Дисертації з теми "Computational approaches"
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Banks, Eric 1976. "Computational approaches to gene finding." Thesis, Massachusetts Institute of Technology, 2000. http://hdl.handle.net/1721.1/81523.
Повний текст джерелаShutova, Ekaterina. "Computational approaches to figurative language." Thesis, University of Cambridge, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.609681.
Повний текст джерелаWynn, Hamish Henry. "Computational approaches to peptidomimetic design." Thesis, University of Cambridge, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.621332.
Повний текст джерелаTraore, Seydou. "Computational approaches toward protein design." Thesis, Toulouse, INSA, 2014. http://www.theses.fr/2014ISAT0033/document.
Повний текст джерелаComputational Protein Design (CPD) is a very young research field which aims at providing predictive tools to complementprotein engineering. Indeed, in addition to the theoretical understanding of fundamental properties and function of proteins,protein engineering has important applications in a broad range of fields, including biomedical applications, biotechnology,nanobiotechnology and the design of green reagents. CPD seeks at accelerating the design of proteins with wanted propertiesby enabling the exploration of larger sequence space while limiting the financial and human costs at experimental level.To succeed this endeavor, CPD requires three ingredients to be appropriately conceived: 1) a realistic modeling of the designsystem; 2) an accurate definition of objective functions for the target biochemical function or physico-chemical property; 3)and finally an efficient optimization framework to handle large combinatorial sizes.In this thesis, we addressed CPD problems with a special focus on combinatorial optimization. In a first series of studies, weapplied for the first time the Cost Function Network optimization framework to solve CPD problems and found that incomparison to other existing methods, it brings several orders of magnitude speedup on a wide range of real CPD instancesthat include the stability design of proteins, protein-protein and protein-ligand complexes. A tailored criterion to define themutation space of residues was also introduced in order to constrain output sequences to those expected by natural evolutionthrough the integration of some structural properties of amino acids in the protein environment. The developed methods werefinally integrated into a CPD-dedicated software in order to facilitate its accessibility to the scientific community
Moreno, Nascimento Érica Cristina. "Understanding Acetylcholinesterase Inhibitors: Computational Modeling Approaches." Doctoral thesis, Universitat Jaume I, 2017. http://hdl.handle.net/10803/406125.
Повний текст джерелаPérez, Llamas Christian 1976. "Computational approaches for integrative cancer genomics." Doctoral thesis, Universitat Pompeu Fabra, 2015. http://hdl.handle.net/10803/328729.
Повний текст джерелаDavant de la complexitat i heterogeneitat del cancer, el desenvolupament de noves tecnologies per l'estudi de genomes, ha obert noves posibilitats. Diversos projectes al voltant del mon les fan servir per generar quantitats de dades de genomes de cancer mai vistes abans. En aquest treball, primer presentem Gitools, una eina que permet obtenir dades de bases de dades en biologia, anal itzar dades genomiques, i visual itzar els resul tats multidimensionals mitjançant mapes de calor interactius. Després mostrem IntOGen, les metodologies per obtenir i organitzar les dades, els metodes per el seu analisi, i com es van possar a disposició d'altres investigadors. Finalment, comparem diversos metods de predicció de l'impacte de les mutacions no sinonimes, que ens mostra com nou metods desenvolupats per cancer funcionen millor que els utilitzats tradicionalment per enfermetats generals, aixis com la necesitat de recorrer a altres fonts d'informació per tenir millor prediccions per mutacions de cancer.
Cid, Samper Fernando 1991. "Computational approaches to characterize RNP granules." Doctoral thesis, Universitat Pompeu Fabra, 2020. http://hdl.handle.net/10803/668449.
