Publications

Published articles:

KUTNJAK, Denis, TAMISIER, Lucie, ADAMS, Ian, BOONHAM, Neil, CANDRESSE, Thierry, CHIUMENTI, Michela, DE JONGHE, Kris, KREUZE, Jan F., LEFEBVRE, Marie, SILVA, Goncalo, MALAPI-WIGHT, Martha, MARGARIA, Paolo, MAVRIČ PLEŠKO, Irena, MCGREIG, Sam, MIOZZI, Laura, REMENANT, Benoit, REYNARD, Jean-Sébastien, ROLLIN, Johan, ROTT, Mike, SCHUMPP, Olivier, MASSART, Sébastien, HAEGEMAN, Annelies. A primer on the analysis of high-throughput sequencing data for detection of plant viruses. Microorganisms. 14 Apr. 2021, vol. 9, iss. 4, str. 1-31, ilustr. ISSN 2076-2607. https://www.mdpi.com/2076-2607/9/4/841, DOI: 10.3390/microorganisms9040841.

PECMAN, Anja, ADAMS, Ian, GUTIÉRREZ-AGUIRRE, Ion, FOX, Adrian, BOONHAM, Neil, RAVNIKAR, Maja, KUTNJAK, Denis. Systematic comparison of nanopore and illumina sequencing for the detection of plant viruses and viroids using total RNA sequencing approach. Frontiers in microbiology. 2022, vol. 13, str. 1-14, ilustr. ISSN 1664-302X. https://www.frontiersin.org/articles/10.3389/fmicb.2022.883921/full.

GRBIN, Dorotea, PECMAN, Anja, ŠERUGA MUSIĆ, Martina, KUTNJAK, Denis, ŠKORIĆ, Dijana. First report of potato virus S and potato virus Y in tomatoes from Croatia. Plant disease. 2022, str. 1-2,. ISSN 0191 2917. https://doi.org/10.1094/PDIS 06 22 1390 PDN.


KOGEJ ZWITTER, Zala, SELJAK, Gabrijel, JAKOMIN, Tjaša, BRODARIČ, Jakob, VUČUROVIĆ, Ana, PEDEMAY, Sandra, SALAR, Pascal, MALEMBIC MAHER, Sylvie, FOISSAC, Xavier, MEHLE, Nataša. Epidemiology of flavescence dorée and hazelnut decline in Slovenia : geographica l distribution and genetic diversity of the associated 16SrV phytoplasmas. Frontiers in plant science . 2023, vol. 14, [art.] 1217425, str. 1-12, ilustr. ISSN 1664-462X. https://doi.org/10.3389/fpls.2023.1217425

RIVAREZ, Mark Paul Selda, PECMAN, Anja, BAČNIK, Katarina, MAKSIMOVIĆ, Olivera, VUČUROVIĆ, Ana, SELJAK, Gabrijel, MEHLE, Nataša, GUTIÉRREZ AGUIRRE, Ion, RAVNIKAR, Maja, KUTNJAK, Denis. In depth study of tomato and weed viromes reveals undiscovered plant vir us diversity in an agroecosystem. Microbiome . 2023, vol. 11, art. 60, str. 1- 24, ilustr. ISSN 2049 2618. https://doi.org/10.1186/s40168-023-01500-6

KOGEJ ZWITTER, Zala, JAKOŠ, Nejc, MEHLE, Nataša. Unravelling the puzzle of 16SrV phytoplasma in hazelnuts : a systematic study of sampling and detection. Phytopathogenic mollicutes . Jun. 2023, vol. 13, iss. 1, str. 139-140. ISSN 2249-4669. http://dx.doi.org/10.5958/2249-4677.2023.00070.1


HAEGEMAN, Annelies, FOUCART, Yoika, DE JONGHE, Kris, GOEDEFROIT, Thomas, AL-RWAHNIH, Maher, BOONHAM, Neil, CANDRESSE, Thierry, GAAFAR, Yahya, HURTADO GONZALES, Oscar, KOGEJ ZWITTER, Zala, KUTNJAK, Denis, LAMOVŠEK, Janja, MAVRIČ PLEŠKO, Irena, et al. Looking beyond virus detection in RNA sequencing data : lessons learned from a community based effort to detect cellular plant pathogens and pests. Plants. Jun. 2023, iss. 11, art. 2135, str. [1]-20, ilustr. ISSN 2223-7747. DOI: https://dx.doi.org/10.3390/plants12112139 .


