About

We Want To Understand How Cells Compute

Throughout their lives cells sense and respond to their environment, communicate with each other, and regulate their internal states in response to molecular signals. Many aspects of cellular life can be understood in terms of computing, especially analog computing: essential cell functions need to be maintained; availability of nutrients needs to be tracked; cells have to divide and proliferate in an orderly manner; immune cells must locate, identify, neutralise and clean up infections and wounds; and in complex multi-cellular organisms, specialised cells — stem cells — are responsible for producing different cell types, creating, and maintaining tissues.

In humans, for example, a single fertilised egg cell gives rise to thousands of different cell types and 15 trillion cells in total. By some, only in rough outline understood process, these different cells end up in their right numbers, at the right time, in the right place. One reason for why we do not yet understand this beautifully choreographed and apparently robust process, despite the vast and rapidly growing body of experimental work, is that we lack a mechanistic and predictive theory of life at the cellular level. And there can be no doubt that we need such a theory: understanding how cells compute — sense their environment or physiological state and adapt their behaviour accordingly — will have profound implications across the life sciences, but especially in microbial, cell, developmental, systems, and synthetic biology.

The Theoretical Systems Biology Group is led by Michael Stumpf at The University of Melbourne.

About Michael

Professional History

  • Sept. 2018 – Present: Professor for Theoretical Systems Biology, University of Melbourne

  • 2007 – Aug 2018: Professor for Theoretical Systems Biology (HEFCE-funded)

  • 2003 – 2006: Reader in Bioinformatics, Imperial College London

  • 2003 – 2006: Wellcome Trust Career Development Fellow, Department of Biology, Imperial College London

  • 2002 – 2003: Wellcome Trust Career Development Fellow, Department of Biology, University College London

  • 1999 – 2002: Wellcome Trust Research Training Fellow in Mathematical Biology, Department of Zoology, University of Oxford with Professor Lord May of Oxford

Qualifications

  • 1995 – 1999: DPhil in Condensed Matter Theory, University of Oxford

  • 1990 – 1995: Dipl. Phys., Physics (1st Class), Universität Tübingen, Universität Göttingen and Max-Planck Institute for Fluid Dynamics

Research Interests

  • Biological Research

    • Cell Fate Decision Making Processes; Gene Regulation and Signalling During Stem Cell Differentiation; Ecological Dynamics of Stem Cells; Multiscale Modelling of in vivo Processes in Development and Immunology; Data Integration and Fusion in Cell and Developmental Biology; Analysis of Single Cell Transcriptomic and Proteomic Data; Synthetic Biology; Engineering Biology to Tackle Global Warming

  • Theoretical Research

    • Stability and Robustness of Stochastic Dynamical Systems; Control of Dynamical Systems and Networks; Differential Topology of Epigenetic Landscapes

  • Methodology Development

    • Statistical Inference; Approximate Bayesian Computation; Empirical Bayes; Data Fusion; Multiscale Modelling; Probabilistic Graphical Models; Network Inference and Analysis; Multivariate Information Measures in Inference and Machine Learning; Reachability Analysis

Selected Recent Grants

  • 2017-2020: Next generation approaches to connect models and quantitative data, BBSRC, £790k (PI)

  • 2017-2021: A synthetic approach towards understanding the robust formation of Turing patterns in developmental biology, Volkswagen Stiftung, €1.4Million (PI)

  • 2016-2020: A systems Biology Approach to Islet Biology, EU H2020,€4.7Million (co-I)

  • 2015-2019: Managing the Nitrogen economy of bacteria, BBSRC, £3.7Million (co-PI)

  • 2014-2017: In vivo and in silico analysis of the haematopoietic stem cell niche, BBSRC, £860k (PI)

  • 2013-2017: Statistical modelling of in vivo immune response dynamics in zebrafish to multiple stimuli, BBSRC, £800k (PI)

  • 2013-2017: Connecting in-vivo optical imaging with dynamic modelling of host-pathogen interaction during bacterial infection, MRC, £380,000 (Biocomputing Fellowship to Dr. Angelique Ale, co-PI)

  • 2012-2015: BioTransistors, BBSRC, £360k (PI)

  • 2011-2014: Cellular decision making: from noise to robust phenotypes, HFSP, $1.2Million (PI)

  • 2011-2014: Robust analysis of signal transduction underlying cellular variability in stem cells, MRC, £371,000 (Biocomputing Fellowship for Dr. Sarah Filippi, co-I)

  • 2011-2013: Social Networks and the Digital Economy, EPSRC, £1.1Million (co-I)

  • 2010-2013: Reverse engineering of complex systems in nature, Leverhulme Trust, £240k (PI)

  • 2009-2013: Mapping combinatorial stress response in E. coli and M. tuberculosis using chimeric proteins and probabilistic modelling, BBSRC, £3 Million (co-PI)

  • 2009-2012: Development of immunofluorescence and stochastic modelling approaches to study mammalian signalling processes, BBSRC-JAIST partnering award, £50k (PI)

  • 2009-2012: Inference-based modelling in systems and population biology, BBSRC, £780k (PI)

Awards and Honours

  • 2013: Miegunyah Distinguished Visiting Fellowship, University of Melbourne

  • 2011: Elected Fellow of the Society of Biology

  • 2010: Rector’s Medal for Excellence in Research Supervision

  • 2009-2014: Royal Society Wolfson Research Merit Award

  • 2005-2008: EMBO Young Investigator

  • 2000-2003: EPA Cephalosporin Junior Research Fellow, Linacre College Oxford

  • 1996-1998: Balliol College Jowett Exhibitioner for Science

  • 1995-1999: Kekulé PhD Fellowship, University of Oxford

Selected Offices and Committee Membership

  • 2018-Present: Editorial Board Member, Cell Systems

  • 2017: Site Review Committee Member, Structural and Mathematical Biology, The Francis Crick Institute

  • 2012-2018: Editor in Chief, Statistical Applications in Genetics and Molecular Biology

  • 2012-2015: Member of the Luxembourg Science Foundation Lifescience Panel

  • 2012-Present: Faculty Member of Faculty 1000 (Population Biology; Systems Biology).

  • 2011-2014: Royal Society Newton International Fellowship Committee

  • 2010-Present: Associate Editor, BMC Systems Biology, BMC Bioinformatics, Human Genomics

  • 2008-2014: Member of the BBSRC Training and Awards Committee, now Committee E.

  • 2006-2008: Member of the BBSRC Engineering and Biological Systems Committee

THE THEORETICAL SYSTEMS BIOLOGY GROUP IS OPEN FOR COLLABORATIONS

If you are interested in working together with the group please get in touch.