Selected publications with BBMRI.at partner contribution

2024

Ryan et al, Securing the future of microbiome research and innovation: the need for biobanking infrastructure in the UK, CABI (2024). doi:10.1079/20240382445

Shekhovtsov, V.A.; Slajcho, B.; Sacherer, A.; Eder, J. CollectionLocator Level 1: Metadata-Based Search for Collections in Federated Biobanks Cornell University, 2024, doi: 10.48550/arXiv.2408.16422

Groiss S, Viertler C, Kap M, Bernhardt G et al. Inter-patient heterogeneity in the hepatic ischemia-reperfusion injury transcriptome: Implications for research and diagnostics. New Biotechnology, Volume 79, 2024, Pages 20-29, ISSN 1871-6784. doi: 10.1016/j.nbt.2023.12.001, PMID: 38072306.

2023

Bonstingl L, Skofler C, Ulz C, Zinnegger M et al. Clinical application of ISO and CEN/TS standards for liquid biopsies – information everybody wants but nobody wants to pay for. medRxiv 2023.12.04.23299422. doi: 10.1101/2023.12.04.23299422.

L’Imperio V, Wulczyn E, Plass M, et al. Pathologist Validation of a Machine Learning-Derived Feature for Colon Cancer Risk Stratification. JAMA Netw Open. 2023;6(3):e2254891. doi:10.1001/jamanetworkopen.2022.54891, PMID: 36917112.

Wittner, R.; Holub, P.; Müller, H.; Geiger, J. et al. ISO 23494: Biotechnology – Provenance Information Model for Biological Specimen And Data. In: Glavic, B., Braganholo, V., Koop, D. (eds) Provenance and Annotation of Data and Processes. IPAW IPAW 2020 2021. Lecture Notes in Computer Science(), vol 12839. Springer, Cham. doi: 10.1038/s41597-022-01537-6. PMID: 35977957.

Wittner, R.; Holub, P.; Mascia, C.; Frexia, F.; Müller, H.; Plass, M. et al. Towards a common standard for data and specimen provenance in life sciences. Learning Health Systems, 2023 [e10365]. Published 2023 April 18. doi: 10.1002/lrh2.10365.

Holub P, Müller H, Bíl T, et al. Privacy risks of whole-slide image sharing in digital pathology. Nat Commun. 2023;14(1):2577. Published 2023 May 4. doi: 10.1038/s41467-023-37991-y. PMID: 37142591.

Holzinger A, Keiblinger K, Holub P, Zatloukal K, Müller H. AI for life: Trends in artificial intelligence for biotechnology. N Biotechnol. 2023;74:16-24. doi: 10.1016/j.nbt.2023.02.001. PMID: 36754147.

Abuja, P.M.; Pabst, D.; Bourgeois, B.; Loibner, M.; Ulz, C.; Kufferath, I.; Fackelmann, U.; Stumptner, C.; Kraemer, R.; Madl, T.; Zatloukal, K. Residual Humidity in Paraffin-Embedded Tissue Reduces Nucleic Acid Stability. Int. J. Mol. Sci. 2023, 24, 8010. doi: 10.3390/ijms24098010. PMID: 37175716.

Vanessa Frey, Patrick Langthaler, Emanuel Raphaelis et al. Paracelsus 10,000: A prospective cohort study based on the population of Salzburg, Austria. Rationale, objectives and study design, Paracelsus Proceedings of Experimental Medicine 2023;1:1-17; doi: 10.33594/000000600.

Kargl M, Plass M, Müller H. A Literature Review on Ethics for AI in Biomedical Research and Biobanking. Yearb Med Inform. 2022 Aug;31(1):152-160. doi: 10.1055/s-0042-1742516. Epub 2022 Dec 4. PMID: 36463873.

