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Relevant bibliographies by topics / Molecular biology – Data processing – Research / Dissertations / Theses

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Dissertations / Theses on the topic 'Molecular biology – Data processing – Research'

Author: Grafiati

Published: 4 June 2021

Last updated: 17 February 2022

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1

Schabort, Willem Petrus Du Toit. "Integration of kinetic models with data from 13C-metabolic flux experiments." Thesis, Link to the online version, 2007. http://hdl.handle.net/10019/707.

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2

Pafilis, Evangelos. "Web-based named entity recognition and data integration to accelerate molecular biology research." [S.l. : s.n.], 2008. http://nbn-resolving.de/urn:nbn:de:bsz:16-opus-89706.

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3

Jungfer, Kim Michael. "Semi automatic generation of CORBA interfaces for databases in molecular biology." Thesis, University College London (University of London), 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.272561.

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4

Archer, Emory Scott. "Development of graphical software tools for molecular biology." Thesis, Hong Kong : University of Hong Kong, 1997. http://sunzi.lib.hku.hk/hkuto/record.jsp?B19974218.

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5

Yim, Cheuk-hon Terence, and 嚴卓漢. "Approximate string alignment and its application to ESTs, mRNAs and genome mapping." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2004. http://hub.hku.hk/bib/B31455736.

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6

Olivier, Brett Gareth. "Simulation and database software for computational systems biology : PySCes and JWS Online." Thesis, Stellenbosch : Stellenbosch University, 2005. http://hdl.handle.net/10019.1/50449.

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Thesis (PhD)--Stellenbosch University, 2005.<br>ENGLISH ABSTRACT: Since their inception, biology and biochemistry have been spectacularly successful in characterising the living cell and its components. As the volume of information about cellular components continues to increase, we need to ask how we should use this information to understand the functioning of the living cell? Computational systems biology uses an integrative approach that combines theoretical exploration, computer modelling and experimental research to answer this question. Central to this approach is the development o

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7

Ho, Ngai-lam, and 何毅林. "Algorithms on constrained sequence alignment." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2004. http://hub.hku.hk/bib/B30201949.

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8

Santos, Karina Baptista dos. "Predição de estruturas de proteínas utilizando restrições de ângulo diedrais." Laboratório Nacional de Computação Científica, 2014. https://tede.lncc.br/handle/tede/204.

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Submitted by Maria Cristina (library@lncc.br) on 2015-04-10T18:35:20Z No. of bitstreams: 1 Karina_Dissertacao_versao_final.pdf: 14328590 bytes, checksum: b09ee552401b05045498580540b46215 (MD5)<br>Approved for entry into archive by Maria Cristina (library@lncc.br) on 2015-04-10T18:35:35Z (GMT) No. of bitstreams: 1 Karina_Dissertacao_versao_final.pdf: 14328590 bytes, checksum: b09ee552401b05045498580540b46215 (MD5)<br>Made available in DSpace on 2015-04-10T18:35:48Z (GMT). No. of bitstreams: 1 Karina_Dissertacao_versao_final.pdf: 14328590 bytes, checksum: b09ee552401b05045498580540b46215 (MD

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9

Moix, Jeremy Michael. "Molecular Dynamics and Stochastic Simulations of Surface Diffusion." Diss., Georgia Institute of Technology, 2007. http://hdl.handle.net/1853/14580.

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Despite numerous advances in experimental methodologies capable of addressing the various phenomenon occurring on metal surfaces, atomic scale resolution of the microscopic dynamics remains elusive for most systems. Computational models of the processes may serve as an alternative tool to fill this void. To this end, parallel molecular dynamics simulations of self-diffusion on metal surfaces have been developed and employed to address microscopic details of the system. However these simulations are not without their limitations and prove to be computationally impractical for a variety of chemi

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10

Custódio, Fábio Lima. "Algoritmos genéticos para predição ab initio de estrutura de proteínas." Laboratório Nacional de Computação Científica, 2008. http://www.lncc.br/tdmc/tde_busca/arquivo.php?codArquivo=159.

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Métodos de predição ab initio de estrutura de proteínas (PSP) buscam prever, baseando-se em primeiros princípios, a estrutura tridimensional que uma dada seqüência de aminoácidos irá adotar no espaço. Os métodos de predição ab initio atualmente possuem aplicações biotecnológicas que envolvem desde a criação de novas proteínas, o auxílio no desenho racional de fármacos (estrutura do receptor), o refinamento de modelos teóricos e a obtenção de estruturas a partir de dados experimentais incompletos. Entretanto, a predição envolve um problema de otimização que lida com milhares de graus de liberda

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11

Dessailly, Benoît. "Binding sites in protein structures: characterisation and relation with destabilising regions." Doctoral thesis, Universite Libre de Bruxelles, 2007. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/210668.

