Jonas Paulsen

Image of Jonas Paulsen
Norwegian version of this page
Phone +47 22859105
Room 4206
Visiting address Blindernveien 31 0371 Oslo
Postal address Postboks 1066 Blindern 0316 Oslo

Academic interests

My research focuses on how the three-dimensional (3D) organization of DNA inside the nucleus relates to critical functions in the eukaryotic cell, including epigenetic gene expression regulation. I develop computational tools and bioinformatics software to explore the comparative genomics of the 3D genome across cell-types, tissues and species. Read more about research group here.

Courses taught

Former courses taught

  • Epigenetic analysis in stem- and cancer cells (MED3003)

  • Medisinstudiet, Modul 1 (MED1100)



  • Liyakat Ali, Tharvesh Moideen; Brunet, Annaëlle; Collas, Philippe & Paulsen, Jonas (2021). TAD cliques predict key features of chromatin organization. BMC Genomics. ISSN 1471-2164. 22(1). doi: 10.1186/s12864-021-07815-8. Full text in Research Archive
  • Di Stefano, Marco; Paulsen, Jonas; Jost, Daniel & Marti-Renom, Marc A. (2020). 4D nucleome modeling. Current Opinion in Genetics and Development. ISSN 0959-437X. 67, p. 25–32. doi: 10.1016/j.gde.2020.10.004. Full text in Research Archive
  • Paulsen, Jonas; Liyakat Ali, Tharvesh Moideen; Nekrasov, Maxim; Delbarre, Erwan; Baudement, Marie-Odile & Kurscheid, Sebastian [Show all 8 contributors for this article] (2019). Long-range interactions between topologically associating domains shape the four-dimensional genome during differentiation. Nature Genetics. ISSN 1061-4036. 51(5), p. 835–843. doi: 10.1038/s41588-019-0392-0.
  • Briand, Nolwenn; Cahyani, Inswasti; Madsen-Østerbye, Julia-Kristina Jensen; Paulsen, Jonas; Rønningen, Torunn & Sørensen, Anita Løvstad [Show all 7 contributors for this article] (2018). Lamin A, Chromatin and FPLD2:Not ust a Peripheral Ménage-à-Trois. Frontiers in Cell and Developmental Biology. ISSN 2296-634X. 6. doi: 10.3389/fcell.2018.00073. Full text in Research Archive
  • Briand, Nolwenn; Guénantin, Anne-Claire; Jeziorowska, Dorota; Shah, Akshay; Mantecon, Matthieu & Capel, Emilie [Show all 12 contributors for this article] (2018). The lipodystrophic hotspot lamin A p.R482W mutation deregulates the mesodermal inducer T/Brachyury and early vascular differentiation gene networks. Human Molecular Genetics. ISSN 0964-6906. 27(8), p. 1447–1459. doi: 10.1093/hmg/ddy055.
  • Paulsen, Jonas; Liyakat Ali, Tharvesh Moideen & Collas, Philippe (2018). Computational 3D genome modeling using Chrom3D. Nature Protocols. ISSN 1754-2189. 13(5), p. 1137–1152. doi: 10.1038/nprot.2018.009.
  • Garcia-Nieto, Pablo E; Schwartz, Erin K; King, Devin A; Paulsen, Jonas; Collas, Philippe & Herrera, Rafael E [Show all 7 contributors for this article] (2017). Carcinogen susceptibility is regulated by genome architecture and predicts cancer mutagenesis. EMBO Journal. ISSN 0261-4189. 36(19), p. 2829–2843. doi: 10.15252/embj.201796717.
  • Paulsen, Jonas; Sekelja, Monika; Oldenburg, Anja; Barateau, Alice; Briand, Nolwenn & Delbarre, Erwan [Show all 11 contributors for this article] (2017). Chrom3D: Three-dimensional genome modeling from Hi-C and nuclear lamin-genome contacts. Genome Biology. ISSN 1465-6906. 18:21, p. 1–15. doi: 10.1186/s13059-016-1146-2.