Niedrist T, Kriegl L, Zurl CJ, Schmidt F, Perkmann-Nagele N, Mucher P, Repl M, Flieder I, Radakovics A, Sieghart D, Radner H, Aletaha D, Binder CJ, Gülly C, Krause R, Herrmann M, Wagner OF, Perkmann T, Haslacher H. Preanalytical stability of SARS-CoV-2 anti-nucleocapsid antibodies. Clin Chem Lab Med. 2022 Nov 4. doi: 10.1515/cclm-2022-0875. Epub ahead of print. PMID: 36323338.

Müller H, Holzinger A, Plass M, Brcic L, Stumptner C, Zatloukal K. Explainability and causability for artificial intelligence-supported medical image analysis in the context of the European In Vitro Diagnostic Regulation. N Biotechnol. 2022 Sep 25;70:67-72. doi: 10.1016/j.nbt.2022.05.002. Epub 2022 May 6. PMID: 35526802.

Wieser M, Burger S, Ertl R, Kummer S, Stargardt M, Walter I. Example for process validation in biobanking: Fit for purpose testing of a cryopreservation method without isopentane. Front Mol Biosci. 2022 Sep 30;9:876670. doi: 10.3389/fmolb.2022.876670. PMID: 36250023.

Shekhovtsov, V.A.; Eder, J. Metadata Quality for Biobanks. Appl. Sci. 2022, 12, 9578. doi: 10.3390/app12199578.

Wittner R, Mascia C, Gallo M, Frexia F, Müller H, Plass M, Geiger J, Holub P. Lightweight Distributed Provenance Model for Complex Real-world Environments. Sci Data. 2022 Aug 17;9(1):503. doi: 10.1038/s41597-022-01537-6. PMID: 35977957.

Perkmann T, Koller T, Perkmann-Nagele N, […] Helmuth Haslacher. Increasing test specificity without impairing sensitivity: lessons learned from SARS-CoV-2 serology. Journal of Clinical Pathology Published Online First: 30 August 2022. doi: 10.1136/jcp-2022-208171. PMID: 36041815.

Stumptner, C; Stadlbauer, V; O’Neil, D; Gessner, A; Hiergeist, A; Zatloukal, K; Abuja, P.M. The Pre-Analytical CEN/TS Standard for Microbiome Diagnostics—How Can Research and Development Benefit? Nutrients 2022, 14, 1976. doi: 10.3390/nu14091976. PMID: 35565946.

Eva M. Matzhold, Günther F. Körmöczi, Chiara Banfi, Marlies Schönbacher, Camilla Drexler, Helmberg, Ivo Steinmetz, Andrea Berghold, Peter Schlenke, Gabriel E. Wagner, Anja Stoisser, Barbara Kleinhappl, Wolfgang R. Mayr and Thomas Wagner. Lower Levels of ABO Anti-A and Anti-B of IgM, IgG and IgA Isotypes in the Serum but Not the Saliva of COVID-19 Convalescents. J. Clin. Med. 2022, 11(15), 4513 doi: 10.3390/jcm11154513. PMID: 35956128.

Perkmann T, Mucher P, Perkmann-Nagele N, Radakovics A, Repl M, Koller T, Schmetterer KG, Bigenzahn JW, Leitner F, Jordakieva G, Wagner OF, Binder CJ, Haslacher H. The Comparability of Anti-Spike SARS-CoV.2 Antibody Tests is Time-Dependent: a Prospective Observational Study. Microbiology Spectrum. 2022. doi: 10.1128/spectrum.01402-21. PMID: 35196824.

Golke T, Mucher P, Schmidt P, Radakovics A, Repl M, Hofer P, Perkmann T, Fondi M, Schmetterer KG, Haslacher H. Delays during PBMC isolation have a moderate effect on yield, but severly compromise cell viability. Clin Chem Lab Med. 2022 Jan 27. doi: 10.1515/cclm-2022-0003. Epub ahead of print. PMID: 35085430.

