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Showing results 1-24 of 24
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2023
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Raffo, Andrea; Paulsen, Jonas. The shape of chromatin: insights from computational recognition of geometric patterns in Hi-C data. Briefings in Bioinformatics 2023 ;Volume 24.(5) p. 1-14 UiO
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Rossini, Roberto; Oshaghi, Mohammadsaleh; Nekrasov, Maxim; Bellanger, Aurelie Nathalie Pascale; Domaschenz, Renae; Dijkwel, Yasmin; Abdelhalim, Mohamed Ibrahim Mohamed; Collas, Philippe; Tremethick, David; Paulsen, Jonas. Multi-level 3D genome organization deteriorates during breast cancer progression.. bioRxiv 2023 p. - UiO
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2022
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Paulsen, Jonas; Collas, Philippe. Modeling the 3D Genome Using Hi-C and Nuclear Lamin-Genome Contacts. I: Hi-C Data Analysis Methods and Protocols. Humana Press 2022 ISBN 978-1-0716-1390-0. p. 337-352 UiO OUS
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Rossini, Roberto; Kumar, Vipin; Mathelier, Anthony; Rognes, Torbjørn; Paulsen, Jonas. MoDLE: high-performance stochastic modeling of DNA loop extrusion interactions. Genome Biology 2022 ;Volume 23.(1) p. - UiO OUS
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2021
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Liyakat Ali, Tharvesh Moideen; Brunet, Annaëlle; Collas, Philippe; Paulsen, Jonas. TAD cliques predict key features of chromatin organization. BMC Genomics 2021 ;Volume 22.(1) p. - UiO OUS
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2020
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Di Stefano, Marco; Paulsen, Jonas; Jost, Daniel; Marti-Renom, Marc A.. 4D nucleome modeling. Current Opinion in Genetics and Development 2020 ;Volume 67. p. 25-32 UiO
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2019
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Paulsen, Jonas; Liyakat Ali, Tharvesh Moideen; Nekrasov, Maxim; Delbarre, Erwan; Baudement, Marie-Odile; Kurscheid, Sebastian; Tremethick, David; Collas, Philippe. Long-range interactions between topologically associating domains shape the four-dimensional genome during differentiation. Nature Genetics 2019 ;Volume 51.(5) p. 835-843 UiO OUS
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2018
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8. |
Briand, Nolwenn; Cahyani, Inswasti; Madsen-Østerbye, Julia-Kristina Jensen; Paulsen, Jonas; Rønningen, Torunn; Sørensen, Anita Løvstad; Collas, Philippe. Lamin A, Chromatin and FPLD2:Not ust a Peripheral Ménage-à-Trois.. Frontiers in Cell and Developmental Biology 2018 ;Volume 6. p. - OUS UiO
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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. The lipodystrophic hotspot lamin A p.R482W mutation deregulates the mesodermal inducer T/Brachyury and early vascular differentiation gene networks. Human Molecular Genetics 2018 ;Volume 27.(8) p. 1447-1459 UiO OUS
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10. |
Paulsen, Jonas; Liyakat Ali, Tharvesh Moideen; Collas, Philippe. Computational 3D genome modeling using Chrom3D. Nature Protocols 2018 ;Volume 13.(5) p. 1137-1152 UiO OUS
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2017
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11. |
Garcia-Nieto, Pablo E; Schwartz, Erin K; King, Devin A; Paulsen, Jonas; Collas, Philippe; Herrera, Rafael E; Morrison, Ashby J. Carcinogen susceptibility is regulated by genome architecture and predicts cancer mutagenesis. EMBO Journal 2017 ;Volume 36.(19) p. 2829-2843 UiO
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12. |
Paulsen, Jonas; Sekelja, Monika; Oldenburg, Anja; Barateau, Alice; Briand, Nolwenn; Delbarre, Erwan; Shah, Akshay; Sørensen, Anita Løvstad; Vigouroux, Corinne; Buendia, Brigitte; Collas, Philippe. Chrom3D: Three-dimensional genome modeling from Hi-C and nuclear lamin-genome contacts. Genome Biology 2017 ;Volume 18:21. p. 1-15 UiO OUS
