Ruslan Kalendar

2025

157. Kalendar R 2025. Comprehensive web-based platform for advanced PCR design, genotyping, synthetic biology, molecular diagnostics, and sequence analysis. Molecular Therapy Nucleic Acids, 36(4): 102716. DOI:10.1016/j.omtn.2025.102716

156. Kalendar R, Shevtsov V, Ismailova A 2025. An assay for variable fragment length allele-specific genotyping. Methods in Molecular Biology, Ed. Anthony Torres, book: Genotyping: Methods and Protocols, volume 2943, 1-17. DOI:10.1007/978-1-0716-4642-7_1

155. Makhmetov S, Temirkhanova K, Rakhimova S, Satvaldina N, Kalendar R, Kozhamkulov U, Bolatov AK, Bayanova M, Bazenova A, Nazarova L, Akilzhanova A, Kairov U 2025. Novel nonsense mutation in gene CHRNA2 identified by whole-genome sequencing in infant with epilepsy disorder: A case report. Heliyon, 11(1): e41484. DOI:10.1016/j.heliyon.2024.e41484

2024

154. Kalendar R, Kairov U 2024. Genome-wide tool for sensitive de novo identification and visualisation of interspersed and tandem repeats. Bioinformatics and biology insights, 18: 1-11. DOI:10.1177/11779322241306391

153. Kalendar R, Ivanov K I, Akhmetollayev I, Kairov U, Samuilova O, Burster T, Zamyatnin A 2024. An improved method and device for nucleic acid isolation using a high-salt gel electroelution trap. Analytical Chemistry, 96(39): 15526-15530. DOI:10.1021/acs.analchem.4c03720

152. Abileva G, Turzhanova A, Zhamangara A, Khapilina O, Kalendar R 2024. Environmental DNA reveals the ecology and seasonal migration of a rare sturgeon species in the Ural River. Environmental DNA, 6(2): e535. DOI:10.1002/edn3.535

151. Kalendar R, Shevtsov A, Otarbay Z, Ismailova A 2024. In silico PCR analysis: a comprehensive bioinformatics tool for enhancing nucleic acid amplification assays. Frontiers in Bioinformatics, 4: 1464197. DOI:10.3389/fbinf.2024.1464197

150. Kalendar R, Levei E, Cadar O, Senila M 2024. Editorial: Trends and Challenges in Plant Biomonitoring, Bioremediation and Biomining. Frontiers in Plant Science, 15: 1486752. DOI:10.3389/fpls.2024.1486752

149. Tao D, Kalendar R, Paterson AH 2024. Editorial: Interspecific Hybridization in Plant Biology, Volume II. Frontiers in Plant Science, 15: 1412622. DOI:10.3389/fpls.2024.1412622

148. Yerezhepov D, Gabdulkayum A, Akhmetova A, Kozhamkulov U, Rakhimova SE, Kairov U, Zhunussova G, Kalendar R, Akilzhanova A 2024. Pulmonary tuberculosis epidemiology and genetics in Kazakhstan. Frontiers in Public Health, 12: 1340673. DOI:10.3389/fpubh.2024.1340673

147. Assylbekova A, Allayarova M, Konysbekova M, Bekturgan A, Makhanova A, Brown S, Kalbacher H, Kalendar R, Burster T 2024. The proteolytic activity of neutrophil-derived serine proteases bound to the cell surface arming lung epithelial cells for viral defense. Molecules, 29(18): 4449. DOI:10.3390/molecules29184449

146. Yerezhepov D, Gabdulkayum A, Akhmetova A, Kozhamkulov U, Rakhimova S, Kairov U, Zhunussova G, Kalendar R, Akilzhanova A 2024. Vitamin D status, VDR and TLR polymorphisms and pulmonary tuberculosis epidemiology in Kazakhstan. Nutrients, 16(4): 558. DOI:10.3390/nu16040558

145. Vasileva Y, Zhulanov A, Chertov N, Sboeva Y, Boronnikova S, Pechenkina V, Nechaeva Y, Kalendar R 2024. Identification of SNPs Associated with Drought Resistance in Hybrid Populations of Picea abies (L.) H. Karst.– P. obovata (Ledeb.). Genes, 15(11): 1440. DOI:10.3390/genes15111440

144. Chertov N, Sboeva Y, Nechaeva Y, Boronnikova S, Zhulanov A, Pechenkina V, Kalendar R 2024. Polymorphic Loci of Adaptively Significant Genes Selection for Determining Nucleotide Polymorphism of Pinus sylvestris L. Populations in the Urals. Genes, 15(10): 1343. DOI:10.3390/genes15101343

2023

143. Kalendar R, Ivanov KI, Samuilova O, Kairov U, Zamyatnin A 2023. Isolation of high-molecular-weight DNA for long-read sequencing using a high-salt gel electroelution trap. Analytical Chemistry, 95(48): 17818-17825. DOI:10.1021/acs.analchem.3c03894

142. Kalendar R, Karlov GI (Eds.) 2023. Mobile Elements and Plant Genome Evolution, Comparative Analyses and Computational Tools, Volume II. Frontiers Research Topics, Lausanne: Frontiers Media SA. ISBN 978-2-8325-4016-9 DOI:10.3389/978-2-8325-4016-9

141. Belyayev A, Kalendar R, Josefiová J, Paštová L, Habibi F, Mahelka V, Mandák B, Krak K 2023. Telomere sequence variability in genotypes from natural plant populations: unusual block-organized double-monomer terminal telomeric arrays. BMC Genomics, 24: 572. DOI:10.1186/s12864-023-09657-y

140. Kalendar R, Kairov U, Karabayev D, Aitkulova AM, Tynyshtykbayeva N, Daniyarov A, Otarbay Z, Rakhimova S, Akilzhanova A, Sarbassov D 2023. Universal whole-genome Oxford nanopore sequencing of SARS-CoV-2 using tiled amplicons. Scientific Reports, 13: 10334. DOI:10.1038/s41598-023-37588-x

