The University of NottinghamResearch
It is intrinsic to the MyCIB philosophy to conduct research through collaboration. We also wish to contribute to data and information standards so that integrative biology modeling development can proceed more efficiently.
Staff Research Interests
Professor Charlie Hodgman
Professor Charlie Hodgman has a longstanding reputation for elucidating the structure and function of biomolecular sequences. Orginally this was primarily at the protein sequence level, but more recently it concerns gene regulatory regions and multimolecular complexes.
I have been promoting Integrative Systems Biology since I joined GlaxoWellcome in 1995, paying particular emphasis on the development of informatics approaches to turn what is an otherwise manual-developed industry into an industrial process in which representative models can be generated automatically. This will be necessary if bio-systems modelling is to keep pace with the rate of data generation. Owing to my diverse background, I am not wedded to any particular branch of the life sciences and welcome collaborative projects where they are of most benefit, especially with industry.
Specific Projects
Director of the Centre of Plant Integrative Biology CPIB.
Software pipelines for:
1. increasing the productivity of biopharmaceutical development.
2. elucidation of changes in biological function arising from single nucleotide polymorphisms.
3. in silico cDNA cloning from expressed sequence tags.
Holistic biological network models of various organisms, including Arabidopsis, Dog, Cow, Haloferax, Tea and Wheat.
Data acquisition and the development of dynamic models of plant root growth.
Web services for network construction and feature detection and gene regulatory region analysis.
Predictive tools to support biopharmaceutical development.
Click on the following link to view Professor Charlie Hodgman's publications.
Contact Professor Charlie Hodgman:
Dr. Chungui Lu
Dr Chungui Lu graduated with an MSc in Plant Science from Yangzhou University, China in 1992. He gained a Ph.D.
in Plant Molecular Biology from the University of Nottingham in 1999. Following positions at the University of
Wales in Bangor, Rothamsted Research and the University of Bristol he took up his current post as Lecturer in
Integrative Biology in 2006.
Dr Lu's current research concentrates of the use of post-genomic technologies (cDNA microarray,
Affymetrix) to monitor expression profiles and patterns of wheat genes under cold stress (freezing-tolerance
and vernalization) and different level nitrogen fertiliser. He also has an on-going interest in the study the
roles of miRNAs in controlling the regulation of nitrogen assimilation in organic and inorganic crops. Dr. Lu
has developed a highly efficient 2-step single cell RT-PCR technique (SC-RT-PCR) and is in the process of
developing single-cell microarray analysis which will provide a powerful tool for functional genomic
characterisation of the many signaling pathways that function in plant cell and provide a basis for cell
type specific genomic scale analyses of gene function. Dr Lu's current research interests include Wheat Vernalisation, Tomato ripening and Human Cancer research.
Contact Dr Chungui Lu:
Dr. Dov Stekel
Dr Stekel's research interests include Modelling and analysis of transcription networks and gene regulation; evolution of real and artificial regulatory networks; bioinformatics and systems biology.
Our research group uses mathematical and computer modelling to simulate, discover and understand the mechanisms by which biological systems are organized. We work collaboratively with experimental groups using locally generated data, with large-scale public databases, and with artificial systems that we simulate ourselves. Current projects include:
Modelling gene regulatory networks
We develop mathematical models of biological systems with a particular interest in prokaryotic gene regulation. This includes modelling gene regulation in RK2 plasmids in collaboration with Chris Thomas and modelling acid stress response in pathogenic and non-pathogenic E coli in collaboration with Pete Lund. We use both deterministic and stochastic models and our interest in stochastic methods has led us to form the STOMP network to bring together experimental and theoretical scientists with an interest in stochastic models of prokaryotic gene regulation.
Evolution of artificial regulatory networks
We develop evolvable computer models of artificial regulatory networks, with an interest in adaptation to environments with varying nutritional content and/or stresses. This allows us to carry out experiments in evolution not possible in experimental systems and we relate our work back to real networks.
Comparative microbial genomics
An interest in comparative genomics, and in particular in comparing transcription regulatory networks in different strains of the same microbial species, has led us to involvement in the xBASE project in collaboration with Mark Pallen
Click on the following link to view Dr Stekel's publications.
Contact Dr Dov Stekel:
Dr Jaume Bacardit
Dr Jaume Bacardit is part of both the Automated Scheduling, Optimization and Planning (ASAP) research group
and MyCIB Centre.
Dr Bacardit is a Lecturer in Bioinformatics has been jointly appointed between the Schools of Computer Science and Biosciences of the University of Nottingham. His role is to facilitate and encourage interdisciplinary research involving both schools.
Click on the following link to view Dr Bacardit's homepage and publications.
Contact Dr Jaume Bacardit: