Alen Suljič

1. SULJIČ, Alen. Vpliv uporabe informacije o času preleta v rekonstrukcijskih metodah na kakovost PET/CT slike : magistrsko delo = The impact of time of flight information used in reconstruction algorithms on PET/CT image quality : master thesis. Ljubljana: [A. Suljič], 2014. 62 f., [24] f. pril., graf. prikazi. https://repozitorij.uni-lj.si/IzpisGradiva.php?id=72069&lang=slv, Repository of the University of Ljubljana – RUL . [COBISS.SI-ID 4728683]

2. SULJIČ, Alen, TOMŠE, Petra, JENSTERLE, Luka, ŠKRK, Damijan. The impact of reconstruction algorithms and time of flight information on PET/CT image quality. Radiology and oncology. [Print ed.]. Sep. 2015, vol. 49, no. 3, str. 227-233, ii, ilustr. ISSN 1318-2099. http://ojs.szd.si/index.php/ro/article/view/2248/1781, DiRROS - Digital repository of Slovenian research organizations, http://www.dlib.si/details/URN:NBN:SI:DOC-FGMMP90L. [COBISS.SI-ID 281478912]

3. BOLHA, Luka, HOČEVAR, Alojzija, SULJIČ, Alen, JURČIĆ, Vesna (author, corresponding author). Inflammatory cell composition and immune-related microRNA signature of temporal artery biopsies from patients with giant cell arteritis. Frontiers in immunology. Dec. 2021, vol. 12, str. 1-13, ilustr. ISSN 1664-3224. https://www.frontiersin.org/articles/10.3389/fimmu.2021.791099/full, Repository of the University of Ljubljana – RUL , DOI: 10.3389/fimmu.2021.791099. [COBISS.SI-ID 90790915]
project: funder: Slovenian Research Agency

4. ZOREC, Tomaž Mark, SULJIČ, Alen, ZAKOTNIK, Samo. scov2-spikeScreen. Ljubljana: Medicinska fakulteta, Inštitut za mikrobiologijo, 2021. Spletni vir. GitHub.com. https://github.com/IMIMF-UNILJSI/scov2-spikeScreen. [COBISS.SI-ID 92288003]

5. KORVA, Miša, KNAP, Nataša, RESMAN RUS, Katarina, ZAKOTNIK, Samo, SULJIČ, Alen, KOGOJ, Rok, AVŠIČ-ŽUPANC, Tatjana. From genotype to phenotype : characterization of different SARS-CoV-2 variants. In: ZORC, Minja (ed.), DOVČ, Peter (ed.). Proceedings of Genetika 2022 : 9th Congress of the Genetic Society of Slovenia and [9th] meeting of the Slovenian Society for Human Genetics with international participation : Ljubljana, September 28-30, 2022. Ljubljana: Genetic Society of Slovenia, 2022. Str. 38. ISBN 978-961-93545-7-5. [COBISS.SI-ID 126394883]

6. BOLHA, Luka, HOČEVAR, Alojzija, SULJIČ, Alen, JURČIĆ, Vesna. Interrelation between immune-related microRNA signature and inflammatory histopathological features of giant cell arteritis. In: Autoimmunity, autoinflammation and immunodeficiency in vasculitis : abstracts of the 20th International Vasculitis & ANCA Workshop, Dublin, Ireland 3 - 6 April 2022. 20th International Vasculitis & ANCA Workshop, Dublin, Ireland 3 - 6 April 2022. [S. l.: s. n., 2022]. Str. 101-102. https://zenodo.org/record/6381941#.Y2zIOHbMIuU. [COBISS.SI-ID 128808707]

7. SULJIČ, Alen, SOČAN, Maja, MRZEL, Maja, LUNAR, Maja M., KORVA, Miša, ŠTORMAN, Alenka, PROSENC, Katarina, JANEŽIČ, Sandra, ŽOHAR ČRETNIK, Tjaša, ZUPANIČ, Tina, POLJAK, Mario, AVŠIČ-ŽUPANC, Tatjana. Milder outcomes of SARS-CoV-2 genetically confirmed reinfections compared to primary infections with the delta variant : a retrospective case-control study. Frontiers in medicine. 2022, vol. 9, str. 1-12, ilustr. ISSN 2296-858X. https://www.frontiersin.org/articles/10.3389/fmed.2022.962653/full, DOI: 10.3389/fmed.2022.962653. [COBISS.SI-ID 124639747]
project: European Virus Archive GLOBAL; funder: Slovenian Research Agency; European Union’s Horizon 2020

8. ULINICI, Mariana, SULJIČ, Alen, POGGIANELLA, Monica, BONOTTO, Rafaela, RESMAN RUS, Katarina, PARASCHIV, Angela, BONETTI, Amedeo Marco, TODIRAS, Mihail, CORLATEANU, Alexandru, PETROVEC, Miroslav, et al. Characterisation of the Antibody Response in Sinopharm (BBIBP-CorV) recipients and COVID-19 Convalescent Sera from the Republic of Moldova. Vaccines. 2023, vol. 11, iss. 3, [article no.] 637, str. 1-18, ilustr. ISSN 2076-393X. https://www.mdpi.com/2076-393X/11/3/637, DOI: 10.3390/vaccines11030637. [COBISS.SI-ID 159859203]
project: D78D20000020009; funder: Autonomous Region of Friuli Venezia Giulia-Regional Law 19/2000
project: Financerji: SNAM Foundation, CARIPLO (INNATE-CoV) and the FarmaCovid crowdfunding initiative

9. ZAKOTNIK, Samo, KNAP, Nataša, SULJIČ, Alen, VLAJ, Doroteja, BOGOVIČ, Petra, STRLE, Franc, KORVA, Miša, AVŠIČ-ŽUPANC, Tatjana. Complete genome sequencing of tick-borne encephalitis virus reveals potential mutations in viral genome associated with disease course. In: 15th International symposium on the ticks and tick-borne diseases : ISTTBD-XV : abstracts : Weimar, Germany, 29-31 March, 2023. Weimar: German Society for Parasitology, 2023. Str.55-56. [COBISS.SI-ID 159925763]

10. SULJIČ, Alen. Enhancing NGS monitoring of SARS-CoV-2 variants (spike-screen) : UK-ICN Virtual Monthly Seminar Series, 29th June, 2023. 1 spletni vir (1 video datoteka (23 min 46 sek)). https://www.youtube.com/watch?v=qjSCAIj8C4c. [COBISS.SI-ID 177736451]

11. SULJIČ, Alen, HOČEVAR, Alojzija, JURČIĆ, Vesna, BOLHA, Luka (author, corresponding author). Evaluation of arterial histopathology and microRNA expression that underlie ultrasonography findings in temporal arteries of patients with giant cell arteritis. International journal of molecular sciences. Jan. 2023, vol. 24, iss. 2, 1-19, ilustr. ISSN 1422-0067. https://www.mdpi.com/1422-0067/24/2/1572, Repository of the University of Ljubljana – RUL , DOI: 10.3390/ijms24021572. [COBISS.SI-ID 137871107]
project: funder: Slovenian Research Agency

12. ALREZAIHI, Abdulrahman, PENTRICE-RANDAL, Rebekah, ZAKOTNIK, Samo, SULJIČ, Alen, PETROVEC, Miroslav, HISCOX, Julian A., KORVA, Miša, AVŠIČ-ŽUPANC, Tatjana. Exploring microbiome differences in upper and lower respiratory tract of COVID-19 patients. In: UK international coronavirus network big data : coronaviruses at multiple scales workshop (sponsored by Zoetis) ; Annual general meeting : Scientific Conference and Annual General Meeting, 13th-15th September 2023, Ljubljana, Slovenia. Scientific Conference and Annual General Meeting, 13th-15th September 2023, Ljubljana, Slovenia. Ljubljana: Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Slovenia, 2023. Str. 44. [COBISS.SI-ID 166119683]