139. Kalendar R, Karlov GI 2023. Editorial: Mobile Elements and Plant Genome Evolution, Comparative Analyses and Computational Tools, Volume II. Frontiers in Plant Science, 14: 1308536. DOI:10.3389/fpls.2023.1308536

138. Blume R, Kalendar R, Guo L, Cahoon E, Blume Y 2023. Overcoming genetic paucity of Camelina sativa: possibilities for interspecific hybridization conditioned by the genus evolution pathway. Frontiers in Plant Science, 14: 1259431. DOI:10.3389/fpls.2023.1259431

137. Arvas YE, Marakli S, Kaya Y, Kalendar R 2023. The power of retrotransposons in high-throughput genotyping and sequencing. Frontiers in Plant Science, 14: 1174339. DOI:10.3389/fpls.2023.1174339

136. Zhulanov A, Chertov N, Nechaeva Y, Pechenkina V, Zhulanova L, Boronnikova S, Kalendar R, 2023. Genetic uniqueness and genetic structure of populations of Picea obovata Ledeb. and Larix sibirica Ledeb. in the northern and middle Urals. Forests, 14(9): 1822. DOI:10.3390/f14091822

135. Terletskaya N, Turzhanova A, Khapilina O, Zhumagul M, Meduntseva N, Kudrina N, Korbozova N, Kubentayev S, Kalendar R 2023. Genetic diversity in natural populations of Rhodiola species of different adaptation strategies. Genes, 14(4): 794. DOI:10.3390/genes14040794

134. Pozharskiy A, Kostyukova V, Khusnitdinova M, Adilbayeva K, Nizamdinova G, Kapytina A, Kerimbek N, Taskuzhina A, Kolchenko M, Abdrakhmanova A, Kisselyova N, Kalendar R, Gritsenko D 2023. Genetic diversity of the breeding collection of tomato varieties in Kazakhstan assessed using SSR, SCAR and CAPS markers. PeerJ, 11: e15683. DOI:10.7717/peerj.15683

133. Gritsenko D, Daurova A, Pozharskiy A, Nizamdinova G, Khusnitdinova M, Sapakhova Z, Daurov D, Zhapar K, Shamekova M, Kalendar R, Zhambakin K 2023. Investigation of mutation load and rate in androgenic mutant lines of rapeseed in early generations evaluated by high-density SNP genotyping. Heliyon, 9: e14065. DOI:10.1016/j.heliyon.2023.e14065

132. Rehman S, Ahmad Z, Ramakrishnan M, Kalendar R, Zhuge, Q 2023. Regulation of epigenetic memory in plants in response to cold and heat stress: towards climate resilient agriculture. Functional and Integrative Genomics, 23(4): 298. DOI:10.1007/s10142-023-01219-5

131. Ramakrishnan M, Papolu PK, Mullasseri S, Zhou M, Wei Q, Sharma A, Ahmad Z, Satheesh V, Kalendar R, Wei Q 2023. The role of LTR retrotransposons in plant genetic engineering: How to control their transposition in the genome. Plant Cell Reports, 42(1): 3-15. DOI:10.1007/s00299-022-02945-z

2022

130. Paterson AH, Tao D, Kalendar R (Eds.) 2022. Interspecific Hybridization in Plant Biology. Frontiers Research Topics, Lausanne: Frontiers Media SA. ISBN 978-2-83250-237-2 DOI:10.3389/978-2-83250-237-2

129. Papolu PK, Ramakrishnan M, Mullasseri S, Kalendar R, Wei Q, Zou LH, Ahmad Z, Ping Y, Vinod KK, Zhou M 2022. Retrotransposons: How the continuous evolutionary front shapes plant genomes for response to heat stress. Frontiers in Plant Science, 13: 1064847. DOI:10.3389/fpls.2022.1064847

128. Ramakrishnan M, Zhang Z, Mullasseri S, Kalendar R, Sharma A, Liu G, Zhou M, Wei Q 2022. Epigenetic stress memory: A new approach to study cold and heat stress responses in plants. Frontiers in Plant Science, 13: 1075279. DOI: 10.3389/fpls.2022.1075279

127. Kalendar R, Ghamkhar K, Franceschi P, Egea-Cortines M 2022. Editorial: Spectroscopy for Crop and Product Phenotyping. Frontiers in Plant Science, 13: 1058333. DOI:10.3389/fpls.2022.1058333

126. Kalendar R, Hunter Ch, Orbovic V 2022. Editorial: Innovative Applications of Sequencing Technologies in Plant Science. Frontiers in Plant Science, 13: 1058347. DOI:10.3389/fpls.2022.1058347

125. Kalendar R, Orbovic V, Egea-Cortines M, Song G-Q 2022. Editorial: Recent Advances in Plant Genetic Engineering and Innovative Applications. Frontiers in Plant Science, 13: 1045417. DOI:10.3389/fpls.2022.1045417

124. Tao D, Kalendar R, Paterson AH 2022. Editorial: Interspecific Hybridization in Plant Biology. Frontiers in Plant Science, 13: 1026492. DOI:10.3389/fpls.2022.1026492

123. Vostrikova A, Pechenkina V, Danilova M, Boronnikova S, Kalendar R, 2022. Gene polymorphism and total genetic score in martial arts athletes with different athletic qualifications. Genes, 13(9): 1677. DOI:10.3390/genes13091677

122. Kushiyev R, Tunçer C, Özdemir İO, Erper İ, Kalendar R, Alkan M, Özer G 2022. Molecular characterisation of native entomopathogenic fungi from ambrosia beetles in hazelnut orchards of Turkey and evaluation of their in vitro efficacy. Insects, 13(9): 824. DOI:10.3390/insects13090824

