Articles producció científica> Enginyeria Informàtica i Matemàtiques

MONET: a toolbox integrating top-performing methods for network modularization

  • Datos identificativos

    Identificador: imarina:6685009
    Autores:
    Tomasoni, MattiaGomez, SergioCrawford, JakeZhang, WeijiaChoobdar, SarvenazMarbach, DanielBergmann, Sven
    Resumen:
    © The Author(s) 2020. Published by Oxford University Press. SUMMARY: We define a disease module as a partition of a molecular network whose components are jointly associated with one or several diseases or risk factors thereof. Identification of such modules, across different types of networks, has great potential for elucidating disease mechanisms and establishing new powerful biomarkers. To this end, we launched the 'Disease Module Identification (DMI) DREAM Challenge', a community effort to build and evaluate unsupervised molecular network modularization algorithms. Here, we present MONET, a toolbox providing easy and unified access to the three top-performing methods from the DMI DREAM Challenge for the bioinformatics community. AVAILABILITY AND IMPLEMENTATION: MONET is a command line tool for Linux, based on Docker and Singularity containers; the core algorithms were written in R, Python, Ada and C++. It is freely available for download at https://github.com/BergmannLab/MONET.git. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
  • Otros:

    Autor según el artículo: Tomasoni, Mattia; Gomez, Sergio; Crawford, Jake; Zhang, Weijia; Choobdar, Sarvenaz; Marbach, Daniel; Bergmann, Sven
    Departamento: Enginyeria Informàtica i Matemàtiques
    Autor/es de la URV: Gómez Jiménez, Sergio
    Palabras clave: Software Community structure Algorithms
    Resumen: © The Author(s) 2020. Published by Oxford University Press. SUMMARY: We define a disease module as a partition of a molecular network whose components are jointly associated with one or several diseases or risk factors thereof. Identification of such modules, across different types of networks, has great potential for elucidating disease mechanisms and establishing new powerful biomarkers. To this end, we launched the 'Disease Module Identification (DMI) DREAM Challenge', a community effort to build and evaluate unsupervised molecular network modularization algorithms. Here, we present MONET, a toolbox providing easy and unified access to the three top-performing methods from the DMI DREAM Challenge for the bioinformatics community. AVAILABILITY AND IMPLEMENTATION: MONET is a command line tool for Linux, based on Docker and Singularity containers; the core algorithms were written in R, Python, Ada and C++. It is freely available for download at https://github.com/BergmannLab/MONET.git. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
    Áreas temáticas: Statistics and probability Statistics & probability Odontología Nutrição Molecular biology Medicina veterinaria Medicina ii Medicina i Mathematics, interdisciplinary applications Mathematical & computational biology Matemática / probabilidade e estatística Interdisciplinar General medicine Engenharias iv Economia Computer science, interdisciplinary applications Computer science applications Computational theory and mathematics Computational mathematics Ciências biológicas iii Ciências biológicas ii Ciências biológicas i Ciências agrárias i Ciência da computação Biotecnología Biotechnology & applied microbiology Biology, miscellaneous Biodiversidade Biochemistry Biochemical research methods Astronomia / física
    Acceso a la licencia de uso: https://creativecommons.org/licenses/by/3.0/es/
    ISSN: 1367-4803
    Direcció de correo del autor: sergio.gomez@urv.cat
    Identificador del autor: 0000-0003-1820-0062
    Página final: 3921
    Fecha de alta del registro: 2024-10-26
    Volumen de revista: 36
    Versión del articulo depositado: info:eu-repo/semantics/publishedVersion
    Enlace a la fuente original: https://academic.oup.com/bioinformatics/article/36/12/3920/5818484
    URL Documento de licencia: https://repositori.urv.cat/ca/proteccio-de-dades/
    Referencia al articulo segun fuente origial: Bioinformatics. 36 (12): 3920-3921
    Referencia de l'ítem segons les normes APA: Tomasoni, Mattia; Gomez, Sergio; Crawford, Jake; Zhang, Weijia; Choobdar, Sarvenaz; Marbach, Daniel; Bergmann, Sven (2020). MONET: a toolbox integrating top-performing methods for network modularization. Bioinformatics, 36(12), 3920-3921. DOI: 10.1093/bioinformatics/btaa236
    DOI del artículo: 10.1093/bioinformatics/btaa236
    Entidad: Universitat Rovira i Virgili
    Año de publicación de la revista: 2020
    Página inicial: 3920
    Tipo de publicación: Journal Publications
  • Palabras clave:

    Biochemical Research Methods,Biochemistry,Biology, Miscellaneous,Biotechnology & Applied Microbiology,Computational Mathematics,Computational Theory and Mathematics,Computer Science Applications,Computer Science, Interdisciplinary Applications,Mathematical & Computational Biology,Mathematics, Interdisciplinary Applications,Molecular Biolog
    Software
    Community structure
    Algorithms
    Statistics and probability
    Statistics & probability
    Odontología
    Nutrição
    Molecular biology
    Medicina veterinaria
    Medicina ii
    Medicina i
    Mathematics, interdisciplinary applications
    Mathematical & computational biology
    Matemática / probabilidade e estatística
    Interdisciplinar
    General medicine
    Engenharias iv
    Economia
    Computer science, interdisciplinary applications
    Computer science applications
    Computational theory and mathematics
    Computational mathematics
    Ciências biológicas iii
    Ciências biológicas ii
    Ciências biológicas i
    Ciências agrárias i
    Ciência da computação
    Biotecnología
    Biotechnology & applied microbiology
    Biology, miscellaneous
    Biodiversidade
    Biochemistry
    Biochemical research methods
    Astronomia / física
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