In vivo kinetics of transcription initiation of the lar promoter in Escherichia coli. Evidence for a sequential mechanism with two rate-limiting steps. - Meenakshisundaram Kandhavelu; Henrik Mannerström; Abhishekh Gupta; Antti Häkkinen; Jason Lloyd-Price; Olli Yli-Harja; Andre S. Ribeiro (BMC Syst. Biol., 2011)

Inference of Kinetic Parameters of Delayed Stochastic Models of Gene Expression Using a Markov Chain Approximation. - Henrik Mannerström; Olli Yli-Harja; Andre S. Ribeiro (EURASIP J. Bioinform. Syst. Biol., 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)

Non-Stationary Gaussian Process Regression with Hamiltonian Monte Carlo. - Markus Heinonen; Henrik Mannerström; Juho Rousu; Samuel Kaski; Harri Lähdesmäki (AISTATS, 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)

Bayesian metabolic flux analysis reveals intracellular flux couplings. - Markus Heinonen; Maria Osmala; Henrik Mannerström; Janne Wallenius; Samuel Kaski; Juho Rousu; Harri Lähdesmäki (Bioinform., 2019)

An interpretable probabilistic machine learning method for heterogeneous longitudinal studies. - Juho Timonen; Henrik Mannerström; Aki Vehtari; Harri Lähdesmäki (CoRR, 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)

lgpr: an interpretable non-parametric method for inferring covariate effects from longitudinal data. - Juho Timonen; Henrik Mannerström; Aki Vehtari; Harri Lähdesmäki (Bioinform., 2021)

PairGP: Gaussian process modeling of longitudinal data from paired multi-condition studies. - Michele Vantini; Henrik Mannerström; Sini Rautio; Helena Ahlfors; Brigitta Stockinger; Harri Lähdesmäki (Comput. Biol. Medicine, 2022)