2022

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  • Meister, T; Pisarev, H; Kolde, R; Kalda, R; Suija, K; Milani, L; Karo-Astover, L; Piirsoo, M; Uusküla, A. (2022). Clinical characteristics and risk factors for COVID-19 infection and disease severity: A nationwide observational study in Estonia. PLoS ONE, 17, e0270192. DOI: 10.1371/journal.pone.0270192.
  • Uusküla, A; Jürgenson T; Pisarev H; Kolde, R; Meister, T; Tisler, A; Suija, K; Kalda, R; Piirsoo, M; Fischer K (2022). Long-term mortality following COVID-19 infection: a national cohort study from Estonia. The Lancet Regional Health – Europe, x, 100394. DOI: 10.1016/j.lanepe.2022.100394.
  • Künnapuu, K; Ioannou, S; Ligi, K; Kolde, R; Laur, S; Vilo, J; Rijnbeek, P; Reisberg, S (2021). Design of a framework to detect temporal clinical event trajectories from health data standardized to the OMOP CDM. OHDSI Global Symposium 2021.
  • Yang, C; Williams, Ross D; Swerdel, JN; Almeida, JR; Brouwer, ES.; Burn, E; Carmona, L; Chatzidionysiou, K; Duarte-Salles, T; Fakhouri, W; Hottgenroth, A; Jani, M; Kolde, R; Kors, JA; Kullamaa, L; Lane, J; Marinier, K; Michel, A; Stewart, HM; Prats-Uribe, A … Rijnbeek, PR. (2022). Development and external validation of prediction models for adverse health outcomes in rheumatoid arthritis: A multinational real-world cohort analysis. Seminars in Arthritis and Rheumatism, 56, 152050. DOI: 10.1016/j.semarthrit.2022.152050.
  • Künnapuu, K; Ioannou, S; Ligi, K; Kolde, R; Laur, S; Vilo, J; Rijnbeek, PR; Reisberg, S (2022). Trajectories: a framework for detecting temporal clinical event sequences from health data standardized to the Observational Medical Outcomes Partnership (OMOP) Common Data Model. JAMIA Open, 5 (1), 1−11. DOI: 10.1093/jamiaopen/ooac021
2021
  • Ostrak, A; Randmets, J; Sokk, V; Laur, S; Kamm, L (2021). Implementing Privacy-Preserving Genotype Analysis with Consideration for Population Stratification. Cryptography, 5 (3), ARTN 21. DOI: 10.3390/cryptography5030021.
2020
  • Tamm, S; Raie, E; Käär, R; Oja, M; Reisberg, S (2020). Eesti eelkooliealiste laste hõlmatus immuniseerimiskava vaktsiinidega 2010. aasta sünnikohordi põhjal Eesti Haigekassa raviarvete alusel. Eesti Arst, 99 (1), 6−15.
  • Laur, S; Orasmaa, S; Särg, D; Tammo, P (2020). EstNLTK 1.6: Remastered Estonian NLP Pipeline. Proceedings of the 12th Language Resources and Evaluation Conference: International Conference on Language Resources and Evaluation (LREC), Marseille, France, 2020. European Language Resources Association, 7152−7160.
  • Krebs, K; Bovijn, J; Zheng, N; Lepamets, M; Censin, JC; Jürgenson, T; Särg, D; Abner, E; Laisk, T; Luo, Y; Skotte, L; Geller, F; Feenstra, B; Wang, W; Auton, A;  Raychaudhuri, S; Esko, T; Metspalu, A; Laur, S… Fadista, J (2020). Genome-wide Study Identifies Association between HLA-B∗55:01 and Self-Reported Penicillin Allergy. The American Journal of Human Genetics, 107 (4), 612−621. DOI: 10.1016/j.ajhg.2020.08.008.
2019
  • James, G; Reisberg, S; Lepik, K; Galwey, N; Avillach, P; Kolberg, L; Mägi, R; Esko, T; Alexander, M; Waterworth, D; Loomis, AK; Vilo, J (2019). An exploratory phenome wide association study linking asthma and liver disease genetic variants to electronic health records from the Estonian Biobank. PLoS ONE, 14 (4), ARTN e0215026. DOI: 10.1371/journal.pone.0215026.