13. SULJIČ, Alen. Histopatološke spremembe temporalnih arterij v povezavi s spremenjenim izražanjem mikro RNA, klinično sliko in ultrazvočno preiskavo pri gigantoceličnem arteritisu = Histopathological changes of temporal arteries in relation to the altered expression of microRNA, clinical manifestations and ultrasound examination in the giant cell arteritis : doktorska disertacija. Ljubljana: [A. Suljič], 2023. 116 str., ilustr. https://repozitorij.uni-lj.si/IzpisGradiva.php?id=147610&lang=slv. [COBISS.SI-ID 159706627]

14. BOSILJ, Martin, SULJIČ, Alen, ZAKOTNIK, Samo. MetaAll. Ljubljana: Medicinska fakulteta, Inštitut za mikrobiologijo in imunologijo, 2023. 1 spletni vir. GitHub.com, NGS-bioinf. https://github.com/NGS-bioinf/MetaAll. [COBISS.SI-ID 195631363]

15. KOGOJ, Rok, GRAŠEK, Manja, SULJIČ, Alen, ZAKOTNIK, Samo, KOTNIK KOMAN, Kaja, PETROVEC, Miroslav, FAFANGEL, Mario, AVŠIČ-ŽUPANC, Tatjana, KORVA, Miša. Molecular analysis of SARS-CoV-2 introductions in Slovenian long-term care facilities. In: UK international coronavirus network big data : coronaviruses at multiple scales workshop (sponsored by Zoetis) ; Annual general meeting : Scientific Conference and Annual General Meeting, 13th-15th September 2023, Ljubljana, Slovenia. Scientific Conference and Annual General Meeting, 13th-15th September 2023, Ljubljana, Slovenia. Ljubljana: Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Slovenia, 2023. Str. 50. [COBISS.SI-ID 166119939]

16. RESMAN RUS, Katarina, ZAKOTNIK, Samo, SAGADIN, Martin, KNAP, Nataša, SULJIČ, Alen, ZOREC, Tomaž Mark, MASTNAK, Maja, PETROVEC, Miroslav, POLJAK, Mario, KORVA, Miša, AVŠIČ-ŽUPANC, Tatjana, et al. Molecular epidemiology of the 2022 monkeypox virus outbreak in Slovenia. Acta dermatovenerologica Alpina, Panonica et Adriatica. 2023, vol. 32, iss. 3, str. 111-117, ilustr. ISSN 1318-4458. https://www.acta-apa.org/journals/acta-dermatovenerol-apa/papers/10.15570/actaapa.2023.21/actaapa.2023.21.pdf, http://www.dlib.si/details/URN:NBN:SI:doc-0Q7BXRM5, DOI: 10.15570/actaapa.2023.21. [COBISS.SI-ID 167495683]
project: Institute of Microbiology and Immunology, Faculty of Medicine, Unicersity of Ljubljana
project: P3-0083; funder: Slovenian Research and Innovation Agency
project: 871029; funder: European Virus Archive; European Union's Horizon 2020

17. OŠEP, Anja, GOLDSWAIN, Hannah, SULJIČ, Alen, BOSILJ, Martin, ZAKOTNIK, Samo, KORVA, Miša, HISCOX, Julian A., URŠIČ, Tina, PETROVEC, Miroslav. Design pf primer pairs for whole genome sequencing of coronavirus HKU1 from clinical samples. In: UK international coronavirus network : [abstracts book] : Annual General Meeting, 17th-18th September 2024, Edinburgh, Great Britain. Annual General Meeting, 17th-18th September 2024, Edinburgh. Great Britain. Edinburgh: Biotechnology and Biological Sciences Research Council, 2024. Str. 46. [COBISS.SI-ID 233101059]