Повний текст джерелаLos gránulos ribonucleoproteicos (gránulos RNP, por sus siglas en inglés) son complejos producidos mediante separación líquido-líquido y están constituidos principalmente por proteínas y ARN. Son responsables de numerosos procesos involucrados con la regulación del ARN. Alteraciones en la dinámica de estos complejos de proteínas y ARN están asociadas con la aparición de diversas enfermedades neurodegenerativas como el ELA o FXTAS. Sin embargo, todavía se desconocen muchos aspectos relativos a su organización interna así como las contribuciones específicas del RNA en la formación y funcionamiento de estos complejos. A fin de estudiar la estructura y formación de los gránulos RNP, hemos integrado varias bases de datos de alto rendimiento de reciente aparición. Esto incluye datos sobre la composición proteica y en ARN de los RNP, sobre la interacción de proteínas y ARN extraída de experimentos de eCLIP y sobre la estructura secundaria del transcriptoma (producida mediante PARS). Todos estos datos han sido procesados para comprender las propiedades fundamentales de los ARNs que integran los gránulos, mediante el empleo de métodos computacionales como el análisis de redes o algoritmos de agrupamiento. De esta manera, hemos producido un modelo que integra varias de estas propiedades e identifica candidatos denominados ARNs de andamiaje. Definimos ARNs de andamiaje como moléculas de ARN con una alta propensión a formar gránulos y reclutar un gran número de componentes proteicos a los gránulos RNP. También hemos encontrado que las interacciones proteína-ARN conectan los principales componentes proteicos de consenso de los gránulos de estrés (un tipo específico de gránulos RNP). También hemos estudiado la contribución de las interacciones ARN-ARN y las modificaciones post-transcriptionales del RNA en la organización interna del gránulo. Hemos aplicado estos resultados para la comprensión de la fisiopatología molecular de FXTAS, empleando también algunos datos experimentales originales. En FXTAS, una mutación en el gen FMR1 produce una repetición de microsatélite en 5´ que incrementa su capacidad como ARN de andamiaje. Este mARN mutado es capaz de secuestrar algunas proteínas importantes como TRA2A (un factor de ayuste alternativo) en gránulos RNP nucleares, impidiendo su normal funcionamiento y por consiguiente produciendo algunos síntomas asociados con el progreso de la enfermedad. Una mejor comprensión de los principios que gobiernan la formación y estructura de los gránulos puede permitir desarrollar nuevas terapias (ej: aptámeros) para mitigar el desarrollo de diversas enfermedades neurodegenerativas.
Fang, Jianzhong. "Computational approaches to visual object detection." Thesis, University of Nottingham, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.416393.
Повний текст джерелаVartapetiance, Anna. "Computational approaches for verbal deception detection." Thesis, University of Surrey, 2015. http://epubs.surrey.ac.uk/807037/.
Повний текст джерелаKaimal, Vivek. "Computational approaches to study microRNA networks." University of Cincinnati / OhioLINK, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1298041682.
Повний текст джерелаStetson, Lindsay C. "Computational Approaches for Cancer Precision Medicine." Case Western Reserve University School of Graduate Studies / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=case1428050439.
Повний текст джерелаSmith, Kevin J. "Computational approaches to fragment based screening." Thesis, University of Essex, 2016. http://repository.essex.ac.uk/17574/.
Повний текст джерелаKhabirova, Eleonora. "Models of neurodegeneration using computational approaches." Thesis, University of Cambridge, 2016. https://www.repository.cam.ac.uk/handle/1810/274157.
Повний текст джерелаMarchese, Robinson Richard Liam. "Computational approaches to predicting drug induced toxicity." Thesis, University of Cambridge, 2013. https://www.repository.cam.ac.uk/handle/1810/244242.
Повний текст джерелаSlade, Jr Wayne Homer. "Computational Intelligence Approaches to Ocean Color Inversion." Fogler Library, University of Maine, 2004. http://www.library.umaine.edu/theses/pdf/SladeWH2004.pdf.
Повний текст джерелаAndronescu, Mirela Stefania. "Computational approaches for RNA energy parameter estimation." Thesis, University of British Columbia, 2008. http://hdl.handle.net/2429/2794.
Повний текст джерелаClegg, Andrew Brian. "Computational-linguistic approaches to biological text mining." Thesis, Birkbeck (University of London), 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.500019.
Повний текст джерелаHan, Ningren. "Computational and statistical approaches to optical spectroscopy." Thesis, Massachusetts Institute of Technology, 2018. http://hdl.handle.net/1721.1/120432.
Повний текст джерелаCataloged from PDF version of thesis.
Includes bibliographical references (pages 223-236).