121. Kairov U, Amanzhanova A, Karabayev D, Rakhimova S, Aitkulova AM, Samatkyzy D, Kalendar R, Kozhamkulov U, Molkenov A, Gabdulkayum A, Sarbassov D, Akilzhanova A 2022. A high scale SARS-CoV-2 profiling by its whole-genome sequencing using Oxford Nanopore Technology in Kazakhstan. Frontiers in Genetics, 13: 906318. DOI:10.3389/fgene.2022.906318

120. Sboeva Y, Chertov N, Nechaeva Y, Valeeva A, Boronnikova S, Kalendar R 2022. Genetic diversity, structure, and differentiation of Pinus sylvestris L. populations in the East European Plain and the Middle Urals. Forests, 13(11): 1798. DOI:10.3390/f13111798

119. Chertov N, Nechaeva Y, Vasilyeva Y, Zhulanov A, Pystogova N, Danilova M, Boronnikova S, Kalendar R 2022. Genetic structure of Pinus populations in the Urals. Forests, 13(8): 1278. DOI:10.3390/f13081278

118. Pozharskiy A, Kostyukova V, Taskuzhina A, Nizamdinova G, Kisselyova N, Kalendar R, Karimov N, Gritsenko D 2022. Screening a collection of local and foreign varieties of Solanum lycopersicum L. in Kazakhstan for genetic markers of resistance against three tomato viruses. Heliyon, 8(8): e10095. DOI:10.1016/j.heliyon.2022.e10095

117. Pozharskiy A, Kostyukova V, Nizamdinova G, Kalendar R, Gritsenko D 2022. MLO proteins from tomato (Solanum lycopersicum L.) and related species in the broad phylogenetic context. Plants, 11(12):1588. DOI:10.3390/plants11121588

116. Belyayev A, Josefiová J, Jandová M, Kalendar R, Mahelka V, Mandák B, Krak K 2022. The structural diversity of CACTA transposons in genomes of Chenopodium (Amaranthaceae, Caryophyllales) species: specific traits and comparison with the similar elements of Angiosperms. Mobile DNA, 13:8. DOI:10.1186/s13100-022-00265-3

115. Kalendar R, Shustov AV, Akhmetollaev IA, Kairov U 2022. Designing allele-specific competitive-extension PCR-based assays for high-throughput genotyping and gene characterization. Frontiers Molecular Biosciences, 9:773956. DOI:10.3389/fmolb.2022.773956

114. Kalendar R, Baidyussen A, Serikbay D, Zotova L, Khassanova G, Kuzbakova M, Kurishbayev A, Jatayev S, Hu Y-G, Schramm C, Anderson PA, Jenkins CLD, Soole KL, Shavrukov Y 2022. Modified ‘Allele-specific qPCR’ method for SNP genotyping based on FRET. Frontiers in Plant Science, 12:747886. DOI:10.3389/fpls.2021.747886

113. Kalendar R 2022. A guide to using FASTPCR software for PCR, in silico PCR, and oligonucleotide analysis. Methods in molecular biology, 2392: 223-243. DOI:10.1007/978-1-0716-1799-1_16

2021

112. Papolu PK, Ramakrishnan M, Wei Q, Vinod KK, Yrjala K, Kalendar R, Zhou M 2021. Long terminal repeats (LTR) and transcription factors regulate PHRE1 and PHRE2 activity in Moso bamboo under heat stress. BMC Plant Biology, 21:585. DOI:10.1186/s12870-021-03339-1

111. Ramakrishnan M, Satish L, Kalendar R, Mathiyazhagan N, Sabariswaran K, Sharma A, Emamverdian A, Wei Q, Zhou M 2021. The dynamism of transposon methylation for plant development and stress adaptation. International Journal of Molecular Sciences, 22(21):11387. DOI:10.3390/ijms222111387

110. Kalendar R, Sabot F, Rodriguez F, Karlov GI, Natali L, Alix K 2021. Editorial: Mobile elements and plant genome evolution, comparative analyzes and computational tools. Frontiers in Plant Science, 12:735134. DOI:10.3389/fpls.2021.735134

109. Kalendar R, Shustov AV, Schulman AH 2021. Palindromic sequence-targeted (PST) PCR, version 2: an advanced method for high-throughput targeted gene characterization and transposon display. Frontiers in Plant Science, 12: 691940. DOI:10.3389/fpls.2021.691940

108. Chertov N, Vasilyeva Y, Zhulanov A, Nechaeva Y, Boronnikova S, Kalendar R 2021. Genetic structure and geographical differentiation of Larix sibirica Ledeb. in the Urals. Forests, 12(10): 1401. DOI:10.3390/f12101401

107. Vasilyeva Y, Chertov N, Nechaeva Y, Sboeva Y, Pystogova N, Boronnikova S, Kalendar R 2021. Genetic structure, differentiation and originality of Pinus sylvestris L. populations in the East of the East European Plain. Forests, 12(8): 999. DOI:10.3390/f12080999

106. Shevtsov V, Kairzhanova A, Shevtsov A, Shustov A, Kalendar R, Abdrakhmanov S, Lukhnova L, Izbanova U, Ramankulov Y, Vergnaud G 2021. Genetic diversity of Francisella tularensis subsp. holarctica in Kazakhstan. PLoS Neglected Tropical Diseases, 15(5): e0009419. DOI:10.1371/journal.pntd.0009419

105. Erper I, Ozer G, Kalendar R, Avci S, Yildirim E, Alkan M, Turkkan M 2021. Genetic diversity and pathogenicity of Rhizoctonia spp. isolates associated with red cabbage in Samsun (Turkey). Journal of Fungi, 7(3): 234. DOI:10.3390/jof7030234