Niedrist T, Drexler C, Torreiter PP, Matejka J, Strahlhofer-Augsten M, Kral S, Riegler S, Gülly C, Zurl C, Kriegl L, Krause R, Berghold A, Steinmetz I, Schlenke P, Herrmann M. Longitudinal comparison of automated SARS-CoV-2 serology assays in assessing virus neutralization capacity in COVID-19 convalescent sera. Arch Pathol Lab Med. 2022 Jan 27. doi: 10.5858/arpa.2021-0604-SA. Epub ahead of print. PMID: 35085385.

E Schulz et al. CD19+IgD+CD27- Naïve B Cells as Predictors of Humoral Response to COVID 19 mRNA Vaccination in Immunocompromised Patients; Front. Immunol., 07 December 2021. doi: 10.3389/fimmu.2021.803742. PMID: 34950155.

Denk, H; Pabst, D; Abuja, PM; Reihs, R; Tessaro, B; Zatloukal, K; Lackner, C. Senescence markers in focal nodular hyperplasia of the liver: pathogenic considerations on the basis of immunohistochemical results. Mod Pathol 2021 Oct 13. doi: 10.1038/s41379-021-00940-5. PMID: 34645984.

Ghini, V; Abuja, PM; Polasek, O; Kozera, L; Laiho, P; Anton, G; Zins, M; Klovins, J; Metspalu, A; Wichmann, HE; Gieger, C; Luchinat, C; Zatloukal, K; Turano, P. Metabolomic Fingerprints in Large Population Cohorts: Impact of Preanalytical Heterogeneity. Clin Chem. 2021; Aug 5; 67(8): 1153-1155. 2021. doi: 0.1093/clinchem/hvab092. PMID: 34223627.

Perkmann T, Perkmann-Nagele N, Mucher P, Radakovics A, Repl M, Koller T, Jordakieva G, Wagner OF, Binder CJ, Haslacher H. Initial SARS-CoV-2 vaccination response can predict booster response for BNT162b2 but not for AZD1222. Int J Infect Dis. 2021 Sep;110:309-313. doi: 10.1016/j.ijid.2021.07.063. Epub 2021 Jul 28. PMID: 34332084.

Zacharias, M; Stangl, V; Thüringer, A; Loibner, M; Wurm, P; Wolfgruber, S; Zatloukal, K; Kashofer, K; Gorkiewicz, G. Rapid Antigen Test for Postmortem Evaluation of SARS-CoV-2 Carriage. Emerg Infect Dis. 2021; Jun 27(6):1734-1737. doi: 10.3201/eid2706.210226. PMID: 33848454.

Perkmann T, Mucher P, Perkmann-Nagele N, Radakovics A, Repl M, Koller T, Schmetterer KG, Bigenzahn JW, Leitner F, Jordakieva G, Wagner OF, Binder CJ, Haslacher H. The comparability of Anti-Spike SARS-CoV-2 antibody tests is time-dependent: a prospective observational study. Microbiol Spectr. 2022;10(1):e0140221. doi: 10.1128/spectrum.01402-21. PMID: 35196824.

Kral S, Banfi C, Niedrist T, Sareban N, Guelly C, Kriegl L, Schiffmann S, Zurl C, Herrmann M, Steinmetz I, Schlenke P, Berghold A, Krause R. Long-lasting immune response to a mild course of PCR-confirmed SARS-CoV-2 infection: A cohort study. J Infect. 2021 Nov;83(5):607-635. doi: 10.1016/j.jinf.2021.08.030. Epub 2021 Aug 22. PMID: 34433071.

Perkmann T, Perkmann-Nagele N, Koller T, Mucher P, Radakovics A, Marculescu R, Wolzt M, Wagner OF, Binder CJ, Haslacher H. Anti-Spike Protein Assays to Determine SARS-CoV-2 Antibody Levels: a Head-to-Head Comparison of Five Quantitative Assays. Microbiol Spectr. 2021 Sep 3;9(1):e0024721. doi: 10.1128/Spectrum.00247-21. Epub 2021 Jun 30. PMID: 34190591.

