2023

Uusküla, A; Oja, M; Tamm, S; Tisler, A; Laanpere, M; Padrik, L; Nygard, M; Reisberg, S; Vilo, J; Kolde, R.

Prevaccination Prevalence of Type-Specific Human Papillomavirus Infection by Grade of Cervical Cytology in Estonia

JAMA Network Open, 2023:6 (2), e2254075. DOI: 10.1001/jamanetworkopen.2022.54075

Media coverage (in Estonian)

2022
Repeatable ETL process to transform Estonian data to OMOP CDM

Meister, T; Pisarev, H; Kolde, R; Kalda, R; Suija, K; Milani, L; Karo-Astover, L; Piirsoo, M; Uusküla, A.

Clinical characteristics and risk factors for COVID-19 infection and disease severity: A nationwide observational study in Estonia

PLoS ONE, 2022:17, 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

Long-term mortality following COVID-19 infection: a national cohort study from Estonia

The Lancet Regional Health – Europe, 2022:100394. DOI: 10.1016/j.lanepe.2022.100394.

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. 

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, 2022:56, 152050. DOI: 10.1016/j.semarthrit.2022.152050

Künnapuu, K; Ioannou, S; Ligi, K; Kolde, R; Laur, S; Vilo, J; Rijnbeek, PR; Reisberg, S

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, 2022:5 (1), 1−11. DOI: 10.1093/jamiaopen/ooac021

2021

Ostrak, A; Randmets, J; Sokk, V; Laur, S; Kamm, L.

Implementing Privacy-Preserving Genotype Analysis with Consideration for Population Stratification

Cryptography, 2021:5 (3), ARTN 21. DOI: 10.3390/cryptography5030021.

2020

Laur, S; Orasmaa, S; Särg, D; Tammo, P

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

Genome-wide Study Identifies Association between HLA-B∗55:01 and Self-Reported Penicillin Allergy

The American Journal of Human Genetics, 2020:107 (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

An exploratory phenome wide association study linking asthma and liver disease genetic variants to electronic health records from the Estonian Biobank

PLoS ONE, 2019:14 (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

Integration of genomic and clinical data augments surveillance of healthcare-acquired infections

Infection Control and Hospital Epidemiology, 2019:40 (6), 649−655. DOI: 10.1017/ice.2019.7

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.

Reporting genetic risks to participants of the Estonian Biobank, Genome Center

European Journal of Human Genetics, 2019:27 (1), 544−545

Reisberg, S; Krebs, K; Lepamets, M; Kals, M; Mägi, R; Metsalu, K; Lauschke, VM; Vilo, J; Milani, L

Translating genotype data of 44,000 biobank participants into clinical pharmacogenetic recommendations: challenges and solutions

Genetics in Medicine, 2019 DOI: 10.1038/s41436-018-0337-5

2018

Mooses, K; Oja, M; Reisberg, S; Vilo, J; Kull, M

Validating Fitbit Zip for monitoring physical activity of children in school: a cross-sectional study

BMC Public Health, 2018:18. DOI: 10.1186/s12889-018-5752-7.

Bogdanov, D; Kamm, L; Laur, S; Sokk, V

Implementation and Evaluation of an Algorithm for Cryptographically Private Principal Component Analysis on Genomic Data

IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2018:15 (5), 1427−1432. DOI: 10.1109/TCBB.2018.2858818.

Bogdanov, D; Kamm, L; Laur, S; Sokk, V

Rmind: A Tool for Cryptographically Secure Statistical Analysis

IEEE Transactions on Dependable and Secure Computing, 2018:15 (3), 481−495. DOI: 10.1109/TDSC.2016.2587623

2017

Reisberg, S; Iljasenko, T; Läll, K; Fischer, K; Vilo, J

Comparing distributions of polygenic risk scores of type 2 diabetes and coronary heart disease within different populations

PLoS ONE, 2+17:12 (7), e0179238−e0179238. DOI: 10.1371/journal.pone.0179238.

Muromägi, A; Sirts, K; Laur, S

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

g:Profiler-a web server for functional interpretation of gene lists (2016 update)

Nucleic Acids Research, 2016, 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. 

Identifying Cases of Type 2 Diabetes in Heterogeneous Data Sources: Strategy from the EMIF Project

PLoS ONE, 2016:11 (8), e0160648. DOI: 10.1371/journal.pone.0160648.

Orasmaa, S; Petmanson, T; Tkatšenko, A; Laur, S; Kaalep, HJ

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

seqlm: an MDL based method for identifying differentially methylated regions in high density methylation array data

Bioinformatics, 2016, btw304. DOI: 10.1093/bioinformatics/btw304.

2015
2014

Bogdanov, D; Kamm, L; Laur, S; Pruulmann-Vengerfeldt, P; Talviste, R; Willemson, J

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

Elektrooniliste terviselugude analüüsimise võimalused Tartu perearstide infosüsteemi näitel

Eesti Arst, 2013:92 (8), 452−459.

Kamm, L; Bogdanov, D; Laur, S; Vilo, J

A new way to protect privacy in large-scale genome-wide association studies

Bioinformatics, 2013:29 (7), 886−893. DOI: 10.1093/bioinformatics/btt066.

Tkachenko, A; Petmanson, T; Laur, S

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

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

Robust Rank Aggregation for gene list integration and meta-analysis

Bioinformatics, 2012:28 (4), 573−580. DOI: 10.1093/bioinformatics/btr709

2011

Tretyakov, K.; Laur, S.; Vilo, J

G = MAT: Linking Transcription Factor Expression and DNA Binding Data

PLoS ONE, 2011:6 (1), e14559. DOI: 10.1371/journal.pone.0014559.

Ilmjärv, S; Luuk, H; Laur, S; Vasar, E; Vilo, J

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), 2011.

2008

Jänes, J; Laur, S; Kolka, I

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

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

Cryptographically Private Support Vector Machines

KDD-2006: The Twelfth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, Philadelphia, USA, 2006, 618−624.

2005

Lipmaa, H; Mielikäinen, T; Laur, S

Private Itemset Support Counting

Seventh International Conference on Information and Communications Security, ICICS ’05, 2005:97−111.