104. Malaviya DR, Roy AK, Kaushal P, Pathak S, Kalendar R 2021. Phenotype study of multifoliolate leaf formation in Trifolium alexandrinum L. PeerJ, 9: e10874. DOI:10.7717/peerj.10874

103. Khapilina O, Raiser O, Danilova A, Shevtsov V, Turzhanova A, Kalendar R 2021. DNA profiling and assessment of genetic diversity of relict species Allium altaicum Pall. on the territory of Altai. PeerJ, 9: e10674. DOI:10.7717/peerj.10674

102. Khapilina O, Turzhanova A, Danilova A, Tumenbayeva A, Shevtsov V, Kotukhov Y, Kalendar R 2021. Primer Binding Site (PBS) profiling of genetic diversity of natural populations of endemic species Аllium ledebourianum Schult.. BioTech, 10(4): 23. DOI:10.3390/biotech10040023

101. Kalendar R, Kospanova D, Schulman AH 2021. Transposon-based tagging in silico using FastPCR software. Methods in molecular biology, 2250: 245-256. DOI:10.1007/978-1-0716-1134-0_23

100. Kalendar R, Muterko A, Boronnikova S 2021. Retrotransposable Elements: DNA Fingerprinting and the Assessment of Genetic Diversity. Methods in molecular biology, 2222: 263-286. DOI:10.1007/978-1-0716-0997-2_15

99. Kalendar R, Boronnikova S, Seppänen M 2021. Isolation and purification of DNA from complicated biological samples. Methods in molecular biology, 2222: 57-67. DOI:10.1007/978-1-0716-0997-2_3

2020

98. Kulyyassov A, Kalendar R 2020. In silico estimation of the abundance and phylogenetic significance of the composite Oct4-Sox2 binding motifs within a wide range of species. Data, 5(4): 111. DOI:10.3390/data5040111

97. Kirillov S, Daniyarov A, Turgimbayeva A, Ramankulov Y, Kalendar R, Abeldenov S 2020. Draft genome sequence of Lactobacillus salivarius KZ-NCB, isolated from chicken cecum. Microbiology Resource Announcements, 9: e01129-20. DOI:10.1128/MRA.01129-20

96. Belyayev A, Jandová M, Josefiová J, Kalendar R, Mahelka V, Mandák B, Krak K 2020. The major satellite DNA families of the diploid Chenopodium album aggregate species: Arguments for and against the “library hypothesis”. Plos One, 15(10): e0241206. DOI:10.1371/journal.pone.0241206

95. Voronova A, Rendón-Anaya M, Ingvarsson P, Kalendar R, Rungis D 2020. Comparative study of pine reference genomes reveals transposable element interconnected gene networks. Genes, 11(10): 1216. DOI:10.3390/genes11101216

94. Alm E, Broberg EK, Connor T, Hodcroft EB, Komissarov AB, Maurer-Stroh S, Melidou A, Neher RA, O'Toole Á, Pereyaslov D, The WHO European Region sequencing laboratories and GISAID EpiCoV group (Investigators) 2020. Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020. Eurosurveillance, 25(32): 2001410. DOI:10.2807/1560-7917.ES.2020.25.32.2001410

93. Gorbikova E, Samsonov SA, Kalendar R, 2020. Probing the proton-loading site of cytochrome c oxidase using Time-Resolved Fourier Transform Infrared spectroscopy. Molecules, 25(15): 3393. DOI:10.3390/molecules25153393

92. Gorbikova E, Kalendar R 2020. Comparison between O and OH intermediates of cytochrome c oxidase studied by FTIR spectroscopy. Frontiers in Chemistry, 8:387. DOI:10.3389/fchem.2020.00387 Frontiers in Chemistry (Chemical Biology) the Research Topic Chemical Biology Editor’s Pick 2021

91. Turzhanova A, Khapilina O, Tumenbayeva A, Shevtsov V, Raiser O, Kalendar R 2020. Genetic diversity of Alternaria species associated with black point in wheat grains. PeerJ, 8:e9097. DOI:10.7717/peerj.9097

90. Kalendar R, Raskina O, Belyayev A, Schulman AH 2020. Long tandem arrays of Cassandra retroelements and their role in genome dynamics in plants. International Journal of Molecular Sciences, 21(8): 2931. DOI:10.3390/ijms21082931

89. Ghonaim M, Kalendar R, Barakat H, Elsherif N, Ashry N, Schulman AH 2020. High-throughput retrotransposon-based genetic diversity of maize germplasm assessment and analysis. Molecular Biology Reports, 47: 1589-1603. DOI:10.1007/s11033-020-05246-4

88. Li Sh, Ramakrishnan M, Vinod KK, Kalendar R, Yrjälä K, Zhou M 2020. Development and deployment of high-throughput retrotransposon-based markers reveal genetic diversity and population structure of Asian bamboo. Forests, 11(1): 31. DOI:10.3390/f11010031

87. Doungous O, Kalendar R, Filippova N, Ngane BK 2020. Utility of iPBS retrotransposons markers for molecular characterization of African Gnetum species. Plant Biosystems, 154(5): 587-592. DOI:10.1080/11263504.2019.1651782

86. Kalendar R, Vottonen LL, Seppänen MM 2020. Genetic diversity and distribution of the VRN1 gene within timothy (Phleum pratense L.) accessions. Grassland Science in Europe, 25: 94-96. 28th General Meeting on "Meeting the future demands for grassland production”, 19-21 October 2020, University of Helsinki, Finland.

