Computation in Living Systems

Cell Identity Dynamics

The evolution of multicellular organisms depends on the differentiation of genetically identical cells into specialised types. We develop coarse-graining methods to model these dynamics and establish mechanistic links with associative memory networks, aiming to formulate a general theory of cell identity dynamics.

Relevant publications:

Hierarchical cell identities emerge from animal gene regulatory mechanisms

EnhancerNet: a predictive model of cell identity dynamics through enhancer selection

Computation and Learning in Biological Memory Systems

Many biological systems, such as the adaptive immune system and epigenetic gene silencing, rely on long-term memory. We are developing theoretical approaches to study how the combination of stochastic production and competition between memory units shapes memory repertoires.

Relevant publications:

Epigenetic inheritance of gene silencing is maintained by a self-tuning mechanism based on resource competition

Tuning of plasma cell lifespan by competition explains the longevity and heterogeneity of antibody persistence

Movement Regulation

We are interested in understanding the principles underlying biological circuits that control movement, drawing connections with reinforcement learning and sampling algorithms.

Relevant publications:

The dopamine circuit as a reward-taxis navigation system.

Temporal fluctuations in chemotaxis gain implement a simulated-tempering strategy for efficient navigation in complex environments.

Systems Medicine and Ageing

We develop mathematical models of physiological circuits to understand how diseases arise from the dysregulation of dynamical mechanisms over long timescales, including models for biological ageing.

Relevant publications:

Tuning of plasma cell lifespan by competition explains the longevity and heterogeneity of antibody persistence

A new model for the HPA axis explains dysregulation of stress hormones on the timescale of weeks.

Senescent cell turnover slows with age providing an explanation for the Gompertz law.

Senescent cells and the incidence of age-related diseases.

Postdoctoral Researchers

The college offers several open positions for postdoctoral fellowships. Below is a list of opportunities. Please follow the provided links for official deadlines and application information.

Chapman Fellowships

A 2-year independent fellowship with teaching duties. Applications typically open annually around September.

Chapman-Schmidt AI in Science Postdoctoral Fellows

A 2-year fellowship for researchers applying AI to science. Links: Associate | Fellow.

Eric and Wendy Schmidt AI in Science Postdoctoral Fellows

A 2-year fellowship to use AI for advancing science or engineering. Links: Associate | Fellow.

Eric and Wendy Schmidt AI in Science Fellowship (Linked with AIMS South Africa)

A 1-year fellowship at Imperial College with a linked 1-year appointment at AIMS South Africa.

I am also happy to support candidates in their applications for external fellowships, such as Marie Curie, EMBO, and HFSP. Please get in touch to discuss potential projects.