Belief propagation for graph partitioning - Petr Sulc; Lenka Zdeborová (CoRR, 2009)

Quantifying Slow Evolutionary Dynamics in RNA Fitness Landscapes. - Petr Sulc; Andreas Wagner; Olivier C. Martin (J. Bioinform. Comput. Biol., 2010)

Options for Control of Reactive Power by Distributed Photovoltaic Generators. - Konstantin S. Turitsyn; Petr Sulc; Scott Backhaus; Michael Chertkov (Proc. IEEE, 2011)

Optimal Distributed Control of Reactive Power via the Alternating Direction Method of Multipliers. - Petr Sulc; Scott Backhaus; Michael Chertkov (CoRR, 2013)

Simulating a burnt-bridges DNA motor with a coarse-grained DNA model. - Petr Sulc; Thomas E. Ouldridge; Flavio Romano; Jonathan P. K. Doye; Ard A. Louis (Nat. Comput., 2014)

A comparison between parallelization approaches in molecular dynamics simulations on GPUs. - Lorenzo Rovigatti; Petr Sulc; István Z. Reguly; Flavio Romano (J. Comput. Chem., 2015)

Pre-stressed rubber material constant estimation for resilient wheel application. - Petr Sulc; Ludek Pesek; Vítezslav Bula; Jan Cibulka; Tomás Bohác; Hubert Tasek (Adv. Eng. Softw., 2017)

TacoxDNA: A user-friendly web server for simulations of complex DNA structures, from single strands to origami. - Antonio Suma; Erik Poppleton; Michael Matthies; Petr Sulc; Flavio Romano; Ard A. Louis; Jonathan P. K. Doye; Cristian Micheletti; Lorenzo Rovigatti (J. Comput. Chem., 2019)

OxDNA.org: a public webserver for coarse-grained simulations of DNA and RNA nanostructures. - Erik Poppleton; Roger Romero; Aatmik Mallya; Lorenzo Rovigatti; Petr Sulc (Nucleic Acids Res., 2021)

ExpertRNA: A New Framework for RNA Secondary Structure Prediction. - Menghan Liu; Erik Poppleton; Giulia Pedrielli; Petr Sulc; Dimitri P. Bertsekas (INFORMS J. Comput., 2022)

Nanobase.org: a repository for DNA and RNA nanostructures. - Erik Poppleton; Aatmik Mallya; Swarup Dey; Joel Joseph; Petr Sulc (Nucleic Acids Res., 2022)

Generative and interpretable machine learning for aptamer design and analysis of in vitro sequence selection. - Andrea Di Gioacchino; Jonah Procyk; Marco Molari; John S. Schreck; Yu Zhou; Yan Liu; Rémi Monasson; Simona Cocco; Petr Sulc (PLoS Comput. Biol., 2022)

Coarse-Grained Simulations Of Dna And Rna Systems With Oxdna And Oxrna Models: Tutorial. - Matthew L. Sample; Michael Matthies; Petr Sulc (WSC, 2023)

oxDNA: coarse-grained simulations of nucleic acids made simple. - Erik Poppleton; Michael Matthies; Debesh Mandal; Flavio Romano; Petr Sulc; Lorenzo Rovigatti (J. Open Source Softw., 2023)

Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations. - Zhengyue Zhang; Jirí Sponer; Giovanni Bussi; Vojtech Mlýnský; Petr Sulc; Chad R. Simmons; Nicholas Stephanopoulos; Miroslav Krepl (J. Chem. Inf. Model., 2023)

Preface. - Matthew R. Lakin; Petr Sulc (Nat. Comput., 2024)

Evolving to Find Optimizations Humans Miss: Using Evolutionary Computation to Improve GPU Code for Bioinformatics Applications. - Jhe-Yu Liou; Muaaz Awan; Kirtus G. Leyba; Petr Sulc; Steven A. Hofmeyr; Carole-Jean Wu; Stephanie Forrest (ACM Trans. Evol. Learn. Optim., 2024)