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Dissertations / Theses on the topic 'Bioinformatics tools'

Author: Grafiati

Published: 4 June 2021

Last updated: 26 July 2025

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1

Sentausa, Erwin. "Time course simulation replicability of SBML-supporting biochemical network simulation tools." Thesis, University of Skövde, School of Humanities and Informatics, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-33.

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<p>Background: Modelling and simulation are important tools for understanding biological systems. Numerous modelling and simulation software tools have been developed for integrating knowledge regarding the behaviour of a dynamic biological system described in mathematical form. The Systems Biology Markup Language (SBML) was created as a standard format for exchanging biochemical network models among tools. However, it is not certain yet whether actual usage and exchange of SBML models among the tools of different purpose and interfaces is assessable. Particularly, it is not clear whether dyna

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2

Berry, Eric Zachary 1980. "Bioinformatics and database tools for glycans." Thesis, Massachusetts Institute of Technology, 2004. http://hdl.handle.net/1721.1/27085.

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Thesis (M. Eng. and S.B.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2004.<br>Includes bibliographical references (leaves 75-76).<br>Recent advances in biology have afforded scientists with the knowledge that polysaccharides play an active role in modulating cellular activities. Glycosaminoglycans (GAGs) are one such family of polysaccharides that play a very important role in regulating the functions of numerous important signaling molecules and enzymes in the cell. Developing bioinformatics tools has been integral to advancing genomics and p

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3

Meng, Da. "Bioinformatics tools for evaluating microbial relationships." Pullman, Wash. : Washington State University, 2009. http://www.dissertations.wsu.edu/Dissertations/Spring2009/d_meng_042209.pdf.

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Thesis (Ph. D.)--Washington State University, May 2009.<br>Title from PDF title page (viewed on June 8, 2009). "School of Electrical Engineering and Computer Science." Includes bibliographical references.

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4

Martini, Paolo. "Dissecting the transcriptome complexity with bioinformatics tools." Doctoral thesis, Università degli studi di Padova, 2012. http://hdl.handle.net/11577/3422923.

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Bioinformatics has acquired a lot of importance especially with the advent of genomic approaches. The large amount of data produced by ``omics'' experiments requires appropriate frameworks to handle, store and mine the information and to derive appropriate work hypotheses. Transcriptome is defined as the whole amount of RNA molecules produced by a cell that provides the bridge between the genome and proteins. RNA molecules can be divided in two major classes: protein coding RNAs or messenger RNAs (mRNAs) and non-coding RNAs (ncRNAs). While the first class has been the most studied in the last

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5

Strafford, J. "Docking and bioinformatics tools to guide enzyme engineering." Thesis, University College London (University of London), 2012. http://discovery.ucl.ac.uk/1339145/.

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The carbon-carbon bond forming ability of transketolase (TK), along with its broad substrate specificity, makes it very attractive as a biocatalyst in industrial organic synthesis. Through the production of saturation mutagenesis libraries focused on individual active site residues, several variants of TK have been discovered with enhanced activities on non-natural substrates. We have used computational and bioinformatics tools to increase our understanding of TK and to guide engineering of the enzyme for further improvements in activity. Computational automated docking is a powerful technique

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6

Petri, Eric D. C. "Bioinformatics Tools for Finding the Vocabularies of Genomes." Ohio University / OhioLINK, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1213730223.

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7

Mahram, Atabak. "FPGA acceleration of sequence analysis tools in bioinformatics." Thesis, Boston University, 2013. https://hdl.handle.net/2144/11126.

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Thesis (Ph.D.)--Boston University<br>With advances in biotechnology and computing power, biological data are being produced at an exceptional rate. The purpose of this study is to analyze the application of FPGAs to accelerate high impact production biosequence analysis tools. Compared with other alternatives, FPGAs offer huge compute power, lower power consumption, and reasonable flexibility. BLAST has become the de facto standard in bioinformatic approximate string matching and so its acceleration is of fundamental importance. It is a complex highly-optimized system, consisting of tens of t

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8

Stenberg, Johan. "Software Tools for Design of Reagents for Multiplex Genetic Analyses." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-6832.

