Next Generation Sequencing for Detection and Discovery of Plant Viruses and Viroids: Comparison of Two Approaches
Pecman, Anja, Kutnjak, Denis, Gutiérrez-Aguirre, Ion, Adams, Ian, Fox, Adrian, Boonham, Neil, Ravnikar, Maja
Published in Frontiers in microbiology (13.10.2017)
Published in Frontiers in microbiology (13.10.2017)
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Journal Article
Transmission modes affect the population structure of potato virus Y in potato
da Silva, Washington, Kutnjak, Denis, Xu, Yi, Xu, Yimin, Giovannoni, James, Elena, Santiago F., Gray, Stewart
Published in PLoS pathogens (01.06.2020)
Published in PLoS pathogens (01.06.2020)
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Journal Article
DNA barcoding insufficiently identifies European wild bees (Hymenoptera, Anthophila) due to undefined species diversity, genus‐specific barcoding gaps and database errors
Janko, Šet, Rok, Šturm, Blaž, Koderman, Danilo, Bevk, Andrej, Gogala, Denis, Kutnjak, Klemen, Čandek, Matjaž, Gregorič
Published in Molecular ecology resources (01.07.2024)
Published in Molecular ecology resources (01.07.2024)
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Journal Article
Deep sequencing of virus-derived small interfering RNAs and RNA from viral particles shows highly similar mutational landscapes of a plant virus population
Kutnjak, Denis, Rupar, Matevž, Gutierrez-Aguirre, Ion, Curk, Tomaž, Kreuze, Jan F, Ravnikar, Maja
Published in Journal of virology (01.05.2015)
Published in Journal of virology (01.05.2015)
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Journal Article
In-depth study of tomato and weed viromes reveals undiscovered plant virus diversity in an agroecosystem
Rivarez, Mark Paul Selda, Pecman, Anja, Bačnik, Katarina, Maksimović, Olivera, Vučurović, Ana, Seljak, Gabrijel, Mehle, Nataša, Gutiérrez-Aguirre, Ion, Ravnikar, Maja, Kutnjak, Denis
Published in Microbiome (28.03.2023)
Published in Microbiome (28.03.2023)
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Journal Article
Systematic Comparison of Nanopore and Illumina Sequencing for the Detection of Plant Viruses and Viroids Using Total RNA Sequencing Approach
Pecman, Anja, Adams, Ian, Gutiérrez-Aguirre, Ion, Fox, Adrian, Boonham, Neil, Ravnikar, Maja, Kutnjak, Denis
Published in Frontiers in microbiology (11.05.2022)
Published in Frontiers in microbiology (11.05.2022)
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Journal Article
Escaping to the summits: Phylogeography and predicted range dynamics of Cerastium dinaricum, an endangered high mountain plant endemic to the western Balkan Peninsula
Kutnjak, Denis, Kuttner, Michael, Niketić, Marjan, Dullinger, Stefan, Schönswetter, Peter, Frajman, Božo
Published in Molecular phylogenetics and evolution (01.09.2014)
Published in Molecular phylogenetics and evolution (01.09.2014)
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Journal Article
High Similarity of Novel Orthoreovirus Detected in a Child Hospitalized with Acute Gastroenteritis to Mammalian Orthoreoviruses Found in Bats in Europe
Steyer, Andrej, Gutiérrez-Aguire, Ion, Kolenc, Marko, Koren, Simon, Kutnjak, Denis, Pokorn, Marko, Poljšak-Prijatelj, Mateja, Racki, Nejc, Ravnikar, Maja, Sagadin, Martin, Fratnik Steyer, Adela, Toplak, Nataša
Published in Journal of Clinical Microbiology (01.11.2013)
Published in Journal of Clinical Microbiology (01.11.2013)
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Journal Article
Tomato brown rugose fruit virus in aqueous environments - survival and significance of water-mediated transmission
Mehle, Nataša, Bačnik, Katarina, Bajde, Irena, Brodarič, Jakob, Fox, Adrian, Gutiérrez-Aguirre, Ion, Kitek, Miha, Kutnjak, Denis, Loh, Yue Lin, Maksimović Carvalho Ferreira, Olivera, Ravnikar, Maja, Vogel, Elise, Vos, Christine, Vučurović, Ana
Published in Frontiers in plant science (02.06.2023)
Published in Frontiers in plant science (02.06.2023)
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Journal Article
In-Depth Comparison of Adeno-Associated Virus Containing Fractions after CsCl Ultracentrifugation Gradient Separation