2019

85. Kalendar R, Shustov AV, Seppänen MM, Schulman AH, Stoddard FL 2019. Palindromic sequence-targeted (PST) PCR: a rapid and efficient method for high-throughput gene characterization and genome walking. Scientific Reports, 9: 17707. DOI:10.1038/s41598-019-54168-0

84. Nováková E, Zablatzká L, Brus J, Nesrstová V, Hanáček P, Kalendar R, Cvrčková F, Majeský Ľ, Smýkal P 2019. Allelic diversity of Acetyl coenzyme A carboxylase accD/bccp genes implicated in nuclear-cytoplasmic conflict in the wild and domesticated pea (Pisum sp.). International Journal of Molecular Sciences, 20(7): 1773. DOI:10.3390/ijms20071773

83. Belyayev A, Josefiová J, Jandová M, Kalendar R, Krak K, Mandák B 2019. Natural history of a satellite DNA family: from the ancestral genome component to species-specific sequences, concerted and non-concerted evolution. International Journal of Molecular Sciences, 20(5): 1201. DOI:10.3390/ijms20051201

82. Milovanov A, Zvyagin A, Daniyarov A, Kalendar R, Troshin L 2019. Genetic analysis of the grapevine genotypes of the Russian Vitis ampelographic collection using iPBS markers. Genetica, 147(1): 91-101. DOI:10.1007/s10709-019-00055-5

81. Kalendar R, Amenov A, Daniyarov A 2019. Use of retrotransposon-derived genetic markers to analyze genomic variability in plants. Functional Plant Biology, 46(1): 15-29. DOI:10.1071/FP18098

80. Kalendar R, Vottonen LL, Seppänen MM 2019. Quantification of roots in soil, plant-fungal symbioses and in mixed plant populations with real-time PCR. Grassland Science in Europe, 24: 458-460. EGF-EUCARPIA Joint Symposium 2019, Zurich, Switzerland. DOI:10.3929/ethz-b-000369264

2018

79. Vuorinen AL, Kalendar R, Fahima T, Korpelainen H, Nevo E, Schulman AH 2018. Retrotransposon-based genetic diversity assessment in wild emmer wheat (Triticum turgidum ssp. dicoccoides). Agronomy, 8(7): 107. DOI:10.3390/agronomy8070107

78. Baranova T, Kalendar R, Kalayev V, Sorokopudov V, Burmenko J 2018. Relationship between cytogenetic characteristics and molecular-genetic differences in species of the genus Rhododendron L. when introduced. Agricultural Biology, 53(3): 511-520. DOI:10.15389/agrobiology.2018.3.511eng

2017

77. Kalendar R, Samuilova O, Ivanov KI 2017. FastPCR: an in silico tool for fast primer and probe design and advanced sequence analysis. Genomics, 109: 312-319. DOI:10.1016/j.ygeno.2017.05.005

76. Kalendar R, Muterko A, Shamekova M, Zhambakin K 2017. In silico PCR tools a fast primer, probe and advanced searching. Methods in Molecular Biology, 1620: 1-31. DOI:10.1007/978-1-4939-7060-5_1

75. Kalendar R, Tselykh T, Khassenov B, Ramanculov EM 2017. Introduction on using the FastPCR software and the related Java web tools for PCR, in silico PCR, and oligonucleotide assembly and analysis. Methods in Molecular Biology, 1620: 33-64. DOI:10.1007/978-1-4939-7060-5_2

74. Kalendar R, Aizharkyn KS, Khapilina ON, Amenov AA, Tagimanova DS 2017. Plant diversity and transcriptional variability assessed by retrotransposon-based molecular markers. Vavilov Journal of Genetics and Breeding, 21(1): 128-134. DOI:10.18699/VJ17.231

73. Kalendar R, Belyayev A, Zachepilo T, Maidanyuk D, Vaido A, Schulman AH, Dyuzhikova N 2017. Copy-number variation of housekeeping gene rpl13a in rat strains selected for nervous system excitability. Molecular and Cellular Probes, 33: 11-15. DOI:10.1016/j.mcp.2017.02.004

2016

72. Drábek J, Jaluvková M, Kalendar R, Pinto LFA, Pavlousek P, Klepárník K, Frébort I 2016. Design and validation of STR hexaplex assay for DNA profiling of grapevine cultivars. Electrophoresis, 37(23-24): 3059–3067. DOI:10.1002/elps.201600068

71. Muterko A, Kalendar R, Salina E 2016. Allelic variation at the VERNALIZATION-A1, VRN-B1, VRN-B3, and PHOTOPERIOD-A1 genes in cultivars of Triticum durum Desf.. Planta, 244(6): 1253-1263. DOI:10.1007/s00425-016-2584-5

70. Tanhuanpää P, Erkkilä M, Kalendar R, Schulman A, Manninen O 2016. Assessment of genetic diversity in Nordic timothy (Phleum pratense L.). Hereditas, 153:5. DOI:10.1186/s41065-016-0009-x

69. Muterko A, Kalendar R, Salina E 2016. Novel alleles of the VERNALIZATION1 genes in wheat are associated with modulation of DNA curvature and flexibility in the promoter region. BMC Plant Biology, 16(1): 65-81. DOI:10.1186/s12870-015-0691-2

2015

68. Oumar D, Kalendar R, Adiobo A, Schulman AH 2015. Retrotransposon molecular markers resolve cocoyam (Xanthosoma sagittifolium) and taro (Colocasia esculenta) by type and variety. Euphytica, 206(2): 541-554. DOI:10.1007/s10681-015-1537-6

67. Muterko A, Kalendar R, Cockram J, Balashova I 2015. Discovery, evaluation and distribution of haplotypes and new alleles of the Photoperiod-A1 gene in wheat. Plant Molecular Biology, 88(1-2): 149-164. DOI:10.1007/s11103-015-0313-2 Supplementary

66. Muterko A, Balashova I, Cockram J, Kalendar R, Sivolap Yu 2015. The new wheat vernalization response allele Vrn-D1 is caused by DNA transposon insertion within the first intron. Plant Molecular Biology Reporter, 33(2): 294-303. DOI:10.1007/s11105-014-0750-0