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9

Parida, Mrutyunjaya. "Exploring and analyzing omics using bioinformatics tools and techniques." Diss., University of Iowa, 2018. https://ir.uiowa.edu/etd/6244.

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During the Human Genome Project the first hundred billion bases were sequenced in four years, however, the second hundred billion bases were sequenced in four months (NHGRI, 2013). As efforts were made to improve every aspect of sequencing in this project, cost became inversely proportional to the speed (NHGRI, 2013). Human Genome Project ended in April 2003 but research in faster and cheaper ways to sequence the DNA is active to date (NHGRI, 2013). On the one hand, these advancements have allowed the convenient and unbiased generation and interrogation of a variety of omics datasets; on the o

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10

Malatras, Apostolos. "Bioinformatics tools for the systems biology of dysferlin deficiency." Thesis, Paris 6, 2017. http://www.theses.fr/2017PA066627/document.

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Le but de mon projet est de créer et d’appliquer des outils pour l’analyse de la biologie des systèmes musculaires en utilisant différentes données OMICS. Ce projet s’intéresse plus particulièrement à la dysferlinopathie due la déficience d’une protéine appelée dysferline qui est exprimée principalement dans les muscles squelettiques et cardiaque. La perte du dysferline due à la mutation (autosomique-récessive) du gène DYSF entraîne une dystrophie musculaire progressive (LGMD2B, MM, DMAT). Nous avons déjà développé des outils bio-informatiques qui peuvent être utilisés pour l’analyse fonctionn

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11

Malatras, Apostolos. "Bioinformatics tools for the systems biology of dysferlin deficiency." Electronic Thesis or Diss., Paris 6, 2017. https://accesdistant.sorbonne-universite.fr/login?url=https://theses-intra.sorbonne-universite.fr/2017PA066627.pdf.

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Le but de mon projet est de créer et d’appliquer des outils pour l’analyse de la biologie des systèmes musculaires en utilisant différentes données OMICS. Ce projet s’intéresse plus particulièrement à la dysferlinopathie due la déficience d’une protéine appelée dysferline qui est exprimée principalement dans les muscles squelettiques et cardiaque. La perte du dysferline due à la mutation (autosomique-récessive) du gène DYSF entraîne une dystrophie musculaire progressive (LGMD2B, MM, DMAT). Nous avons déjà développé des outils bio-informatiques qui peuvent être utilisés pour l’analyse fonctionn

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12

Chiara, M. "BIOINFORMATIC TOOLS FOR NEXT GENERATION GENOMICS." Doctoral thesis, Università degli Studi di Milano, 2012. http://hdl.handle.net/2434/173424.

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New sequencing strategies have redefined the concept of “high-throughput sequencing” and many companies, researchers, and recent reviews use the term “Next-Generation Sequencing” (NGS) instead of high-throughput sequencing. These advances have introduced a new era in genomics and bioinformatics⁠⁠. During my years as PhD student I have developed various software, algorithms and procedures for the analysis of Nest Generation sequencing data required for distinct biological research projects and collaborations in which our research group was involved. The tools and algorithms are thus presented

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13

Lopes, Pinto Fernando. "Development of Molecular Biology and Bioinformatics Tools : From Hydrogen Evolution to Cell Division in Cyanobacteria." Doctoral thesis, Uppsala universitet, Institutionen för fotokemi och molekylärvetenskap, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-110842.

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The use of fossil fuels presents a particularly interesting challenge - our society strongly depends on coal and oil, but we are aware that their use is damaging the environment. Currently, this awareness is gaining momentum, and pressure to evolve towards an energetically cleaner planet is very strong. Molecular hydrogen (H2) is an environmentally suitable energy carrier that could initially supplement or even substitute fossil fuels. Ideally, the primary energy source to produce hydrogen gas should be renewable, and the process of conversion back to energy without polluting emissions, making

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14

DePasquale, Erica. "Development of Computational Tools for Single-Cell Discovery." University of Cincinnati / OhioLINK, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1614021318421845.

