A method to infer positive selection from marker dynamics in an asexual population. - Christopher J. R. Illingworth; Ville Mustonen (Bioinform., 2012)

GraphAlignment: Bayesian pairwise alignment of biological networks. - Michal Kolár; Jörn Meier; Ville Mustonen; Michael Lässig; Johannes Berg (BMC Syst. Biol., 2012)

Identifying Selection in the Within-Host Evolution of Influenza Using Viral Sequence Data. - Christopher J. R. Illingworth; Andrej Fischer; Ville Mustonen (PLoS Comput. Biol., 2014)

Prediction of antibiotic resistance in Escherichia coli from large-scale pan-genome data. - Danesh Moradigaravand; Martin Palm; Anne Farewell; Ville Mustonen; Jonas Warringer; Leopold Parts (PLoS Comput. Biol., 2018)

Contrasting the impact of cytotoxic and cytostatic drug therapies on tumour progression. - Jani V. Anttila; Mikhail Shubin; Johannes Cairns; Florian Borse; Qingli Guo; Tommi Mononen; Ignacio Vázquez-García; Otto Pulkkinen; Ville Mustonen (PLoS Comput. Biol., 2019)

The evolutionary history of 2,658 cancers. - Moritz Gerstung; Clemency Jolly; Ignaty Leshchiner; Stefan C. Dentro; Santiago Gonzalez; Thomas J. Mitchell; Yulia Rubanova; Pavana Anur; Kaixian Yu; Maxime Tarabichi; Amit G. Deshwar; Jeff Wintersinger; et al. (Nat., 2020)

Multiobjective optimization identifies cancer-selective combination therapies. - Otto Pulkkinen; Prson Gautam; Ville Mustonen; Tero Aittokallio (PLoS Comput. Biol., 2020)

Drug-induced resistance evolution necessitates less aggressive treatment. - Teemu Kuosmanen; Johannes Cairns; Robert Noble; Niko Beerenwinkel; Tommi Mononen; Ville Mustonen (PLoS Comput. Biol., 2021)

Identification of multiplicatively acting modulatory mutational signatures in cancer. - Dovydas Kiciatovas; Qingli Guo; Miika Kailas; Henri Pesonen; Jukka Corander; Samuel Kaski; Esa Pitkänen; Ville Mustonen (BMC Bioinform., 2022)

Time-travelling pathogens and their risk to ecological communities. - Giovanni Strona; Corey J. A. Bradshaw; Pedro Cardoso; Nicholas Gotelli; Frédéric Guillaume; Federica Manca; Ville Mustonen; Luis Zaman (PLoS Comput. Biol., 2023)

Quantifying massively parallel microbial growth with spatially mediated interactions. - Florian Borse; Dovydas Kiciatovas; Teemu Kuosmanen; Mabel Vidal; Guillermo Cabrera-Vives; Johannes Cairns; Jonas Warringer; Ville Mustonen (PLoS Comput. Biol., 2024)