sepal: identifying transcript profiles with spatial patterns by diffusion-based modeling. - Alma Andersson; Joakim Lundeberg (Bioinform., 2021)

Computational methods for analysis of spatial transcriptomics data: An exploration of the spatial gene expression landscape. - Alma Andersson (2022)

Markov state modelling reveals heterogeneous drug-inhibition mechanism of Calmodulin. - Annie M. Westerlund; Akshay Sridhar; Leo Dahl; Alma Andersson; Anna-Yaroslava Bodnar; Lucie Delemotte (PLoS Comput. Biol., 2022)

Benchmarking and Evaluation of AI Models in Biology: Outcomes and Recommendations from the CZI Virtual Cells Workshop. - Elizabeth Fahsbender; Alma Andersson; Jeremy Ash; Polina Binder; Daniel Burkhardt; Benjamin Chang; Georg K. Gerber; Anthony Gitter; Patrick Godau; Ankit Gupta; Genevieve Haliburton; Siyu He; et al. (CoRR, 2025)