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15

Furió, Tarí Pedro. "Development of bioinformatic tools for massive sequencing analysis." Doctoral thesis, Universitat Politècnica de València, 2020. http://hdl.handle.net/10251/152485.

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[EN] Transcriptomics is one of the most important and relevant areas of bioinformatics. It allows detecting the genes that are expressed at a particular moment in time to explore the relation between genotype and phenotype. Transcriptomic analysis has been historically performed using microarrays until 2008 when high-throughput RNA sequencing (RNA-Seq) was launched on the market, replacing the old technique. However, despite the clear advantages over microarrays, it was necessary to understand factors such as the quality of the data, reproducibility and replicability of the analyses and potent

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16

Garma, L. D. (Leonardo D. ). "Structural bioinformatics tools for the comparison and classification of protein interactions." Doctoral thesis, Oulun yliopisto, 2017. http://urn.fi/urn:isbn:9789526216065.

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Abstract Most proteins carry out their functions through interactions with other molecules. Thus, proteins taking part in similar interactions are likely to carry out related functions. One way to determine whether two proteins do take part in similar interactions is by quantifying the likeness of their structures. This work focuses on the development of methods for the comparison of protein-protein and protein-ligand interactions, as well as their application to structure-based classification schemes. A method based on the MultiMer-align (or MM-align) program was developed and used to compare

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17

Malatras, Apostolos [Verfasser]. "Bioinformatics tools for the systems biology of dysferlin deficiency / Apostolos Malatras." Berlin : Freie Universität Berlin, 2018. http://d-nb.info/1171431333/34.

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18

Cabrera, Cárdenas Claudia Paola. "Bioinformatics tools for the genetic dissection of complex traits in chickens." Thesis, University of Edinburgh, 2009. http://hdl.handle.net/1842/3864.

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This thesis explores the genetic characterization of the mechanisms underlying complex traits in chicken through the use and development of bioinformatics tools. The characterization of quantitative trait loci controlling complex traits has proven to be very challenging. This thesis comprises the study of experimental designs, annotation procedures and functional analyses. These represent some of the main ‘bottlenecks’ involved in the integration of QTLs with the biological interpretation of high-throughput technologies. The thesis begins with an investigation of the bioinformatics tools and p

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19

García, Recio Adrián. "Bioinformatics tools for membrane proteins: from sequences to structure and function." Doctoral thesis, Universitat de Vic - Universitat Central de Catalunya, 2022. http://hdl.handle.net/10803/673699.

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Les proteïnes de membrana són un gran grup de proteïnes que tenen un paper essencial a la cèl·lula. Aquest grup inclou receptors, canals iònics, transportadors i enzims, que representen el 25% de les proteïnes del genoma humà. Al voltant del 50% de les proteïnes de membrana són dianes farmacològiques per a diverses malalties. A més, hi ha mutacions patògenes que afecten el seu plegament, estabilitat i funció per al 90% de les proteïnes de membrana. La investigació sobre proteïnes de membrana ha crescut al llarg dels darrers anys. juntament amb el desenvolupament d'eines computacionals per trac

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20

Pierleoni, Andrea <1979&gt. "Design and implementation of bioinformatics tools for large scale genome annotation." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2008. http://amsdottorato.unibo.it/695/1/Tesi_Pierleoni_Andrea.pdf.

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The continuous increase of genome sequencing projects produced a huge amount of data in the last 10 years: currently more than 600 prokaryotic and 80 eukaryotic genomes are fully sequenced and publically available. However the sole sequencing process of a genome is able to determine just raw nucleotide sequences. This is only the first step of the genome annotation process that will deal with the issue of assigning biological information to each sequence. The annotation process is done at each different level of the biological information processing mechanism, from DNA to protein, and ca

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21

Pierleoni, Andrea <1979&gt. "Design and implementation of bioinformatics tools for large scale genome annotation." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2008. http://amsdottorato.unibo.it/695/.