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An increasing number of proteins with unknown function have their three-dimensional structure solved at high resolution. This situation, largely due to structural genomics initiatives, has been stimulating the development of automated structure-based function prediction methods. Knowledge of residues important for function – and more particularly – for binding can help automated prediction of function in different ways. The properties of a binding site such as its shape or amino acid composition can provide clues on the ligand that may bind to it. Also, having information on functionally impor

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12

Foose, Daniel Patrick. "Vespucci: A free, cross-platform software tool for spectroscopic data analysis and imaging." Wright State University / OhioLINK, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=wright1472823712.

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13

Deatherage, Daniel E. "TGFΒ/SMAD4 Signaling and Altered Epigenetics Contribute to Increased Ovarian Cancer Severity". The Ohio State University, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=osu1306860253.

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14

Bauer-Mehren, Anna. "Integrative approaches to investigate the molecular basis of diseases and adverse drug reactions: from multivariate statistical analysis to systems biology." Doctoral thesis, Universitat Pompeu Fabra, 2010. http://hdl.handle.net/10803/7219.

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Despite some great success, many human diseases cannot be effectively treated, prevented or cured, yet. Moreover, prescribed drugs are often not very efficient and cause undesired side effects. Hence, there is a need to investigate the molecular basis of diseases and adverse drug reactions in more detail. For this purpose, relevant biomedical data needs to be gathered, integrated and analysed in a meaningful way. In this regard, we have developed novel integrative analysis approaches based on both perspectives, classical multivariate statistics and systems biology. A novel multilevel statistic

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15

Andén, Olivia. "Structural basis of modulation by pH and calcium in a ligand-gated ion channel." Thesis, KTH, Genteknologi, 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-299889.

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Pentameriska ligandstyrda jonkanaler (pLGICs) är avgörande för omvandlingen av kemisk till elektrisk signalöverföring i djurs nervsystem. Dysfunktion i dessa kanaler har visat sig vara kopplad till flera sjukdomar inklusive epilepsi, schizofreni, Alzheimers och autism, vilket gör dem till en måltavla för en mängd olika läkemedel. Att studera eukaryota kanaler är dock mycket utmanande, så upptäckten av prokaryota homologer, som är mycket lättare att studera, har därmed bidragit mycket till förståelsen för struktur och funktion hos proteiner i denna familj. I detta projekt producerades och renad

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16

Desai, Akshay A. "Data analysis and creation of epigenetics database." Thesis, 2014. http://hdl.handle.net/1805/4452.

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Indiana University-Purdue University Indianapolis (IUPUI)<br>This thesis is aimed at creating a pipeline for analyzing DNA methylation epigenetics data and creating a data model structured well enough to store the analysis results of the pipeline. In addition to storing the results, the model is also designed to hold information which will help researchers to decipher a meaningful epigenetics sense from the results made available. Current major epigenetics resources such as PubMeth, MethyCancer, MethDB and NCBI’s Epigenomics database fail to provide holistic view of epigenetics. They provide d

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17

Huang, Fei. "Optimizing hydropathy scale to improve IDP prediction and characterizing IDPs' functions." Thesis, 2014. http://hdl.handle.net/1805/5191.

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Indiana University-Purdue University Indianapolis (IUPUI)<br>Intrinsically disordered proteins (IDPs) are flexible proteins without defined 3D structures. Studies show that IDPs are abundant in nature and actively involved in numerous biological processes. Two crucial subjects in the study of IDPs lie in analyzing IDPs’ functions and identifying them. We thus carried out three projects to better understand IDPs. In the 1st project, we propose a method that separates IDPs into different function groups. We used the approach of CH-CDF plot, which is based the combined use of two predictors and

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18

Thomson, Karen J. "A Computational Study of the Mechanism for F1-ATPase Inhibition by the Epsilon Subunit." Thesis, 2013. http://hdl.handle.net/1805/5024.