Compact and smart optical sensors have had a major impact on people's lives over the last decade. Although the spatial information provided by optical imaging systems has already had a major impact, there is untapped potential in the spectroscopic domain. By transforming molecular information into wavelength-domain data, optical spectroscopy techniques have become some of the most popular scientific tools for examining the composition and nature of materials and chemicals in a non-destructive and non-intrusive manner. However, unlike imaging, spectroscopic techniques have not achieved the same level of penetration due to multiple challenges. These challenges have ranged from a lack of sensitive, miniaturized, and low-cost systems, to the general reliance on domain-specific expertise for interpreting complex spectral signals. In this thesis, we aim to address some of these challenges by combining modern computational and statistical techniques with physical domain knowledge. In particular, we focus on three aspects where computational or statistical knowledge have either enabled realization of a new instrument-with a compact form factor yet still maintaining a competitive performance-or deepened statistical insights of analyte detection and quantification in highly mixed or heterogeneous environments. In the first part, we utilize the non-paraxial Talbot effect to build compact and high-performance spectrometers and wave meters that use computational processing for spectral information retrieval without the need for a full-spectrum calibration process. In the second part, we develop an analyte quantification algorithm for Raman spectroscopy based on spectral shaping modeling. It uses a hierarchical Bayesian inference model and reversible-jump Markov chain Monte Carlo (RJMCMC) computation with a minimum training sample size requirement. In the last part, we numerically investigate the spectral characteristics and signal requirements for universal and predictive non-invasive glucose estimation with Raman spectroscopy, using an in vivo skin Raman spectroscopy dataset. These results provide valuable advancements and insights in bringing forth smart compact optical spectroscopic solutions to real-world applications.
by Ningren Han.
Ph. D.
Sorathiya, Anilkumar. "Computational modelling approaches to HIV-1 dynamics." Thesis, University of Cambridge, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.609918.
Повний текст джерелаScoggins, Randy Keith. "SIGNAL PROCESSING APPROACHES FOR APPEARANCE MATCHING." MSSTATE, 2003. http://sun.library.msstate.edu/ETD-db/theses/available/etd-04162003-143335/.
Повний текст джерелаAndersen, Malin. "Computational and experimental approaches to regulatory genetic variation." Doctoral thesis, Stockholm : Bioteknologi, Kungliga Tekniska högskolan, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-4593.
Повний текст джерелаVaz, Junior M. "Computational approaches to simulation of metal cutting processes." Thesis, Swansea University, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.639305.
Повний текст джерелаMeasures, Kathryn M. "Computational approaches to studying protein structures and reactivity." Thesis, University of Nottingham, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.321374.
Повний текст джерелаTodorov, Ilian Todorov. "Computational approaches to disordered compounds and solid solutions." Thesis, University of Bristol, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.268776.
Повний текст джерелаDiaz, Artiles Ana. "Exercise under artificial gravity - experimental and computational approaches." Thesis, Massachusetts Institute of Technology, 2015. http://hdl.handle.net/1721.1/98799.
Повний текст джерелаCataloged from PDF version of thesis.
Includes bibliographical references (pages 185-191).
Humans experience strong physiological deconditioning during space missions, primarily due to the weightlessness conditions. Some of these adverse consequences include bone loss, muscle atrophy, sensory-motor deconditioning, and cardiovascular adaptation, which may lead to orthostatic intolerance when astronauts are back on Earth. In order to mitigate the negative effects of weightlessness, several countermeasures are currently in place, particularly very intensive exercise protocols. However, despite these countermeasures, astronaut physiological deconditioning persists, highlighting the need for new approaches to maintain the astronauts' physiological state within acceptable limits. Artificial gravity has long been suggested as a comprehensive countermeasure that is capable of challenging all the physiological systems at the same time, therefore maintaining overall health during extended weightlessness. Ground studies have shown that intermittent artificial gravity using a short-radius centrifuge combined with ergometer exercise is effective in preventing cardiovascular and musculoskeletal deconditioning. However, these studies have been done in very different conditions, and confounding factors between the studies (including centrifuge configuration, exposure time, gravity level, gravity gradient, and use/intensity of exercise) make it very difficult to draw clear conclusions about the stimuli needed to maintain physiological conditioning in space. The first objective of this research effort is to analyze the effects of different artificial gravity levels and ergometer exercise workload on musculoskeletal and cardiovascular functions, motion sickness and comfort. Human experiments are conducted using a new configuration of the MIT Compact Radius Centrifuge, which has been constrained to a radius of 1.4 meters, the upper radial limit to fit within an ISS module without extensive structural alterations. The second objective is to develop a computational model of the cardiovascular system to gain a better understanding of the effects of exercise under a high gravity gradient on the cardiovascular system. The gravity gradient generated when using a short-radius centrifuge has not previously been investigated in detail. The model is validated with the experimental measurements from the MIT CRC. Then, the model is used to explore the cardiovascular responses to new centrifuge configurations and from 0g adapted subjects.
by Ana Diaz Artiles.
