Bibliografija osebe. Seznam zajema vsa gradiva in ne le tista, kje je oseba mentor.

Doktorska dela (7)

1. Kristjan Jarni: Genetska struktura gozdnih semenskih objektov divje češnje (Prunus avium L.) v Sloveniji
2. Vid Jelen: Primerjava mitohondrijskih genomov in analiza mutacij jedrnih genov šestih sevov fitopatogene glive Verticillium albo-atrum
3. Tjaša Rešetič: Analiza transkriptoma plodu oljke (Olea europaea L.) s pirosekvenciranjem
4. Matjaž Hladnik: Proučevanje bolezni razbrazdanja lesa vinske trte (Vitis spp.) na nivoju transkriptoma in karakterizacija tipov sorte žlahtne vinske trte Refošk (Vitis vinifera L.)
5. Aljaž Majer: Identifikacija genov za odpornost na hmeljevo uvelost
6. Alenka Baruca Arbeiter: Razvoj in karakterizacija funkcijskih markerjev za genetske študije oljke (Olea europaea L.)
7. Mateja Zupin: Odziv navadnega fižola (Phaseolus vulgaris L.) na sušni stres

Magistrska dela (3)

1. Maja Peternelj: Arabidopsis thaliana transformation by Agrobacterium tumefaciens - Escherichia coli co-infection
2. Taja Jeseničnik: Identifikacija in diferenciacija patogenih gliv rodu Verticillium z uporabo novih enostavnih in multipleks PCR označevalcev
3. Ana Ogrinc: Izdelava genomskega atlasa kandidatnih genov za reprodukcijo pri moškem spolu sesalcev

Diplomska dela (10)

1. Lidija Berke: Bioinformacijska analiza oznak izraženih zaporedij (EST) hmelja (Humulus lupulus L.) in njihova aplikacija pri razvoju molekularnih markerjev
2. Katja Koncilja: Analiza znotrajvrstne variabilnosti žlahtne vinske trte (Vitis vinifera L.) sorte 'Merlot' z mikrosatelitskimi markerji
3. Goran Markučič: Primerjava različnih tipov žlahtne vinske trte (Vitis vinifera L.) sorte 'Cipro' v Slovenski Istri
4. Matevž Rupar: Molekulska raznovrstnost slovenskih izolatov fitoplazme, povzročiteljice zlate trsne rumenice
5. Maruša Lampič: Vpliv polimorfizma genov HLA na dovzetnost za Hashimotov tiroiditis pri otrocih s sladkorno boleznijo tipa 1
6. Mojca Tomšič: Karakterizacija kariotipa hermafroditnih rastlin hmelja (Humulus lupulus L.) z uporabo pretočne citometrije in štetja kromosomov
7. Tine Pokorn: Genotipizacija kultivarjev hmelja (Humulus lupulus L.) s fluorescentnimi mikrosatelitnimi markerji
8. Daša Perko: Uporaba molekularnih markerjev za detekcijo povzročiteljev verticilijske uvelosti hmelja (Verticillium albo-atrum in V. dahliae) v tleh
9. Anela Kaurin: Razvoj in uporaba novih mikrosatelitnih markerjev za analizo genetske variabilnosti fitopatogenih gliv rodu Verticillium
10. Sara Cregeen: Diferencialno izražanje genov hmelja po okužbi z glivo Verticillium albo-atrum

Druga dela (57)

