CROPPER: a metagene creator resource for cross-platform and cross-species compendium studies. - Jussi Paananen; Markus Storvik; Garry Wong (BMC Bioinform., 2006)

FORG3D: Force-directed 3D graph editor for visualization of integrated genome scale data. - Jussi Paananen; Garry Wong (BMC Syst. Biol., 2009)

Varietas: a functional variation database portal. - Jussi Paananen; Robert Ciszek; Garry Wong (Database J. Biol. Databases Curation, 2010)

TAFFEL: Independent Enrichment Analysis of gene sets. - Mitja I. Kurki; Jussi Paananen; Markus Storvik; Seppo Ylä-Herttuala; Juha E. Jääskeläinen; Mikael von und zu Fraunberg; Garry Wong; Petri Pehkonen (BMC Bioinform., 2011)

Varanto: variant enrichment analysis and annotation. - Oskari Timonen; Mikko Särkkä; Tibor Fülöp; Anton Mattsson; Juha Kekäläinen; Jussi Paananen (Bioinform., 2019)

Random forest-based imputation outperforms other methods for imputing LC-MS metabolomics data: a comparative study. - Marietta Kokla; Jyrki Virtanen; Marjukka Kolehmainen; Jussi Paananen; Kati Hanhineva (BMC Bioinform., 2019)

An omics perspective on drug target discovery platforms. - Jussi Paananen; Vittorio Fortino (Briefings Bioinform., 2020)

ThETA: transcriptome-driven efficacy estimates for gene-based TArget discovery. - Mario Failli; Jussi Paananen; Vittorio Fortino (Bioinform., 2020)

Detection of medications associated with Alzheimer's disease using ensemble methods and cooperative game theory. - B. Braithwaite; Jussi Paananen; Heidi Taipale; Antti Tanskanen; Jari Tiihonen; Sirpa Hartikainen; Anna-Maija Tolppanen (Int. J. Medical Informatics, 2020)

Validating and Extracting Information from National Identification Numbers in R: The Case of Finland and Sweden. - Pyry Kantanen; Erik Bülow; Aleksi Lahtinen; Måns Magnusson; Jussi Paananen; Leo Lahti (R J., 2025)