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3. Markov modeling for cost-effectiveness using federated health data network

Author

Haug, Markus, primary, Oja, Marek, additional, Pajusalu, Maarja, additional, Mooses, Kerli, additional, Reisberg, Sulev, additional, Vilo, Jaak, additional, Giménez, Antonio Fernández, additional, Falconer, Thomas, additional, Danilović, Ana, additional, Maljkovic, Filip, additional, Dawoud, Dalia, additional, and Kolde, Raivo, additional

Published
2024
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4. Transforming Estonian health data to the Observational Medical Outcomes Partnership (OMOP) Common Data Model: lessons learned

Author

Oja, Marek, primary, Tamm, Sirli, additional, Mooses, Kerli, additional, Pajusalu, Maarja, additional, Talvik, Harry-Anton, additional, Ott, Anne, additional, Laht, Marianna, additional, Malk, Maria, additional, Lõo, Marcus, additional, Holm, Johannes, additional, Haug, Markus, additional, Šuvalov, Hendrik, additional, Särg, Dage, additional, Vilo, Jaak, additional, Laur, Sven, additional, Kolde, Raivo, additional, and Reisberg, Sulev, additional

Published
2023
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5. Building an international consortium for tracking coronavirus health status

Author

Segal, Eran, Zhang, Feng, Lin, Xihong, King, Gary, Shalem, Ophir, Shilo, Smadar, Allen, William E., Alquaddoomi, Faisal, Altae-Tran, Han, Anders, Simon, Balicer, Ran, Bauman, Tal, Bonilla, Ximena, Booman, Gisel, Chan, Andrew T., Cohen, Ori, Coletti, Silvano, Davidson, Natalie, Dor, Yuval, Drew, David A., Elemento, Olivier, Evans, Georgina, Ewels, Phil, Gale, Joshua, Gavrieli, Amir, Geiger, Benjamin, Grad, Yonatan H., Greene, Casey S., Hajirasouliha, Iman, Jerala, Roman, Kahles, Andre, Kallioniemi, Olli, Keshet, Ayya, Kocarev, Ljupco, Landua, Gregory, Meir, Tomer, Muller, Aline, Nguyen, Long H., Oresic, Matej, Ovchinnikova, Svetlana, Peterson, Hedi, Prodanova, Jana, Rajagopal, Jay, Rätsch, Gunnar, Rossman, Hagai, Rung, Johan, Sboner, Andrea, Sigaras, Alexandros, Spector, Tim, Steinherz, Ron, Stevens, Irene, Vilo, Jaak, and Wilmes, Paul

Published
2020
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6. #383 BioEndoCar: identifying candidate biomarkers for diagnosis and prognosis of endometrial carcinoma using machine learning and artificial intelligence

Author

Kokol, Marko, primary, Romano, Andrea, additional, Werner, Erica, additional, Smrkolj, Špela, additional, Roškar, Luka, additional, Pirš, Boštjan, additional, Semczuk, Andrzej, additional, Kaminska, Aleksandra, additional, Adamiak-Godlewska, Aneta, additional, Fishman, Dmytro, additional, Vilo, Jaak, additional, Lowy, Camille, additional, Griesbeck, Anne, additional, Schroeder, Christoph, additional, Tokarz, Janina, additional, Adamski, Jerzy, additional, Weinberger, Vit, additional, Bednaríková, Markéta, additional, Vinklerova, Petra, additional, Ferrero, Simone, additional, Barra, Fabio, additional, Takac, Iztok, additional, Sobocan, Monika, additional, Knez, Jure, additional, and Rižner, Tea Lanišnik, additional

Published
2023
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10. From Genomes to Vaccines: Leishmania as a Model

Author

Almeida, Renata, Norrish, Alan, Levick, Mark, Vetrie, David, Freeman, Tom, Vilo, Jaak, Ivens, Alasdair, Lange, Uta, Stober, Carmel, McCann, Sharon, and Blackwell, Jenefer M.

