. 1-14 14 p., 634.

Research output: Contribution to journalArticle

Open Access

On-target CRISPR/CAS9 activity can cause undesigned large deletion in mouse zygotes

Korablev, A., Lukyanchikova, V., Serova, I. & Battulin, N., 20 May 2020, In : International Journal of Molecular Sciences. 21, 10, 3604.

Research output: Contribution to journalArticle

Open Access

PlantLayout - программное средство для моделирования распределения веществ в тканях различной структуры

Translated title of the contribution: PlantLayout pipeline to model tissue patterningSavina, M. S. & Mironova, V. V., 1 Jan 2020, In : Vavilovskii Zhurnal Genetiki i Selektsii. 24, 1, p. 102-107 6 p.

Research output: Contribution to journalArticle

Open Access

Specification and regulation of vascular tissue identity in the Arabidopsis embryo

Smit, M. E., Llavata-Peris, C. I., Roosjen, M., van Beijnum, H., Novikova, D., Levitsky, V., Sevilem, I., Roszak, P., Slane, D., Jürgens, G., Mironova, V., Brady, S. M. & Weijers, D., 20 Apr 2020, In : Development (Cambridge). 147, 8, 15 p., dev186130.

Research output: Contribution to journalArticle

Open Access

The Effect of Meditation on Comprehension of Statements About One-Self and Others: A Pilot ERP and Behavioral Study

Savostyanov, A., Tamozhnikov, S., Bocharov, A., Saprygin, A., Matushkin, Y., Lashin, S., Kolpakova, G., Sudobin, K. & Knyazev, G., 9 Jan 2020, In : Frontiers in Human Neuroscience. 13, 12 p., 437.

Research output: Contribution to journalArticle

Open Access
2019
2 Citations (Scopus)
1 Citation (Scopus)

A single ChIP-seq dataset is sufficient for comprehensive analysis of motifs co-occurrence with MCOT package

Levitsky, V., Zemlyanskaya, E., Oshchepkov, D., Podkolodnaya, O., Ignatieva, E., Grosse, I., Mironova, V. & Merkulova, T., 2 Dec 2019, In : Nucleic Acids Research. 47, 21, p. e139 14 p.

Research output: Contribution to journalArticle

Open Access
2 Citations (Scopus)

Capturing Auxin Response Factors Syntax Using DNA Binding Models

Stigliani, A., Martin-Arevalillo, R., Lucas, J., Bessy, A., Vinos-Poyo, T., Mironova, V., Vernoux, T., Dumas, R. & Parcy, F., 3 Jun 2019, In : Molecular Plant. 12, 6, p. 822-832 11 p.

Research output: Contribution to journalArticle

6 Citations (Scopus)

Fluorescent labeling of ursolic acid with FITC for investigation of its cytotoxic activity using confocal microscopy

Frolova, T. S., Lipeeva, A. V., Baev, D. S., Baiborodin, S. I., Orishchenko, К. E., Kochetov, A. V. & Sinitsyna, O. I., 1 Jun 2019, In : Bioorganic Chemistry. 87, p. 876-887 12 p.

Research output: Contribution to journalArticle

Genetic control of anthocyanin pigmentation of potato tissues

Strygina, K. V., Kochetov, A. V. & Khlestkina, E. K., 18 Mar 2019, In : BMC Genetics. 20, Suppl 1, p. 27 9 p., 27.

Research output: Contribution to journalArticle

1 Citation (Scopus)

Genotoxic activity of 1,2,3-triazolyl modified furocoumarins and 2,3-dihydrofurocoumarins

Kremis, S. A., Baev, D. S., Lipeeva, A. V., Shults, E. E., Tolstikova, T. G., Sinitsyna, O. I., Kochetov, A. V. & Frolova, T. S., 1 Nov 2019, In : Journal of Biochemical and Molecular Toxicology. 33, 11, p. e22396 e22396.

Research output: Contribution to journalArticle

Image-based analysis of quantitative morphological characteristics of wild potato tubers using the desktop application SeedСounter

Ivanova, K. A., Komyshev, E. G., Genaev, M. A., Egorova, A. A., Koloshina, K. A., Chalaya, N. A., Afonnikov, D. A., Kochetov, A. V., Rogozina, E. V. & Gerasimova, S. V., 1 Jan 2019, In : Vavilovskii Zhurnal Genetiki i Selektsii. 23, 5, p. 519-526 8 p.