PECMAN, Anja. Characterization of plant viromes using different viral nucleic acids enrichment strategies and high-throughput sequencing platforms : doctoral dissertation = Karakterizacija rastlinskega viroma z uporabo različnih strategij obogatitve virusnih nuklenskih kislin in platform visoko pretočnega sekvenciranja : doktorska disertacija

RIVAREZ, Mark Paul Selda. Diversity of viruses infecting tomato and weed plants in agroecosystems : doctoral dissertation = Raznolikost virusov paradižnika in plevelnih rastlin v kmetijskih ekosistemih : doktorska disertacija. Ljubljana: [M. P. Selda Rivarez], 2022. XIII, 247 str., ilustr., tabele. [COBISS.SI-ID 126513411]

Book chapter

PECMAN, Anja, MEHLE, Nataša, KUTNJAK, Denis. Detection of plant viruses using nanopore sequencing based metagenomic approach. V: PANTALEO, Vitantonio (ur.), MIOZZI, Laura (ur.). Viral metagenomics: methods and protocols. Methods in molecular biology. Springer (revised, in press)

Conference presentations:

PECMAN, Anja, KUTNJAK, Denis, ADAMS, Ian, GUTIÉRREZ-AGUIRRE, Ion, FOX, Adrian, BOONHAM, Neil, RAVNIKAR, Maja. How does nanopore sequencing compare to Illumina sequencing for detection of plant viruses and viroids. V: Programme and abstracts : International Advances in Plant Virology 202: virtually via Zoom: 20 th April – 22 nd April 2021. [S. l.: Association of Applied Biologists], 2021. Str. 116. https://custom.cvent.com/05F40F40EA964BBB968323D70A3E1C38/files/event/ef4ceb27d30d4676a7f14cb5d4dd7663/bd3a825c81194b88a904a9bd5738cd44.pdf.

PECMAN, Anja, KUTNJAK, Denis, ADAMS, Ian, GUTIÉRREZ-AGUIRRE, Ion, FOX, Adrian, BOONHAM, Neil, RAVNIKAR, Maja. On the way to fast “on-site” detecion of plant viruses and viroids. V: HORVAT, Monika (ur.), et al. Cutting Edge 2021 : Scientific conference for young researchers : Independent in science : Thursday, 16. 09. 21, virtual conference : book of abstracts. Ljubljana: Fakulteta za kemijo in kemijsko tehnologijo, 2021. Str. 15, ilustr. ISBN 978-961-7078-21-3. [COBISS.SI-ID 78086403]

KOGEJ, Zala, SELJAK, Gabrijel, RAVNIKAR, Maja, VUČUROVIĆ, Ana, JAKOMIN, Tjaša, BRODARIČ, Jakob, OREŠEK, Erika, MEHLE, Nataša. Raznolikost fitoplazem skupine 16SrV v trtah, leskah in njihovih prenašalcih = Diversity of 16SrV phytoplasma group in grapevine, hazelnut and its vectors. V: TRDAN, Stanislav (ur.). 15. slovensko posvetovanje o varstvu rastlin z mednarodno udeležbo = 15th Slovenian Conference on Plant Protection with International Participation : izvlečki referatov = abstract volume : 1.-2. marec 2022, Portorož, Slovenija. Ljubljana: Društvo za varstvo rastlin Slovenije: = Plant Protection Society of Slovenia, 2022. Str. 108-109. ISBN 978-961-93447-8-1. [COBISS.SI-ID 100485123]

KOGEJ, Zala, SELJAK, Gabrijel, JAKOMIN, Tjaša, BRODARIČ, Jakob, VUČUROVIĆ, Ana, RAVNIKAR, Maja, KUTNJAK, Denis, MEHLE, Nataša. Investigation of the diversity of the destructive 16SrV phytoplasma group in grapevine, hazelnut and leafhoppers. V: Epidemiology and management of plant viruses under a changing climate : book of abstracts. 15th ISPVE Madrid 2022, Madrid, Spain, 5-8th June, 2022. [S. l.: s. n., 2022]. Str. 118. [COBISS.SI-ID 111930371]

PECMAN, Anja, KOGEJ ZWITTER, Zala, MEHLE, Nataša, VUČUROVIĆ, Ana, RAVNIKAR, Maja, KUTNJAK, Denis. Uporaba visokozmogljivega sekvenciranja za iskanje karantenskih rastlinskih virusov = The use of high-throughput sequencing for detection of quarantine plant viruses. V: TRDAN, Stanislav (ur.). 15. slovensko posvetovanje o varstvu rastlin z mednarodno udeležbo = 15th Slovenian Conference on Plant Protection with International Participation : izvlečki referatov = abstract volume : 1.-2. marec 2022, Portorož, Slovenija. Ljubljana: Društvo za varstvo rastlin Slovenije: = Plant Protection Society of Slovenia, 2022. Str. 84-85. ISBN 978-961-93447-8-1. [COBISS.SI-ID 100509699]