Published
2002

13. Additional file 1 of Common clinical blood and urine biomarkers for ischemic stroke: an Estonian Electronic Health Records database study

Author

Kurvits, Siim, Harro, Ainika, Reigo, Anu, Ott, Anne, Laur, Sven, Särg, Dage, Tampuu, Ardi, Alasoo, Kaur, Vilo, Jaak, Milani, Lili, and Haller, Toomas

Abstract

Additional file 1: Table S1. Abbreviations used in the article. Table S2. Clinical parameters mentioned in the article. Text S3. Raw data extraction workflow. Text S4. Semi-automatic pipeline for cleaning raw tabular EHR data for downstream analyses of IS. Fig. S5. Sources for phenotype information from the EstBB. Text S6. Filters used in Association Rule Mining (ARM) to identify potentially interesting rules for further testing. Text S7. R script to transform numerical clinical data for Logistic Regression (LR). Text S8. R script used for Cox Proportinal Hazards (CPH) model and Kaplan-Meier (K-M) graphs. Text S9. Deep neural networks (DNN) implementation. Table S10. Five association rules (ARMs) identified. Fig. S11. Lowess curve examples. Table S12. Summary of lowess. Table S13. Summary of Logistic Regression (LR). Fig. S14. Kaplan-Meier graphs for CPs with P

Published
2023
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15. Omics-informed CNV calls reduce false-positive rates and improve power for CNV-trait associations

Author

Lepamets, Maarja, primary, Auwerx, Chiara, additional, Nõukas, Margit, additional, Claringbould, Annique, additional, Porcu, Eleonora, additional, Kals, Mart, additional, Jürgenson, Tuuli, additional, Morris, Andrew Paul, additional, Võsa, Urmo, additional, Bochud, Murielle, additional, Stringhini, Silvia, additional, Wijmenga, Cisca, additional, Franke, Lude, additional, Peterson, Hedi, additional, Vilo, Jaak, additional, Lepik, Kaido, additional, Mägi, Reedik, additional, and Kutalik, Zoltán, additional

Published
2022
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16. Publisher Correction: Building an international consortium for tracking coronavirus health status

Author

Segal, Eran, Zhang, Feng, Lin, Xihong, King, Gary, Shalem, Ophir, Shilo, Smadar, Allen, William E., Alquaddoomi, Faisal, Altae-Tran, Han, Anders, Simon, Balicer, Ran, Bauman, Tal, Bonilla, Ximena, Booman, Gisel, Chan, Andrew T., Cohen, Ori, Coletti, Silvano, Davidson, Natalie, Dor, Yuval, Drew, David A., Elemento, Olivier, Evans, Georgina, Ewels, Phil, Gale, Joshua, Gavrieli, Amir, Geiger, Benjamin, Grad, Yonatan H., Greene, Casey S., Hajirasouliha, Iman, Jerala, Roman, Kahles, Andre, Kallioniemi, Olli, Keshet, Ayya, Kocarev, Ljupco, Landua, Gregory, Meir, Tomer, Muller, Aline, Nguyen, Long H., Oresic, Matej, Ovchinnikova, Svetlana, Peterson, Hedi, Prodanova, Jana, Rajagopal, Jay, Rätsch, Gunnar, Rossman, Hagai, Rung, Johan, Sboner, Andrea, Sigaras, Alexandros, Spector, Tim, Steinherz, Ron, Stevens, Irene, Vilo, Jaak, and Wilmes, Paul

Published
2020
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17. An Evolutionary Model of DNA Substring Distribution

Author

Kull, Meelis, Tretyakov, Konstantin, Vilo, Jaak, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Elomaa, Tapio, editor, Mannila, Heikki, editor, and Orponen, Pekka, editor

Published
2010
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20. Trajectories:A framework for detecting temporal clinical event sequences from health data standardized to the Observational Medical Outcomes Partnership (OMOP) Common Data Model

Author

Künnapuu, Kadri, Ioannou, Solomon, Ligi, Kadri, Kolde, Raivo, Laur, Sven, Vilo, Jaak, Rijnbeek, Peter R., Reisberg, Sulev, Künnapuu, Kadri, Ioannou, Solomon, Ligi, Kadri, Kolde, Raivo, Laur, Sven, Vilo, Jaak, Rijnbeek, Peter R., and Reisberg, Sulev

Abstract

Objective: To develop a framework for identifying temporal clinical event trajectories from Observational Medical Outcomes Partnership-formatted observational healthcare data. Materials and Methods: A 4-step framework based on significant temporal event pair detection is described and implemented as an open-source R package. It is used on a population-based Estonian dataset to first replicate a large Danish population-based study and second, to conduct a disease trajectory detection study for type 2 diabetes patients in the Estonian and Dutch databases as an example. Results: As a proof of concept, we apply the methods in the Estonian database and provide a detailed breakdown of our findings. All Estonian population-based event pairs are shown. We compare the event pairs identified from Estonia to Danish and Dutch data and discuss the causes of the differences. The overlap in the results was only 2.4%, which highlights the need for running similar studies in different populations. Conclusions: For the first time, there is a complete software package for detecting disease trajectories in health data.

