The use of machine learning to discover regulatory networks controlling biological systems.

Journal: Molecular cell
Published Date: Jan 10, 2022

Abstract

Biological systems are composed of a vast web of multiscale molecular interactors and interactions. High-throughput technologies, both bulk and single cell, now allow for investigation of the properties and quantities of these interactors. Computational algorithms and machine learning methods then provide the tools to derive meaningful insights from the resulting data sets. One such approach is graphical network modeling, which provides a computational framework to explicitly model the molecular interactions within and between the cells comprising biological systems. These graphical networks aim to describe a putative chain of cause and effect between interacting molecules. This feature allows for determination of key molecules in a biological process, accelerated generation of mechanistic hypotheses, and simulation of experimental outcomes. We review the computational concepts and applications of graphical network models across molecular scales for both intracellular and intercellular regulatory biology, examples of successful applications, and the future directions needed to overcome current limitations.

Authors

  • Rossin Erbe
    Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA; Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA; Convergence Institute, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA.
  • Jessica Gore
    Institute for Genome Sciences, University of Maryland Medical Center, Baltimore, MD, USA.
  • Kelly Gemmill
    Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA; Convergence Institute, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA.
  • Daria A Gaykalova
    Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA; Convergence Institute, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA; Institute for Genome Sciences, University of Maryland Medical Center, Baltimore, MD, USA; Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland Medical Center, Baltimore, MD, USA; Marlene & Stewart Greenebaum Comprehensive Cancer Center, University of Maryland Medical Center, Baltimore, MD, USA.
  • Elana J Fertig
    Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA; Convergence Institute, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA; Department of Applied Mathematics and Statistics, Johns Hopkins University, Baltimore, MD, USA; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA. Electronic address: ejfertig@jhmi.edu.

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