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Dr Kevin Bryson
Appointment
  • Senior Lecturer
  • Dept of Computer Science
  • Faculty of Engineering Science
Biography
Kevin Bryson has over 20 years of experience modelling biological systems using mathematical, statistical and computational approaches. This ranges from modelling small molecules at the molecular orbital level using quantum mechanical packages, through atomic-level modelling of DNA and proteins using classical molecular dynamics, through genome and transcriptome analysis, ODE-modelling of signalling, gene regulatory and metabolic pathways, to macroscopic modelling of mixed populations of discrete bacteria using hand-crafted agent-based simulators.


He received a BSc (1st class) in Mathematics and Computer Science from Heriot-Watt University, Edinburgh, in 1991 and a DPhil in Physics from the University of York in 1996. His doctoral studies were followed by a period in industry at Oxford Molecular Ltd. developing bioinformatics and molecular dynamics software. This was followed by three postdoctoral positions: a BBSRC Fellowship at the University of Warwick, an Individual EU Marie Curie Fellowship at INRA in France and a Senior Wellcome Trust Fellowship at University College London. He was promoted to a Lecturer in Bioinformatics and Systems Biology at University College London in 2005.

Research Summary

Our lab focuses on applying mathematical, statistical and computational approaches to understand clinically relevant biological systems with the aim to integrate diverse data sources and techniques to develop models that can predict the normal and dysfunctional behaviour.

A number of ongoing projects in the lab include:


  1. Modelling the quorum mechanism of Streptococcus pneumonia. The aim of this project is to understand changes in the population level behaviour of Streptococcus pneumonia (such as competence, fractricide and biofilm formation) from changes occurring at the molecular level within the quorum signalling pathway. To accomplish this we are integrating genomic data, cis-regulatory motif, microarray, ODE-based modelling of the signalling and gene regulation pathways and agent-based modelling approaches. This is a collaborative project with Dr Bambos Charalambous in Department of Infection.
  2. Modelling the phosphatidylinositol (PI) / Calcium signalling in human and its control by Arf proteins. The PI cycle is a metabolic signalling pathway which is stimulated by a diverse range of hormones and growth factors and controls cell growth and differentiation. Arf1 and Arf6 are small GTPases which have been shown to stimulate PLD activity and thus regulate the PI signalling pathway. Arf exists in both extracellular and membrane-attached states with the enzymatic process being membrane-bound. This membrane-bound reaction provides modelling challenges. We are developing predictive ODE-based models with parameters determined both via literature searching and fitting experimental NMR data with species identified via QM calculations using Gaussian. This is a collaborative CoMPLEX project with Dr Geraint Thomas in Cell & Development Biology.
  3. Understanding the ER/mitochondrial intra-cellular signalling pathways in human. Signalling between the ER and mitochondria under stress conditions are important mechanisms within cancer and neurodegeration - leading to either adaptation or apoptosis. The aim of this project is to determine pathways involved in these processes by applying machine learning to public microarray data over cancer cell lines. Any tentative pathways will then be experimentally confirmed within cell cultures. This is a collaborative CoMPLEX project with Dr Gyorgy Szabadkai in Cell & Development Biology.
  4. Modelling the purine metabolic pathway in human. Purine metabolism is implicated in a variety of cancers such as acute myeloid cancer where drug treatments which inhibit IMPDH, one of the key purine metabolic enzymes, have been shown to stop cell proliferation. The aim of this project is to develop ODE models, parameterized using literature and RNASeq data, to predict the overall metabolic effects of inhibiting particular enzymes, potentially revealing other drug targets within the network. This is a collaborative CoMPLEX project with Dr Geraint Thomas in Cell & Development Biology.
  5. Protein structure modelling for misfolding diseases. The lab has a general interest in neurodegenerative diseases involving protein misfolding and amyloid formation such as Huntington’s disease. The signalling and metabolic pathways mentioned previously are all implicated in these diseases and we also have developed sequence-based predictors of amyloidogenesis using machine learning approaches to better understand this process.

Teaching Summary
Kevin Bryson is the director of the MSc Computer Science and MSc Financial Computing degrees and also the 1st year coordinator for the undergraduate BSc and MEng programmes within the Computer Science department.

As part of the BCB, he directs the Introduction to Bioinformatics (I2B) Graduate School Course which is taken by UCL/Birkbeck PhD students, RAs and staff.


He is the module coordinator for two modules:
  • COMP1001 (1st year Computer Architecture) using assembly language programming to explain the underlying working of the MIPS processor (and processors in general).
  • COMP2007 (2nd year Networking and Concurrency) teaching Java Concurrent Programming and introduces the concepts of computer networking by developing concurrent Java simulators demonstrating the key principles.

He also teaches on the following modules:
  • BIOC3010 (3rd year Computational and Systems Biology within the Department of Structural and Molecular Biology) teaching transcriptomics and systems biology.
  • COMPGI10 (MSc Machine Learning, Bioinformatics module) teaching the application of machine learning to high-throughput and biological network data.
  • WIBRG001 (MSc Drug Design within the Wolfson Institute of Medical Research) teaching introductory bioinformatics.
  • CPLXG001 (MRes Advanced Biological Modelling and Bioinformatics within CoMPLEX) teaching bioinformatics.
  • CPLXG003 (MRes Transferrable Skills Module within CoMPLEX) teaching the application of SQL relational databases within bioinformatics.
  • Birkbeck MSc in Bioinformatics and Systems Biology teaching biological networks and mathematical modelling.

Previously he taught on the following modules:
  • COMP3006 (Advanced Mathematics) where he taught advanced linear algebra and vector calculus.
  • INFN3004 (MSc and Intercalating Medical BSc in Immunology and Cell Pathology and Infection) where he taught introductory bioinformatics.


Academic Background
2007 PGCLTHE Postgraduate Certificate in Learning and Teaching in Higher Education – Education - Postgraduate University College London
1996 DPhil Doctor of Philosophy – Physics University of York
1991 BSc Hons Bachelor of Science (Honours) – Mathematics with Computer Science Heriot-Watt University
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