Ph. D.
Puvanendrampillai, Dushyanthan. "Novel computational approaches to understanding protein-ligand interactions." Thesis, University of Cambridge, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.614917.
Повний текст джерелаMirina, Alexandra. "Computational approaches for intelligent processing of biomedical data." Thesis, Yeshiva University, 2015. http://pqdtopen.proquest.com/#viewpdf?dispub=3664552.
Повний текст джерелаThe rapid development of novel experimental techniques has led to the generation of an abundance of biological data, which holds great potential for elucidating many scientific problems. The analysis of such complex heterogeneous information, which we often have to deal with, requires appropriate state-of-the-art analytical methods. Here we demonstrate how an unconventional approach and intelligent data processing can lead to meaningful results.
This work includes three major parts. In the first part we describe a correction methodology for genome-wide association studies (GWAS). We demonstrate the existing bias for the selection of larger genes for downstream analyses in GWA studies and propose a method to adjust for this bias. Thus, we effectively show the need for data preprocessing in order to obtain a biologically relevant result. In the second part, building on the results obtained in the first part, we attempt to elucidate the underlying mechanisms of aging and longevity by conducting a longevity GWAS. Here we took an unconventional approach to the GWAS analysis by applying the idea of genetic buffering. Doing this allowed us to identify pairs of genetic markers that play a role in longevity. Furthermore, we were able to confirm some of them by means of a downstream network analysis. In the third and final part, we discuss the characteristics of chronic lymphocytic leukemia (CLL) B-cells and perform clustering analysis based on immunoglobulin (Ig) mutation patterns. By comparing the sequences of Ig of CLL patients and healthy donors, we show that different Ig heavy chain (IGHV) regions in CLL exhibit similarities with different B-cell subtypes of healthy donors, which raised a question about the single origin of CLL cases.
Mehio, Wissam. "Computational approaches for identifying inhibitors of protein interactions." Thesis, University of Edinburgh, 2011. http://hdl.handle.net/1842/9503.
Повний текст джерелаCao, Yi. "Computational approaches for detecting manipulations in capital markets." Thesis, Ulster University, 2015. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.675472.
Повний текст джерелаBajuri, Mohd Nazri Bin. "Mechanobiological analyses of healing tendons using computational approaches." Thesis, University of Oxford, 2016. https://ora.ox.ac.uk/objects/uuid:c6daa0b7-4875-4056-b05e-c35097988b72.
Повний текст джерелаYang, Guoli. "Learning in adaptive networks : analytical and computational approaches." Thesis, University of Edinburgh, 2016. http://hdl.handle.net/1842/20956.
Повний текст джерелаZhou, Mengshi. "Integrated Computational Drug Discovery Approaches for Neuropsychiatric Disorders." Case Western Reserve University School of Graduate Studies / OhioLINK, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=case1595622079403654.
Повний текст джерелаMapiye, Darlington Shingirirai. "Computational genomics approaches for kidney diseases in Africa." University of the Western Cape, 2015. http://hdl.handle.net/11394/4958.
