Classification of DNA sequences using Bloom filters. - Henrik Stranneheim; Max Käller; Tobias Allander; Björn Andersson; Lars Arvestad; Joakim Lundeberg (Bioinform., 2010)

Improved gap size estimation for scaffolding algorithms. - Kristoffer Sahlin; Nathaniel Street; Joakim Lundeberg; Lars Arvestad (Bioinform., 2012)

BESST - Efficient scaffolding of large fragmented assemblies. - Kristoffer Sahlin; Francesco Vezzi; Björn Nystedt; Joakim Lundeberg; Lars Arvestad (BMC Bioinform., 2014)

ST Pipeline: an automated pipeline for spatial mapping of unique transcripts. - José Fernández Navarro; Joel Sjöstrand; Fredrik Salmén; Joakim Lundeberg; Patrik L. Ståhl (Bioinform., 2017)

ST Spot Detector: a web-based application for automatic spot and tissue detection for spatial Transcriptomics image datasets. - Kim Wong; José Fernández Navarro; Ludvig Bergenstråhle; Patrik L. Ståhl; Joakim Lundeberg (Bioinform., 2018)

ST viewer: a tool for analysis and visualization of spatial transcriptomics datasets. - José Fernández Navarro; Joakim Lundeberg; Patrik L. Ståhl (Bioinform., 2019)

SpatialCPie: an R/Bioconductor package for spatial transcriptomics cluster evaluation. - Joseph Bergenstråhle; Ludvig Bergenstråhle; Joakim Lundeberg (BMC Bioinform., 2020)

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

Learning Stationary Markov Processes with Contrastive Adjustment. - Ludvig Bergenstråhle; Jens Lagergren; Joakim Lundeberg (CoRR, 2023)

Semla: a versatile toolkit for spatially resolved transcriptomics analysis and visualization. - Ludvig Larsson; Lovisa Franzén; Patrik L. Ståhl; Joakim Lundeberg (Bioinform., 2023)