65. Stratula OR, Kalendar RN, Sivolap YuM 2015. Allelic variants of the gene bamy1 barley in eastern European and central Asian areas. Cytology and Genetics, 49(2): 80-89. DOI:10.3103/S0095452715020103

64. Abdollahi Mandoulakani B, Yaniv E, Kalendar R, Raats D, Bariana HS, Reza Bihamta M, Schulman AH 2015. Development of IRAP- and REMAP-derived SCAR markers for marker-assisted selection of the strip rust resistance gene Yr15 derived from wild emmer wheat. Theoretical and Applied Genetics, 128(2): 211-219. DOI:10.1007/s00122-014-2422-8

2014

63. Stratula O, Cockram J, Kalendar R 2014. Molecular genetic analysis of cereal b-amylase genes using exon-primed inter-crossing (EPIC) PCR. Field and Vegetable Crops Research, 51(3): 175-189. DOI:10.5937/ratpov51-6808

62. Baranova TV, Kalendar RN, Kalaev VN 2014. The phylogeny study of the genus Rhododendron L. based on studies sequence spacers ITS1-ITS2. Siberian Journal of Forest Science, 1(6): 29-45.

61. Zachepilo T, Kalendar R, Schulman AH, Vaido A, Dyuzhikova N 2014. Emotionally painful stress causes changes in L1 insertion pattern in the hippocampus in rats with different nervous system excitability. European Neuropsychopharmacology, Abstracts of the 27th ECNP Congress (Poster sessions), 24(Supplement 2): S163. DOI:10.1016/S0924-977X(14)70247-0

60. Balážová Ž, Trebichalský A, Gálová Z, Kalendar R, Schulman AH, Stratula O, Chňapek M 2014. Genetic diversity of triticale cultivars based on microsatellite and retrotransposon-based markers. The Journal of Microbiology, Biotechnology and Food Sciences, 3(2): 58-60.

59. Moisy C, Schulman AH, Kalendar R, Buchmann JP, Pelsy F 2014. The Tvv1 retrotransposon family is conserved between plant genomes separated by over 100 million years. Theoretical and Applied Genetics, 127(5): 1223-1235. DOI:10.1007/s00122-014-2293-z

58. Kalendar R, Lee D, Schulman AH 2014. FastPCR software for PCR, in silico PCR, and oligonucleotide assembly and analysis. Methods in Molecular Biology, 1116: 271-302. DOI:10.1007/978-1-62703-764-8_18

57. Kalendar R, Schulman AH 2014. Transposon based tagging: IRAP, REMAP, and iPBS. Methods in Molecular Biology, 1115: 233-255. DOI:10.1007/978-1-62703-767-9_12

2013

56. Kuras A, Antonius K, Kalendar R, Kruczynska D, Korbin M Application of five DNA marker techniques to distinguish between five apple (Malus X domestica Borkh.) cultivars and their sports. Journal of Horticultural Science and Biotechnology, 88(6): 790-794. DOI:10.1080/14620316.2013.11513040

55. Trebichalsky A, Kalendar R, Schulman A, Stratula O, Galova Z, Balazova Z, Chnapek M 2013. Detection of genetic relationships among spring and winter Triticale (x Triticosecale Witt.) and rye cultivars (Secale cereale L.) by using retrotransposon-based markers. Czech Journal of genetics and plant breeding, 49(4): 171-174. DOI:10.17221/56/2013-CJGPB

54. Bublyk OM, Andreev IO, Kalendar RN, Spiridonova KV, Kunakh VA 2013. Efficiency of different PCR-based marker systems for assessment of Iris pumila genetic diversity. Biologia, 68(4): 613-620. DOI:10.2478/s11756-013-0192-4

2012

53. Trebichalský A, Schulman AH, Kalendar R, Stratula O, Gálová Z 2012. Exploration of genetic relations between winter triticale (x Triticosecale witt.) and rye (Secale cereale l.) cultivars using retrotransposon-based markers. The Journal of Microbiology, Biotechnology and Food Sciences, 1(4): 711-716.

52. Hosid E, Brodsky L, Kalendar R, Raskina O, Belyayev A 2012. Diversity of Long Terminal Repeat Retrotransposon Genome Distribution in Natural Populations of the Wild Diploid Wheat Aegilops speltoides. Genetics, 190(1): 263-274. DOI:10.1534/genetics.111.134643

2011

51. Kalendar R 2011. The use of retrotransposon-based molecular markers to analyze genetic diversity. Field and Vegetable Crops Research, 48(2): 261-274. DOI:10.5937/ratpov1102261K

50. Kalendar R, Lee D, Schulman AH 2011. Java web tools for PCR, in silico PCR, and oligonucleotide assembly and analysis. Genomics, 98(2): 137-144. DOI:10.1016/j.ygeno.2011.04.009

49. Tenhola-Roininen T, Kalendar R, Schulman AH, Tanhuanpaa P. 2011. A doubled haploid rye linkage map with a QTL affecting α-amylase activity. Journal of Applied Genetics, 52(3): 299-304. DOI:10.1007/s13353-011-0029-1

48. Smykal P, Bacova-Kerteszova N, Kalendar R, Corander J, Schulman A, Pavelek M 2011. Genetic diversity of cultivated flax (Linum usitatissimum L.) germplasm assessed by retrotransposon-based markers. Theoretical and Applied Genetics, 122(7): 1385-1397. DOI:10.1007/s00122-011-1539-2

47. Kalendar R, Flavell A, Ellis THN, Sjakste T, Moisy C, Schulman AH 2011. Analysis of plant diversity with retrotransposon-based molecular markers. Heredity, 106: 520-530. DOI:10.1038/hdy.2010.93

46. Sivolap YM, Kozhuhova N, Kalendar RN 2011. Variability and specificity of the genomes of crops plants. Kiev, Astroprint, P. 336. ISBN 978-966-190-274-8.