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The continuous increase of genome sequencing projects produced a huge amount of data in the last 10 years: currently more than 600 prokaryotic and 80 eukaryotic genomes are fully sequenced and publically available. However the sole sequencing process of a genome is able to determine just raw nucleotide sequences. This is only the first step of the genome annotation process that will deal with the issue of assigning biological information to each sequence. The annotation process is done at each different level of the biological information processing mechanism, from DNA to protein, and ca

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22

Liu, Youfang. "Analytical tools for population-based association studies." NCSU, 2008. http://www.lib.ncsu.edu/theses/available/etd-08182008-161113/.

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Disease gene fine mapping is an important task in human genetic research. Association analysis is becoming a primary approach for localizing disease loci, especially when abundant SNPs are available due to the well improved genotyping technology during the last decades. Despite the rapid improvement of detection ability, there are many limitations of association strategy. In this dissertation, we focused on three different topics including haplotype similarity based test, association test incorporating genotyping error and simulation tool for large data set. 1) Previous haplotype similarity ba

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23

Marani, Paola <1970&gt. "From "wet biology" to statistical analysis of structural features with bioinformatics tools." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2008. http://amsdottorato.unibo.it/689/1/Tesi_Marani_Paola.pdf.

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Many new Escherichia coli outer membrane proteins have recently been identified by proteomics techniques. However, poorly expressed proteins and proteins expressed only under certain conditions may escape detection when wild-type cells are grown under standard conditions. Here, we have taken a complementary approach where candidate outer membrane proteins have been identified by bioinformatics prediction, cloned and overexpressed, and finally localized by cell fractionation experiments. Out of eight predicted outer membrane proteins, we have confirmed the outer membrane localization for five

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Marani, Paola <1970&gt. "From "wet biology" to statistical analysis of structural features with bioinformatics tools." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2008. http://amsdottorato.unibo.it/689/.

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Many new Escherichia coli outer membrane proteins have recently been identified by proteomics techniques. However, poorly expressed proteins and proteins expressed only under certain conditions may escape detection when wild-type cells are grown under standard conditions. Here, we have taken a complementary approach where candidate outer membrane proteins have been identified by bioinformatics prediction, cloned and overexpressed, and finally localized by cell fractionation experiments. Out of eight predicted outer membrane proteins, we have confirmed the outer membrane localization for five

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25

Meraba, Rebone Leboreng. "Evaluating the predictive performance of cytotoxic T lymphocyte epitope prediction tools using Elispot assay data." Master's thesis, University of Cape Town, 2018. http://hdl.handle.net/11427/27972.

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Computational T-cell epitope prediction tools have been previously devised to predict potential human leukocyte antigen (HLA) binding peptides from protein sequences. These tools are complements of Enzyme-linked immunosorbent spot (ELISpot) assays - a very commonly applied immunological technique that is used both to identify regions of pathogen genomes that trigger an immune response and to characterize the relationships between an individual's complement of HLA alleles and the degree of immunity that they display. If computational tools could accurately predict HLA-peptide binding, then thes

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26

Shi, Jieming. "Novel bioinformatics tools for miRNA-Seq analysis, RNA structure visualization, and genome-wide repeat detection." Miami University / OhioLINK, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=miami15003113547315.

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27

Murat, Katarzyna. "Bioinformatics analysis of epigenetic variants associated with melanoma." Thesis, University of Bradford, 2018. http://hdl.handle.net/10454/17220.

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The field of cancer genomics is currently being enhanced by the power of Epigenome-wide association studies (EWAS). Over the last couple of years comprehensive sequence data sets have been generated, allowing analysis of genome-wide activity in cohorts of different individuals to be increasingly available. Finding associations between epigenetic variation and phenotype is one of the biggest challenges in biomedical research. Laboratories lacking dedicated resources and programming experience require bioinformatics expertise which can be prohibitively costly and time-consuming. To addres

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28

Wang, Kai. "DEVELOPMENT OF MACHINE LEARNING BASED BIOINFORMATICS TOOLS FORCRISPR DETECTION, PIRNA IDENTIFICATION, AND WHOLE-GENOME BISULFITESEQUENCING DATA ANALYSIS." Miami University / OhioLINK, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=miami1546437447863901.