Published
2022

21. Expression Profiler

Author

Vilo, Jaak, Kapushesky, Misha, Kemmeren, Patrick, Sarkans, Ugis, Brazma, Alvis, Dietz, K., editor, Gail, M., editor, Krickeberg, K., editor, Samet, J., editor, Tsiatis, A., editor, Parmigiani, Giovanni, editor, Garrett, Elizabeth S., editor, Irizarry, Rafael A., editor, and Zeger, Scott L., editor

Published
2003
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22. Microarray Data Representation, Annotation and Storage

Author

Brazma, Alvis, Sarkans, Ugis, Robinson, Alan, Vilo, Jaak, Vingron, Martin, Hoheisel, Jörg, Fellenberg, Kurt, Scheper, T., editor, Babel, W., editor, Blanch, H. W., editor, Endo, I., editor, Enfors, S. -O., editor, Fiechter, A., editor, Hoare, M., editor, Mattiasson, B., editor, Sahm, H., editor, Schügerl, K., editor, Stephanopoulos, G., editor, von Stockar, U., editor, Tsao Director, G. T., editor, Villadsen, J., editor, Wandrey, C., editor, Hoheisel, Jörg, editor, Brazma, A., editor, Büssow, K., editor, Cantor, C. R., editor, Christians, F. C., editor, Chui, G., editor, Diaz, R., editor, Drmanac, R., editor, Drmanac, S., editor, Eickhoff, H., editor, Fellenberg, K., editor, Hannenhalli, S., editor, Hoheisel, J., editor, Hou, A., editor, Hubbell, E., editor, Jin, H., editor, Jin, P., editor, Jurinke, C., editor, Konthur, Z., editor, Köster, H., editor, Kwon, S., editor, Lacy, S., editor, Lehrach, H., editor, Lipshutz, R., editor, Little, D., editor, Lueking, A., editor, McGall, G. H., editor, Moeur, B., editor, Nordhoff, E., editor, Nyarsik, L., editor, Pevzner, P. A., editor, Robinson, A., editor, Sarkans, U., editor, Shafto, J., editor, Sohail, M., editor, Southern, E. M., editor, Swanson, D., editor, Ukrainczyk, T., editor, van den Boom, D., editor, Vilo, J., editor, Vingron, M., editor, Walter, G., editor, and Xu, C., editor

Published
2002
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25. Pattern discovery in biosequences

Author

Brāzma, Alvis, Jonassen, Inge, Vilo, Jaak, Ukkonen, Esko, Carbonell, Jaime G., editor, Siekmann, Jörg, editor, Goos, G., editor, Hartmanis, J., editor, van Leeuwen, J., editor, Honavar, Vasant, editor, and Slutzki, Giora, editor

Published
1998
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30. The 1st year of the COVID-19 epidemic in Estonia: an interrupted time series of population based nationwide cross-sectional studies.

Author

Uuskula, Anneli, primary, Kalda, Ruth, additional, Solvak, Mihkel, additional, Jurisson, Mikk, additional, Kaarik, Meelis, additional, Fischer, Krista, additional, Keis, Aime, additional, Raudvere, Uku, additional, vilo, Jaak, additional, Peterson, Hedi, additional, Kaarik, Ene, additional, Metspalu, Mait, additional, Jurgenson, Tuuli, additional, Milani, Lili, additional, Kolberg, Liis, additional, Tiit, Ene-Margit, additional, and Vassil, Kristjan, additional

Published
2021
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31. Abstract 464: BioEndoCar: in search of new Biomarkers for Diagnosis and Prognosis of Endometrial Carcinoma

Author

Hafner, Eva, primary, Smrkolj, Špela, additional, Romano, Andrea, additional, Werner, Henrica MJ, additional, Semczuk, Andrzej, additional, Kaminska, Aleksandra, additional, Adamiak-Godlewska, Aneta, additional, Fishman, Dmytro, additional, Vilo, Jaak, additional, Lowy, Camille, additional, Schröder, Christoph, additional, Tokarz, Janina, additional, Adamski, Jerzy, additional, Weinberger, Vít, additional, Bednaříková, Markéta, additional, Vinklerova, Petra, additional, Ferrero, Simone, additional, Barra, Fabio, additional, Takač, Iztok, additional, Knez, Jure, additional, and Rižner, Tea Lanišnik, additional