Research output: Contribution to journalArticle

Open Access

MIGREW: Database on molecular identification of genes for resistance in wheat

Kazantsev, F. V., Skolotneva, E. S., Kelbin, V. N., Salina, E. A. & Lashin, S. A., 5 Feb 2019, In : BMC Bioinformatics. 20, Suppl 1, 8 p., 36.

Research output: Contribution to journalArticle

1 Citation (Scopus)

Morphometry of the wheat spike by analyzing 2D images

Genaev, M. A., Komyshev, E. G., Smirnov, N. V., Kruchinina, Y. V., Goncharov, N. P. & Afonnikov, D. A., 17 Jul 2019, In : Agronomy. 9, 7, 390.

Research output: Contribution to journalArticle

Open Access
1 Citation (Scopus)

New insights from Opisthorchis felineus genome: update on genomics of the epidemiologically important liver flukes

Ershov, N. I., Mordvinov, V. A., Prokhortchouk, E. B., Pakharukova, M. Y., Gunbin, K. V., Ustyantsev, K., Genaev, M. A., Blinov, A. G., Mazur, A., Boulygina, E., Tsygankova, S., Khrameeva, E., Chekanov, N., Fan, G., Xiao, A., Zhang, H., Xu, X., Yang, H., Solovyev, V., Lee, S. M. Y. & 3 others, Liu, X., Afonnikov, D. A. & Skryabin, K. G., 22 May 2019, In : BMC Genomics. 20, 1, p. 399 22 p., 399.

Research output: Contribution to journalArticle

Open Access
3 Citations (Scopus)

Phylostratigraphic analysis shows the earliest origination of the abiotic stress associated genes in a. Thaliana

Mustafin, Z. S., Zamyatin, V. I., Konstantinov, D. K., Doroshkov, A. V., Lashin, S. A. & Afonnikov, D. A., 22 Nov 2019, In : Genes. 10, 12, 27 p., 963.

Research output: Contribution to journalArticle

Open Access
Open Access

Salicylic Acid Affects Root Meristem Patterning via Auxin Distribution in a Concentration-Dependent Manner

Pasternak, T., Groot, E. P., Kazantsev, F. V., Teale, W., Omelyanchuk, N., Kovrizhnykh, V., Palme, K. & Mironova, V. V., 1 Jul 2019, In : Plant Physiology. 180, 3, p. 1725-1739 15 p.

Research output: Contribution to journalArticle

12 Citations (Scopus)

The evolution of gene regulatory networks controlling Arabidopsis thaliana L. trichome development

Doroshkov, A. V., Konstantinov, D. K., Afonnikov, D. A. & Gunbin, K. V., 15 Feb 2019, In : BMC Plant Biology. 19, Suppl 1, 15 p., 53.

Research output: Contribution to journalArticle

4 Citations (Scopus)
Open Access
1 Citation (Scopus)

Прогресс в секвенировании геномов растений – направления исследований

Translated title of the contribution: Progress in plant genome sequencing: Research directionsBragina, M. K., Afonnikov, D. A. & Salina, E. A., 1 Jan 2019, In : Vavilovskii Zhurnal Genetiki i Selektsii. 23, 1, p. 38-48 11 p.

Research output: Contribution to journalArticle

Open Access
1 Citation (Scopus)

Системный подход к моделированию развития листостебельных грибных инфекций пшеницы

Translated title of the contribution: A system approach to the modeling of fungal infections of the wheat leafNikolaev, S. V., Zubairova, U. S., Skolotneva, E. S., Orlova, E. A. & Afonnikov, D. A., 1 Jan 2019, In : Vavilovskii Zhurnal Genetiki i Selektsii. 23, 1, p. 100-109 10 p.

