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 55 for “"protein interaction networks"”.
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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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Algorithms for the analysis of protein interaction networks
… of systems biology: the understanding of protein interactions. Such understanding is valuable: interactions between proteins are fundamental to many cellular processes. Over the last decade, high-throughput experimental techniques have allowed us to collect a large amount of …
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On the structure and evolution of protein interaction networks
The study of protein interactions from the networks point of view has yielded new insights into systems biology [Bar03, MA03, RSM+02, WS98]. In particular, "network motifs" become apparent as a useful and systematic tool for describing and exploring networks [BP06, MKFV06, MSOI+02, SOMMA02, SV06]. …
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Parameter Identifiability and Estimation in Gene and Protein Interaction Networks
… with respect to different measurements (proteins and mRNA), and propose a working definition for "biologically meaningful estimation". We also analyze the correlations between parameters, and use this analysis to consider effective approaches to determining parameters with biological …
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Characterization of Protein Complexes and Protein Interaction Networks by Mass Spectrometry
… experimental proteomics approach for deciphering protein complexes and protein interaction networks in the budding and fission yeasts. Key steps of the employed analytical routine, including the purification of complexes and mass spectrometric identification of their subunits, were investigated in …
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Web servers, databases, and algorithms for the analysis of protein interaction networks
… have generated large amounts of data on protein-protein interactions (PPI) for many organisms. We focus on the sub-domain of systems biology related to understanding the interactions between proteins that ultimately drive all cellular processes. Representing PPIs as a protein interaction …
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Pathosystems Biology: Computational Prediction and Analysis of Host-Pathogen Protein Interaction Networks
… of systems biology is the elucidation of the protein-protein interactions (PPIs) that control important biological processes within a cell and between organisms. In particular, at the cellular and molecular level, interactions between a pathogen and its host play a vital role in initiating …
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Mechanisms of binding diversity in protein disorder : molecular recognition features mediating protein interaction networks
Intrinsically disordered proteins are proteins characterized by lack of stable tertiary structures under physiological conditions. Evidence shows that disordered proteins are not only highly involved in protein interactions, but also have the capability to associate with more than one partner. …
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Unraveling the Structure and Assessing the Quality of Protein Interaction Networks with Power Graph Analysis
… experiments focused on specific genes and proteins to genome and proteome-wide screens. One result of this endeavor is the compilation of complex networks of interacting proteins. Molecular biologists hope to understand life's complex molecular machines by studying these networks. This …
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Development and Application of a quantitative Mass spectrometry based Platform for Thermodynamic Analysis of Protein interaction Networks
<p>The identification and quantification of protein-protein interactions in large scale is critical to understanding biological processes at a systems level. Current approaches for the analysis of protein -protein interactions are generally not quantitative and largely limited to certain types of …
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Inference frameworks in computational biology: from protein-protein interaction networks using machine learning to carbon footprint estimation.
Protein-protein interactions (PPIs) are essential to understanding biological pathways and their roles in development and disease. Computational tools have been successful at predicting PPIs in silico, but the lack of consistent and reliable frameworks for this task has led to network models that …
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The Betweenness Centrality Of Biological Networks
… experiments have generated genome-wide protein interaction networks for many organisms including Saccharomyces cerevisiae (baker's yeast), Caenorhabditis elegans (worm) and Drosophila melanogaster (fruit fly). In this thesis, we examine the vertex and edge betweenness centrality measures …
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Incorporating diverse data to improve genetic network alignment with IsoRank
… to simultaneously align multiple unrelated networks over the same set of nodes. In addition to the original protein-interaction networks, I align genetic-interaction networks, gene-expression correlations, and chromosome localization data to improve the functional similarity of aligned …
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Biological Networks: Modeling and Structural Analysis
<p>Biological networks are receiving increased attention due to their importance in understanding life at the cellular level. There exist many different kinds of biological networks, and different models have been proposed for them. In this dissertation we focus on suitable network models for …
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Network tools forthe analysis and prediction of protein-protein interactions
… simplifies many common operations on biological networks. As a demonstration of FNAC, we investigate the properties of several prominent protein function and protein-protein interaction networks. In doing so, we uncover evidence suggesting that a recently-developed technique for annotating …
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BIOINFORMATICS TOOL AND MODEL DEVELOPMENT FOR STUDYING BIOLOGICAL NETWORKS AND PROTEIN-PROTEIN INTERACTIONS
… needs of quantitative analysis of biological networks, PROFEAT webserver was developed for computing the network descriptors, which offers distinguished advantages over the others by: providing the most comprehensive (up-to 379) network descriptors at node/edge/network-levels; supporting …
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Benchmarking Methods For Predicting Phenotype Gene Associations
… These methods are evaluated on multiple protein interaction networks and feature representations. We empirically evaluate the performance of multiple prediction tasks using two evaluation experiments: cross-fold validation and the more stringent temporal holdout. We demonstrate that all …
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Investigating Modular Structure and Function in Biology: from Immunology to Cognition
… and has been especially studied in biological networks, including metabolic circuits, protein-protein interaction networks, ecological food webs, and human brain networks. However, beyond simply quantifying the organization of these different systems, modularity plays an important role in …
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Using network inference to discover molecular pathways underlying cytokine synergism and age-related neurodegeneration
… modeling method that provides high-confidence subnetworks of physically interacting molecules by integrating diverse "omics" data with prior knowledge from protein-protein interaction networks (PPIs). However, PCSF is sensitive to initial parameterization and generating biological hypotheses from …
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Numerical Methods for the Chemical Master Equation
… mathematical models of gene regulatory networks and protein-protein interaction networks, where the numbers of molecules of most species are around tens or hundreds. However, solving the master equation directly suffers from the so called "curse of dimensionality" issue. This thesis …
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