Published
2021
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41. Human embryonic stem cell-derived test systems for developmental neurotoxicity: a transcriptomics approach

Author

Krug, Anne K., Kolde, Raivo, Gaspar, John A., Rempel, Eugen, Balmer, Nina V., Meganathan, Kesavan, Vojnits, Kinga, Baquié, Mathurin, Waldmann, Tanja, Ensenat-Waser, Roberto, Jagtap, Smita, Evans, Richard M., Julien, Stephanie, Peterson, Hedi, Zagoura, Dimitra, Kadereit, Suzanne, Gerhard, Daniel, Sotiriadou, Isaia, Heke, Michael, Natarajan, Karthick, Henry, Margit, Winkler, Johannes, Marchan, Rosemarie, Stoppini, Luc, Bosgra, Sieto, Westerhout, Joost, Verwei, Miriam, Vilo, Jaak, Kortenkamp, Andreas, Hescheler, Jürgen, Hothorn, Ludwig, Bremer, Susanne, van Thriel, Christoph, Krause, Karl-Heinz, Hengstler, Jan G., Rahnenführer, Jörg, Leist, Marcel, and Sachinidis, Agapios

Published
2013
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44. Healthspan pathway maps in C. elegans and humans highlight transcription, proliferation/biosynthesis and lipids

Author

Möller, Steffen, Saul, Nadine, Cohen, Alan A., Köhling, Rüdiger, Sender, Sina, Murua Escobar, Hugo, Junghanss, Christian, Cirulli, Francesca, Berry, Alessandra, Antal, Peter, Adler, Priit, Vilo, Jaak, Boiani, Michele, Jansen, Ludger, Repsilber, Dirk, Grabe, Hans Jörgen, Struckmann, Stephan, Barrantes, Israel, Hamed, Mohamed, Wouters, Brecht, Schoofs, Liliane, Luyten, Walter, Fuellen, Georg, Möller, Steffen, Saul, Nadine, Cohen, Alan A., Köhling, Rüdiger, Sender, Sina, Murua Escobar, Hugo, Junghanss, Christian, Cirulli, Francesca, Berry, Alessandra, Antal, Peter, Adler, Priit, Vilo, Jaak, Boiani, Michele, Jansen, Ludger, Repsilber, Dirk, Grabe, Hans Jörgen, Struckmann, Stephan, Barrantes, Israel, Hamed, Mohamed, Wouters, Brecht, Schoofs, Liliane, Luyten, Walter, and Fuellen, Georg

Abstract

The molecular basis of aging and of aging-associated diseases is being unraveled at an increasing pace. An extended healthspan, and not merely an extension of lifespan, has become the aim of medical practice. Here, we define health based on the absence of diseases and dysfunctions. Based on an extensive review of the literature, in particular for humans and C. elegans, we compile a list of features of health and of the genes associated with them. These genes may or may not be associated with survival/lifespan. In turn, survival/lifespan genes that are not known to be directly associated with health are not considered. Clusters of these genes based on molecular interaction data give rise to maps of healthspan pathways for humans and for C. elegans. Overlaying healthspan-related gene expression data onto the healthspan pathway maps, we observe the downregulation of (pro-inflammatory) Notch signaling in humans and of proliferation in C. elegans. We identify transcription, proliferation/biosynthesis and lipids as a common theme on the annotation level, and proliferation-related kinases on the gene/protein level. Our literature-based data corpus, including visualization, should be seen as a pilot investigation of the molecular underpinnings of health in two different species., Funding Agencies:Fonds de la Recherche en Sante du QuebecEstonian Research Agency grant IUT34-4FWO 11A5420NBME NC TKP2020 grant of NKFIH Hungary BME-Biotechnology FIKP grant of EMMI (BME FIKP-BIO) Orszagos Tudomanyos Kutatasi Alapprogramok (OTKA) K119866

Published
2020
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50. Mechanisms of IFN-γ–induced apoptosis of human skin keratinocytes in patients with atopic dermatitis

Author

Rebane, Ana, Zimmermann, Maya, Aab, Alar, Baurecht, Hansjörg, Koreck, Andrea, Karelson, Maire, Abram, Kristi, Metsalu, Tauno, Pihlap, Maire, Meyer, Norbert, Fölster-Holst, Regina, Nagy, Nikoletta, Kemeny, Lajos, Kingo, Külli, Vilo, Jaak, Illig, Thomas, Akdis, Mübeccel, Franke, Andre, Novak, Natalija, Weidinger, Stephan, and Akdis, Cezmi A.

Published
2012
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