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29

Roche, Daniel Barry. "The development of bioinformatics tools for the rapid identification of novel cellulase sequences." Thesis, University of Reading, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.558725.

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The main aim of this project was to develop bioinformatics tools to rapidly identify novel cellulases sequences for use in next generation biofuels production. Firstly, a detailed analysis of the sequences and folds of structurally elucidated cellulases was undertaken. From this analysis it was discovered that cellulases are structurally diverse and are classified into 19 different CA TH superfamilies. The study of cellulase fold space was subsequently utilized for the development of a cellulase specific fold recognition tool, CellulaseFOLD. CellulaseFOLD was found to be over 30% faster than t

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30

Binatti, Andrea. "The genomic landscape of solid and hematologic malignancies characterized by new bioinformatics tools." Doctoral thesis, Università degli studi di Padova, 2018. http://hdl.handle.net/11577/3424919.

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Whole Exome Sequencing (WES) has high power to discover variants in cancer cells, allowing the identification of molecular features underlying diseases development and progression, with important outcomes for cancer diagnosis/prognostication as well as for development and selection of molecularly targeted therapies in personalized medicine. WES projects pose as well different challenges due to biological factors, such as tumour heterogeneity, altered ploidy, low tumor purity, and technical artifacts, that make not obvious the identification of relevant variants. IWhale, an easy-to-use and cus

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31

Arango, Argoty Gustavo Alonso. "Computational Tools for Annotating Antibiotic Resistance in Metagenomic Data." Diss., Virginia Tech, 2019. http://hdl.handle.net/10919/88987.

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Metagenomics has become a reliable tool for the analysis of the microbial diversity and the molecular mechanisms carried out by microbial communities. By the use of next generation sequencing, metagenomic studies can generate millions of short sequencing reads that are processed by computational tools. However, with the rapid adoption of metagenomics a large amount of data has been generated. This situation requires the development of computational tools and pipelines to manage the data scalability, accessibility, and performance. In this thesis, several strategies varying from command line, w

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32

Adwik, G. A. "Use of molecular and bioinformatics tools for developing methods of epidemiological identification of trypanosomes." Thesis, University of Salford, 2016. http://usir.salford.ac.uk/37755/.

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Human African trypanosomiasis (HAT), also known as sleeping sickness, has been a major health problem for populations in Africa caused by the Trypanosoma brucei spp parasite. Although, the current number of the reported cases is on the decrease, more efforts are required to try to control or eliminate the disease. The recent advances in molecular techniques have contributed towards identifying taxonomic groups at all levels (species, subspecies, populations, strains and isolates). Commonly, field samples are collected and stored using Whatman FTA cards. Many molecular epidemiological tools are

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33

Motro, Yair. "Comparative genomics analysis and development of bioinformatics tools for two newly sequenced spirochaete species." Thesis, Motro, Yair (2008) Comparative genomics analysis and development of bioinformatics tools for two newly sequenced spirochaete species. PhD thesis, Murdoch University, 2008. https://researchrepository.murdoch.edu.au/id/eprint/41679/.

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The bacterial family Spirochaetales contains a number of potent pathogens responsible for serious and well-known diseases, such as tick Lyme disease (Borrelia burgdoferri), leptospirosis (Leptospira interrogens), and sypillis (Treponema pallidum). Though the mentioned species have been extensively investigated, there still remain spirochaete genera, and the spirochaete family as a whole, that have been minimally characterised. The Brachyspira genera includes species primarily responsible for gastro-intestinal diseases. Some biological characteristics of the two species B. hyodysenteriae and B.

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34

Carraro, Marco. "Development of bioinformatics tools to predict disease predisposition from Next Generation Sequencing (NGS) data." Doctoral thesis, Università degli studi di Padova, 2018. http://hdl.handle.net/11577/3426807.