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Indiana University-Purdue University Indianapolis (IUPUI)<br>The multi-protein complex of F0F1 ATP synthase has been of great interest in the fields of microbiology and biochemistry, due to the ubiquitous use of ATP as a biological energy source. Efforts to better understand this complex have been made through structural determination of segments based on NMR and crystallographic data. Some experiments have provided useful data, while others have brought up more questions, especially when structures and functions are compared between bacteria and species with chloroplasts or mitochondria. T

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19

Hsu, Wei-Lun. "Mechanisms of binding diversity in protein disorder : molecular recognition features mediating protein interaction networks." Thesis, 2014. http://hdl.handle.net/1805/4035.

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Indiana University-Purdue University Indianapolis (IUPUI)<br>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. Short disordered protein fragments, called “molecular recognition features” (MoRFs), were hypothesized to facilitate the binding diversity of highly-connected proteins termed “hubs”. MoRFs often couple folding with binding while forming interac

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20

"The applications of image processing in biology and relevant data analysis." 2007. http://library.cuhk.edu.hk/record=b5893361.

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Wang, Zexi.<br>Thesis (M.Phil.)--Chinese University of Hong Kong, 2007.<br>Includes bibliographical references (leaves 63-64).<br>Abstract --- p.i<br>Acknowledgement --- p.iii<br>Chapter 0 --- Introduction --- p.1<br>Chapter 1 --- The Design of the Experiments --- p.4<br>Chapter 1.1 --- Flies and the Devices --- p.5<br>Chapter 1.2 --- Parameter Settings and Interested Information --- p.8<br>Chapter 2 --- Video Processing --- p.11<br>Chapter 2.1 --- "Videos, Computer Vision and Image Processing" --- p.11<br>Chapter 2.2 --- Details in Video Processing --- p.14<br>Chapter 3 --- Data Anal

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21

de, Gannes Matthew K. "Rapid Method of Processing Sperm for Nucleic Acid Extraction in Clinical Research." 2014. https://scholarworks.umass.edu/masters_theses_2/9.

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Background: Sperm contain highly compact nuclei, inhibiting DNA extraction using traditional techniques. Current methods extracting sperm DNA involve lengthy lysis and no means of stabilizing DNA, hindering clinical research. Objective: We sought to optimize an efficient method of extracting high quality human sperm DNA. Methods: Sperm from three volunteers were isolated using PureCeption. We tested 1) proteinase K with DNA/RNA Shield, 2) DTT and TCEP as reducing agents, 3) QIAshredder homogenization, and 4) stability of sperm DNA fresh (baseline) or after 4 weeks of storage at 4OC in DNA/RNA

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22

Pafilis, Evangelos [Verfasser]. "Web-based named entity recognition and data integration to accelerate molecular biology research / presented by Evangelos Pafilis." 2009. http://d-nb.info/992296714/34.

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23

Suphavilai, Chayaporn. "Computational development of regulatory gene set networks for systems biology applications." Thesis, 2014. http://hdl.handle.net/1805/6163.

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Indiana University-Purdue University Indianapolis (IUPUI)<br>In systems biology study, biological networks were used to gain insights into biological systems. While the traditional approach to studying biological networks is based on the identification of interactions among genes or the identification of a gene set ranking according to differentially expressed gene lists, little is known about interactions between higher order biological systems, a network of gene sets. Several types of gene set network have been proposed including co-membership, linkage, and co-enrichment human gene set netwo

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24

Sanjeev, B. S. "Computational Studies On Eosinophil Associated Ribonucleases : Insights Into Dynamics And Catalysis Through Molecular Dynamics Simulations." Thesis, 2004. http://etd.iisc.ernet.in/handle/2005/1187.

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25

Philips, Santosh. "Computational biology approaches in drug repurposing and gene essentiality screening." Diss., 2016. http://hdl.handle.net/1805/10978.

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Indiana University-Purdue University Indianapolis (IUPUI)<br>The rapid innovations in biotechnology have led to an exponential growth of data and electronically accessible scientific literature. In this enormous scientific data, knowledge can be exploited, and novel discoveries can be made. In my dissertation, I have focused on the novel molecular mechanism and therapeutic discoveries from big data for complex diseases. It is very evident today that complex diseases have many factors including genetics and environmental effects. The discovery of these factors is challenging and cr

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26

Huang, Hui. "System biology modeling : the insights for computational drug discovery." Thesis, 2014. http://hdl.handle.net/1805/5612.