Eder Johann, Shekhovtsov Vladimir A. Data quality for federated medical data lakelands. International Journal of Web Information Systems Vol. 17 No. 5, 2021 pp. 407-426; Emerald Publishing Limited 1744-0084; doi 10.1108/IJWIS-03-2021-0026.

Mucher P, Batmyagmar D, Perkmann T, Repl M, Radakovics A, Ponocny-Seliger E, Lukas I, Fritzer-Szekeres M, Lehrner J, Knogler T, Tscholakoff D, Fondi M, Wagner OF, Winker R, Haslacher H. Basal myokine levels are associated with quality of life and depressed mood in older adults. Psychophysiology. 2021 May;58(5):e13799. doi: 10.1111/psyp.13799. PMID: 33655551.

Altmann P, Ponleitner M, Rommer PS, Haslacher H, Mucher P, Leutmezer F, Petzold A, Wotawa C, Lanzenberger R, Berger T, Zetterberg H, Bsteh G. Seven day pre-analytical stability of serum and plasma neurofilament light chain. Sci Rep. 2021 May 26;11(1):11034. doi: 10.1038/s41598-021-90639-z. PMID: 34040118.

Popper, H; Zacharias, M; Brcic, L; Marsh, L; Lehrach, H; Schutte, M; Kwapiszewska, G; Timmermann, B; Kashofer, K; Nerlich, A; Regitnig, P; Kenner, L; Zatloukal, K. Different types of immune system regulations in severe Coronavirus disease 2019. VIRCHOWS ARCH. 2021; 479(SUPPL 1): S50-S50.

Perkmann T, Perkmann-Nagele N, Koller T, Mucher P, Radakovics A, Wolzt M, Wagner OF, Binder CJ, Haslacher H. Serum antibody response to BNT162b2 after natural SARS-CoV-2 infection. Eur J Clin Invest. 2021 Aug 1:e13632. doi: 10.1111/eci.13632. Epub ahead of print. PMID: 34337738.

Reihs R, Proynova R, Maqsood S, Ataian M, Lablans M, Quinlan PR, Lawrence E, Bowman E, van Enckevort E, Bučík DF, Müller H, Holub P. BBMRI-ERIC Negotiator: Implementing Efficient Access to Biobanks. Biopreserv Biobank. 2021 Jun 28. doi: 10.1089/bio.2020.0144. Epub ahead of print. PMID: 34182766.

Wulczyn E, Steiner DF, Moran M, Plass M, Reihs R, Tan F, Flament-Auvigne I, Brown T, Regitnig P, Chen PC, Hegde N, Sadhwani A, MacDonald R, Ayalew B, Corrado GS, Peng LH, Tse D, Müller H, Xu Z, Liu Y, Stumpe MC, Zatloukal K, Mermel CH. Interpretable survival prediction for colorectal cancer using deep learning. NPJ Digit Med. 2021 Apr 19;4(1):71. doi: 10.1038/s41746-021-00427-2. PMID: 33875798.

Loibner M, Langner C, Regitnig P, Gorkiewicz G, Zatloukal K. Biosafety Requirements for Autopsies of Patients with COVID-19: Example of a BSL-3 Autopsy Facility Designed for Highly Pathogenic Agents. Pathobiology. 2021;88(1):37-45. doi: 10.1159/000513438. Epub 2020 Dec 9. PMID: 33296902.

Holub P, Kozera L, Florindi F, van Enckevort E, Swertz M, Reihs R, Wutte A, Valík D, Mayrhofer MT; BBMRI-ERIC community. BBMRI-ERIC’s contributions to research and knowledge exchange on COVID-19. Eur J Hum Genet. 2020 Jun;28(6):728-731. doi: 10.1038/s41431-020-0634-8. PMID: 32444797.