Повний текст джерелаEnd stage renal disease (ESRD), a more severe form of kidney disease, is considered to be a complex trait that may involve multiple processes which work together on a background of a significant genetic susceptibility. Black Africans have been shown to bear an unequal burden of this disease compared to white Europeans, Americans and Caucasians. Despite this, most of the genetic and epidemiological advances made in understanding the aetiology of kidney diseases have been done in other populations outside of sub-Saharan Africa (SSA). Very little research has been undertaken to investigate key genetic factors that drive ESRD in Africans compared to patients from rest of world populations. Therefore, the primary aim of this Bioinformatics thesis was twofold: firstly, to develop and apply a whole exome sequencing (WES) analysis pipeline and use it to understand a genetic mechanism underlying ESRD in a South African population of mixed ancestry. As I hypothesized that the pipeline would enable the discovery of highly penetrate rare variants with large effect size, which are expected to explain an important fraction of the genetic aetiology and pathogenesis of ESRD in these African patients. Secondly, the aim was to develop and set up a multicenter clinical database that would capture a plethora of clinical data for patients with Lupus, one of the risk factors of ESRD. From WES of six family members (five cases and one control); a total of 23 196 SNVs, 1445 insertions and 1340 deletions, overlapped amongst all affected family members. The variants were consistent with an autosomal dominant inheritance pattern inferred in this family. Of these, only 1550 SNVs, 67 insertions and 112 deletions were present in all affected family members but absent in the unaffected family member. Following detailed evaluation of evidence for variant implication and pathogenicity, only 3 very rare heterozygous missense variants in 3 genes COL4A1 [p.R476W], ICAM1 [p.P352L], COL16A1 [p.T116M] were considered potentially disease causing. Computational relatedness analysis revealed approximate amount of DNA shared by family members and confirmed reported relatedness. Genotyping for the Y chromosome was additionally performed to assist in sample identity. The clinical database has been designed and is being piloted at Groote Schuur medical Hospital at the University of Cape Town. Currently, about 290 patients have already been entered in the registry. The resources and methodologies developed in this thesis have the potential to contribute not only to the understanding of ESRD and its risk factors, but to the successful application of WES in clinical practice. Importantly, it contributes significant information on the genetics of ESRD based on an African family and will also improve scientific infrastructure on the African continent. Clinical databasing will go a long way to enable clinicians to collect and store standardised clinical data for their patients.
Sohn, Michael B. "Novel Computational and Statistical Approaches in Metagenomic Studies." Diss., The University of Arizona, 2015. http://hdl.handle.net/10150/556866.
Повний текст джерелаWallace, Ian Patrick. "Improved computational approaches to classical electric energy problems." Thesis, University of Edinburgh, 2017. http://hdl.handle.net/1842/28922.
Повний текст джерелаLi, Hao. "On Wave Based Computational Approaches For Heterogeneous Media." Thesis, Université Paris-Saclay (ComUE), 2017. http://www.theses.fr/2017SACLN001/document.
Повний текст джерелаThis thesis develops numerical approaches to solve mid-frequency heterogeneous Helmholtz problem. When the square of wave number varies linearly in the media, one considers an extended Variational Theory of Complex Rays(VTCR) with shape functions namely Airy wave functions, which satisfy the governing equation. Then a general way to handle heterogeneous media by the Weak Trefftz Discontinuous Galerkin (WTDG) is proposed. There is no a priori restriction for the wave number. One locally develops general approximated solution of the governing equation, the gradient of the wave number being the small parameter. In this way, zero order and first order approximations are defined, namely Zero Order WTDG and First Order WTDG. Their shape functions only satisfy the local governing equation in average sense.Theoretical demonstration and academic examples of approaches are addressed. Then the extended VTCR and the WTDG are both applied to solve a harbor agitation problem. Finally, a FEM/WAVE WTDG is further developed to achieve a mix use of the Finite Element method(FEM) approximation and the wave approximation in the same subdomains, at the same time for frequency bandwidth including LF and MF
Parra, Farré Genís. "Computational identification of genes: ab initio and comparative approaches." Doctoral thesis, Universitat Pompeu Fabra, 2004. http://hdl.handle.net/10803/7082.
Повний текст джерелаThe motivation of this thesis is to give a little insight in how genes are encoded and recognized by the cell machinery and to use this information to find genes in unannotated genomic sequences. One of the objectives is the development of tools to identify eukaryotic genes through the modeling and recognition of their intrinsic signals and properties. This thesis addresses another problem: how the sequence of related genomes can contribute to the identification of genes. The value of comparative genomics is illustrated by the sequencing of the mouse genome for the purpose of annotating the human genome. Comparative gene predictions programs exploit this data under the assumption that conserved regions between related species correspond to functional regions (coding genes among them). Thus, this thesis also describes a gene prediction program that combines ab initio gene prediction with comparative information between two genomes to improve the accuracy of the predictions.
Carl, Merlin [Verfasser]. "Alternative Finestructural and Computational Approaches to Constructibility / Merlin Carl." Bonn : Universitäts- und Landesbibliothek Bonn, 2011. http://d-nb.info/1016012713/34.