1. Andreja Čerenak, Jernej Jakše, Nataša Štajner, Branka Javornik: Vrednotenje genskih virov hmelja z molekulskimi markerji
2. Ajay Kumar Mishra, Atul Kumar, Deepti Mishra, Vishnu Sukumari Nath, Jernej Jakše, Tomáš Kocábek, Uday Kumar Killi, Filis Morina, Jaroslav Matoušek: Genome-wide transcriptomic analysis reveals insights into the response to Citrus bark cracking viroid (CBCVd) in hop (Humulus lupulus L.)
3. Jernej Jakše, Jenelle D. F. Meyer, Go Suzuki, A. John McCallum, Foo Cheung, Christopher Town, Michael J. Havey: Pilot sequencing of onion genomic DNA reveals fragments of transposable elements, low gene densities, and significant gene enrichment after methyl filtration
4. Andreja Čerenak, Zlatko Šatović, Jernej Jakše, Zlata Luthar, Klaudija Carović-Stanko, Branka Javornik: Identification of QTLs for alpha acid content and yield in hop (Humulus lupulus L.)
5. Pablo Hirschegger, Jernej Jakše, Peter Trontelj, Borut Bohanec: Origins of Allium ampeloprasum horticultural groups and a molecular phylogeny of the section Allium (Allium: Alliacea)
6. Jernej Jakše, Nataša Štajner, Zlata Luthar, Jean-Marc Jeltsch, Branka Javornik: Development of transcript-associated microsatellite markers for diversity and linkage mapping studies in hop (Humulus lupulus L.)
7. E. L. Howard, S. Whittock, Jernej Jakše, J. Carling, P. Matthews, G. Probasco, J. A. Henning, Peter E. Darby, Andreja Čerenak, Branka Javornik, A. Kilian, Anthony Koutoulis: High-throughput genotyping of hop (Humulus lupulus L.) utilising diversity arrays technology (DArT)
8. Ivan Radosavljević, Zlatko Satović, Jernej Jakše, Branka Javornik, Danijela Greguraš, Marija Jug-Dujaković, Zlatko Liber: Development of new microsatellite markers for Salvia officinalis L. and its potential use in conservation-genetic studies of narrow endemic Salvia brachyodon Vandas
9. Jernej Jakše, Andreja Čerenak, Sebastjan Radišek, Zlatko Satović, Zlata Luthar, Branka Javornik: Identification of quantitative trait loci for resistance to Verticillium wilt and yield parameters in hop (Humulus lupulus L.)
10. Erin L. McAdam, Jules S. Freeman, Simon P. Whittock, Emily J. Buck, Jernej Jakše, Andreja Čerenak, Branka Javornik, Andrzej Lilian, Cai-Hong Wang, Dave Andersen, René E. Vaillancourt, Jason Carling, Ron Beatson, Lawrence Graham, Donna Graham, Peter E. Darby, Anthony Koutoulis: Quantitative trait loci in hop (Humulus lupulus L.) reveal complex genetic architecture underlying variation in sex, yield and cone chemistry
11. Jernej Jakše, Nataša Štajner, Lidija Tomić, Branka Javornik: Application of microsatellite markers in grapevine and olives
12. Ajay Kumar Mishra, Tomáš Kocábek, Vishnu Sukumari Nath, Praveen Awasthi, Ankita Shrestha, Uday Kumar Killi, Jernej Jakše, Josef Patzak, Karel Krofta, Jaroslav Matoušek: Dissection of dynamic transcriptome landscape of leaf, bract, and lupulin gland in hop (Humulus lupulus L.)
13. Tim Weber, Jernej Jakše, Barbara Sladonja, Dario Hruševar, Nediljko Landeka, Slavko Brana, Borut Bohanec, Milenko Milović, Dalibor Vladović, Božena Mitić, Danijela Poljuha: Molecular study of selected taxonomically critical taxa of the genus Iris L. from the broader Alpine-Dinaric area
14. Urban Kunej, Jernej Jakše, Sebastjan Radišek, Nataša Štajner: Identification and characterization of Verticillium nonalfalfae-responsive microRNAs in the roots of resistant and susceptible hop cultivars
15. Ante Turudić, Zlatko Liber, Martina Grdiša, Jernej Jakše, Filip Varga, Zlatko Šatović: The complete chloroplast genome of dalmatian pyrethrum (Tanacetum cinerariifolium (Trevir.) Sch. Bip. (Asteraceae)), the source of the natural insecticide pyrethrin
16. Anže Švara, Jernej Jakše, Nataša Štajner: Confirming infection of hop plants inoculated with Verticilium nonalfalfae
17. Taja Jeseničnik, Anela Kaurin, Zarja Grgič, Sebastjan Radišek, Jernej Jakše, Nataša Štajner: Novel identification of the collection of pathogenic fungal species Verticillium with the development of species-specific SSR markers
18. Urška Ribič, Jernej Jakše, Nataša Toplak, Simon Koren, Minka Kovač, Anja Klančnik, Barbara Jeršek: Transporters and efflux pumps are the main mechanisms involved in Staphylococcus epidermidis adaptation and tolerance to didecyldimethylammonium chloride