Thomas Perkmann, Nicole Perkmann-Nagele, Maria Ozsvar-Kozma, Thomas Koller, Marie-Kathrin Breyer, Robab Breyer-Kohansal, Otto C Burghuber, Sylvia Hartl, Daniel Aletaha, Daniela Sieghart, Peter Quehenberger, Rodrig Marculescu, Patrick Mucher, Astrid Radakovics, Robert Strassl, Gerda Leitner, Oswald F Wagner, Christoph J Binder, Helmuth Haslacher. Increasing test specificity without impairing sensitivity: lessons learned from SARS-CoV-2 serology [published online ahead of print, 2022 Aug 30]. J Clin Pathol. 2022;jclinpath-2022-208171. doi: 10.1136/jcp-2022-208171. PMID: 36041815.

Eder, J., Shekhovtsov, V.A. (2020). Data Quality for Medical Data Lakelands. In: Dang, T.K., Küng, J., Takizawa, M., Chung, T.M. (eds) Future Data and Security Engineering. FDSE 2020. Lecture Notes in Computer Science(), vol 12466. Springer, Cham. doi: 10.1007/978-3-030-63924-2_2.

Perkmann T, Perkmann-Nagele N, Breyer MK, Breyer-Kohansal R, Burghuber OC, Hartl S, Aletaha D, Sieghart D, Quehenberger P, Marculescu R, Mucher P, Strassl R, Wagner OF, Binder CJ, Haslacher H. Side-by-Side Comparison of Three Fully Automated SARS-CoV-2 Antibody Assays with a Focus on Specificity. Clin Chem. 2020 Nov 1;66(11):1405-1413. doi: 10.1093/clinchem/hvaa198. PMID: 32777031.

Müller H, Dagher G, Loibner M, Stumptner C, Kungl P, Zatloukal K. Biobanks for life sciences and personalized medicine: importance of standardization, biosafety, biosecurity, and data management. Curr Opin Biotechnol. 2020 Oct;65:45-51. doi: 10.1016/j.copbio.2019.12.004. PMID: 31896493.

Karine Sargsyan, Brigitte Jaksa, Gabriele Hartl and Tanja Macheiner. Risk Management in Biobanks. Intechopen, doi: 10.5772/intechopen.91463.

Harutyunyan A, Urlesberger B, Muradyan A, Hovhannisyan M, Badalyan A, Kalenteryan H, Haxhija E, Sargsyan K, Yenkoyan K, Babloyan A. Introducing multi-modal enteral medication reduced morbidity and mortality associated with necrotising enterocolitis. Acta Paediatr. 2021 Feb;110(2):458-464. doi: 10.1111/apa.15466. PMID: 32640087.

Pichler H, Eder J. Supporting the Donation of Health Records to Biobanks for Medical Research. Springer International Publishing. doi: 10.1007/978-3-030-50402-1_3.

Lim MS, Beyer T, Babayan A, Bergmann M, Brehme M, Buyx A, Czernin J, Egger G, Elenitoba-Johnson KSJ, Gückel B, Jačan A, Haslacher H, Hicks RJ, Kenner L, Langanke M, Mitterhauser M, Pichler BJ, Salih HR, Schibli R, Schulz S, Simecek J, Simon J, Soares MO, Stelzl U, Wadsak W, Zatloukal K, Zeitlinger M, Hacker M. Advancing Biomarker Development Through Convergent Engagement: Summary Report of the 2nd International Danube Symposium on Biomarker Development, Molecular Imaging and Applied Diagnostics; March 14-16, 2018; Vienna, Austria. Mol Imaging Biol. 2020 Feb;22(1):47-65. doi: 10.1007/s11307-019-01361-2. PMID: 31049831.

Stumptner C, Pabst D, Loibner M, Viertler C, Zatloukal K. The impact of crosslinking and non-crosslinking fixatives on antigen retrieval and immunohistochemistry. N Biotechnol. 2019 Sep 25;52:69-83. doi: 10.1016/j.nbt.2019.05.003. Epub 2019 May 11. PMID: 31082574.