Research output: Contribution to journalArticle

Open Access
2018

An integrated information system on bioresource collections of the FASO of Russia

Lashin, S. A., Afonnikov, D. A., Genaev, M. A., Kazantsev, F. V., Komyshev, E. G., Oschepkova, E. A., Petrov, A. V., Rasskazov, D. A., Smirnova, A. A. & Kolchanov, N. A., 1 Jan 2018, In : Vavilovskii Zhurnal Genetiki i Selektsii. 22, 3, p. 386-393 8 p.

Research output: Contribution to journalArticle

Genetic Organization of Open Chromatin Domains Situated in Polytene Chromosome Interbands in Drosophila

Zykova, T. Y., Popova, O. O., Khoroshko, V. A., Levitsky, V. G., Lavrov, S. A. & Zhimulev, I. F., 1 Nov 2018, In : Doklady Biochemistry and Biophysics. 483, 1, p. 297-301 5 p.

Research output: Contribution to journalArticle

2 Citations (Scopus)

Haplotype analysis of APOE intragenic SNPs

Babenko, V. N., Afonnikov, D. A., Ignatieva, E. V., Klimov, A. V., Gusev, F. E. & Rogaev, E. I., 19 Apr 2018, In : BMC Neuroscience. 19, Suppl 1, p. 16 12 p., 16.

Research output: Contribution to journalArticle

4 Citations (Scopus)
1 Citation (Scopus)

Information system on microbial collections as a part of bioresource collections portal for Russia’s FASO organizations: A working protocol

Kazantsev, F. V., Smirnova, A. A., Rozanov, A. S., Uvarova, Y. E., Afonnikov, D. A., Peltek, S. E. & Lashin, S. A., 1 Jan 2018, In : Vavilovskii Zhurnal Genetiki i Selektsii. 22, 2, p. 279-284 6 p.

Research output: Contribution to journalArticle

MAMMOTh: A new database for curated mathematical models of biomolecular systems

Kazantsev, F., Akberdin, I., Lashin, S., Ree, N., Timonov, V., Ratushny, A., Khlebodarova, T. & Likhoshvai, V., 1 Feb 2018, In : Journal of Bioinformatics and Computational Biology. 16, 1, 16 p., 1740010.

Research output: Contribution to journalArticle

4 Citations (Scopus)

Marital Structure, Genetic Fitness, and the GJB2 Gene Mutations among Deaf People in Yakutia (Eastern Siberia, Russia)

Romanov, G. P., Barashkov, N. A., Teryutin, F. M., Lashin, S. A., Solovyev, A. V., Pshennikova, V. G., Bondar, A. A., Morozov, I. V., Sazonov, N. N., Tomsky, M. I., Dzhemileva, L. U., Khusnutdinova, E. K., Posukh, O. L. & Fedorova, S. A., 1 May 2018, In : Russian Journal of Genetics. 54, 5, p. 554-561 8 p.

Research output: Contribution to journalArticle

1 Citation (Scopus)

Pluripotency gene network dynamics: System views from parametric analysis

Akberdin, I. R., Omelyanchuk, N. A., Fadeev, S. I., Leskova, N. E., Oschepkova, E. A., Kazantsev, F. V., Matushkin, Y. G., Afonnikov, D. A. & Kolchanov, N. A., 29 Mar 2018, In : PLoS ONE. 13, 3, p. e0194464 24 p., 0194464.

Research output: Contribution to journalArticle

4 Citations (Scopus)

Residue coevolution reveals functionally important intramolecular interactions in formamidopyrimidine-DNA glycosylase

Endutkin, A. V., Koptelov, S. S., Popov, A. V., Torgasheva, N. A., Lomzov, A. A., Tsygankova, A. R., Skiba, T. V., Afonnikov, D. A. & Zharkov, D. O., 1 Sep 2018, In : DNA Repair. 69, p. 24-33 10 p.

Research output: Contribution to journalArticle

1 Citation (Scopus)

Spatial specificity of auxin responses coordinates wood formation

Brackmann, K., Qi, J., Gebert, M., Jouannet, V., Schlamp, T., Grünwald, K., Wallner, E. S., Novikova, D. D., Levitsky, V. G., Agustí, J., Sanchez, P., Lohmann, J. U. & Greb, T., 28 Feb 2018, In : Nature Communications. 9, 1, p. 875 15 p., 875.

