Jonas Paulsen

Bilde av Jonas Paulsen
English version of this page
Telefon +47 22859105
Brukernavn
Besøksadresse Blindernveien 31 0371 Oslo
Postadresse Postboks 1066 Blindern 0316 OSLO
Andre tilknytninger Institutt for pedagogikk (Student)

Faglige interesser

Min forskning fokuserer på hvordan den tredimensjonale (3D) organiseringen til DNA inne i cellekjernen relaterer seg til kritiske funksjoner i den eukaryote cellen, inkludert epigenetisk regulering av genuttrykk. Jeg utvikler bioinformatikk-software for å utforske komparativ 3D genomikk på tvers av celletyper, vev og arter.

Undervisning

 

Publikasjoner

  • 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 Fulltekst i vitenarkiv.
  • 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 Fulltekst i vitenarkiv.
  • 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 Vis sammendrag
  • 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 Fulltekst i vitenarkiv.
  • 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 Fulltekst i vitenarkiv. Vis sammendrag
  • 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 Vis sammendrag
  • 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 Fulltekst i vitenarkiv.

Se alle arbeider i 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.

Se alle arbeider i Cristin

Publisert 3. jan. 2020 14:09 - Sist endret 5. jan. 2020 11:42