2010

45. Kalendar R, Antonius K, Smykal P, Schulman AH 2010. iPBS: A universal method for DNA fingerprinting and retrotransposon isolation. Theoretical and Applied Genetics, 121(8): 1419-1430. DOI:10.1007/s00122-010-1398-2

44. Belyayev A, Kalendar R, Brodsky L, Nevo E, Schulman AH, Raskina O 2010. Transposable elements in a marginal plant population: temporal fluctuations provide new insights into genome evolution of wild diploid wheat. Mobile DNA, 1:6. DOI:10.1186/1759-8753-1-6

43. Boronnikova SV, Kalendar RN 2010. Using IRAP markers for analysis of genetic variability in populations of resource and rare species of plants. Russian Journal of Genetics, 46(1): 36-42. DOI:10.1134/S1022795410010060

2009

42. Kalendar R, Lee D, Schulman AH 2009. FastPCR software for PCR primer and probe design and repeat search. Genes, Genomes and Genomics, 3(1): 1-14.

41. Vukich M, Schulman AH, Giordani T, Natali L, Kalendar R, Cavallini A 2009. Genetic variability in sunflower and in the Helianthus genus as assessed by retrotransposon-based molecular markers. Theoretical and Applied Genetics, 19(6): 1027-1038. DOI:10.1007/s00122-009-1106-2

40. Smýkal P, Kalendar R, Ford R, Macas J, Griga M 2009. Evolutionary conserved lineage of Angela-family retrotransposons as a genome-wide microsatellite repeat dispersal agent. Heredity, 103: 157-167. DOI:10.1038/hdy.2009.45

2008

39. Kalendar R, Tanskanen J, Chang W, Antonius K, Sela H, Peleg O, Schulman AH 2008. Cassandra retrotransposons carry independently transcribed 5S RNA. Proceedings of the National Academy of Sciences of the United States of America, 105(15): 5833-5838. DOI:10.1073/pnas.0709698105

38. Ramallo E, Kalendar R, Schulman AH, and Martínez-Izquierdo JA 2008. Reme1, a Copia retrotransposon in melon, is transcriptionally induced by UV light. Plant Molecular Biology, 66 (1-2): 137-150. DOI:10.1007/s11103-007-9258-4

37. Tanhuanpää P, Kalendar R, Schulman AH, Kiviharju E 2008. The first double haploid linkage map for cultivated oat. Genome, 51(8): 560-569. DOI:10.1139/G08-040

2007

36. Tanhuanpää P, Kalendar R, Schulman AH, Kiviharju E 2007. A major gene for grain cadmium accumulation in oat (Avena sativa L.). Genome 50:588-594. DOI:10.1139/G07-036

35. Kalendar R, Boronnikova SV, Kokaeva ZG, Gostimskij SA, Mikheeva OV 2007. "Molecular genetics". Perm State University and Moscow State University, ISBN 5-7944-0913-4.

2006

34. Sabot F, Kalendar R, Jääskeläinen M, Chang W, Tanskanen J, Schulman AH 2006. Retrotransposons: metaparasites and agents of genome evolution. Israel Journal of Ecology and Evolution, 52(3-4): 319-330. DOI:10.1560/IJEE_52_3-4_319

33. Manninen OM, Jalli M, Kalendar R, Schulman A, Afanasenko O, Robinson J 2006. Mapping of major spot-type and net-type netblotch resistance genes in the Ethiopian barley line CI 9819. Genome, 49: 1564-1571. DOI:10.1139/G06-119

32. Kalendar R, Schulman AH 2006. IRAP and REMAP for retrotransposon-based genotyping and fingerprinting. Nature Protocols,1(5): 2478-2484. DOI:10.1038/nprot.2006.377

31. Tanhuanpaa P, Kalendar R, Laurila J, Schulman AH, Manninen O, Kiviharju E 2006. Generation of SNP markers for short straw in oat (Avena sativa L.). Genome, 49(3): 282-287. DOI:10.1139/G05-100

30. Antonius-Klemola K, Kalendar R, Schulman AH 2006. TRIM retrotransposons occur in apple and are polymorphic between varieties but not sports. Theoretical and Applied Genetics, 112(6): 999-1008. DOI:10.1007/s00122-005-0203-0

29. Brik AF, Kalendar RN, Stratula OR, Sivolap YuM 2006. IRAP and REMAP analyses of barley varieties of Odessa breeding. Cytology and Genetics, 3: 24-33.

2005

28. Teo CH, Tan SH, Ho CL, Faridah QZ, Othman YR, Heslop-Harrison JS, Kalendar R, Schulman AH 2005. Genome constitution and classification using retrotransposon-based markers in the orphan crop banana. Journal of Plant Biology, 48(1): 96-105. DOI:10.1007/BF03030568

27. Vicient CM, Kalendar R, Schulman AH 2005. Variability, recombination and mosaic evolution of the rarley BARE-1 retrotransposon. Journal of Molecular Evolution, 61(3): 275-91. DOI:10.1007/s00239-004-0168-7

26. Schulman AH, Kalendar R. 2005. A movable feast: Diverse retrotransposons and their contribution to barley genome dynamics. Cytogenetic and Genome Research, 110 (1-4): 598-605. DOI:10.1159/000084993

1994-2004

25. Kalendar R, Vicient CM, Peleg O, Anamthawat-Jonsson K, Bolshoy A, Schulman AH 2004. Large retrotransposon derivatives: abundant, conserved but nonautonomous retroelements of barley and related genomes. Genetics, 166(3): 1437-1450. DOI:10.1534/genetics.166.3.1437

24. Leigh F, Kalendar R Lea V, Lee D, Donini P, Schulman AH 2003. Comparison of the utility of barley retrotransposon families for genetic analysis by molecular marker techniques. Molecular Genetics and Genomics, 269(3): 464-474. DOI:10.1007/s00438-003-0850-2

23. Baumel A, Ainouch M, Kalendar R, Schulman AH 2002. Retrotransposons and genomic stability in populations of the young allopolyploid species Spartina anglica Hubard (Poaceae). Molecular Biology and Evolution, 19 (8): 1218-1227. DOI:10.1093/oxfordjournals.molbev.a004182

22. Boyko E, Kalendar R, Korzun V, Korol A, Schulman AH, Gill BS 2002. A high-density cytogenetic map of the Aegilops tauschii genome incorporating retrotransposons and defence related genes: insights into cereal chromosome structure and function. Plant Molecular Biology, 48: 767-790. DOI:10.1023/A:1014831511810 Cover

21. Календарь РН, Глазко ВИ 2002. Типы молекулярно-генетических маркеров и их применение. Физиология и биохимия культурных растений, 34(4): 279-296.