Повний текст джерелаHartford, Alan Hughes. "Computational approaches for maximum likelihood estimation for nonlinearmixed models." NCSU, 2000. http://www.lib.ncsu.edu/theses/available/etd-20000719-081254.
Повний текст джерелаThe nonlinear mixed model is an important tool for analyzingpharmacokinetic and other repeated-measures data.In particular, these models are used when the measured response for anindividual,,has a nonlinear relationship with unknown, random, individual-specificparameters,.Ideally, the method of maximum likelihood is used to find estimates forthe parameters ofthe model after integrating out the random effects in the conditionallikelihood. However, closed form solutions tothe integral are generally not available. As a result, methods have beenpreviously developed to find approximatemaximum likelihood estimates for the parameters in the nonlinear mixedmodel. These approximate methods include FirstOrder linearization, Laplace's approximation, importance sampling, andGaussian quadrature. The methods are availabletoday in several software packages for models of limited sophistication;constant conditional error variance is requiredfor proper utilization of most software. In addition, distributionalassumptions are needed. This work investigates howrobust two of these methods, First Order linearization and Laplace'sapproximation, are to these assumptions. The findingis that Laplace's approximation performs well, resulting in betterestimation than first order linearization when bothmodels converge to a solution.
A method must provide good estimates of the likelihood at points inthe parameter space near the solution. This workcompares this ability among the numerical integration techniques,Gaussian quadrature, importance sampling, and Laplace'sapproximation. A new "scaled" and "centered" version of Gaussianquadrature is found to be the most accurate technique.In addition, the technique requires evaluation of the integrand at onlya few abscissas. Laplace's method also performswell; it is more accurate than importance sampling with even 100importance samples over two dimensions. Even so,Laplace's method still does not perform as well as Gaussian quadrature.Overall, Laplace's approximation performs betterthan expected, and is shown to be a reliable method while stillcomputationally less demanding.
This work also introduces a new method to maximize the likelihood.This method can be sharpened to any desired levelof accuracy. Stochastic approximation is incorporated to continuesampling until enough information is gathered to resultin accurate estimation. This new method is shown to work well for linearmixed models, but is not yet successful for thenonlinear mixed model.
Dulk, Paul den. "Computational approaches to affective processes evolutionary and neural perspectives /." [S.l. : Amsterdam : s.n.] ; Universiteit van Amsterdam [Host], 2002. http://dare.uva.nl/document/61946.
Повний текст джерелаSwett, Rebecca Jane. "Computational approaches to anti-toxin therapies and biomarker identification." Thesis, Wayne State University, 2013. http://pqdtopen.proquest.com/#viewpdf?dispub=3601751.
Повний текст джерелаThis work describes the fundamental study of two bacterial toxins with computational methods, the rational design of a potent inhibitor using molecular dynamics, as well as the development of two bioinformatic methods for mining genomic data. Clostridium difficile is an opportunistic bacillus which produces two large glucosylating toxins. These toxins, TcdA and TcdB cause severe intestinal damage. As Clostridium difficile harbors considerable antibiotic resistance, one treatment strategy is to prevent the tissue damage that the toxins cause. The catalytic glucosyltransferase domain of TcdA and TcdB was studied using molecular dynamics in the presence of both a protein-protein binding partner and several substrates. These experiments were combined with lead optimization techniques to create a potent irreversible inhibitor which protects 95% of cells in vitro. Dynamics studies on a TcdB cysteine protease domain were performed to an allosteric communication pathway. Comparative analysis of the static and dynamic properties of the TcdA and TcdB glucosyltransferase domains were carried out to determine the basis for the differential lethality of these toxins. Large scale biological data is readily available in the post-genomic era, but it can be difficult to effectively use that data. Two bioinformatics methods were developed to process whole-genome data. Software was developed to return all genes containing a motif in single genome. This provides a list of genes which may be within the same regulatory network or targeted by a specific DNA binding factor. A second bioinformatic method was created to link the data from genome-wide association studies (GWAS) to specific genes. GWAS studies are frequently subjected to statistical analysis, but mutations are rarely investigated structurally. HyDn-SNP-S allows a researcher to find mutations in a gene that correlate to a GWAS studied phenotype. Across human DNA polymerases, this resulted in strongly predictive haplotypes for breast and prostate cancer. Molecular dynamics applied to DNA Polymerase Lambda suggested a structural explanation for the decrease in polymerase fidelity with that mutant. When applied to Histone Deacetylases, mutations were found that alter substrate binding, and post-translational modification.