18. SULJIČ, Alen, ZOREC, Tomaž Mark, ZAKOTNIK, Samo, VLAJ, Doroteja, KOGOJ, Rok, KNAP, Nataša, PETROVEC, Miroslav, POLJAK, Mario, AVŠIČ-ŽUPANC, Tatjana, KORVA, Miša (author, corresponding author). Efficient SARS-CoV-2 variant detection and monitoring with Spike Screen next-generation sequencing. Briefings in bioinformatics. [Online ed.]. 2024, vol. 25, iss. 4, [article no.] bbae263, str.1-13, ilustr. ISSN 1477-4054. https://academic.oup.com/bib/article/25/4/bbae263/7687614?login=false, Repository of the University of Ljubljana – RUL , DOI: 10.1093/bib/bbae263. [COBISS.SI-ID 199443203]
project: P3-0083; funder: Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Slovenian Research and Innovation Agency
project: MRIC-UL-IC-BSL3+; funder: Network of Infrastructure Centres of the University of Ljubljana
project: 871029 EVA GLOBAL project; funder: European Union’s Horizon 2020 research and innovation program

19. ALREZOIHI, Abdulrahman, PENRICE-RANDAL, Rebekah, DONG, Xiaofeng, PRINCE, Tessa, RANDLE, Nadine, ZAKOTNIK, Samo, SULJIČ, Alen, AVŠIČ-ŽUPANC, Tatjana, PETROVEC, Miroslav, KORVA, Miša. Enrichment of SARS-CoV-2 sequence from nasopharyngeal swabs whilst identifying the nasal microbiome. Journal of clinical virology. [Print ed.]. Apr. 2024, vol. 171, iss. [article no.] 105620, str. 1-9. ISSN 1386-6532. https://www.sciencedirect.com/science/article/abs/pii/S1386653223002433?via%3Dihub, DOI: 10.1016/j.jcv.2023.105620. [COBISS.SI-ID 177869571]

20. KORVA, Miša, BOLTEŽAR, Lučka, TOMAŽIČ, Janez, MALI, Polonca, KOGOJ, Rok, BOSILJ, Martin, SULJIČ, Alen, RESMAN RUS, Katarina, AVŠIČ-ŽUPANC, Tatjana. Evolutionary dynamics of SARS-CoV-2 and microbial background in lymphoma patient with prolonged COVID-19. In: UK international coronavirus network : [abstracts book] : Annual General Meeting, 17th-18th September 2024, Edinburgh, Great Britain. Annual General Meeting, 17th-18th September 2024, Edinburgh. Great Britain. Edinburgh: Biotechnology and Biological Sciences Research Council, 2024. Str. 28. [COBISS.SI-ID 233095427]

21. GRUBELNIK, Gašper, KOGOJ, Rok, SULJIČ, Alen, TOZON, Nataša, PAVLIN, Darja, SLAVEC, Brigita, AVŠIČ-ŽUPANC, Tatjana, KORVA, Miša. Feline coronavirus (FCoV) and SARS-CoV-2 - has recombination occurred between the two viruses in domestic cats with feline infectious peritonitis?. In: UK-ICN ECR conference programme : scientific meeting, 1st March, 2024, Liverpool. Liverpool: Biotechnology and Biological Research Council (BBSRC) and the Department of Environment, Food and Rural Affairs (DEFRA), 2024. Str. 14. [COBISS.SI-ID 189879555]

22. LUŠTREK, Manca, PRESTOR, Zala, SULJIČ, Alen, KOGOJ, Rok, KNAP, Nataša, JEVŠNIK VIRANT, Monika, URŠIČ, Tina, PETROVEC, Miroslav, AVŠIČ-ŽUPANC, Tatjana, KORVA, Miša (author, corresponding author). Influenza A, Influenza B, human respiratory syncytial virus and SARSCoV-2 molecular diagnostics and epidemiology in the post COVID-19 era. Respiratory research. 2024, vol. 25, iss. 1, [article no.] 234, str.1-9, tabele, graf. prikazi. ISSN 1465-993X. https://respiratory-research.biomedcentral.com/articles/10.1186/s12931-024-02862-7, DOI: 10.1186/s12931-024-02862-7. [COBISS.SI-ID 199445507]
project: P3-0083, V3-2034; funder: Slovenian Research and Innovation Agency
project: 871029 EVA GLOBAL project; funder: European Union’s Horizon 2020 research and innovation program

