Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 20 of 34 for “"protein networks"”.
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Biological Network-based Approaches to The Functional Analysis of miRNAs in Prostate Cancer
… and integrating heterogenous interaction networks and expression data reveals a system-level understanding of the cell behavior. This thesis focuses on integrating multiple heterogenous biological networks, in particular protein networks and miRNA-target interactions, to facilitate miRNA …
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Using Persistent Homology for Topological Analysis of Protein Interaction Network of Candida Antarctica Lipase B Molecular Dynamic Simulation Model
… to analyze the conformational changes of the protein and probe its unusual high-temperature activity. Next, we build the protein interaction network of amino acids for CalB to study pairwise interactions between amino acids (nodes) and probe the protein in terms of statistical features of …
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Using network clustering to predict copy number variations associated with health disparities
… health disparities from the perspective of gene networks. We inferred network clusters from two different human gene/protein networks. We then evaluated each network cluster for the occurrences of known pathogenic genes and genes located in CNVs with different population frequencies, and used …
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Identifying Evolutionarily Conserved Protein Interaction Networks
Our goal is to investigate protein networks conserved between different organisms. Given the protein interaction networks for two species and a list of homologous pairs of protein in the two species, we propose a model for measuring whether two subnetworks, one in each protein interaction network, …
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Network Based Prediction of Protein Localization Using Diffusion Kernel
… localization of both monoplex and multiplex proteins. Most of current localization prediction algorithms employ features derived from protein sequence data and external functional annotations such as gene ontology or physicochemical properties. However, there is no method that can exploit …
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Identification of Novel Drivers of Haematopoietic Stem Cell Fate Using Low Cell Number Proteomics and Single Cell Profiling
… have prevented comprehensive characterisation of protein networks governing HSC fate. To overcome these technical limitations, we developed an optimised mass spectrometry workflow to interrogate as few as 10,000 HSCs and multiplex up to 16 cell fractions. Using this approach, we were able to …
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A comprehensive study of multiplicative attribute graph model
… to describe social, technological and biological networks, with nodes representing agents (people, websites, gene, etc.) and edges (or links) representing relations (or interactions) between agents. Examples of real-world networks include social networks, the World Wide Web, collaboration …
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Study of the cell cycle interactome of Arabidopsis thaliana through a targeted proteomics approach
Defining protein complexes is critical to virtually all aspects of cell biology, because many cellular processes are regulated by stable protein complexes and their identification often provides insights into their function. In the introduction of the thesis, an overview is given on proteomic …
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Distributed graph decomposition algorithms on Apache Spark
… triangles or graphlets, spectral analysis of networks using eigenvectors of graph Laplacian, and finding highly connected subgraphs such as cliques and quasi cliques. Unfortunately, the algorithms for solving most of the above tasks are quite costly, which makes them not-scalable to large …
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Collective analog bioelectronic computation
… integrated-circuit models of protein-protein and gene-protein networks inside a cell. Due to a natural mapping between the Poisson statistics of molecular flows in a chemical reaction and Poisson statistics of electronic current flow in a transistor, stochastic effects are …
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Principles for the design and construction of synthetic circuits utilizing protein-protein interactions in Saccharomyces cerevisiae
… biology, significant progress in creating networks using transcriptional and translational control has been made, but a network comprised solely of protein-protein interactions has not yet been built. To realize this goal, new design rules for assembling and connecting protein devices into …
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Mathematical modeling approaches for dynamical analysis of protein regulatory networks with applications to the budding yeast cell cycle and the circadian rhythm in cyanobacteria
… to study regulatory interactions within gene-protein networks. From the modeler's perspective, two challenges arise in the process of building a mathematical model. First, the same regulatory network can be translated into different types of models at different levels of detail, and the …
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Biochemical Characterization of Hydroxyproline-rich Glycoproteins in the Arabidopsis Root Cell Wall
… of the plant cell wall hydroxyprolinerich glycoproteins (HRGPs) superfamily and presumably functions by self-assembling into a scaffold that forms a covalently cross-linked wall network. Here, the self-assembly of extensins from Arabidopsis, tomato, tobacco and maize and extensin analogs from …
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Structural and Dynamic Proximal Proteomic Analysis of TRPV2 Ion Channel Activation
… in channel function is to identify TRPV2’s protein effectors and impacted signaling pathways. To achieve this, we sought to identify TRPV2’s dynamic proximal interactome by employing the catalytically active peroxidase, APEX, to tag proteins proximal to TRPV2. By comparing the protein …
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Relating topology and dynamics in cell signaling networks
… at three scales: the detailed biochemistry of protein-protein interactions, the complex, interlocked feedback loops of transcriptionally regulated signaling pathways, and the multiple mechanisms of connection that link distinct pathways together into a full cell decision process. In this …
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Scale-Free Networks in Molecular Biology: Algorithms and Random Walks Analyses
… mean field analysis of algorithms for scale-free networks in molecular biology and II) the analysis of biological networks using random walks and related algorithms. I: Many systems in nature and society are described by means of complex networks. Research indicates that these complex networks …
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Fast simulation of stochastic biochemical reaction networks on cytomorphic chips
… large-scale simulation of biochemical reaction networks in cells is important in pathway discovery in medicine, in analyzing complex cell function in systems biology, and in the design of synthetic biological circuits in living cells. However, cells can undergo many trillions of reactions over …
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Dynamics of spectral algorithms for distributed routing
… to organically changing social, economic and protein networks. This transition has been overwhelming in many ways at once. Dynamic, heterogeneous, irregular topologies have taken the place of static, homogeneous, regular ones. Asynchronous, ad hoc peer-to-peer networks have replaced carefully …
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Stochastic Modeling and Simulation of Multiscale Biochemical Systems
… arise in modeling and simulation as biochemical networks are discovered with increasing complexities and unknown mechanisms. With the improvement in experimental techniques, biologists are able to quantify genes and proteins and their dynamics in a single cell, which calls for quantitative …
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