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The sequencing of the human genome has opened up completely new avenues in research and the notion of personalized medicine has become common. DNA Sequencing technology has evolved by several orders of magnitude, coming into the range of $1,000 for a complete human genome. The promise of identifying genetic variants that influence our lifestyles and make us susceptible to diseases is now becoming reality. However, genome interpretation remains one the most challenging problems of modern biology. The focus of my PhD project is the development of bioinformatics tools to predict diseases predispo

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35

Verma, Rajni [Verfasser]. "Development and Application of Novel Bioinformatics and Computational Modeling Tools for Protein Engineering Advanced Computational Tools for Protein Engineering / Rajni Verma." Bremen : IRC-Library, Information Resource Center der Jacobs University Bremen, 2013. http://d-nb.info/103526966X/34.

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Greated, Alicia. "The IncP-9 plasmid group : characterisation of genomic sequences and development of tools for environmental monitoring." Thesis, University of Birmingham, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.366379.

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Blischak, Paul David. "Developing Computational Tools for Evolutionary Inferences in Polyploids." The Ohio State University, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=osu1531400134548368.

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Hossain, A. S. Md Mukarram. "Scalable tools for high-throughput viral sequence analysis." Thesis, University of Cambridge, 2017. https://www.repository.cam.ac.uk/handle/1810/276228.

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Viral sequence data are increasingly being used to estimate evolutionary and epidemiological parameters to understand the dynamics of viral diseases. This thesis focuses on developing novel and improved computational methods for high-throughput analysis of large viral sequence datasets. I have developed a novel computational pipeline, Pipelign, to detect potentially unrelated sequences from groups of viral sequences during sequence alignment. Pipelign detected a large number of unrelated and mis-annotated sequences from several viral sequence datasets collected from GenBank. I subsequently dev

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Kamepalli, Phanindra. "User Interface and Modified Testbench to Support Comprehensive Analysis of Protein Structural Alignment Tools." University of Cincinnati / OhioLINK, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1313766325.

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Faust, Karoline. "Development, assessment and application of bioinformatics tools for the extraction of pathways from metabolic networks." Doctoral thesis, Universite Libre de Bruxelles, 2010. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/210054.

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Genes can be associated in numerous ways, e.g. by co-expression in micro-arrays, co-regulation in operons and regulons or co-localization on the genome. Association of genes often indicates that they contribute to a common biological function, such as a pathway. The aim of this thesis is to predict metabolic pathways from associated enzyme-coding genes. The prediction approach developed in this work consists of two steps: First, the reactions are obtained that are carried out by the enzymes coded by the genes. Second, the gaps between these seed reactions are filled with intermediate compounds

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Cheng, Kei Chin. "Analysis of gene expression data in transgenic and non- transgenic soybean cultivars using bioinformatics tools." Thesis, McGill University, 2007. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=18455.

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Current safety assessment for novel crops, including transgenic crops, uses a targeted approach, which determines crop safeness by assessing the content of a few specific chemical components. However, microarray technology can simultaneously assess the whole transcriptome and can therefore be used to analyze target genes as well as unintended effects. In this study, we used this technique as a non-targeted approach. Gene expression data from a microarray experiment with five soybean cultivars was analyzed using bioinformatics. Two cultivars were transgenic (RoundUp®) and three were non-transge

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Khalid, Sabah. "Design, Development And Implementation Of Bioinformatics Tools For The Mining Of Microarray Gene Expression Data." Thesis, Brunel University, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.487014.

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The aspiration to understand the molecular complexities of the human body to the highest level in an efficient manner creates unique problems for the scientist in the design and implementation offunctional genomic studies. Furthermore with the involvement many hundreds ofgenes in even the simplest biological processes, how does one begin to identify the genes from the entire genome that playa significant role within a particular biological phenomena. The answer lies with microarray technology providing a resourceful solution enabling the simultaneous isolation ofgenes that may participate in a

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Patel, Hitesh [Verfasser], and Irmgard [Akademischer Betreuer] Merfort. "Use and development of chem-bioinformatics tools and methods for drug discovery and target identification." Freiburg : Universität, 2015. http://d-nb.info/1115495917/34.

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PIRRO', STEFANO. "HiPPO and Panda: two bioinformatics tools to support analysis of high-dimensional mass cytometry data." Doctoral thesis, Università degli Studi di Roma "Tor Vergata", 2016. http://hdl.handle.net/2108/201732.

