Jonas Paulsen

Image of Jonas Paulsen
Norwegian version of this page
Phone +47 22859105
Room 4206
Username
Visiting address Blindernveien 31 None 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)

 

Publications

  • Paulsen, Jonas; Liyakat Ali, Tharvesh Moideen; Nekrasov, Maxim; Delbarre, Erwan; Baudement, Marie-Odile; Kurscheid, Sebastian; Tremethick, David & Collas, Philippe (2019). Long-range interactions between topologically associating domains shape the four-dimensional genome during differentiation. Nature Genetics.  ISSN 1061-4036.  51(5), s 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 & Collas, Philippe (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; Garcia, Maria; Oldenburg, Anja; Paulsen, Jonas; Hulot, Jean-Sébastien; Vigouroux, Corinne & Collas, Philippe (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), s 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), s 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 & Morrison, Ashby J (2017). Carcinogen susceptibility is regulated by genome architecture and predicts cancer mutagenesis. EMBO Journal.  ISSN 0261-4189.  36(19), s 2829- 2843 . doi: 10.15252/embj.201796717
  • Paulsen, Jonas; Sekelja, Monika; Oldenburg, Anja; Barateau, Alice; Briand, Nolwenn; Delbarre, Erwan; Shah, Akshay; Sørensen, Anita Løvstad; Vigouroux, Corinne; Buendia, Brigitte & Collas, Philippe (2017). Chrom3D: Three-dimensional genome modeling from Hi-C and nuclear lamin-genome contacts. Genome Biology.  ISSN 1465-6906.  18:21, s 1- 15 . doi: 10.1186/s13059-016-1146-2
  • 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), s 1743- 1745 . doi: 10.1093/bioinformatics/btw042
  • 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
  • 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; Mikkelsen, Tarjei S.; Myklebost, Ola & Meza, Leonardo Zepeda (2014). The regulatory landscape of osteogenic differentiation. Stem Cells.  ISSN 1066-5099.  32(10), s 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.  ISSN 0305-1048.  42(18), s e143 . doi: 10.1093/nar/gku738 Show summary
  • 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), s 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; Holden, Marit; Liestøl, Knut; Nygård, Ståle; Nygaard, Vegard; Paulsen, Jonas; Rydbeck, Halfdan; Trengereid, Kai; Clancy, Trevor; Drabløs, Finn; Ferkingstad, Egil; Kalaš, Matúš; Lien, Tonje Gulbrandsen; Rye, Morten Beck; Frigessi, Arnoldo & Hovig, Johannes Eivind (2013). The Genomic HyperBrowser: an analysis web server for genome-scale data. Nucleic Acids Research.  ISSN 0305-1048.  41(W1), s W133- W141 . doi: 10.1093/nar/gkt342 Full text in Research Archive. Show summary
  • Paulsen, Jonas; Lien, Tonje Gulbrandsen; Sandve, Geir Kjetil; Holden, Lars; Borgan, Ørnulf; Glad, Ingrid Kristine & Hovig, Johannes Eivind (2013). Handling realistic assumptions in hypothesis testing of 3D co-localization of genomic elements. Nucleic Acids Research.  ISSN 0305-1048.  41(10), s 5164- 5174 . doi: 10.1093/nar/gkt227 Show summary
  • 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.  ISSN 0305-1048.  40(21), s 10950- 10963 . doi: 10.1093/nar/gks839 Full text in Research Archive.

View all works in Cristin

  • Paulsen, Jonas (2014). Inferential analysis of genomic 3D organization.
  • Star, Bastiaan; Nederbragt, Alexander Johan; Jentoft, Sissel; Grimholt, Unni; Malmstrøm, Martin; Gregers, Tone Fredsvik; Rounge, Trine Ballestad; Solbakken, Monica Hongrø; Paulsen, Jonas; Lagesen, Karin; Tooming-Klunderud, Ave; Tina, Kirubakaran G.; Espelund, Mari; Skage, Morten; Berg, Paul Ragnar; Omholt, Stig W; Stenseth, Nils Christian & Jakobsen, Kjetill Sigurd (2011). The genome of Atlantic cod reveals a unique immune system.

View all works in Cristin

Published Jan. 3, 2020 2:07 PM - Last modified Aug. 5, 2020 2:31 PM