23. BOSILJ, Martin, SULJIČ, Alen, ZAKOTNIK, Samo, SLUNEČKO, Jan, KOGOJ, Rok, KORVA, Miša (author, corresponding author). MetaAll : integrative bioinformatics workflow for analysing clinical metagenomic data. Briefings in bioinformatics. [Online ed.]. 2024, vol. 25, iss. 6, [article no.] e597, str.1-14, ilustr. ISSN 1477-4054. https://academic.oup.com/bib/article/25/6/bbae597/7901732?login=false, Repository of the University of Ljubljana – RUL , DOI: 10.1093/bib/bbae597. [COBISS.SI-ID 217049091]
project: P3-0083, J3-2515, J3-50101; funder: Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Slovenian Research and Innovation Agency

24. KOGOJ, Rok, SULJIČ, Alen, ZAKOTNIK, Samo, KNAP, Nataša, BOSILJ, Martin, SLUNEČKO, Jan, GRUBELNIK, Gašper, VLAJ, Doroteja, KORVA, Miša. Near real-time SARS-CoV-2 genetic variant surveillance system during and in the wake of the COVID-19 pandemic. Clinical chemistry and laboratory medicine, Austrian Society for Laboratory Medicine and Clinical Chemistry, Medical University Graz, June 13-june 14, Graz, Austria. [Online ed.]. 2024, vol. 62, iss. 6, str. ea206. ISSN 1437-4331. https://www.degruyter.com/document/doi/10.1515/cclm-2024-0438/html, DOI: 10.1515/cclm-2024-0438. [COBISS.SI-ID 199735811]

25. BOSILJ, Martin, SULJIČ, Alen. PatDetect. Ljubljana: Medicinska fakulteta, Inštitut za mikrobiologijo in imunologijo, 2024. 1 spletni vir. GitHub.com, NGS-bioinf. https://github.com/NGS-bioinf/PatDetect. [COBISS.SI-ID 202424835]

26. KOGOJ, Rok, GRAŠEK, Manja, SULJIČ, Alen, ZAKOTNIK, Samo, VLAJ, Doroteja, KOTNIK KOMAN, Kaja, FAFANGEL, Mario, PETROVEC, Miroslav, AVŠIČ-ŽUPANC, Tatjana, KORVA, Miša (author, corresponding author). Sequencing analysis of SARS-CoV-2 cases in Slovenian long-term care facilities to support outbreak control. Frontiers in public health. May 2024, vol. 12, iss. [article no.] 1406777, str. 1-13, ilustr. ISSN 2296-2565. https://www.frontiersin.org/journals/public-health/articles/10.3389/fpubh.2024.1406777/full, DOI: 10.3389/fpubh.2024.1406777. [COBISS.SI-ID 197563395]
project: This work was funded by the Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana
project: P3-0083, V3-2034; funder: Slovenian Research Agency
project: no. 871029 European Virus Archive - GLOBAL project; funder: Union's Horizon 2020

27. SLUNEČKO, Jan, KOGOJ, Rok, ZAKOTNIK, Samo, SULJIČ, Alen, KNAP, Nataša, BOSILJ, Martin, STRLE, Franc, AVŠIČ-ŽUPANC, Tatjana, BOGOVIČ, Petra (author, corresponding author), KORVA, Miša (author, corresponding author). Development and performance evaluation of a clinical metagenomics approach for identifying pathogens in the whole blood from patients with undifferentiated fever. Frontiers in cellular and infection microbiology. 2025, vol. 15, no. [article no.] 1667422, str. 1-11, ilustr. ISSN 2235-2988. https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2025.1667422/full, DiRROS - Digital repository of Slovenian research organizations, Repository of the University of Ljubljana – RUL , DOI: 10.3389/fcimb.2025.1667422. [COBISS.SI-ID 251524099]
project: P3-0083, P3-0296, J3-50101; funder: Slovenian Research and Innovation Agency (ARIS)
project: 20230154; funder: University Medical Center Ljubljana
project: IP-022 MRIC-UL-IC-BSL3+; funder: Network of Infrastructure Centers of the University of Ljubljana

