Empirical comparison of structure-based pathway methods. - Maria K. Jaakkola; Laura L. Elo (Briefings Bioinform., 2016)

Comparison of methods to detect differentially expressed genes between single-cell populations. - Maria K. Jaakkola; Fatemeh Seyednasrollah; Arfa Mehmood; Laura L. Elo (Briefings Bioinform., 2017)

ROTS: An R package for reproducibility-optimized statistical testing. - Tomi Suomi; Fatemeh Seyednasrollah; Maria K. Jaakkola; Thomas Faux; Laura L. Elo (PLoS Comput. Biol., 2017)

Crowdsourcing digital health measures to predict Parkinson's disease severity: the Parkinson's Disease Digital Biomarker DREAM Challenge. - Solveig K. Sieberts; Jennifer Schaff; Marlena Duda; Bálint Á Pataki; Ming Sun; Phil Snyder; Jean-Francois Daneault; Federico Parisi; Gianluca Costante; Udi Rubin; Peter Banda; Yooree Chae; et al. (npj Digit. Medicine, 2021)

Estimating cell type-specific differential expression using deconvolution. - Maria K. Jaakkola; Laura L. Elo (Briefings Bioinform., 2022)

Segmentation of Dynamic Total-Body [18F]-FDG PET Images Using Unsupervised Clustering. - Maria K. Jaakkola; Maria Rantala; Anna Jalo; Teemu Saari; Jaakko Hentilä; Jatta S. Helin; Tuuli A. Nissinen; Olli Eskola; Johan Rajander; Kirsi A. Virtanen; Jarna C. Hannukainen; Francisco López-Picón; et al. (Int. J. Biomed. Imaging, 2023)

Quantitative evaluation of unsupervised clustering algorithms for dynamic total-body PET image analysis. - Oona Rainio; Maria K. Jaakkola; Riku Klén (CoRR, 2025)