Overview
The cell is the structural and
functional unit of all living organisms, acting as the "building block of
life." The Human Genome Project has identified 20,-25,000 genes in human
(NHGRI) , and we are now attempting to understand how these genes interact with
each other, with proteins, hormones, drugs, metabolites etc. and how these
interaction control/regulate cell functions.
To gain understanding about the
dynamical behaviour of cells in a living organisms, we are taking a Systems
Biology approach incorporating computational, modern control engineering
and systems sciences approaches.
The main aim of our research is to
construct genetic networks, incorporating gene co-expression network, gene
regulatory network, and the interaction network of proteins, to help
us understand the mechanism controlling genome expression, i.e. given a set of
genome expression data (such as microarray data) to answer 'how genes are
expressed?'. Such investigation may ultimately tell us what are the main
factors leading to disease and how we may correct the problem with drugs or
gene therapies. 
Background: The cell biology theory states that all organisms
are composed of one or more cells and all cells come from pre-existing cells.
All vital functions of an organism occur within cells, and cells contain the
hereditary information necessary for regulating cell functions and for
transmitting information to the next generation of cells. All cells possess DNA
that is the hereditary material of genes, and RNA that contain the information
necessary to build various proteins such as enzymes (the cell's primary
machinery.) A DNA is responsible for the genetic propagation of most inherited
traits, ranging from hair colour to disease susceptibility. The genetic
information encoded by an organism's DNA is called its genome.
DNA consists of a pair of molecules
organized as strands, which is a chain of chemical "building blocks",
called nucleotides, of which there are four types: adenine (abbreviated A),
cytosine (C), guanine (G) and thymine (T). A strand of DNA contains genes,
areas that regulate genes, and areas that either have no function, or a
function yet unknown. Genes are the units of heredity and can be loosely viewed
as the organism's "cookbook", and thus DNA is often referred to as
the molecule of heredity.
How does the sequence of a strand of DNA correspond to the amino
acid sequence of a protein? This concept is explained by the central
dogma of molecular biology, which states as: DNA -> RNA ->
Protein, describing the normal flow of
biological information: DNA can be copied to DNA (DNA replication), DNA
information can be copied into messager RNA - mRNA (transcription), and
proteins can be synthesized using the information in mRNA as a template
(translation). In other words, DNA is transcribed to RNA which is translated to
protein. Protein is never translated back to RNA or DNA; and except for
retroviruses, DNA is never created from RNA. Furthermore, DNA is never directly
translated to protein. DNA to RNA to protein. The amount of protein that a cell
expresses depends on the tissue, the developmental stage of the organism and
the metabolic or physiologic state of the cell.
Systems biology is a new field that aims to gain system-level understanding of
complex functions of biological systems and biological processes, ranging from
molecules to cells, tissues, or entire organisms. From the systems science
point of view, many important properties of a complex system emerge from the
interaction of the system components and, therefore, rather than investigating
the characteristics of isolated system parts separately, systems biologists
focus on discovering emergent properties and functions that do not appear in
individual components, but are driven by the interactions among all the system
components or component groups.
Thanks to the development of high-throughput ¡®-omics¡¯ technologies, such as
genomic sequences gathered by the Human Genome Project, gene expression data
from microarray experiments, proteome databases and protein interaction
databases, together with large volume of digital textural documents such as the
PubMed, have created an unprecedented opportunity to apply computational
techniques/tools for a comprehensive study of the structure and dynamics of
system components, and thus provides a foundation to systems biology.
¡¡
Computational and System Biology Research
(CSBR) working group aims to foster cross disciplinary
collaboration between the biomedical sciences, informatics, computational
science and a variety of other disciplines at the University of Bradford,
including mathematical, and engineering sciences.
Our main research is to develop new
computational approach called integrative data mining that can assist systems
biologists to direct the whole investigation process from information
gathering, analysis and interpretation and incrementally improve our
understanding and eventually gain a panorama of the biological systems. The
integrative data mining approach can be generally described by there main
steps: (1) identifying elements/components of the system; (2) describing the
system using connective networks, in which nodes represent the system
components and edges represent interactions between nodes. The network
describes the functional relationship among the system components, and the
interactions ultimately determine an organism¡¯s behaviour and functions; (3)
gaining insights into emergent properties of biological systems by means of
analyzing structural properties and dynamics of the network.
This is a website for a working group, funded by the PVC-RI Interdisciplinary Research Award 2005 and
2008 at the University of Bradford, jointly supervised by Dr Yonghong Peng from
the School of Informatics, Prof Des Tobin and Prof Vladimir Botchkarev from the School of Life
Science.
NB: Pages are under construction.