  • Ward, DV; Hoss, AG; Kolde, R; van Aggelen, HC; Loving, J; Smith, SA; Mack, DA; Kathirvel, R; Halperin, JA; Buell, DJ; Wong, BE; Ashworth, JL; Fortunato-Habib, MM; Xu, L; Barton, BA; Lazar, P; Carmona, JJ; Mathew, J; Salgo, IS; Gross, BD … Ellison, RT, III (2019). Integration of genomic and clinical data augments surveillance of healthcare-acquired infections. Infection Control and Hospital Epidemiology, 40 (6), 649−655. DOI: 10.1017/ice.2019.75.
  • Liivlaid, H; Eigo, N; Reisberg, S (2019). Eriarstiabi haigestumusstatistika võrdlus Tervise Arengu Instituudi ja Eesti Haigekassa andmetel. Eesti Arst, 1, 17−26.
  • Palover, M; Leitsalu, L; Krebs, K; Lall, K; Kals, M; Nikopensius, T; Reigo, A; Milani, L; Fischer, K; Magi, R; Allik, A; Kolk, B; Metsalu, K; Puusepp, M; Mikkel, K; Tammesoo, M; Pintsaar, E; Temberg, T; Reisberg, S; Vilo, J … Metspalu, A. (2019). Reporting genetic risks to participants of the Estonian Biobank, Genome Center. European Journal of Human Genetics, 27 (1), 544−545.
  • Reisberg, S; Krebs, K; Lepamets, M; Kals, M; Mägi, R; Metsalu, K; Lauschke, VM; Vilo, J; Milani, L; (2019). Translating genotype data of 44,000 biobank participants into clinical pharmacogenetic recommendations: challenges and solutions. Genetics in Medicine. DOI: 10.1038/s41436-018-0337-5.
2018
  • Mooses, K; Oja, M; Reisberg, S; Vilo, J; Kull, M (2018). Validating Fitbit Zip for monitoring physical activity of children in school: a cross-sectional study. BMC Public Health, 18. DOI: 10.1186/s12889-018-5752-7.
  • Bogdanov, D; Kamm, L; Laur, S; Sokk, V (2018). Implementation and Evaluation of an Algorithm for Cryptographically Private Principal Component Analysis on Genomic Data. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 15 (5), 1427−1432. DOI: 10.1109/TCBB.2018.2858818.
  • Bogdanov, D; Kamm, L; Laur, S; Sokk, V (2018). Rmind: A Tool for Cryptographically Secure Statistical Analysis. IEEE Transactions on Dependable and Secure Computing, 15 (3), 481−495. DOI: 10.1109/TDSC.2016.2587623.
2017
  • Reisberg, S; Iljasenko, T; Läll, K; Fischer, K; Vilo, J (2017). Comparing distributions of polygenic risk scores of type 2 diabetes and coronary heart disease within different populations. PLoS ONE, 12 (7), e0179238−e0179238. DOI: 10.1371/journal.pone.0179238.
  • Muromägi, A; Sirts, K; Laur, S (2017). Linear Ensembles of Word Embedding Models. Proceedings of the 21st Nordic Conference on Computational Linguistics: NoDaLiDa, Gothenburg, Sweden, 22.-24.05.2017. Linköping University Electronic Press, 96−104.
2016
  • Reimand J; Arak T; Adler P; Kolberg L; Reisberg S; Peterson H; Vilo J (2016). g:Profiler-a web server for functional interpretation of gene lists (2016 update). Nucleic Acids Research, gkw199. DOI: 10.1093/nar/gkw199.
  • Roberto, G; Leal, I; Sattar, N; Loomis, AK; Avillach, P; Egger, P; van Wijngaarden, R; Ansell, D; Reisberg, S; Tammesoo, ML; Alavere, H; Pasqua, A; Pedersen, L; Cunningham, J; Tramontan, L; Mayer, MA; Herings, R; Coloma, P; Lapi, F; Sturkenboom, M … Gini, R. (2016). Identifying Cases of Type 2 Diabetes in Heterogeneous Data Sources: Strategy from the EMIF Project. PLoS ONE, 11 (8), e0160648. DOI: 10.1371/journal.pone.0160648.
