Long-range interactions between topologically associating domains shape the four-dimensional genome during differentiation von Paulsen, Jonas, Liyakat Ali, Tharvesh M., Nekrasov, Maxim, Delbarre, Erwan, Baudement, Marie-Odile, Kurscheid, Sebastian, Tremethick, David, Collas, Philippe

Volltext

Chrom3D: three-dimensional genome modeling from Hi-C and nuclear lamin-genome contacts von Paulsen, Jonas, Sekelja, Monika, Oldenburg, Anja R, Barateau, Alice, Briand, Nolwenn, Delbarre, Erwan, Shah, Akshay, Sørensen, Anita L, Vigouroux, Corinne, Buendia, Brigitte, Collas, Philippe

Volltext

MoDLE: high-performance stochastic modeling of DNA loop extrusion interactions von Rossini, Roberto, Kumar, Vipin, Mathelier, Anthony, Rognes, Torbjørn, Paulsen, Jonas

Volltext

Manifold Based Optimization for Single-Cell 3D Genome Reconstruction von Paulsen, Jonas, Gramstad, Odin, Collas, Philippe

Volltext

Hi-C-constrained physical models of human chromosomes recover functionally-related properties of genome organization von Di Stefano, Marco, Paulsen, Jonas, Lien, Tonje G., Hovig, Eivind, Micheletti, Cristian

Volltext

4D nucleomes in single cells: what can computational modeling reveal about spatial chromatin conformation? von Sekelja, Monika, Paulsen, Jonas, Collas, Philippe

Volltext

TAD cliques predict key features of chromatin organization von Liyakat Ali, Tharvesh M, Brunet, Annaël, Collas, Philippe, Paulsen, Jonas

Volltext

A statistical model of ChIA-PET data for accurate detection of chromatin 3D interactions von Paulsen, Jonas, Rødland, Einar A, Holden, Lars, Holden, Marit, Hovig, Eivind

Volltext

The Regulatory Landscape of Osteogenic Differentiation von Håkelien, Anne‐Mari, Bryne, Jan Christian, Harstad, Kristine G., Lorenz, Susanne, Paulsen, Jonas, Sun, Jinchang, Mikkelsen, Tarjei S., Myklebost, Ola, Meza‐Zepeda, Leonardo A.

Volltext

Hictk: blazing fast toolkit to work with .hic and .cool files von Rossini, Roberto, Paulsen, Jonas

Volltext

The shape of chromatin: insights from computational recognition of geometric patterns in Hi-C data von Raffo, Andrea, Paulsen, Jonas

Volltext

Potentials of mean force for protein structure prediction vindicated, formalized and generalized von Hamelryck, Thomas, Borg, Mikael, Paluszewski, Martin, Paulsen, Jonas, Frellsen, Jes, Andreetta, Christian, Boomsma, Wouter, Bottaro, Sandro, Ferkinghoff-Borg, Jesper

Volltext

Modeling the 3D Genome Using Hi-C and Nuclear Lamin-Genome Contacts von Paulsen, Jonas, Collas, Philippe

Volltext

Modeling properties of chromosome territories using polymer filaments in diverse confinement geometries von Nahali, Negar, Oshaghi, Mohammadsaleh, Paulsen, Jonas

Volltext

4D nucleome modeling von Di Stefano, Marco, Paulsen, Jonas, Jost, Daniel, Marti-Renom, Marc A

Volltext

Lamin A, Chromatin and FPLD2: Not Just a Peripheral Ménage-à-Trois von Briand, Nolwenn, Cahyani, Inswasti, Madsen-Østerbye, Julia, Paulsen, Jonas, Rønningen, Torunn, Sørensen, Anita L, Collas, Philippe

Volltext

Computational 3D genome modeling using Chrom3D von Paulsen, Jonas, Liyakat Ali, Tharvesh Moideen, Collas, Philippe

Volltext

4D nucleome modeling von Marti-Renom, Marc A, Paulsen, Jonas, Jost, Daniel

Volltext

Carcinogen susceptibility is regulated by genome architecture and predicts cancer mutagenesis von García‐Nieto, Pablo E, Schwartz, Erin K, King, Devin A, Paulsen, Jonas, Collas, Philippe, Herrera, Rafael E, Morrison, Ashby J

Volltext

Manifold Based Optimization for Single-Cell 3D Genome Reconstruction: e1004396 von Paulsen, Jonas, Gramstad, Odin, Collas, Philippe

Volltext