Integrative Systems Biology
ISB Research Group
Professor Charlie Hodgman
Associate Professor Dov Stekel
Mr John Veasey
Dr Chungui Lu
Dr Jaume Bacardit
Mr Jim Craigon
Research Overview
Integrative Systems Biology (ISB) is an exciting new approach to making new scientific discoveries in the Life Sciences. This approach involves the collaboration between multiple disciplines to address research issues from different angles simultaneously. This novel approach helps laboratory Biologists to prioritise their laboratory work, and focus their experiments, which are most important in aiding understanding. There are two research groups, both directed by Professor Charlie Hodgman, the first is the ‘Virtual Root’ researched by the Centre of Plant Integrative Biology (CPIB) and secondly several specific research areas in the Multidisciplinary Centre for Integrative Biology (MyCIB).
General Research Themes
Systems Biology, Integrative Biology, Bioinformatics, Mathematical Modelling, Network Biology and Transcriptomics
Current Projects
Mathematical Modelling of the Virtual Root
The Centre for Plant Integrative Biology (CPIB) is one of six UK Centres for Integrative Systems Biology currently funded by BBSRC and EPSRC. The Centre is applying a systems approach – combining the skills of mathematicians, computer scientists, engineers and plant biologists – to answer plant science questions. The core CPIB project involves modelling root growth and development across the physical scales, from the sub-cellular to whole-organ level, using the model plant Arabidopsis thaliana. The resulting ‘virtual root’ will simulate hormone-regulated root growth, providing researchers with a vital tool for investigating and manipulating root development and architecture in crop species. For more information about CPIB and its current activities, please contact the Director Professor Charlie Hodgman, or CPIB's Outreach Officer Dr Susie Lydon by email or phone +44(0)115 9516289.
The Figure above (in clockwise order) shows lateral emergence in an Arabidopsis root, an E. coli gene regulatory network, a wall hanging in the CPIB and MyCIB Center, The Plant Sciences building, part of an outreach program by CPIB, an Arabidopsis metabolic network, an inferred network in Wheat, and finally, the stages of Tomato ripening.
Tomato Ripening
CPIB has a LINK project headed by Professor Charlie Hodgman and Professor Graham Seymour. This projects aims to find the key regulators and downstream targets of tomato ripening from transcriptomic and metabolomic data. This project involves major use of correlation analysis and network inference techniques, which will lead to new discoveries in tomato ripening.
Mathematical and Computational Modelling of Transcription Networks and Gene Regulation
Mathematical and computational modelling of transcriptional regulation is key in understanding the mechanisms by which biological systems are organized. Current research by Associate Professor Dov Stekel involves the modelling of gene regulatory networks, the prediction of transcription factor binding sites and the evolution of artificial regulatory networks.
For more information about Dov Stekel's current research, publications and recent news, please got to the following website: dovlab.wordpress.com/
Wheat Vernalisation
Gene regulatory network have been produced to investigate vernalisation in wheat. We use microarray data to identify target genes, which are associated with vernalisation/cold response and functional interactions between genes by using artificial neural networks. Lecturer Dr Chungui Lu and Professor Charlie Hodgman head this research project with key collaboration in this field.
Biological Data Mining
We live in data-rich times. Thanks to the development of sequencing or microarray technologies, just to mention two of them, we have new data from many different species available to analyse and gain new insight about them. However, traditional techniques cannot cope with this data deluge. Data mining is a computer science discipline that focuses on the automatic identification of new, hidden, information within data without any prior knowledge. This task is highly challenging, as most biological databases are growing at an exponential rate, they often contain inaccurate data and the new knowledge identified by the data mining methods needs to be presented to the domain experts in the way that it can give new insight. Dr Jaume Bacardit heads this research.
MyCIB Support Service
The MyCIB Support Service aims to offer a Transcriptomics, Systems Biology and Bioinformatics-based analytical service for collaborators in both Academia and Industry. This service aims to cover all of life-sciences. Please contact John Veasey or Alex Marshall if you wish to collaborate with the MyCIB Support Service.
External Links
CPIB - CPIB website detailing the project and the different strands of research based on different areas of root development.
MyCIB - MyCIB website with more information about the different MyCIB projects and researchers.
For any further information about any of the above projects, please contact Professor Charlie Hodgman by email or phone +44(0)115 9516290, or CPIB Research Administrator Mirela Axinte by email or phone +44(0)115 9516288.