A nucleotide-level coarse-grained model of RNA
 Šulc, P Romano, F Ouldridge, T Doye, J Louis, A (17 Mar 2014) doi:10.48550/arxiv.1403.4180
Plectoneme tip bubbles: Coupled denaturation and writhing in supercoiled DNA
 Matek, C Ouldridge, T Doye, J Louis, A (10 Apr 2014) doi:10.48550/arxiv.1404.2869
DNA hairpins primarily promote duplex melting rather than inhibiting hybridization
 Schreck, J Ouldridge, T Romano, F Sulc, P Shaw, L Louis, A Doye, J (19 Aug 2014) doi:10.48550/arxiv.1408.4401
Characterizing the bending and flexibility induced by bulges in DNA duplexes
 Schreck, J Ouldridge, T Romano, F Louis, A Doye, J (19 Dec 2014) doi:10.48550/arxiv.1412.6309
Introducing Improved Structural Properties and Salt Dependence into a Coarse-Grained Model of DNA
 Snodin, B Randisi, F Mosayebi, M Sulc, P Schreck, J Romano, F Ouldridge, T Tsukanov, R Nir, E Louis, A Doye, J (03 Apr 2015) doi:10.48550/arxiv.1504.00821
Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self assembly
 Fonseca, P Romano, F Schreck, J Ouldridge, T Doye, J Louis, A (06 Dec 2017) doi:10.48550/arxiv.1712.02161
Coarse-grained modelling of the structural properties of DNA origami
 Snodin, B Schreck, J Romano, F Louis, A Doye, J (22 Sep 2018) doi:10.48550/arxiv.1809.08430
Controlling crystallization and its absence: Proteins, colloids and patchy models
 Doye, J Louis, A Lin, I Allen, L Noya, E Wilber, A Kok, H Lyus, R (04 Jan 2007) doi:10.48550/arxiv.cond-mat/0701074
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