19. Sebastjan Radišek, Jernej Jakše, Branka Javornik, J. De Gruyter: Pojav glive Phoma exigua na hmelju v Sloveniji
20. Taja Jeseničnik, Nataša Štajner, Sebastjan Radišek, Ajay Kumar Mishra, Katarina Košmelj, Urban Kunej, Jernej Jakše: Discovery of microRNA-like small RNAs in pathogenic plant fungus Verticillium nonalfalfae using high-throughput sequencing and qPCR and RLM-RACE validation
21. Dunja Bandelj, Jernej Jakše, Branka Javornik: Amplification of fluorescent-labelled microsatellite markers in olives by a novel, economic method
22. Ante Turudić, Zlatko Liber, Martina Grdiša, Jernej Jakše, Filip Varga, Zlatko Šatović: Variation in chloroplast genome size
23. Jan Otoničar, Maja Hostnik, Maja Grundner, Rok Kostanjšek, Tajda Gredar, Maja Garvas, Zoran Arsov, Zdravko Podlesek, Cene Gostinčar, Jernej Jakše, Steve J. W. Busby, Matej Butala: A method for targeting a specified segment of DNA to a bacterial microorganelle
24. Taja Jeseničnik, Nataša Štajner, Sebastjan Radišek, Jernej Jakše: RNA interference core components identified and characterised in Verticillium nonalfalfae, a vascular wilt pathogenic plant fungi of hops
25. Ankita Shrestha, Ajay Kumar Mishra, Jaroslav Matoušek, Lenka Steinbachová, David Potěšil, Vishnu Sukumari Nath, Praveen Awasthi, Tomáš Kocábek, Jernej Jakše, Lenka Záveská Drábková, Zbyněk Zdráhal, David Honys, Gerhard Steger: Integrated proteo-transcriptomic analyses reveal insights into regulation of pollen development stages and dynamics of cellular response to apple fruit crinkle viroid (AFCVd)-infection in Nicotiana tabacum
26. Kristina Marton, Marko Flajšman, Sebastjan Radišek, Katarina Košmelj, Jernej Jakše, Branka Javornik, Sabina Berne: Comprehensive analysis of Verticillium nonalfalfae in silico secretome uncovers putative effector proteins expressed during hop invasion
27. Vanja Miljanić, Jernej Jakše, Urban Kunej, Denis Rusjan, Andreja Škvarč, Nataša Štajner: Virome status of preclonal candidates of grapevine varieties (Vitis vinifera L.) from the Slovenian wine-growing region Primorska as determined by high-throughput sequencing
28. Aida Dervishi, Jernej Jakše, Hairi Ismaili, Branka Javornik, Nataša Štajner: Genetic structure and core collection of olive germplasm from Albania revealed by microsatellite markers
29. Jernej Jakše, Binu Antony, Alan Soffan, Sulieman Alfaifi, Koko D. Sutanto, Saleh A. Aldosari, Abdulrahman S. Aldawood, Arnab Pain: Genes involved in sex pheromone biosynthesis of Ephestia cautella, an important food storage pest, are determined by transcriptome sequencing
30. Jernej Jakše, Muhammad Anas Khan, Sulieman Alfaifi, Hussein M. Migdadi, Megahed H. Ammar, Ehab H. El-Harty, Mohammad I. Althamrah, Muhammad Afzal, Muhammad M. Javed, Salem S. Alghamdi: Analysis of ESTs from the date palm (Phoenix dactylifera L.) cv. Sukary, an elite variety
31. Tjaša Tolar, Jernej Jakše, Zora Korošec-Koruza: The oldest macroremains of Vitis from Slovenia
32. Martina Grdiša, Zlatko Šatović, Zlatko Liber, Jernej Jakše, Filip Varga, Renata Erhatić, Siniša Srečec: High genetic diversity and low population differentiation in wild hop (Humulus lupulus L.) from Croatia
33. Vishnu Sukumari Nath, Ankita Shrestha, Praveen Awasthi, Ajay Kumar Mishra, Tomáš Kocábek, Jaroslav Matoušek, Andrej Sečnik, Jernej Jakše, Sebastjan Radišek, Vipin Hallan: Mapping the gene expression spectrum of mediator subunits in response to viroid infection in plants
34. Vanja Miljanić, Jernej Jakše, Denis Rusjan, Andreja Škvarč, Nataša Štajner: Small RNA sequencing and multiplex RT-PCR for diagnostics of grapevine viruses and virus-like organisms
35. Sebastjan Radišek, Nataša Ferant, Jernej Jakše, Branka Javornik: Identification of a phytoplasma from the aster yellows group infecting purple coneflower (Echinacea purpurea) in Slovenia
36. Željko Tomanović, Katarina Kos, Andjeljko Petrović, Petr Starý, Nickolas G. Kavallieratos, V. Žikić, Jernej Jakše, Stanislav Trdan, Ana Ivanović: The relationship between molecular variation and variation in the wing shape of three aphid parasitoid species: Aphidius uzbekistanicus Luzhetzki, Aphidius rhopalosiphi De Stefani Perez and Aphidius avenaphis (Fitch) (Hymenoptera: Braconidae: Aphidiinae)
