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)

A systematic evaluation of normalization methods in quantitative label-free proteomics. - Tommi Välikangas; Tomi Suomi; Laura L. Elo (Briefings Bioinform., 2018)

A comprehensive evaluation of popular proteomics software workflows for label-free proteome quantification and imputation. - Tommi Välikangas; Tomi Suomi; Laura L. Elo (Briefings Bioinform., 2018)

Phosphonormalizer: an R package for normalization of MS-based label-free phosphoproteomics. - Sohrab Saraei; Tomi Suomi; Otto Kauko; Laura L. Elo (Bioinform., 2018)

SimPhospho: a software tool enabling confident phosphosite assignment. - Veronika Suni; Tomi Suomi; Tomoya Tsubosaka; Susumu Y. Imanishi; Laura L. Elo; Garry L. Corthals (Bioinform., 2018)

PhosPiR: an automated phosphoproteomic pipeline in R. - Ye Hong; Dani Flinkman; Tomi Suomi; Sami Pietilä; Peter James; Eleanor Coffey; Laura L. Elo (Briefings Bioinform., 2022)

Correction to: PhosPiR: an automated phosphoproteomic pipeline in R. - Ye Hong; Dani Flinkman; Tomi Suomi; Sami Pietilä; Peter James; Eleanor Coffey; Laura L. Elo (Briefings Bioinform., 2022)

ECCB2024: The 23rd European Conference on Computational Biology. - Anu Kukkonen-Macchi; Sampsa Hautaniemi; Katharina F. Heil; Merja Heinäniemi; Lars Juhl Jensen; Sini Junttila; Lukas Käll; Asta Laiho; Peter Maccallum; Matti Nykter; Bengt Persson; Tomi Suomi; et al. (Bioinform., 2024)

A Mosaic of Perspectives: Understanding Ownership in Software Engineering. - Tomi Suomi; Petri Ihantola; Tommi Mikkonen; Niko Mäkitalo (XP, 2025)

Adaptive sequence alignment for metagenomic data analysis. - Sami Pietilä; Tomi Suomi; Niklas Paulin; Asta Laiho; Yannes S. Sclivagnotis; Laura L. Elo (Comput. Biol. Medicine, 2025)