Research output: Contribution to journalArticle

28 Citations (Scopus)

SpikeDroidDB: An information system for annotation of morphometric characteristics of wheat spike

Genaev, M. A., Komyshev, E. G., Hao, F., Koval, V. S., Goncharov, N. P. & Afonnikov, D. A., 1 Jan 2018, In : Vavilovskii Zhurnal Genetiki i Selektsii. 22, 1, p. 132-140 9 p.

Research output: Contribution to journalArticle

2 Citations (Scopus)

The morphogenic potential of Siberian potato cultivars in tissue cultures

Ibragimova, S. M., Romanova, A. V., Myzgina, G. K. & Kochetov, A. V., 1 Jan 2018, In : Vavilovskii Zhurnal Genetiki i Selektsii. 22, 3, p. 316-320 5 p.

Research output: Contribution to journalArticle

1 Citation (Scopus)
2017

3D analysis of mitosis distribution highlights the longitudinal zonation and diarch symmetry in proliferation activity of the Arabidopsis thaliana root meristem

Lavrekha, V. V., Pasternak, T., Ivanov, V. B., Palme, K. & Mironova, V. V., 1 Dec 2017, In : Plant Journal. 92, 5, p. 834-845 12 p.

Research output: Contribution to journalArticle

11 Citations (Scopus)

Achievements and prospects of applying high-throughput sequencing techniques to potato genetics and breeding

Bykova, I. V., Shmakov, N. A., Afonnikov, D. A., Kochetov, A. V. & Khlestkina, E. K., 1 Nov 2017, In : Russian Journal of Genetics: Applied Research. 7, 7, p. 736-743 8 p.

Research output: Contribution to journalArticle

1 Citation (Scopus)

A database on genes increasing the resistance of wheat and its related species against pathogenic fungi

Smirnova, O. G. & Kochetov, A. V., 1 Dec 2017, In : Russian Journal of Genetics: Applied Research. 7, 8, p. 816-821 6 p.

Research output: Contribution to journalArticle

1 Citation (Scopus)

AltORFev facilitates the prediction of alternative open reading frames in eukaryotic mRNAs

Kochetov, A. V., Allmer, J., Klimenko, A. I., Zuraev, B. S., Matushkin, Y. G., Lashin, S. A. & Hancock, J., 15 Mar 2017, In : Bioinformatics. 33, 6, p. 923-925 3 p.

Research output: Contribution to journalArticle

5 Citations (Scopus)

A Sacrifice-for-Survival Mechanism Protects Root Stem Cell Niche from Chilling Stress

Hong, J. H., Savina, M., Du, J., Devendran, A., Kannivadi Ramakanth, K., Tian, X., Sim, W. S., Mironova, V. V. & Xu, J., 29 Jun 2017, In : Cell. 170, 1, p. 102-113.e14 11 p.

Research output: Contribution to journalArticle

33 Citations (Scopus)

Auxin regulates functional gene groups in a fold-change-specific manner in Arabidopsis thaliana roots

Omelyanchuk, N. A., Wiebe, D. S., Novikova, D. D., Levitsky, V. G., Klimova, N., Gorelova, V., Weinholdt, C., Vasiliev, G. V., Zemlyanskaya, E. V., Kolchanov, N. A., Kochetov, A. V., Grosse, I. & Mironova, V. V., 30 May 2017, In : Scientific Reports. 7, 1, p. 2489 11 p., 2489.

Research output: Contribution to journalArticle

11 Citations (Scopus)

Differential expression of NBS-LRR-encoding genes in the root transcriptomes of two Solanum phureja genotypes with contrasting resistance to Globodera rostochiensis

Kochetov, A. V., Glagoleva, A. Y., Strygina, K. V., Khlestkina, E. K., Gerasimova, S. V., Ibragimova, S. M., Shatskaya, N. V., Vasilyev, G. V., Afonnikov, D. A., Shmakov, N. A., Antonova, O. Y., Gavrilenko, T. A., Alpatyeva, N. V., Khiutti, A. & Afanasenko, O. S., 28 Dec 2017, In : BMC Plant Biology. 17, Suppl 2, p. 251 10 p., 251.

Research output: Contribution to journalArticle

6 Citations (Scopus)