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. [COBISS.SI-ID 59812099]

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, DOI: 10.3389/fmicb.2022.883921. [COBISS.SI-ID 108948739]

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, DOI: 10.1094/PDIS-06-22-1390-PDN. [COBISS.SI-ID 116162307]

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 : geographical 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, https://www.frontiersin.org/articles/10.3389/fpls.2023.1217425/full#supplementary-material, https://dirros.openscience.si/IzpisGradiva.php?id=16723. [COBISS.SI-ID 159155203]

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 virus 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, https://dirros.openscience.si/IzpisGradiva.php?id=16442, DOI: 10.1186/s40168-023-01500-6. [COBISS.SI-ID 148647683]

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, DOI: 10.5958/2249-4677.2023.00070.1. [COBISS.SI-ID 154571011]

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: 10.3390/plants12112139. [COBISS.SI-ID 154555651]

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. 2nd ed. New York: Humana Press, 2024. Str. 251-264. Methods in molecular biology, vol. 2732. ISBN 978-1-0716-3515-5, ISBN 1-0716-3515-8. ISSN 1940-6029. https://link.springer.com/protocol/10.1007/978-1-0716-3515-5_17, DOI: 10.1007/978-1-0716-3515-5_17. [COBISS.SI-ID 178294275]

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 2021 : virtually via Zoom : 20th April – 22nd April 2021. [S. l.: Association of Applied Biologists], 2021. Str. 116. https://custom.cvent.com/05F40F40EA964BBB968323D70A3E1C38/files/event/ef4ceb27d30d4676a7f14cb5d4dd7663/bd3a825c81194b88a904a9bd5738cd44.pdf. [COBISS.SI-ID 62641155]

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]

Predstavitev planov in rezultatov dela v WP2 v okviru projekta NanoPhyto na srečanju strokovnjakov s področja fitoplazem, ki so vključeni v Euphresco projekt FLADO-VIGILANT (2020-A-344):

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]

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.). Zbornik predavanj in referatov 15. slovenskega posvetovanja o varstvu rastlin z mednarodno udeležbo, Portorož, 1.-2. marec 2022 = Lectures and papers presented at the 15th Slovenian Conference on Plant Protection with International Participation, Portorož, March 1-2, 2022. Ljubljana: Društvo za varstvo rastlin Slovenije: = Plant Protection Society of Slovenia, 2022. Str. 268-274, ilustr. ISBN 978-961-93447-9-8. [COBISS.SI-ID 149585155]

KOGEJ ZWITTER, 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 ZWITTER, 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]

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]

GRBIN, Dorotea, PECMAN, Anja, ČAJKULIĆ, Ana-Marija, NOVAK, Adrijana, ŠERUGA-MUSIĆ, Martina, KUTNJAK, Denis, ŠKORIĆ, Dijana. First glimpse into the tomato and pepper viromes of Croatia. V: VIROID 2022 : abstracts of papers presented at the VIROID 2022 conference : Viroids, Viroid-like RNAs and RNA viruses : 14-16 September 2022 Crete, Greece. [S. l.: s. n.], 2022. Str. 43. [COBISS.SI-ID 128846851]

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]

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]

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]

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

MAKSIMOVIĆ, Olivera, KUTNJAK, Denis, RAVNIKAR, Maja, GUTIÉRREZ-AGUIRRE, Ion. Advanced sequence detection of plant viruses in water samples : platform comparison between Ilumina and oxford nanopore sequencing. V: STOPNIŠEK, Nejc (ur.). Slovenian Microbiome Network Symposium 2023 : Defining a healthy microbiome : 30. 11. – 1. 12. 2023, Maribor, Slovenia : abstract book. Maribor: Nacionalni laboratorij za zdravje, okolje in hrano, 2023. Str. 60, p8. ISBN 978-961-6148-23-8. https://doi.org/10.5281/zenodo.10214965. [COBISS.SI-ID 174748675]

MEHLE, Nataša, KOGEJ ZWITTER, Zala, KUTNJAK, Denis. Rekonstrukcija fitoplazemskih genomov za epidemiološke raziskave s pomočjo sekvenciranja z nanoporami. V: KUŠAR, Darja (ur.), JAMNIKAR CIGLENEČKI, Urška (ur.). 9. kongres Slovenskega mikrobiološkega društva : knjiga povzetkov : 14.–16. februar 2024. Ljubljana: Slovensko mikrobiološko društvo, 2024. Str. 145. ISBN 978-961-96562-0-4. https://smd2024.si/wp-content/uploads/2024/02/2024-02-12-knjiga-povzetkov-SMD_Compress.pdf. [COBISS.SI-ID 186671619]

MEHLE, Nataša, KOGEJ ZWITTER, Zala, BAJDE, Irena, BRODARIČ, Jakob, VUČUROVIĆ, Ana. Nova spoznanja o epidemiologiji zlate trsne rumenice na osnovi proučevanja genetske raznolikosti povzročitelja bolezni = New insights into the epidemiology of Grapevine flavescence dorée based on a study of the genetic diversity of the causal agent. V: TRDAN, Stanislav (ur.). 16. slovensko posvetovanje o varstvu rastlin z mednarodno udeležbo = 16th Slovenian Conference on Plant Protection with International Participation : izvlečki referatov = abstract volume : 5.-6. marec 2024, Bohinjska Bistrica, Slovenija. Ljubljana: Društvo za varstvo rastlin Slovenije: = Plant Protection Society of Slovenia, 2024. Str. 59-60. ISBN 978-961-96561-0-5. https://dvrs.si/wp-content/uploads/2024_Zbornik_izvleckov_SPVR.pdf. [COBISS.SI-ID 190939651]

MEHLE, Nataša, KOGEJ ZWITTER, Zala, BAJDE, Irena, BRODARIČ, Jakob, VUČUROVIĆ, Ana. Diversity of map genotypes of Grapevine Flavescence dorèe phytoplasma in Slovenian vineyards : lecture at GFD follow-up meeting: Technical consultation on Grapevine flavescence dorée and Scaphoideus titanus, National Institute of Biology (NIB), Ljubljana, Slovenia, April 9, 2024. [COBISS.SI-ID 192429315]

MEHLE, Nataša, KOGEJ ZWITTER, Zala, BAJDE, Irena, BRODARIČ, Jakob, VUČUROVIĆ, Ana. Grapevine Flavescence dorée phytoplasma map genotypes associated with outbreaks in Slovenian vineyards. V: EVEILLARD, Sandrine (ur.). Proceedings of the 6th European Bois Noir Workshop [and] 1st International Pro-AECOGY Conference : Towards the Prophylactic and Agroecological Control of grapevine yellows : 14-16 May 2024, Bordeaux, France. 6th European Bois Noir Workshop and 1st International Pro-AECOGY Conference, Towards the Prophylactic and Agroecological Control of grapevine yellows, 14-16 May 2024, Bordeaux, France. [S. l.: s. n., 2024]. Str. 78-79. https://boisnoirwkshop.sciencesconf.org/data/pages/Proceedings_Sixth_European_Bois_noir_worksho_First_International_Pro_AECOGY_Conference_2025.pdf. [COBISS.SI-ID 196593667]

PhD thesis:

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 nukleinskih kislin in platform visoko zmogljivega sekvenciranja : doktorska disertacija. Ljubljana: [A. Pecman], 2022. XIV, 65 str., ilustr., tabele. [COBISS.SI-ID 133223427]

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]

KOGEJ ZWITTER, Zala: doktorska disertacija (v teku)