| GRNBoost2 and Arboreto: efficient and scalable inference of gene regulatory networks T Moerman, S Aibar Santos, C Bravo González-Blas, J Simm, Y Moreau, ... Bioinformatics 35 (12), 2159-2161, 2019 | 338 | 2019 |
| GRU-ODE-Bayes: Continuous modeling of sporadically-observed time series E De Brouwer, J Simm, A Arany, Y Moreau Advances in neural information processing systems 32, 2019 | 307 | 2019 |
| Characterization of the vaginal micro-and mycobiome in asymptomatic reproductive-age Estonian women T Drell, T Lillsaar, L Tummeleht, J Simm, A Aaspõllu, E Väin, I Saarma, ... PloS one 8 (1), e54379, 2013 | 297 | 2013 |
| Repurposing high-throughput image assays enables biological activity prediction for drug discovery J Simm, G Klambauer, A Arany, M Steijaert, JK Wegner, E Gustin, ... Cell chemical biology 25 (5), 611-618. e3, 2018 | 209 | 2018 |
| Easy hyperparameter search using optunity M Claesen, J Simm, D Popovic, Y Moreau, B De Moor arXiv preprint arXiv:1412.1114, 2014 | 103 | 2014 |
| Evolution of bacterial consortia in spontaneously started rye sourdoughs during two months of daily propagation M Bessmeltseva, E Viiard, J Simm, T Paalme, I Sarand PLoS One 9 (4), e95449, 2014 | 91 | 2014 |
| The influence of different maternal microbial communities on the development of infant gut and oral microbiota T Drell, J Štšepetova, J Simm, K Rull, A Aleksejeva, A Antson, V Tillmann, ... Scientific reports 7 (1), 9940, 2017 | 90 | 2017 |
| Tree-based ensemble multi-task learning method for classification and regression J Simm, IM De Abril, M Sugiyama IEICE TRANSACTIONS on Information and Systems 97 (6), 1677-1681, 2014 | 81 | 2014 |
| Changes in the transcriptome of the human endometrial Ishikawa cancer cell line induced by estrogen, progesterone, tamoxifen, and mifepristone (RU486) as detected by RNA-sequencing K Tamm-Rosenstein, J Simm, M Suhorutshenko, A Salumets, M Metsis PloS one 8 (7), e68907, 2013 | 79 | 2013 |
| The development of gut microbiota in critically ill extremely low birth weight infants assessed with 16S rRNA gene based sequencing T Drell, I Lutsar, J Štšepetova, Ü Parm, T Metsvaht, ML Ilmoja, J Simm, ... Gut microbes 5 (3), 304-503, 2014 | 70 | 2014 |
| High-throughput sequencing approach uncovers the miRNome of peritoneal endometriotic lesions and adjacent healthy tissues M Saare, K Rekker, T Laisk-Podar, D Soritsa, AM Roost, J Simm, ... PLoS One 9 (11), e112630, 2014 | 65 | 2014 |
| Research resource: small RNA-seq of human granulosa cells reveals miRNAs in FSHR and aromatase genes A Velthut-Meikas, J Simm, T Tuuri, JS Tapanainen, M Metsis, A Salumets Molecular endocrinology 27 (7), 1128-1141, 2013 | 63 | 2013 |
| Linking drug target and pathway activation for effective therapy using multi-task learning M Yang, J Simm, CC Lam, P Zakeri, GJP van Westen, Y Moreau, ... Scientific reports 8 (1), 8322, 2018 | 58 | 2018 |
| ChemGrapher: optical graph recognition of chemical compounds by deep learning M Oldenhof, A Arany, Y Moreau, J Simm Journal of chemical information and modeling 60 (10), 4506-4517, 2020 | 56 | 2020 |
| The complex microbiome from native semen to embryo culture environment in human in vitro fertilization procedure J Štšepetova, J Baranova, J Simm, Ü Parm, T Rööp, S Sokmann, ... Reproductive Biology and Endocrinology 18, 1-13, 2020 | 55 | 2020 |
| Hyperparameter tuning in python using optunity M Claesen, J Simm, D Popovic, B Moor Proceedings of the international workshop on technical computing for machine …, 2014 | 52 | 2014 |
| Endometrial transcriptome analysis indicates superiority of natural over artificial cycles in recurrent implantation failure patients undergoing frozen embryo transfer S Altmäe, K Tamm-Rosenstein, FJ Esteban, J Simm, L Kolberg, ... Reproductive biomedicine online 32 (6), 597-613, 2016 | 49 | 2016 |
| Diversity and stability of lactic acid bacteria in rye sourdoughs of four bakeries with different propagation parameters E Viiard, M Bessmeltseva, J Simm, T Talve, A Aaspõllu, T Paalme, ... PloS one 11 (2), e0148325, 2016 | 49 | 2016 |
| Towards practical privacy-preserving genome-wide association study C Bonte, E Makri, A Ardeshirdavani, J Simm, Y Moreau, F Vercauteren BMC bioinformatics 19, 1-12, 2018 | 48 | 2018 |
| Macau: Scalable Bayesian factorization with high-dimensional side information using MCMC J Simm, A Arany, P Zakeri, T Haber, JK Wegner, V Chupakhin, ... 2017 IEEE 27th International Workshop on Machine Learning for Signal …, 2017 | 42 | 2017 |
