The Lagergren lab is concerned with method development in machine learning and probabilistic modeling as well as application of the developed methods. The goal is to facilitate investigations of developmental, temporal, and spatial aspects through analysis of cutting edge biological data that has single cell resolution, in some cases also carrying spatial information. Methodologically, the projects focus on advanced methods for computational inference such as Expectation Maximization, Sequential Markov Chain, Variational Inference, Markov Chain Monte Carlo (MCMC), and Particle MCMC methods. It is also important for us to obtain efficient implementations of our methods by taking advantage of modern computational technology.

Current Projects

The Lagergren lab is currently running or coordinating five computational biology projects, while maintaining collaborations with many research groups in the fields of computational biology and medicine.


CIIR – Tumour-immune interactions and clinical applications, funded by the Swedish Research Council.


CONTRA, funded by the European Union. Coordinated by KTH.

CONTRA (Computational ONcology TRaining Alliance) is an EU funded Innovative Training Network consisting of eight principal investigators from eight major European universities as well as partners from pharmaceutical, biotech-start up, and software development companies. CONTRA has recruited 15 early-stage researchers (Ph.D. candidates), each located and supervised at one of the participating universities.

Single Cell Machine Learning

Single Cell Machine Learning, funded by the Swedish Foundation for Strategic Research.

Mechanisms of antibiotic resistance

Mechanisms for acquisition and transmission of successful antibiotic resistant pneumococcal clones pre- and post-vaccination, funded by the Swedish Research Council.

Models and effective inference: tumour trees and beyond

Models and effective inference: tumour trees and beyond, funded by Swedish Research Council.

Committee service (since 2008)

Program committee Recomb 2018
Program committee Recomb 2017
Program committee Recomb 2016
Program committee Recomb CG 2015
Program committee Recomb 2015
Program committee Recomb 2014
Program committee Recomb 2013
Program committee Recomb 2012
Program committee ISMB 2012
Program committee Recomb 2011
Program committee WABI 2011
Program committee Recomb 2010
Program committee WABI 2010
Program committee Recomb 2009
Program committee, track chair, ISMB 2009
Program committee Recomb 2008
Program committee ISMB 2008
Co-chair program committee WABI 2008
Steering committee Recomb CG


Bioinformatics, Cancer, Cardiovascular disease, genomics, Human genetics, Neurobiology, Systems biology