37. Tjaša Rešetič, Nataša Štajner, Dunja Bandelj, Branka Javornik, Jernej Jakše: Validation of candidate reference genes in RT-qPCR studies of developing olive fruit and expression analysis of four genes involved in fatty acids metabolism
38. Sebastjan Radišek, Gregor Leskošek, Jernej Jakše, Branka Javornik: Occurrence of Cercospora cantuariensis on hop in Austria and Slovenia
39. Aljaž Majer, Branka Javornik, Andreja Čerenak, Jernej Jakše: Development of novel EST-derived resistance gene markers in hop (Humulus lupulus L.)
40. Urban Kunej, Aida Dervishi, Valérie Laucou, Jernej Jakše, Nataša Štajner: The potential of HTS approaches for accurate genotyping in grapevine (Vitis vinifera L.)
41. Kristina Milišić, Branislava Sivčev, Nataša Štajner, Jernej Jakše, Saša Matijašević, Dragan Nikolić, Tatjana Popovič, Zorica Ranković-Vasić: Ampelographic and molecular characterisation of grapevine varieties in the gene bank of the experimental vineyard ‘Radmilovac’ – Serbia
42. Urban Kunej, Jernej Jakše, Sebastjan Radišek, Nataša Štajner: Core RNA interference genes involved in miRNA and ta-siRNA biogenesis in hops and their expression analysis after challenging with Verticillium nonalfalfae
43. Vishnu Sukumari Nath, Ajay Kumar Mishra, Atul Kumar, Jaroslav Matoušek, Jernej Jakše: Revisiting the role of transcription factors in coordinating the defense response against Citrus bark cracking viroid infection in commercial hop (Humulus lupulus L.)
44. Sebastjan Radišek, Gregor Leskošek, Jernej Jakše, Branka Javornik: Cercospora cantuariensis na hmelju v Avstriji in Sloveniji
45. Ante Turudić, Zlatko Liber, Martina Grdiša, Jernej Jakše, Filip Varga, Zlatko Šatović: Towards the well-tempered chloroplast DNA sequences
46. Nataša Štajner, Sebastjan Radišek, Ajay Kumar Mishra, Vishnu Sukumari Nath, Jaroslav Matoušek, Jernej Jakše: Evaluation of disease severity and global transcriptome response induced by Citrus bark cracking viroid, Hop latent viroid, and their co-infection in hop (Humulus lupulus L.)
47. Tanja Guček, Sebastjan Radišek, Jernej Jakše, Branka Javornik: Biologija interakcij med rastlinami in viroidi
48. Filip Varga, Zlatko Liber, Jernej Jakše, Ante Turudić, Zlatko Šatović, Ivan Radosavljević, Nina Jeran, Martina Grdiša: Development of microsatellite markers for Tanacetum cinerariifolium (Trevis.) Sch. Bip., a plant with a large and highly repetitive genome
49. Andrej Sečnik, Nataša Štajner, Sebastjan Radišek, Urban Kunej, Mitja Križman, Jernej Jakše: Cytosine methylation in genomic DNA and characterization of DNA methylases and demethylases and their expression profiles in viroid-infected hop plants (Humulus lupulus var. ‘Celeia’)
50. Ante Turudić, Zlatko Liber, Martina Grdiša, Jernej Jakše, Filip Varga, Zlatko Šatović: Chloroplast genome annotation tools
51. Ivan Radosavljević, Krešimir Križanović, Sara Laura Šarančić, Jernej Jakše: Towards the investigation of the adaptive divergence in a species of exceptional ecological plasticity
52. Herbert Venthur, Ignacio Arias, Paula Lizana, Jernej Jakše, Hatten A. Alharbi, Mohammed Ahmed Ali Alsaleh, Arnab Pain, Binu Antony: Red palm weevil olfactory proteins annotated from the rostrum provide insights into the essential role in chemosensation and chemoreception
53. Špela Mestinšek Mubi, Urban Kunej, Valentin Vogrinčič, Jernej Jakše, Jana Murovec: The effect of phytosulfokine alpha on haploid embryogenesis and gene expression of Brassica napus microspore cultures
54. Ante Turudić, Zlatko Liber, Martina Grdiša, Jernej Jakše, Filip Varga, Igor Poljak, Zlatko Šatović: Dig-up primers
55. Filip Varga, Zlatko Liber, Ante Turudić, Jernej Jakše, Lea Juzbašić, Nina Jeran, Martina Grdiša, Miloš Zbiljić, Zlatko Šatović: Joint identification and application of microsatellite markers in genetic diversity study of closely related species Teucrium montanum, T. capitatum and their natural hybrid
56. Carmen Scieuzo, Jernej Jakše, Patrizia Falabella: Identification of multifunctional putative bioactive peptides in the insect model red palm weevil (Rhynchophorus ferrugineus)
57. Alnilan Cristina Barros Lobato, Ivan Konjević, Sebastjan Radišek, Jernej Jakše, Helena Volk, Monika Hermanová, Miroslav Fojta, Jan Paštika, Zdeněk Sofer, Rui Gusmão, Samo B. Hočevar, Nikola Tasić: Label-free and sensitive detection of Citrus Bark Cracking Viroid in hop using Ti$_3$C$_2$T$_x$ MXene-modified genosensor