Twist-DNA: computing base-pair and bubble opening probabilities in genomic superhelical DNA. - Daniel Jost 002 (Bioinform., 2013)

How epigenome drives chromatin folding and dynamics, insights from efficient coarse-grained models of chromosomes. - Surya K. Ghosh; Daniel Jost 002 (PLoS Comput. Biol., 2018)

Guidelines for cell-type heterogeneity quantification based on a comparative analysis of reference-free DNA methylation deconvolution software. - Clémentine Decamps; Florian Privé; Raphael Bacher; Daniel Jost 002; Arthur Waguet; Eugene Andres Houseman; Eugene Lurie; Pavlo Lutsik; Aleksandar Milosavljevic; Michael Scherer; Michael G. B. Blum; Magali Richard (BMC Bioinform., 2020)

PenDA, a rank-based method for personalized differential analysis: Application to lung cancer. - Magali Richard; Clémentine Decamps; Florent Chuffart; Elisabeth Brambilla; Sophie Rousseaux; Saadi Khochbin; Daniel Jost 002 (PLoS Comput. Biol., 2020)

3DGenBench: a web-server to benchmark computational models for 3D Genomics. - Polina Belokopytova; Emil Viesná; Mateusz Chilinski; Yifeng Qi; Hossein Salari; Marco Di Stefano; Andrea Esposito 001; Mattia Conte; Andrea Maria Chiariello; Vladimir B. Teif; Dariusz Plewczynski; Bin Zhang; et al. (Nucleic Acids Res., 2022)

Dynamical modeling of the H3K27 epigenetic landscape in mouse embryonic stem cells. - Kapil Newar; Amith Zafal Abdulla; Hossein Salari; Eric Fanchon; Daniel Jost 002 (PLoS Comput. Biol., 2022)

3DPolyS-LE: an accessible simulation framework to model the interplay between chromatin and loop extrusion. - Todor Gitchev; Gabriel Zala; Peter Meister; Daniel Jost 002 (Bioinform., 2022)