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2016
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13. |
Børnich, Claus; Grytten, Ivar; Hovig, Johannes Eivind; Paulsen, Jonas; Cech, Martin; Sandve, Geir Kjetil. Galaxy Portal: Interacting with the galaxy platform through mobile devices. Bioinformatics 2016 ;Volume 32.(11) p. 1743-1745 OUS UiO
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14. |
Di Stefano, Marco; Paulsen, Jonas; Lien, Tonje Gulbrandsen; Hovig, Johannes Eivind; Micheletti, Cristian. Hi-C-constrained physical models of human chromosomes recover functionally-related properties of genome organization. Scientific Reports 2016 ;Volume 6. OUS UiO
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15. |
Sekelja, Monika; Paulsen, Jonas; Collas, Philippe. 4D nucleomes in single cells: What can computational modeling reveal about spatial chromatin conformation?. Genome Biology 2016 ;Volume 17:54. p. - UiO
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2015
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16. |
Paulsen, Jonas; Gramstad, Odin; Collas, Philippe. Manifold Based Optimization for Single-Cell 3D Genome Reconstruction. PLoS Computational Biology 2015 ;Volume 11.(8) UiO
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2014
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17. |
Håkelien, Anne-Mari; Bryne, Jan Christian; Harstad, Kristine Gjul; Lorenz, Susanne; Paulsen, Jonas; Sun, Jinchang; Mikkelsen, Tarjei S.; Myklebost, Ola; Meza, Leonardo Zepeda. The regulatory landscape of osteogenic differentiation. Stem Cells 2014 ;Volume 32.(10) p. 2780-2793 OUS UiO
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18. |
Paulsen, Jonas. Inferential analysis of genomic 3D organization. Akademika forlag 2014 (ISBN 978-82-8264-950-6) 143 p. UiO
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19. |
Paulsen, Jonas; Rødland, Einar Andreas; Holden, Lars; Holden, Marit; Hovig, Johannes Eivind. A statistical model of ChIA-PET data for accurate detection of chromatin 3D interactions. Nucleic Acids Research (NAR) 2014 ;Volume 42.(18) p. e143- NR OUS
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20. |
Paulsen, Jonas; Sandve, Geir Kjetil F.; Gundersen, Sveinung; Lien, Tonje Gulbrandsen; Trengereid, Kai; Hovig, Johannes Eivind. HiBrowse: Multi-purpose statistical analysis of genome-wide chromatin 3D organization. Bioinformatics 2014 ;Volume 30.(11) p. 1620-1622 UiO OUS
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2013
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21. |
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. The Genomic HyperBrowser: an analysis web server for genome-scale data. Nucleic Acids Research (NAR) 2013 ;Volume 41.(W1) p. W133-W141 OUS UiT UiB UiO NR NTNU NORCE
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22. |
Paulsen, Jonas; Lien, Tonje Gulbrandsen; Sandve, Geir Kjetil; Holden, Lars; Borgan, Ørnulf; Glad, Ingrid Kristine; Hovig, Johannes Eivind. Handling realistic assumptions in hypothesis testing of 3D co-localization of genomic elements. Nucleic Acids Research (NAR) 2013 ;Volume 41.(10) p. 5164-5174 OUS UiO NR
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2012
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23. |
Nordstrand, Line Mari; Furu, Kari; Paulsen, Jonas; Rognes, Torbjørn; Klungland, Arne. Alkbh1 and Tzfp repress a non-repeat piRNA cluster in pachytene spermatocytes. Nucleic Acids Research (NAR) 2012 ;Volume 40.(21) p. 10950-10963 UiO OUS
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2011
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24. |
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. The genome of Atlantic cod reveals a unique immune system. ESEB; 2011-09-20 - 2011-09-25 FFI OUS UiB UiO
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