Recent research in experimental and computational biology has revealed the necessity of using stochastic modeling and simulation to investigate the functionality and dynamics of gene networks. However, there is no sophisticated stochastic modeling techniques and efficient stochastic simulation algorithms SSA) for analyzing and simulating gene networks. Therefore, the objective of this research is to design …
Tag Archive: Bioinformatics
Mar
12
Design of large scale kinetic metabolic models: Applications in mammalian and algae metabolism
The modeling of cellular metabolism has always been a popular topic among researchers. The existing examples are usually confined to a particular pathway or cellular process. However, the massive research efforts in genetic annotation of the last decade have expanded the field to incorporate genome scale models GSMs), which include the entire cellular metabolism. Due …
Mar
08
Statistical methods for interpretation of high resolution mass spectra
Mass spectrometry is a powerful analytical technique used to characterize various compounds. A mass spectrum is a graph of ion intensity as a function of mass-to-charge ratio. Protein study experiments generate thousands of mass spectra, generating an overload of data that necessitates the development of sophisticated data analysis methods. Our work aims at developing the …
Feb
19
Systems theory for pharmaceutical drug discovery
Biological networks are comprised of thousands of interacting components, and these networks have complicated patterns of feedback and feed-forward motifs. It is practically impossible to use intuition to determine whether simultaneously modifying multiple pharmaceutical targets has a good therapeutic response. Even when a drug is discovered which is safe in humans and highly-effective against its …
Feb
16
Robust Stability Analysis for a Class of Extended Linearization Systems
We consider analysis of nonlinear systems that can be brought into a state dependent representation known as extended linearization. Under this formulation, conventional linear analysis techniques may be adapted to study the stability, optimality, and robustness properties of nonlinear systems. When subject to system uncertainty, estimating the radius of stability for systems under extended linearization …
Feb
16
Probabilistic computational methods for structural alignment of RNA sequences
In this thesis, the problem of structural alignment of homologous RNA sequences is addressed. The structural alignment of a given set of RNA sequences is a secondary structure for each sequence, such that the structures are similar to each other, and a sequence alignment between the sequences that is conforming with the secondary structures. A …
Feb
15
Robust Stability Analysis for a Class of Extended Linearization Systems
We consider analysis of nonlinear systems that can be brought into a state dependent representation known as extended linearization. Under this formulation, conventional linear analysis techniques may be adapted to study the stability, optimality, and robustness properties of nonlinear systems. When subject to system uncertainty, estimating the radius of stability for systems under extended linearization …
Feb
14
Improved Understanding of Apoptosis and Metabolism in Chinese Hamster Ovary Cell Culture
Mammalian cell culture has gained importance in biotechnology for the development of therapeutic and diagnostic agents. Among them, Chinese hamster ovary CHO) cells are regarded as the mammalian cell “workhorse”. The use of CHO cell line for the production of recombinant proteins used in human therapy has reached a level of industrial production. However, a …
Feb
11
Identifying functional modules from biological networks and expression profiles
One of the major goals of systems biology is to understand functional modules, or the mechanisms that carry out life-sustaining biological functions at the molecular level. The term functional modules encompasses not only sets of genes or proteins, but also the interactions between them. This dissertation undertakes the following two strategies to identify these functional …
Feb
11
Identifying functional modules from biological networks and expression profiles
One of the major goals of systems biology is to understand functional modules, or the mechanisms that carry out life-sustaining biological functions at the molecular level. The term functional modules encompasses not only sets of genes or proteins, but also the interactions between them. This dissertation undertakes the following two strategies to identify these functional …