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Inferring Gene Regulatory Networks from Multiple Datasets

  • Christopher A. PenfoldEmail author
  • Iulia Gherman
  • Anastasiya Sybirna
  • David L. Wild
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1883)

Abstract

Gaussian process dynamical systems (GPDS) represent Bayesian nonparametric approaches to inference of nonlinear dynamical systems, and provide a principled framework for the learning of biological networks from multiple perturbed time series measurements of gene or protein expression. Such approaches are able to capture the full richness of complex ODE models, and can be scaled for inference in moderately large systems containing hundreds of genes. Related hierarchical approaches allow for inference from multiple datasets in which the underlying generative networks are assumed to have been rewired, either by context-dependent changes in network structure, evolutionary processes, or synthetic manipulation. These approaches can also be used to leverage experimentally determined network structures from one species into another where the network structure is unknown. Collectively, these methods provide a comprehensive and flexible platform for inference from a diverse range of data, with applications in systems and synthetic biology, as well as spatiotemporal modelling of embryo development. In this chapter we provide an overview of GPDS approaches and highlight their applications in the biological sciences, with accompanying tutorials available as a Jupyter notebook from https://github.com/cap76/GPDS.

Key words

Nonlinear dynamical systems Gaussian process dynamical systems Causal structure identification Learning from multiple data sources Spatiotemporal models 

Notes

Acknowledgements

CAP is supported by the Wellcome Trust (grant 083089/Z/07/Z). IG is supported by EPSRC/BBSRC research grant EP/L016494/1. AS is supported by a 4-year Wellcome Trust PhD Scholarship and Cambridge International Trust Scholarship. DLW acknowledges support from the Engineering and Physical Science Research Council (grant EP/R014337/1).

CAP, IG, and AS BBSRC-EPSRC funded OpenPlant Synthetic Biology Research Centre (BB/L014130/1) through the OpenPlant Fund scheme. CAP and AS also thank M. Azim Surani for his support.

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Christopher A. Penfold
    • 1
    Email author
  • Iulia Gherman
    • 2
  • Anastasiya Sybirna
    • 1
    • 3
    • 4
  • David L. Wild
    • 5
  1. 1.Wellcome/CRUK Gurdon InstituteUniversity of CambridgeCambridgeUK
  2. 2.Warwick Integrative Synthetic Biology Centre, School of EngineeringUniversity of WarwickCoventryUK
  3. 3.Wellcome/MRC Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeUK
  4. 4.Physiology, Development and Neuroscience DepartmentUniversity of CambridgeCambridgeUK
  5. 5.Department of Statistics and Systems Biology CentreUniversity of WarwickCoventryUK

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