Yalamanchili, Hari Krishna. "Computational approaches for protein functions and gene association networks." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2014. http://hdl.handle.net/10722/206477.
Повний текст джерелаpublished_or_final_version
Biochemistry
Doctoral
Doctor of Philosophy
Cross, Simon St John. "Chemical, biological and computational approaches toward novel antibody applications." Thesis, University of Nottingham, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.395456.
Повний текст джерелаChung, Andy Heung Wing. "Novel mathematical and computational approaches for modelling biological systems." Thesis, University of Sussex, 2016. http://sro.sussex.ac.uk/id/eprint/60405/.
Повний текст джерелаMohammed, Shiras Chakkungal. "Digital Detail – Computational Approaches for Multi Performative Building Skins." The Ohio State University, 2009. http://rave.ohiolink.edu/etdc/view?acc_num=osu1262259520.
Повний текст джерелаMoutoussis, Michael. "Defensive avoidance in paranoid delusions : experimental and computational approaches." Thesis, University of Manchester, 2011. https://www.research.manchester.ac.uk/portal/en/theses/defensive-avoidance-in-paranoid-delusions-experimental-and-computational-approaches(e36dbfcf-9341-43a0-be41-087f9b22d994).html.
Повний текст джерелаMoore, Jimmy Daniel. "Computational approaches for the interpretation of ToF-SIMS data." Thesis, University of Manchester, 2014. https://www.research.manchester.ac.uk/portal/en/theses/computational-approaches-for-the-interpretation-of-tofsims-data(2b097f73-f9e8-4870-89d3-35a7ad14546f).html.
Повний текст джерелаYang, Lei. "Understanding protein motions by computational modeling and statistical approaches." [Ames, Iowa : Iowa State University], 2008.
Знайти повний текст джерелаPetrone, Paula Marcela. "Computational approaches to conformational change and specificity in biomolecules /." May be available electronically:, 2009. http://proquest.umi.com/login?COPT=REJTPTU1MTUmSU5UPTAmVkVSPTI=&clientId=12498.
Повний текст джерелаWeirather, Jason Lee. "Computational approaches to the study of human trypanosomatid infections." Thesis, The University of Iowa, 2014. http://pqdtopen.proquest.com/#viewpdf?dispub=3609102.
Повний текст джерелаTrypanosomatids cause human diseases such as leishmaniasis and African trypanosomiasis. Trypanosomatids are protists from the order Trypanosomatida and include species of the genera Trypanosoma and Leishmania, which occupy a similar ecological niche. Both have digenic life-stages, alternating between an insect vector and a range of mammalian hosts. However, the strategies used to subvert the host immune system differ greatly as do the clinical outcome of infections between species. The genomes of both the host and the parasite instruct us about strategies the pathogens use to subvert the human immune system, and adaptations by the human host allowing us to better survive infections. We have applied unsupervised learning algorithms to aid visualization of amino acid sequence similarity and the potential for recombination events within Trypanosoma brucei 's large repertoire of variant surface glycoproteins (VSGs). Methods developed here reveal five groups of VSGs within a single sequenced genome of T. brucei, indicating many likely recombination events occurring between VSGs of the same type, but not between those of different types. These tools and methods can be broadly applied to identify groups of non-coding regulatory sequences within other Trypanosomatid genomes. To aid in the detection, quantification, and species identification of leishmania DNA isolated from environmental or clinical specimens, we developed a set of quantitative-PCR primers and probes targeting a taxonomically and geographically broad spectrum of Leishmania species. This assay has been applied to DNA extracted from both human and canine hosts as well as the sand fly vector, demonstrating its flexibility and utility in a variety of research applications. Within the host genomes, fine mapping SNP analysis was performed to detect polymorphisms in a family study of subjects in a region of Northeast Brazil that is endemic for Leishmania infantum chagasi, the parasite causing visceral leishmaniasis. These studies identified associations between genetic loci and the development of visceral leishmaniasis, with a single polymorphism associated with an asymptomatic outcome after infection. The methods and results presented here have capitalized on the large amount of genomics data becoming available that will improve our understanding of both parasite and host genetics and their role in human disease.