Publications by Jonas Paulsen
25 publications found
Original articles
MoDLE: high-performance stochastic modeling of DNA loop extrusion interactions
Genome Biol, 23 (1), 247
DOI 10.1186/s13059-022-02815-7, PubMed 36451166
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
TAD cliques predict key features of chromatin organization
BMC Genomics, 22 (1), 499
DOI 10.1186/s12864-021-07815-8, PubMed 34217222
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
Computational 3D genome modeling using Chrom3D
Nat Protoc, 13 (5), 1137-1152
DOI 10.1038/nprot.2018.009, PubMed 29700484
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
Carcinogen susceptibility is regulated by genome architecture and predicts cancer mutagenesis
EMBO J, 36 (19), 2829-2843
DOI 10.15252/embj.201796717, PubMed 28814448
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
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
Galaxy Portal: interacting with the galaxy platform through mobile devices
Bioinformatics, 32 (11), 1743-5
DOI 10.1093/bioinformatics/btw042, PubMed 26819474
Manifold Based Optimization for Single-Cell 3D Genome Reconstruction
PLoS Comput Biol, 11 (8), e1004396
DOI 10.1371/journal.pcbi.1004396, PubMed 26262780
The regulatory landscape of osteogenic differentiation
Stem Cells, 32 (10), 2780-93
DOI 10.1002/stem.1759, PubMed 24898411
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
HiBrowse: multi-purpose statistical analysis of genome-wide chromatin 3D organization
Bioinformatics, 30 (11), 1620-2
DOI 10.1093/bioinformatics/btu082, PubMed 24511080
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
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
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
The genome sequence of Atlantic cod reveals a unique immune system
Nature, 477 (7363), 207-10
DOI 10.1038/nature10342, PubMed 21832995
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
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
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
4D nucleome modeling
Curr Opin Genet Dev, 67, 25-32
DOI 10.1016/j.gde.2020.10.004, PubMed 33253996
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
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
Other articles
Multi-level 3D genome organization deteriorates during breast cancer progression
bioRxiv
DOI 10.1101/2023.11.26.568711, PubMed 38076897