Below is a list of our articles published in scientific journals together with a selection of posters presented in various international conferences. View also the list of completed bachelor, masters and doctoral thesis.

2024

Mooses K, Šavrova A, Pajusalu M, Oja M, Tamm S, Haug M, Padrik L, Laanpere M, Uusküla A, Kolde R

Using electronic health records to evaluate the adherence to cervical cancer prevention guidelines: A cross-sectional study

Preventive Medicine, 183, 2024, doi: 10.1016/j.ypmed.2024.107982

Haug M, Oja M, Pajusalu M, Mooses K, Reisberg S, Vilo J, Giménez AF,  Falconer T, Danilović A, Maljkovic F, Dawoud D, Kolde R.

Markov modeling for cost-effectiveness using federated health data network

Journal of the American Medical Informatics Association, 2024; ocae044, doi: 10.1093/jamia/ocae044

Markus AF, Rijnbeek PR, Kors JA Burn E, Duarte-Salles T, Haug M, Kim C, Kolde R, Lee Y, Park HS, Park RW, Prieto-Alhambra D, Reyes C, Krishnan JA, Brusselle GG, Verhamme KMC

Real-world treatment trajectories of adults with newly diagnosed asthma or COPD

Mercadé-Besora N, Li X, Kolde R, Trinh NTH, Sanchez-Santos MT, Man WY, Roel E, Reyes C, Delmestri A, Nordeng HME, Uusküla A, Duarte-Salles T, Prats C, Prieto- Alhambra D, Jödicke AM, Català M

The role of COVID-19 vaccines in preventing post-COVID- 19 thromboembolic and cardiovascular complications

Heart 2024;0:1–9. doi:10.1136/heartjnl-2023-323483

2023

Oja M, Tamm S, Mooses K, Pajusalu M, Talvik HA, Ott A, Laht M, Malk M, Lõo M, Holm J, Haug M, Šuvalov H, Särg D, Vilo J, Laur S, Kolde R, Reisberg S

Transforming Estonian health data to the Observational Medical Outcomes Partnership (OMOP) Common Data Model: lessons learned

JAMIA Open, 2023: 6 (4). DOI: 10.1093/jamiaopen/ooad100

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)

Mooses K; Vesilind, K; Oja M; Tamm S; Haug M; Kalda R; Suija K, Tisler A, Meister T; Malk M, Uusküla A; Kolde R.

The use of prescription drugs and health care services during the 6‑month post‑COVID‑19 period

Scientific Reports, 2023:13, 11638100394. DOI: 10.1038/s41598-023-38691-9.

Gandaglia G, Pellegrino F, Golozar A, De Meulder B, Abbott T, Achtman A, Omar MI, Alshammari T, Areia C, Asiimwe A, Beyer K, Bjartell A, Campi R, Cornford P, Falconer T, Feng Q, Gong M, Herrera R, Hughes N, Hulsen T, Kinnaird A, Lai LYH , Maresca G, Mottet N, Oja M, Prinsen P, Reich C, Remmers S, Roobol MJ, Sakalis V, Seager S, Smith EJ, Snijder R, Steinbeisser C, Thurin NH, Hijazy A, van Bochove K, Van den Bergh RCN, Van Hemelrijck M, Willemse PP, Williams AE, Kermani NZ, Evans-Axelsson S, Briganti A, N’Dow J, on behalf of the PIONEER Consortium

Clinical Characterization of Patients Diagnosed with Prostate Cancer and Undergoing Conservative Management: A PIONEER Analysis Based on Big Data

European Urology, 2023. DOI: 10.1016/j.eururo.2023.06.012

Voss EA, Shoaibi A, Lai LYH,  Blacketer C, Alshammari T, Makadia R, Haynes K, Sena AG, Rao G, van Sandijk S, Fraboulet C,  Boyer L, Le Carrour T, Horban S, Morales DR, Roldán JM, Ramírez-Anguita JM, Mayer A,  de Wilde M, John LH, Duarte-Salles T, Roel E, Pistillo A, Kolde R, Maljkovi F, Denaxas S, Papez V, Kahn MG, Natarajan K, Reich C, Secora A, Minty EP, Shah NH, Posada JD, Morales MTG, Bosca D, Juanino HC, Holgado AD, Jiménez MP, Balazote PS, Barrio NG, Sen S, Üresin AY, Erdogan B, Belmans L, Byttebier G, Malbrain MLNG, Dedman DJ, Cuccu Z, Vashisht R, Butte AJ, Patel A, Dahm L, Hana C, Arshad FBF, Ostropolets A, Nyberg F,  Hripcsak G, Suchard MA,
Prieto-Alhambra D, Rijnbeek PR, Schuemie MJ, Ryan PB

Contextualising adverse events of special interest to characterise the baseline incidence rates in 24 million patients with COVID-19 across 26 databases: a multinational retrospective cohort study

eClinicalMedicine. Part of THE LANCET Discovery Science, 2023:58. DOI: 10.1016/j.eclinm.2023.101932

Rosenberg M, Thetloff M, Tamm S, Kuusk K, Reisberg S, Vilo J

Kroonilise neeruhaiguse levimus Eesti e-tervise andmete alusel

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.