KOGEJ ZWITTER, Zala, SELJAK, Gabrijel, JAKOMIN, Tjaša, BRODARIČ, Jakob, VUČUROVIĆ, Ana, RAVNIKAR, Maja, KUTNJAK, Denis, PEDEMAY, Sandra, SALAR, Pascal, MALEMBIC-MAHER, Sylvie, FOISSAC, Xavier, MEHLE, Nataša. Epidemiology and diversity of 16SrV phytoplasma group infecting grapevine and hazelnut. V: BAEBLER, Špela (ur.), et al. Plants in Changing Environment : international conference of the Slovenian Society of Plant Biology : Biotechnical Faculty, University of Ljubljana, September 15-16, 2022, Ljubljana, Slovenia : [book of abstracts]. 1st electronic ed. Ljubljana: Slovenian Society of Plant Biology, 2022. Str. 45. ISBN 978-961-91014-5-2. https://www.plantslo.org/wp/wp-content/uploads/2022/09/PlantsInChangingEnvironment22AbstractBook.pdf. [COBISS.SI-ID 123154691]

PECMAN, Anja, KOGEJ ZWITTER, Zala, MEHLE, Nataša, VUČUROVIĆ, Ana, RAVNIKAR, Maja, KUTNJAK, Denis. Nanopore sequencing for detection of (quarantine) plant viruses. V: International advances in plant virology 2022 : hybrid event hosted in Ljubljana, Slovenia 5th-7th October 2022 : programme, abstracts and delegate list. Warwick: Association of Applied Biologists, 2022. Str. 63. [COBISS.SI-ID 125013251]

GRBIN, Dorotea, PECMAN, Anja, ČAJKULIČ, Ana-Marija , NOVAK, Adrijana ,ŠERUA MUSIĆ, Martina, KUTNJAK, Denis, ŠKORIČ, Dijana. First glimpse into the tomato and pepper viromes of Croatia. V: International conference VIROID 2022: Viroids, viroid-like RNAs, and RNA viruses (14-16 September 2022 | Heraklion, Greece)

KOGEJ ZWITTER, Zala, BAJDE, Irena, BRODARIČ, Jakob, VUČUROVIĆ, Ana, MEHLE, Nataša. Možnost prenosa fitoplazme Flavescence dorée z ameriškim škržatkom je zapisana v njenem genetskem kodu = The possibility of transmission of Flavescence dorée phytoplasma by the American leafhopper is written in its genetic code. V: VRŠIČ, Stanko (ur.). 6. slovenski vinogradniško-vinarski kongres : zbornik prispevkov : Ptuj, 21.–22. april 2023. Ptuj: Kmetijsko gozdarski zavod, 2023. Str. [335-340], ilustr. ISBN 978-961-91422-7-1. [COBISS.SI-ID 151789059]

KOGEJ ZWITTER, Zala, SELJAK, Gabrijel, JAKOMIN, Tjaša, BRODARIČ, Jakob, VUČUROVIĆ, Ana, MEHLE, Nataša. Propadanje lesk v Sloveniji zaradi okužbe s fitoplazmo, sorodno povzročiteljici zlate trsne rumenice : Strokovni posvet in redna letna skupščina, Slovensko strokovno društvo lupinarjev, 11. marca 2023, na Biotehniški fakulteti, Ljubljana. [COBISS.SI-ID 145970691]

MEHLE, Nataša, KOGEJ ZWITTER, Zala. Genetic diversity of 16SrV phytoplasma infecting grapevines and hazelnuts in Slovenia : Technical consultation on „Grapevine flavescence dorée and Scaphoideus titanus“, May 10th 2023, Zagreb, Croatia. [COBISS.SI-ID 152249091]

ŠKORIC Dijana, GRBIN Dorotea, PUL Patrik, MEHLE Nataša, PECMAN Anja, KOGEJ ZWITTER Zala, KUTNJAK Denis, VUCUROVIC Ana. A search for resistance breaking strains of tomato spotted wilt orthotospovirus in Croatia and Slovenia. V: 12th International congress of plant pathology (ICPP), 20-25.8.2023, Lyon, France. Book of abstracts. Str. 803.

MEHLE Nataša, PECMAN Anja, VUCUROVIC Ana, BUKVIC Veronika, BRODARIC Jakob, BAJDE Irena, RAVNIKAR Maja, KUTNJAK Denis. Nanopore sequencing for the analysis of official samples for the presence of (quarantine) plant viruses. V: 12th International congress of plant pathology (ICPP), 20-25.8.2023, Lyon, France. Book of abstracts. Str. 1256.

HAEGEMAN, Annelies et al. Revisiting high throughput sequencing data used for plant virus detection in order to find evidence of nonviral plant pathogens and pests. V: 12th International congress of plant pathology (ICPP), 20-25.8.2023, Lyon, France. Book of abstracts. Str. 367

MEHLE, Nataša. Euphresco project: 2020-A-344 FLADO-VIGILANT WP2: Survey on the occurrence of 16SrV phytoplasmas on hazelnuts : what we already know about 16SrV phytoplasmas on hazelnuts? : lecture at Online kick off meeting, 18. 5. 2021. [COBISS.SI-ID 64004355]

MEHLE, Nataša. Flado-Vigilant Euphresco project : 2020-A-344 : online meeting of Euphresco Community Network, 15th March 2022. [COBISS.SI-ID 101248259]