  • Orasmaa, S; Petmanson, T; Tkatšenko, A; Laur, S; Kaalep, HJ; (2016). EstNLTK – NLP Toolkit for Estonian. Proceedings of the Tenth International Conference on Language Resources and Evaluation (LREC 2016): The International Conference on Language Resources and Evaluation; Portorož, Slovenia. 2460−2466.
  • Kolde, R; Märtens, K; Lokk, K; Laur, S; Vilo, J (2016). seqlm: an MDL based method for identifying differentially methylated regions in high density methylation array data. Bioinformatics, btw304. DOI: 10.1093/bioinformatics/btw304.
2015
  • Reisberg, S ; Talvik, HA; Koppel, K; Laur, S; Vilo, J (2015). Description of the current status and future needs of the Information Architecture and Data Management solutions for the national personalised medicine pilot project. 1−100.
2014
  • Bogdanov, D; Kamm, L; Laur, S; Pruulmann-Vengerfeldt, P; Talviste, R; Willemson, J (2014). Privacy-preserving statistical data analysis on federated databases. Privacy Technologies and Policy: Annual Privacy Forum 2014, 20.-21. mai 2014, Ateena, Kreeka.  DOI: 10.1007/978-3-319-06749-0_3.
2013
  • Reisberg, S; Sirel, R; Kalda, R; Merzin, M; Pruulmann, J; Vilo, J (2013). Elektrooniliste terviselugude analüüsimise võimalused Tartu perearstide infosüsteemi näitel. Eesti Arst, 92 (8), 452−459.
  • Kamm, L; Bogdanov, D; Laur, S; Vilo, J (2013). A new way to protect privacy in large-scale genome-wide association studies. Bioinformatics, 29 (7), 886−893. DOI: 10.1093/bioinformatics/btt066.
  • Tkachenko, A; Petmanson, T; Laur, S (2013). Named Entity Recognition in Estonian. Proceedings of the 4th Biennial International Workshop on Balto-Slavic Natural Language Processing, Sofia, Bulgaria, 8-9 August 2013.  ACL: Omnipress, 78−83.
2012
  • Bogdanov, D; Jagomägis, R; Laur, S (2012). A universal toolkit for cryptographically secure privacy-preserving data mining. In:  Proceedings of the Pacific Asia Workshop on Intelligence and Security Informatics 2012 (112−126). 
  • Kolde, R; Laur, S; Adler, P; Vilo, J (2012). Robust Rank Aggregation for gene list integration and meta-analysis. Bioinformatics, 28 (4), 573−580. DOI: 10.1093/bioinformatics/btr709.
2011
  • Tretyakov, K.; Laur, S.; Vilo, J. (2011). G = MAT: Linking Transcription Factor Expression and DNA Binding Data. PLoS ONE, 6 (1), e14559. DOI: 10.1371/journal.pone.0014559.
  • Ilmjärv, S; Luuk, H; Laur, S; Vasar, E; Vilo, J (2013). Non-parametric probe-level estimation of differential expression. In: . 19th Annual International Conference on Intelligent Systems for Molecular Biology and 10th European Conference on Computational Biology, Vienna (Austria).
2008
  • Jänes, J; Laur, S; Kolka, I. (2008). Detection and characterisation of Hα emission lines from Gaia BP/RP spectra. C.A.L. Bailer-Jones. Classification and discovery in large astronomical surveys (71−75).  Melville, New York: AIP.
  • Bogdanov, D; Laur, S; Willemson, J (2008). Sharemind: a framework for fast privacy-preserving computations. Computer Security – ESORICS 2008: 13th European Symposium on Research in Computer Security Málaga, Spain, 192−206.  DOI: 10.1007/978-3-540-88313-5_13.
2006
  • Laur, S; Lipmaa, H; Mielikäinen, T (2006). Cryptographically Private Support Vector Machines. KDD-2006: The Twelfth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, Philadelphia, USA, 618−624.
2005
  • Lipmaa, H; Mielikäinen, T; Laur, S (2005). Private Itemset Support Counting. Seventh International Conference on Information and Communications Security, ICICS ’05, 97−111.