Janc, Mojca, Zevnik, Kaja, Dolinar, Ana, Jakomin, Tjaša, Štalekar, Maja, Bačnik, Katarina, Kutnjak, Denis, Žnidarič, Magda Tušek, Zentilin, Lorena, Fedorov, Dmitrii, Dobnik, David
Published in Viruses (31.07.2024)
Published in Viruses (31.07.2024)
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Journal Article
Managing the deluge of newly discovered plant viruses and viroids: an optimized scientific and regulatory framework for their characterization and risk analysis
Fontdevila Pareta, Nuria, Khalili, Maryam, Maachi, Ayoub, Rivarez, Mark Paul S, Rollin, Johan, Salavert, Ferran, Temple, Coline, Aranda, Miguel A, Boonham, Neil, Botermans, Marleen, Candresse, Thierry, Fox, Adrian, Hernando, Yolanda, Kutnjak, Denis, Marais, Armelle, Petter, Françoise, Ravnikar, Maja, Selmi, Ilhem, Tahzima, Rachid, Trontin, Charlotte, Wetzel, Thierry, Massart, Sebastien
Published in Frontiers in microbiology (30.05.2023)
Published in Frontiers in microbiology (30.05.2023)
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Web Resource
Identification of novel reassortant mammalian orthoreoviruses from bats in Slovenia
Naglič, Tina, Rihtarič, Danijela, Hostnik, Peter, Toplak, Nataša, Koren, Simon, Kuhar, Urška, Jamnikar-Ciglenečki, Urška, Kutnjak, Denis, Steyer, Andrej
Published in BMC veterinary research (03.09.2018)
Published in BMC veterinary research (03.09.2018)
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Journal Article
Evaluation of Methods and Processes for Robust Monitoring of SARS-CoV-2 in Wastewater
Maksimovic Carvalho Ferreira, Olivera, Lengar, Živa, Kogej, Zala, Bačnik, Katarina, Bajde, Irena, Milavec, Mojca, Županič, Anže, Mehle, Nataša, Kutnjak, Denis, Ravnikar, Maja, Gutierrez-Aguirre, Ion
Published in Food and environmental virology (01.12.2022)
Published in Food and environmental virology (01.12.2022)
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Journal Article
A Primer on the Analysis of High-Throughput Sequencing Data for Detection of Plant Viruses
Kutnjak, Denis, Tamisier, Lucie, Adams, Ian, Boonham, Neil, Candresse, Thierry, Chiumenti, Michela, De Jonghe, Kris, Kreuze, Jan F, Lefebvre, Marie, Silva, Gonçalo, Malapi-Wight, Martha, Margaria, Paolo, Mavrič Pleško, Irena, McGreig, Sam, Miozzi, Laura, Remenant, Benoit, Reynard, Jean-Sebastien, Rollin, Johan, Rott, Mike, Schumpp, Olivier, Massart, Sébastien, Haegeman, Annelies
Published in Microorganisms (Basel) (14.04.2021)
Published in Microorganisms (Basel) (14.04.2021)
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Web Resource
High-Throughput Sequencing Facilitates Characterization of a "Forgotten" Plant Virus: The Case of a Henbane Mosaic Virus Infecting Tomato
Pecman, Anja, Kutnjak, Denis, Mehle, Nataša, Žnidarič, Magda Tušek, Gutiérrez-Aguirre, Ion, Pirnat, Patricija, Adams, Ian, Boonham, Neil, Ravnikar, Maja
Published in Frontiers in microbiology (19.11.2018)
Published in Frontiers in microbiology (19.11.2018)
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Journal Article
New Insights into the Evolutionary and Genomic Landscape of Molluscum Contagiosum Virus (MCV) based on Nine MCV1 and Six MCV2 Complete Genome Sequences
Zorec, Tomaž M, Kutnjak, Denis, Hošnjak, Lea, Kušar, Blanka, Trčko, Katarina, Kocjan, Boštjan J, Li, Yu, Križmarić, Miljenko, Miljković, Jovan, Ravnikar, Maja, Poljak, Mario
Published in Viruses (26.10.2018)
Published in Viruses (26.10.2018)
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Journal Article
Interlaboratory Comparison Study on Ribodepleted Total RNA High-Throughput Sequencing for Plant Virus Diagnostics and Bioinformatic Competence
Gaafar, Yahya Z. A., Westenberg, Marcel, Botermans, Marleen, László, Krizbai, De Jonghe, Kris, Foucart, Yoika, Ferretti, Luca, Kutnjak, Denis, Pecman, Anja, Mehle, Nataša, Kreuze, Jan, Muller, Giovanna, Vakirlis, Nikolaos, Beris, Despoina, Varveri, Christina, Ziebell, Heiko
Published in Pathogens (Basel) (12.09.2021)
Published in Pathogens (Basel) (12.09.2021)
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