Publication list - Publika - Scientific publications from Oslo University Hospital

Publications by Jonas Paulsen

25 publications found

Original articles

Rossini R, Kumar V, Mathelier A, Rognes T, Paulsen J (2022)
MoDLE: high-performance stochastic modeling of DNA loop extrusion interactions
Genome Biol, 23 (1), 247
DOI 10.1186/s13059-022-02815-7, PubMed 36451166

Paulsen J, Collas P (2022)
Modeling the 3D Genome Using Hi-C and Nuclear Lamin-Genome Contacts
Methods Mol Biol, 2301, 337-352
DOI 10.1007/978-1-0716-1390-0_18, PubMed 34415545

Liyakat Ali TM, Brunet A, Collas P, Paulsen J (2021)
TAD cliques predict key features of chromatin organization
BMC Genomics, 22 (1), 499
DOI 10.1186/s12864-021-07815-8, PubMed 34217222

Paulsen J, Liyakat Ali TM, Nekrasov M, Delbarre E, Baudement MO, Kurscheid S, Tremethick D, Collas P (2019)
Long-range interactions between topologically associating domains shape the four-dimensional genome during differentiation
Nat Genet, 51 (5), 835-843
DOI 10.1038/s41588-019-0392-0, PubMed 31011212

Paulsen J, Liyakat Ali TM, Collas P (2018)
Computational 3D genome modeling using Chrom3D
Nat Protoc, 13 (5), 1137-1152
DOI 10.1038/nprot.2018.009, PubMed 29700484

Briand N, Guénantin AC, Jeziorowska D, Shah A, Mantecon M, Capel E, Garcia M, Oldenburg A, Paulsen J, Hulot JS, Vigouroux C, Collas P (2018)
The lipodystrophic hotspot lamin A p.R482W mutation deregulates the mesodermal inducer T/Brachyury and early vascular differentiation gene networks
Hum Mol Genet, 27 (8), 1447-1459
DOI 10.1093/hmg/ddy055, PubMed 29438482

García-Nieto PE, Schwartz EK, King DA, Paulsen J, Collas P, Herrera RE, Morrison AJ (2017)
Carcinogen susceptibility is regulated by genome architecture and predicts cancer mutagenesis
EMBO J, 36 (19), 2829-2843
DOI 10.15252/embj.201796717, PubMed 28814448

Paulsen J, Sekelja M, Oldenburg AR, Barateau A, Briand N, Delbarre E, Shah A, Sørensen AL, Vigouroux C, Buendia B, Collas P (2017)
Chrom3D: three-dimensional genome modeling from Hi-C and nuclear lamin-genome contacts
Genome Biol, 18 (1), 21
DOI 10.1186/s13059-016-1146-2, PubMed 28137286

Di Stefano M, Paulsen J, Lien TG, Hovig E, Micheletti C (2016)
Hi-C-constrained physical models of human chromosomes recover functionally-related properties of genome organization
Sci Rep, 6, 35985
DOI 10.1038/srep35985, PubMed 27786255

Børnich C, Grytten I, Hovig E, Paulsen J, Čech M, Sandve GK (2016)
Galaxy Portal: interacting with the galaxy platform through mobile devices
Bioinformatics, 32 (11), 1743-5
DOI 10.1093/bioinformatics/btw042, PubMed 26819474

Paulsen J, Gramstad O, Collas P (2015)
Manifold Based Optimization for Single-Cell 3D Genome Reconstruction
PLoS Comput Biol, 11 (8), e1004396
DOI 10.1371/journal.pcbi.1004396, PubMed 26262780

Håkelien AM, Bryne JC, Harstad KG, Lorenz S, Paulsen J, Sun J, Mikkelsen TS, Myklebost O, Meza-Zepeda LA (2014)
The regulatory landscape of osteogenic differentiation
Stem Cells, 32 (10), 2780-93
DOI 10.1002/stem.1759, PubMed 24898411

