The Genomic HyperBrowser: an analysis web server for genome-scale data. - Geir Kjetil Sandve; Sveinung Gundersen; Morten Johansen; Ingrid Kristine Glad; Krishanthi Gunathasan; Lars Holden; Marit Holden; Knut Liestøl; Ståle Nygård; Vegard Nygaard; Jonas Paulsen; Halfdan Rydbeck; et al. (Nucleic Acids Res., 2013)

HiBrowse: multi-purpose statistical analysis of genome-wide chromatin 3D organization. - Jonas Paulsen; Geir Kjetil Sandve; Sveinung Gundersen; Tonje Lien; Kai Trengereid; Eivind Hovig (Bioinform., 2014)

Inferential analysis of genomic 3D organization. - Jonas Paulsen (2014)

Manifold Based Optimization for Single-Cell 3D Genome Reconstruction. - Jonas Paulsen; Odin Gramstad; Philippe Collas (PLoS Comput. Biol., 2015)

Galaxy Portal: interacting with the galaxy platform through mobile devices. - Claus Børnich; Ivar Grytten; Eivind Hovig; Jonas Paulsen; Martin Cech; Geir Kjetil Sandve (Bioinform., 2016)

The shape of chromatin: insights from computational recognition of geometric patterns in Hi-C data. - Andrea Raffo; Jonas Paulsen (Briefings Bioinform., 2023)