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Indiana University-Purdue University Indianapolis (IUPUI)<br>Traditional treatment strategy development for diseases involves the identification of target proteins related to disease states, and the interference of these proteins with drug molecules. Computational drug discovery and virtual screening from thousands of chemical compounds have accelerated this process. The thesis presents a comprehensive framework of computational drug discovery using system biology approaches. The thesis mainly consists of two parts: disease biomarker identification and disease treatment discoveries. The first

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27

Pandit, Yogesh. "Context specific text mining for annotating protein interactions with experimental evidence." Thesis, 2014. http://hdl.handle.net/1805/3809.

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Indiana University-Purdue University Indianapolis (IUPUI)<br>Proteins are the building blocks in a biological system. They interact with other proteins to make unique biological phenomenon. Protein-protein interactions play a valuable role in understanding the molecular mechanisms occurring in any biological system. Protein interaction databases are a rich source on protein interaction related information. They gather large amounts of information from published literature to enrich their data. Expert curators put in most of these efforts manually. The amount of accessible and publicly availabl

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28

Han, Baoguang. "Statistical analysis of clinical trial data using Monte Carlo methods." Thesis, 2014. http://hdl.handle.net/1805/4650.

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Indiana University-Purdue University Indianapolis (IUPUI)<br>In medical research, data analysis often requires complex statistical methods where no closed-form solutions are available. Under such circumstances, Monte Carlo (MC) methods have found many applications. In this dissertation, we proposed several novel statistical models where MC methods are utilized. For the first part, we focused on semicompeting risks data in which a non-terminal event was subject to dependent censoring by a terminal event. Based on an illness-death multistate survival model, we proposed flexible random effects mo

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29

Carter, Megan Elizabeth. "Blood on FTA™ Paper: Does Punch Location Affect the Quality of a Forensic DNA Profile?" 2013. http://hdl.handle.net/1805/3244.

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Indiana University-Purdue University Indianapolis (IUPUI)<br>Forensic DNA profiling is widely used as an identification tool for associating an individual with evidence of a crime. Analysis of a DNA sample involves observation of data in the form of an electropherogram, and subsequently annotating a DNA “profile” from an individual or from the evidence. The profile obtained from the evidence can be compared to reference profiles deposited in a national DNA database, which may include the potential contributor. Following a match, a random match probability is calculated to determine how comm

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30

Chen, Yu-Hsiang. "Analysis of integration sites of transgenic sheep generated by lentiviral vectors using next-generation sequencing technology." Thesis, 2014. http://hdl.handle.net/1805/4834.

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Indiana University-Purdue University Indianapolis (IUPUI)<br>The development of new methods to carry out gene transfer has many benefits to several fields, such as gene therapy, agriculture and animal health. The newly established lentiviral vector systems further increase the efficiency of gene transfer dramatically. Some studies have shown that lentiviral vector systems enhance efficiency over 10-fold higher than traditional pronuclear injection. However, the timing for lentiviral vector integration to occur remains unclear. Integrating in different stages of embryogenesis might lead t

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31

Li, Pin. "Effects of carbon nanotubes on airway epithelial cells and model lipid bilayers : proteomic and biophysical studies." Thesis, 2014. http://hdl.handle.net/1805/5968.

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Indiana University-Purdue University Indianapolis (IUPUI)<br>Carbon nanomaterials are widely produced and used in industry, medicine and scientific research. To examine the impact of exposure to nanoparticles on human health, the human airway epithelial cell line, Calu-3, was used to evaluate changes in the cellular proteome that could account for alterations in cellular function of airway epithelia after 24 h exposure to 10 μg/mL and 100 ng/mL of two common carbon nanoparticles, singleand multi-wall carbon nanotubes (SWCNT, MWCNT). After exposure to the nanoparticles, label-free quantitative

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32

(11198013), Kevin Wee. "Creation, deconstruction, and evaluation of a biochemistry animation about the role of the actin cytoskeleton in cell motility." Thesis, 2021.

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<p>External representations (ERs) used in science education are multimodal ensembles consisting of design elements to convey educational meanings to the audience. As an example of a dynamic ER, an animation presenting its content features (i.e., scientific concepts) via varying the feature’s depiction over time. A production team invited the dissertation author to inspect their creation of a biochemistry animation about the role of the actin cytoskeleton in cell motility and the animation’s implication on learning. To address this, the author developed a four-step methodology entitled the Mult

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33

Heisen, Burkhard Clemens. "New Algorithms for Macromolecular Structure Determination." Doctoral thesis, 2009. http://hdl.handle.net/11858/00-1735-0000-0006-B503-3.

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