Starkbaum J, Felt U. Negotiating the reuse of health-data: Research, Big Data, and the European General Data Protection Regulation. Big Data & Society, SAGEjournals. doi: 10.1177/2053951719862594.

Dagher G, Becker KF, Bonin S, Foy C, Gelmini S, Kubista M, Kungl P, Oelmueller U, Parkes H, Pinzani P, Riegman P, Schröder U, Stumptner C, Turano P, Sjöback R, Wutte A, Zatloukal K. Pre-analytical processes in medical diagnostics: New regulatory requirements and standards. N Biotechnol. 2019 Sep 25;52:121-125. doi: 10.1016/j.nbt.2019.05.002. Epub 2019 May 15. PMID: 31102798.

Haslacher H, Bayer M, Fiegl H, Gerner M, Hofer P, Korb M, Neururer S, Perkmann T, Plattner K, Sargsyan K, Steiner E, Stumptner C, Walter I, Wieser M, Wutte A, Wagner O, Zatloukal K. Quality management at the national biobanking level – establishing a culture of mutual trust and support: the BBMRI.at example. Clin Chem Lab Med. 2019 Nov 26;57(12):e301-e305. doi: 10.1515/cclm-2019-0491. PMID: 31188755.

Peter M. Abuja (Medical University of Graz), Tamara Carapina (EATRIS), Martin de Kort (EATRIS), Michael Raess (INFRAFRONTIER), Chris Tieken (EATRIS), Nigel Wagstaff (EATRIS). Academia – Industry Collaboration Best Practices Guide.

Vogl F and Sargsyan K.: Do we need an expiration date for biobanks? Chapter 12 in Global Genes, Local Concerns; Legal, Ethical, and Scientific Challenges in International Biobanking; Edited by Timo Minssen, Janne R Herrmann and Jens Schovsbo; 26 April 2019, pages 216–228 (13 total). doi: 10.4337/9781788116190.00021.

Stumptner C, Pabst D, Loibner M, Viertler C, Zatloukal K. The impact of crosslinking and non-crosslinking fixatives on antigen retrieval and immunohistochemistry. N Biotechnol. 2019 Sep 25;52:69-83. doi: 10.1016/j.nbt.2019.05.003. Epub 2019 May 11. PMID: 31082574.

Dagher G, Becker KF, Bonin S, Foy C, Gelmini S, Kubista M, Kungl P, Oelmueller U, Parkes H, Pinzani P, Riegman P, Schröder U, Stumptner C, Turano P, Sjöback R, Wutte A, Zatloukal K. Pre-analytical processes in medical diagnostics: New regulatory requirements and standards. N Biotechnol. 2019 Sep 25;52:121-125. doi: 10.1016/j.nbt.2019.05.002. Epub 2019 May 15. PMID: 31102798.

Goisauf M, Durnová AP. From engaging publics to engaging knowledges: Enacting “appropriateness” in the Austrian biobank infrastructure. Public Underst Sci. 2019 Apr;28(3):275-289. doi: 10.1177/0963662518806451. Epub 2018 Oct 16. PMID: 30324869.

Stumptner C, Sargsyan K. Kungl P, Zatloukal K. Crucial Role of High Quality Biosamples; in Handbook of Biomarkers and Precision Medicine; Claudio Carini, ‎Mark Fidock, ‎Alain van Gool; CRC Press 2019.

Hämäläinen I, Törnwall O, Simell B, Zatloukal K, Perola M, van Ommen GB. Role of Academic Biobanks in Public-Private Partnerships in the European Biobanking and BioMolecular Resources Research Infrastructure Community. Biopreserv Biobank. 2019;17(1):46-51. doi: 10.1089/bio.2018.0024. Epub 2018 Nov 30. PMID: 30499696.

Ranasinghe S, Pichler H, Eder J. Report on Data Quality in Biobanks: Problems, Issues, State-of-the-Art; 2018. arXiv:1812.10423 [cs.CY]. doi: 10.48550/arXiv.1812.10423.