Speaking at Workshop: Recent Advances in Statistical Inference for Mathematical Biology

Today I will be presenting at at the Mathematical Biosciences Institute at Ohio State University which this week is hosting the workshop Recent Advances in Statistical Inference for Mathematical Biology. I will be giving a talk about Hiroki’s work (abstract here and below), while Dorota will be presenting a poster about her work.

I am very excited about this workshop as it is the first to my knowledge to bring together mathematical modelling with statistical inference. In my view, this marriage is crucial to the future development of mathematical biology as a field.


Inferring the gap between mechanism and phenotype in dynamical models of gene regulation


Dynamical (differential equation) models in molecular biology are often cast in terms of biological mechanisms such as transcription, translation and protein-protein and protein-DNA interactions. However, most molecular biological measurements are at the phenotypic level, such as levels of gene or protein expression in wild type and chemically or genetically perturbed systems. Mechanistic parameters are often difficult or impossible to measure. We have been combining dynamical models with statistical inference as a means to integrate phenotypic data with mechanistic hypotheses. In doing so we are able to identify key parameters that determine system behaviour, and parameters with insufficient evidence to estimate, and thus make informed predictions for further experimental work. We are also able to use inferred parameters to build stochastic and multi-scale models to investigate behaviour at single-cell level. We apply these ideas to two systems in microbiology: global gene regulation in the antibiotic-resistance bearing RK2 plasmids, and zinc uptake and efflux regulation in Escherichia coli.


Seminars this week at Nottingham and Leicester

I will be delivering two seminars this week.

On Wednesday I will be giving a talk in the local “Knowledge Transfer” series about mathematical modelling in biology. This talk is for general audience: all are welcome. 11:30am, Rushcliffe Restaurant, Sutton Bonington Campus.

Closer to home, on Thursday I will be speaking in the Applied Maths seminar series at the University of Leicester on dynamical models and inference for bacterial gene regulation. 2pm, Room 119, Michael Atiyah Building.

Please come to either or both if you are interested.


Modelling and Microbiology – Conference at the eScience Institute

Tomorrow is the final meeting at the eScience Institute in Edinburgh: our conference on Modelling and Microbiology. Although I am a co-organizer, I am unable to attend for family reasons. We will be ably represented by Dorota Herman, who will be speaking on Tuesday at 3:05pm.

The entire meeting will be webcast and can be watched here. We have many good speakers, so I am posting the full speaker timetable below.

Monday July 4th

1.45-2 Welcome (Rosalind Allen)

2-3 Robert Austin (Princeton)
Darwin, ecology and the emergence of bacterial resistance: an
attempt at a synthesis

3.30-4.15 Martin Howard (John Innes Centre)
Dissecting the dynamics of low copy number plasmid segregation

4.15–5 Tobias Bollenbach (IST Austria)
Microbial responses to antibiotic combinations

Tuesday July 5th

9.30-10.30 Martin Ackermann (ETH Zuerich)
An evolutionary perspective on phenotypic heterogeneity in bacteria

11-11.45 Peter Lund (Birmingham)
Insights into stress response from laboratory-based evolution

11.45-12.05 Sara Mitri (Oxford)
Social evolution in microbial communities

12.05-12.25 Fatima Drubi (Leiden University)
Do bacteria sporulate as a bet-hedging strategy in stochastic

2-2.45 Alexander Morozov (Edinburgh)
Self-assembled bacterial rotors

2.45-3.05 Bartlomiej Waclaw (Edinburgh)
Simple models for bacterial evolution with migration

3.05-3.25 Dorota Herman (Birmingham)
Mathematical model for transcriptional regulation of RK2 plasmids and
its evolutional optimisation

3.55-4.40 Jan Kreft (Birmingham)
Individual-based modelling of horizontal gene transfer in chemostats
and biofilms

4.40-5.15 Phil Aldridge (Newcastle)

Continuous control of flagellar gene expression by the s28-FlgM
regulatory circuit in Salmonella enterica

Wednesday July 6th

9.30-10.30 Oskar Hallatschek (MPI Goettingen)
Genetic drift and selection in growing biofilms

11-11.45 Ian Stansfield (Aberdeen)
Negative feedback loops in the translational control of gene

11.45-12.05 Leena Nieminen (Strathclyde)
Modelling metabolic switching in differentiating bacterium
Streptomyces coelicor

12.05-12.25 David Richards (John Innes)
The mechanistic basis of hyphal branching in Streptomyces

2-2.45 Mamen Romano (Aberdeen)
The dynamics of demand and supply in mRNA translation

2.45-3.05 Dominique Chu (Kent)
Optimisation of gene expression resources in bioprocessing host cell

Thursday July 7th

9.30-10.30 John Little (U. Arizona)
Stochastic modelling of the phage lambda regulatory circuit: prophage
induction and stability

11.00-11.45 Francesco Falciani (Birmingham)
A systems biology approach sheds new light on bacterial acid

11.45-12.30 Kevin Foster (Oxford)
Spatiogenetic structure and cooperation in microbe

New research presentation written

Today I’ve finished writing a new research presentation based on Dorota’s work. I’ve titled it “Deconstructing a Gene Regulatory Network” and it covers Dorota’s work on modelling the IncP1 RK2 plasmid in collaboration with Chris Thomas. The first part looks at our combining of differential equation models with statistical inference techniques and we get some nice results, including two sets of parameters that fit the data, and some experimentally testable hypotheses about what will happen when all regulation of the system is removed. In the second part, we try to ask ‘why’ the system has evolved to be the way it is, and compare various hypotheses in networks with decreasing levels of complexity (away from the real system). All this stuff is yet to be published so I’m being a bit cryptic on line! Most of the slides, of course, have come from Dorota, so credit to where it’s due.

If you’d like to come to the talk, I’ll be giving it for the first time at 1pm on Wednesday 17th November in the Medical School at University Park, Nottingham, and for the second time on Monday 22nd November at the Nara Institute of Science and Technology, Japan. Yup! I can’t wait till the trip 🙂