  • Di Stefano, Marco; Paulsen, Jonas; Lien, Tonje Gulbrandsen; Hovig, Johannes Eivind & Micheletti, Cristian (2016). Hi-C-constrained physical models of human chromosomes recover functionally-related properties of genome organization. Scientific Reports. ISSN 2045-2322. 6. doi: 10.1038/srep35985.
  • Sekelja, Monika; Paulsen, Jonas & Collas, Philippe (2016). 4D nucleomes in single cells: What can computational modeling reveal about spatial chromatin conformation? Genome Biology. ISSN 1465-6906. 17:54. doi: 10.1186/s13059-016-0923-2.
  • Børnich, Claus; Grytten, Ivar; Hovig, Johannes Eivind; Paulsen, Jonas; Cech, Martin & Sandve, Geir Kjetil (2016). Galaxy Portal: Interacting with the galaxy platform through mobile devices. Bioinformatics. ISSN 1367-4803. 32(11), p. 1743–1745. doi: 10.1093/bioinformatics/btw042.
  • Paulsen, Jonas; Gramstad, Odin & Collas, Philippe (2015). Manifold Based Optimization for Single-Cell 3D Genome Reconstruction. PLoS Computational Biology. ISSN 1553-734X. 11(8). doi: 10.1371/journal.pcbi.1004396. Full text in Research Archive
  • Håkelien, Anne-Mari; Bryne, Jan Christian; Harstad, Kristine Gjul; Lorenz, Susanne; Paulsen, Jonas & Sun, Jinchang [Show all 9 contributors for this article] (2014). The regulatory landscape of osteogenic differentiation. Stem Cells. ISSN 1066-5099. 32(10), p. 2780–2793. doi: 10.1002/stem.1759.
  • Paulsen, Jonas; Rødland, Einar Andreas; Holden, Lars; Holden, Marit & Hovig, Johannes Eivind (2014). A statistical model of ChIA-PET data for accurate detection of chromatin 3D interactions. Nucleic Acids Research (NAR). ISSN 0305-1048. 42(18). doi: 10.1093/nar/gku738.
  • Paulsen, Jonas; Sandve, Geir Kjetil F.; Gundersen, Sveinung; Lien, Tonje Gulbrandsen; Trengereid, Kai & Hovig, Johannes Eivind (2014). HiBrowse: Multi-purpose statistical analysis of genome-wide chromatin 3D organization. Bioinformatics. ISSN 1367-4803. 30(11), p. 1620–1622. doi: 10.1093/bioinformatics/btu082. Full text in Research Archive
  • Sandve, Geir Kjetil; Gundersen, Sveinung; Johansen, Morten; Glad, Ingrid Kristine; Gunathasan, Krishanthi & Holden, Lars [Show all 21 contributors for this article] (2013). The Genomic HyperBrowser: an analysis web server for genome-scale data. Nucleic Acids Research (NAR). ISSN 0305-1048. 41(W1), p. W133–W141. doi: 10.1093/nar/gkt342. Full text in Research Archive
  • Paulsen, Jonas; Lien, Tonje Gulbrandsen; Sandve, Geir Kjetil; Holden, Lars; Borgan, Ørnulf & Glad, Ingrid Kristine [Show all 7 contributors for this article] (2013). Handling realistic assumptions in hypothesis testing of 3D co-localization of genomic elements. Nucleic Acids Research (NAR). ISSN 0305-1048. 41(10), p. 5164–5174. doi: 10.1093/nar/gkt227.
  • Nordstrand, Line Mari; Furu, Kari; Paulsen, Jonas; Rognes, Torbjørn & Klungland, Arne (2012). Alkbh1 and Tzfp repress a non-repeat piRNA cluster in pachytene spermatocytes. Nucleic Acids Research (NAR). ISSN 0305-1048. 40(21), p. 10950–10963. doi: 10.1093/nar/gks839. Full text in Research Archive

View all works in Cristin

  • Star, Bastiaan; Nederbragt, Alexander Johan; Jentoft, Sissel; Grimholt, Unni; Malmstrøm, Martin & Gregers, Tone Fredsvik [Show all 18 contributors for this article] (2011). The genome of Atlantic cod reveals a unique immune system.
  • Paulsen, Jonas (2014). Inferential analysis of genomic 3D organization. Akademika forlag. ISSN 978-82-8264-950-6.

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Published Jan. 3, 2020 2:07 PM - Last modified Jan. 29, 2021 1:21 PM