20. Balashova IA, Kalendar RN, Fait V, Sivolap YuM 2002. The design of DNA markers for the Vrn-D1 locus of soft wheat. Biotechnology in Russia, 2: 20-24.

19. Vicient C M, Kalendar R, Schulman AH 2001. Envelope-class retrovirus-like elements are widespread, transcribed and spliced, and insertionally polymorphic in plants. Genome Research, 11: 2041-2049. DOI:10.1101/gr.193301

18. Vicient CM, Jääskeläinen M, Kalendar R, Schulman AH 2001. Active retrotransposons are a common feature of grass genomes. Plant Physiology, 125: 1283-1292. DOI:10.1104/pp.125.3.1283

17. Kalendar R, Tanskanen J, Immonen S, Nevo E, Schulman AH 2000. Genome evolution of wild barley (Hordeum spontaneum) by BARE-1 retrotransposon dynamics in response to sharp microclimatic divergence. Proceedings of the National Academy of Sciences of the United States of America, 97(12), 6603-6607. DOI:10.1073/pnas.110587497 "Further reading": "Science"

16. Manninen O, Kalendar R, Robinson J, Schulman A H 2000. Application of BARE-1 retrotransposon markers to the mapping of a major resistance gene for net blotch in barley. Molecular Genetics and Genomics, 264: 325-334. DOI:10.1007/s004380000326

15. Vicient CM, Kalendar R, Anamthawat-Jónsson K, Suoniemi A, Schulman AH 1999. Structure, functionality, and evolution of the BARE-1 retrotransposon of barley. Genetica, 107(1-3): 53-63. DOI:10.1023/A:1003929913398

14. Jääskeläinen M, Mykkänen A-H, Arna T, Vicient C, Suoniemi A, Kalendar R, Savilahti H, Schulman AH 1999. Retrotransposon BARE-1: Expression of encoded proteins and formation of virus- like particles in barley cells. Plant Journal, 20(4): 413-422. DOI:10.1046/j.1365-313x.1999.00616.x

13. Gribbon BM, Pearce SR, Kalendar R, Schulman AH, Paulin L, Jack P, Kumar A, Flavell AJ 1999. Phylogeny and transpositional activity of Ty1-copia group retrotransposons in cereal genomes. Molecular Genetics and Genomics, 261: 883-891. DOI:10.1007/PL00008635

12. Kalendar R, Grob T, Regina M, Suoniemi A, Schulman AH 1999. IRAP and REMAP: two new retrotransposon-based DNA fingerprinting techniques. Theoretical and Applied Genetics, 98: 704-711. DOI:10.1007/s001220051124

11. Sulima II, Kalendar RN, Sivolap YuM 2000. The mapping of the barley genome by RAPD analysis using double haploid strains. Cytology and Genetics, 34(4): 41-49.

10. Netsvetaev VP, Kalendar RN 1999. The use of collections of self-pollinators for estimating gene linkage. Russian Journal of Genetics, 35(4): 393-402.

9. Glazko VI, Dubin AA, Kalendar RM, Glazko GV, Scherepitko VI 1999. Comparisons analysis of polymorphic bands from different microsetellite loci in soyabean. Cytology and Genetics, 33(5): 47-51.

8. Sivolap YuM, Kalendar RN 1998. Investigations of interspecies polymorphism and identifications of genotypes of barley (Hordeum vulgare L.). Cytology and Genetics, 32(6): 35-41.

7. Sivolap YM, Kalendar RN, Verbitskaya TG, Brik AF, Kozhuhova NE, Solodenko AE, Chebotar SV, Balashova IA, Barisheva IA, Topchieva EA 1998. Use of the polymerase chain reaction analysis for plant breeding and genetics investigation. Kiev, Agrarnaya Nauka, P.156. 0099-6447-P

6. Sivolap YuM, Kalendar RN, Netsvetaev VP 1997. Use of polymerase chain reaction products to map the barley (H.vulgare L.) genome. Russian Journal of Genetics, 33: 43-49.

5. Sivolap YuM, Kalendar RM, Netsvetaev VP, Chaplya AE 1997. The markers analysis of some QTLs of barley with using RAPD and isozymes. Cytology and Genetics, 31: 39-44.

4. Sivolap YuM, Kalendar RN 1995. Genetic polymorphism in barley detected by PCR with arbitrary primers. Russian Journal of Genetics, 31: 1155-1161.

3. Kalendar RN, Sivolap YuM 1995. Polymerase chain reaction with arbitrary oligonucleotide primers. Biopolymers and Cell, 11(3-4): 55-66. DOI:10.1046/10.7124/bc.0003ED

2. Netsvetaev VP, Kalendar RN, Sivolap YuM 1995. ß-amylase polymorphism in barley is detected by PCR with arbitrary primer. Barley Genetics Newsletter, 24: 80-83.

1. Sivolap YuM, Kalendar RN, Chebotar SV 1994. Genetics polymorphism of cereal plant detected by PCR with arbitrary primers. Cytology and Genetics, 28: 54-61.