Paulsen J, Rødland EA, Holden L, Holden M, Hovig E (2014)
A statistical model of ChIA-PET data for accurate detection of chromatin 3D interactions
Nucleic Acids Res, 42 (18), e143
DOI 10.1093/nar/gku738, PubMed 25114054

Paulsen J, Sandve GK, Gundersen S, Lien TG, Trengereid K, Hovig E (2014)
HiBrowse: multi-purpose statistical analysis of genome-wide chromatin 3D organization
Bioinformatics, 30 (11), 1620-2
DOI 10.1093/bioinformatics/btu082, PubMed 24511080

Sandve GK, Gundersen S, Johansen M, Glad IK, Gunathasan K, Holden L, Holden M, Liestøl K, Nygård S, Nygaard V, Paulsen J, Rydbeck H, Trengereid K, Clancy T, Drabløs F, Ferkingstad E, Kalas M, Lien T, Rye MB, Frigessi A, Hovig E (2013)
The Genomic HyperBrowser: an analysis web server for genome-scale data
Nucleic Acids Res, 41 (Web Server issue), W133-41
DOI 10.1093/nar/gkt342, PubMed 23632163

Paulsen J, Lien TG, Sandve GK, Holden L, Borgan O, Glad IK, Hovig E (2013)
Handling realistic assumptions in hypothesis testing of 3D co-localization of genomic elements
Nucleic Acids Res, 41 (10), 5164-74
DOI 10.1093/nar/gkt227, PubMed 23571755

Nordstrand LM, Furu K, Paulsen J, Rognes T, Klungland A (2012)
Alkbh1 and Tzfp repress a non-repeat piRNA cluster in pachytene spermatocytes
Nucleic Acids Res, 40 (21), 10950-63
DOI 10.1093/nar/gks839, PubMed 22965116

Star B, Nederbragt AJ, Jentoft S, Grimholt U, Malmstrøm M, Gregers TF, Rounge TB, Paulsen J, Solbakken MH, Sharma A, Wetten OF, Lanzén A, Winer R, Knight J, Vogel JH, Aken B, Andersen O, Lagesen K, Tooming-Klunderud A, Edvardsen RB, Tina KG, Espelund M, Nepal C, Previti C, Karlsen BO et al. (2011)
The genome sequence of Atlantic cod reveals a unique immune system
Nature, 477 (7363), 207-10
DOI 10.1038/nature10342, PubMed 21832995

Hamelryck T, Borg M, Paluszewski M, Paulsen J, Frellsen J, Andreetta C, Boomsma W, Bottaro S, Ferkinghoff-Borg J (2010)
Potentials of mean force for protein structure prediction vindicated, formalized and generalized
PLoS One, 5 (11), e13714
DOI 10.1371/journal.pone.0013714, PubMed 21103041

Pálsson S, Paulsen J, Arnason E (2008)
Rapid evolution of the intergenic T-P spacer in the mtDNA of Arctic cod Arctogadus glacialis
Mar Biotechnol (NY), 10 (3), 270-7
DOI 10.1007/s10126-007-9058-5, PubMed 18214612

Review articles

Raffo A, Paulsen J (2023)
The shape of chromatin: insights from computational recognition of geometric patterns in Hi-C data
Brief Bioinform, 24 (5)
DOI 10.1093/bib/bbad302, PubMed 37646128

Di Stefano M, Paulsen J, Jost D, Marti-Renom MA (2020)
4D nucleome modeling
Curr Opin Genet Dev, 67, 25-32
DOI 10.1016/j.gde.2020.10.004, PubMed 33253996

Briand N, Cahyani I, Madsen-Østerbye J, Paulsen J, Rønningen T, Sørensen AL, Collas P (2018)
Lamin A, Chromatin and FPLD2: Not Just a Peripheral Ménage-à-Trois
Front Cell Dev Biol, 6, 73
DOI 10.3389/fcell.2018.00073, PubMed 30057899

Sekelja M, Paulsen J, Collas P (2016)
4D nucleomes in single cells: what can computational modeling reveal about spatial chromatin conformation?
Genome Biol, 17, 54
DOI 10.1186/s13059-016-0923-2, PubMed 27052789