Jonas Paulsen
Position: PhD student
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Publications 2017

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
PubMed 28137286

Publications 2016

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
PubMed 26819474

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
PubMed 27786255

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
PubMed 27052789

Publications 2015

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

Publications 2014

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
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
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
PubMed 24511080

Publications 2013

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
PubMed 23571755

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
PubMed 23632163

Publications 2012

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
PubMed 22965116

Publications 2011

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
PubMed 21832995

Publications 2010

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
PubMed 21103041

Publications 2008

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
PubMed 18214612