Computational study of noise in a large signal transduction network. - Jukka Intosalmi; Tiina Manninen; Keijo Ruohonen; Marja-Leena Linne (BMC Bioinform., 2011)

Analyzing Th17 cell differentiation dynamics using a novel integrative modeling framework for time-course RNA sequencing data. - Jukka Intosalmi; Helena Ahlfors; Sini Rautio; Henrik Mannerström; Zhi Jane Chen; Riitta Lahesmaa; Brigitta Stockinger; Harri Lähdesmäki (BMC Syst. Biol., 2015)

A subpopulation model to analyze heterogeneous cell differentiation dynamics. - Yat Hin Chan; Jukka Intosalmi; Sini Rautio; Harri Lähdesmäki (Bioinform., 2016)

Data-driven mechanistic analysis method to reveal dynamically evolving regulatory networks. - Jukka Intosalmi; Kari Nousiainen; Helena Ahlfors; Harri Lähdesmäki (Bioinform., 2016)

Learning unknown ODE models with Gaussian processes. - Markus Heinonen; Çagatay Yildiz; Henrik Mannerström; Jukka Intosalmi; Harri Lähdesmäki (ICML, 2018)

Learning stochastic differential equations with Gaussian Processes without Gradient Matching. - Çagatay Yildiz; Markus Heinonen; Jukka Intosalmi; Henrik Mannerström; Harri Lähdesmäki (MLSP, 2018)

A Mathematical Model for Enhancer Activation Kinetics During Cell Differentiation. - Kari Nousiainen; Jukka Intosalmi; Harri Lähdesmäki (AlCoB, 2019)

A Probabilistic Framework for Molecular Network Structure Inference by Means of Mechanistic Modeling. - Juho Timonen; Henrik Mannerström; Harri Lähdesmäki; Jukka Intosalmi (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)