CITATION.cff

# Copyright (C) 2022 Roberto Rossini <roberros@uio.no>
#
# SPDX-License-Identifier: MIT

cff-version: 1.2.0
message: 'If you use this software, please cite it using the metadata from this file.'
authors:
  - given-names: Roberto
    family-names: Rossini
    orcid: 'https://orcid.org/0000-0003-3096-1470'
    email: roberros@uio.no
    affiliation: 'Department of Biosciences, University of Oslo'
title: MoDLE
abstract: 'High-performance stochastic modeling of DNA loop extrusion interactions.'
doi: '10.5281/zenodo.6424697'
url: 'https://github.com/paulsengroup/modle'
repository-code: 'https://github.com/paulsengroup/modle'
type: software
license: MIT
preferred-citation:
  type: article
  authors:
  - given-names: Roberto
    family-names: Rossini
    orcid: 'https://orcid.org/0000-0003-3096-1470'
    email: roberros@uio.no
    affiliation: 'Department of Biosciences, University of Oslo'
  - given-names: Vipin
    family-names: Kumar
    email: vipin.kumar@ncmm.uio.no
    affiliation: 'Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo'
  - given-names: Anthony
    family-names: Mathelier
    orcid: 'https://orcid.org/0000-0001-5127-5459'
    email: anthony.mathelier@ncmm.uio.no
    affiliation: 'Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo'
  - given-names: Torbjørn
    family-names: Rognes
    orcid: 'https://orcid.org/0000-0002-9329-9974'
    email: torognes@ifi.uio.no
    affiliation: 'Centre for Bioinformatics, Department of Informatics, University of Oslo'
  - given-names: Jonas
    family-names: Paulsen
    orcid: 'https://orcid.org/0000-0002-7918-5495'
    email: jonas.paulsen@ibv.uio.no
    affiliation: 'Department of Biosciences, University of Oslo'
  doi: '10.1186/s13059-022-02815-7'
  url: 'https://doi.org/10.1186/s13059-022-02815-7'
  journal: 'Genome Biology'
  year: 2022
  month: 11
  volume: 23
  number: 1
  pages: 247
  issn: '1474-760X'
  title: 'MoDLE: high-performance stochastic modeling of DNA loop extrusion interactions'
  abstract: 'DNA loop extrusion emerges as a key process establishing genome structure and function. We introduce MoDLE, a computational tool for fast, stochastic modeling of molecular contacts from DNA loop extrusion capable of simulating realistic contact patterns genome wide in a few minutes. MoDLE accurately simulates contact maps in concordance with existing molecular dynamics approaches and with Micro-C data and does so orders of magnitude faster than existing approaches. MoDLE runs efficiently on machines ranging from laptops to high performance computing clusters and opens up for exploratory and predictive modeling of 3D genome structure in a wide range of settings.'