28. KOGOJ, Rok, PETRILLO, Mauro, ZAKOTNIK, Samo, SULJIČ, Alen, KORVA, Miša (author, corresponding author), LEONI, Gabriele (author, corresponding author). Misdetection of frameshifts in SARS-CoV-2 genomes : need for additional harmonisation and efficient monitoring of data workflows. Bioinformatics. [Print ed.]. 2025, vol. 41, iss. 10, [article no.] btaf516, str. 1-5, ilustr. ISSN 1367-4803. https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaf516/8254281?login=false, DOI: 10.1093/bioinformatics/btaf516. [COBISS.SI-ID 253893635]
project: P3-0083, J3-50101; funder: Slovenain Research and Innovation Agency
project: 10112671 HADEA, SLOSEQ; funder: The Ministry of Health of Republic of Slovenia and by the European Union

29. SULJIČ, Alen (author, corresponding author), OŠEP, Anja, KOGOJ, Rok, URŠIČ, Tina, PETROVEC, Miroslav, KORVA, Miša. Mutational dynamics of SARS-CoV-2 in patients with persistent infection. In: Dynamics & Evolution of Human Viruses. [S. l.]: Dynamics & Evolution of Human Viruses. 2025, str. 1, ilustr. https://dynamicsevolution.org/event/5/contributions/244/. [COBISS.SI-ID 239890947]

30. BOLTEŽAR, Lučka, KOGOJ, Rok, RESMAN RUS, Katarina, SULJIČ, Alen, BOSILJ, Martin, KNAP, Nataša, MALI, Polonca, TOMAŽIČ, Janez, AVŠIČ-ŽUPANC, Tatjana, KORVA, Miša (author, corresponding author). Respiratory microbiome alterations, coinfections and virus intra-host evolution in a persistently active SARS-CoV-2 infection. BMC infectious diseases. 2025, vol. 25, iss. 1, [article no.] 932, 1-11 str., ilustr. ISSN 1471-2334. https://bmcinfectdis.biomedcentral.com/articles/10.1186/s12879-025-11355-x, DiRROS - Digital repository of Slovenian research organizations, DOI: 10.1186/s12879-025-11355-x. [COBISS.SI-ID 245172995]
project: P3-0083, P3-0289 J3-50101; funder: Slovenian Research and Innovation Agency (ARIS)
project: IP-022 MRIC-UL-IC-BSL3+; funder: Network of Infrastructure Centers of the University of Ljubljana

31. KORVA, Miša (author, corresponding author), BOGOVIČ, Petra (author, corresponding author), KNAP, Nataša, KOGOJ, Rok, SLUNEČKO, Jan, ZAKOTNIK, Samo, SULJIČ, Alen, RESMAN RUS, Katarina, POZVEK, Patricija, STRLE, Franc, AVŠIČ-ŽUPANC, Tatjana, PETROVEC, Miroslav. Emerging human pathogen : identifying Spiroplasma ixodetis as a frequent cause of unlocalised febrile illness. The Journal of infection. May 2026, vol. 93, iss. 1, [article no.] 106776, str. 1-9, ilustr. ISSN 0163-4453. https://www.journalofinfection.com/article/S0163-4453(26)00101-5/fulltext, Repository of the University of Ljubljana – RUL , DiRROS - Digital repository of Slovenian research organizations, DOI: 10.1016/j.jinf.2026.106776. [COBISS.SI-ID 280582403]

32. SULJIČ, Alen, KOGOJ, Rok, ROJKO, Tereza, ADAMIČ, Peter, LEJKO-ZUPANC, Tatjana, PETROVEC, Miroslav, HISCOX, Julian A., KORVA, Miša. Relaxed selection and convergent evolution shape SARS-CoV-2 variant dynamics in immunocompromised patients. In: Abstract book : The XVIIth International Nidovirus Symposium "NIDO2026", 24 - 27 June 2026, Hong Kong, China. [S. l.: s. n.], 2026. Str. 145-146. https://nido2026.com/wp-content/uploads/2026/07/abstract-book.pdf. [COBISS.SI-ID 285626883]