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Biological processes are often modulated by the interaction of different cell types, in a complex network of relations and dependencies. For this reason, biological research aims to both increase the number of cellular features that can be surveyed simultaneously and the resolution at which such observations are possible. High-dimensional mass cytometry is particularly well suited to tracking cells in complex tissues because more than 40 parameters can be monitored at the same time, on hundreds of thousands of cells per sample. Several computational approaches have been proposed to reduce the

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Pathak, Vaibhav Sanjay. "IDENTIFYING SOMATIC COPY NUMBER ABERRATIONS WITHIN GLIOBLASTOMA MULTIFORME AND LOW GRADE GLIOMAS USING BIOINFORMATICS TOOLS EXCAVATOR AND XHMM." Case Western Reserve University School of Graduate Studies / OhioLINK, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=case1481394117039479.

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46

Das, Abhiram. "Computational tools for the analysis of biological networks in plants." Diss., Georgia Institute of Technology, 2015. http://hdl.handle.net/1853/54340.

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This thesis presents research associated to phenotyping of plants by applying informatics techniques which includes databases, web technologies, image processing and feature measurements of 2D and 3D images. The thesis presents two enabling bioinformatics tools related by a shared set of research objectives and distinct by the nature of their applications. The first project called ClearedLeavesDB, is a common platform for plant biologists to share data and metadata about cleared leaf images. This project resulted in an online interactive database of cleared leaf images. The second project call

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Katz, Lee Scott. "Computational tools for molecular epidemiology and computational genomics of Neisseria meningitidis." Diss., Georgia Institute of Technology, 2010. http://hdl.handle.net/1853/42934.

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Neisseria meningitidis is a gram negative, and sometimes encapsulated, diplococcus that causes devastating disease worldwide. For the worldwide genetic surveillance of N. meningitidis, the gold standard for profiling the bacterium uses genetic loci found around the genome. Unfortunately, the software for analyzing the data for these profiles is difficult to use for a variety of reasons. This thesis shows my suite of tools called the Meningococcus Genome Informatics Platform for the analysis of these profiling data. To better understand N. meningitidis, the CDC Meningitis Laboratory and oth

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Torabi, Moghadam Behrooz. "Computational discovery of DNA methylation patterns as biomarkers of ageing, cancer, and mental disorders : Algorithms and Tools." Doctoral thesis, Uppsala universitet, Institutionen för cell- och molekylärbiologi, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-320720.

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Epigenetics refers to the mitotically heritable modifications in gene expression without a change in the genetic code. A combination of molecular, chemical and environmental factors constituting the epigenome is involved, together with the genome, in setting up the unique functionality of each cell type. DNA methylation is the most studied epigenetic mark in mammals, where a methyl group is added to the cytosine in a cytosine-phosphate-guanine dinucleotides or a CpG site. It has been shown to have a major role in various biological phenomena such as chromosome X inactivation, regulation of gen

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Federation, Alexander Joel. "The Development of Chemical and Computational Tools to Study Transcriptional Regulation in Cancer." Thesis, Harvard University, 2015. http://nrs.harvard.edu/urn-3:HUL.InstRepos:17463980.

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Eukaryotic gene regulation is a complex process requiring the action of many multicomponent complexes in the cell. Specific inhibitors of chromatin-associated factors allow the functional study of protein domains without genetic removal of the entire protein. Here, two small molecule probes were used to study the role of DOT1L and BET proteins in cancer biology. DOT1L is a histone methyltransferase with activity correlating with positive regulation of transcription. In MLL-rearranged leukemia, DOT1L is recruited aberrantly to early developmental transcription factors, leading to their inapprop

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Goldstein, Theodore C. "Tools for extracting actionable medical knowledge from genomic big data." Thesis, University of California, Santa Cruz, 2013. http://pqdtopen.proquest.com/#viewpdf?dispub=3589324.

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<p> Cancer is an ideal target for personal genomics-based medicine that uses high-throughput genome assays such as DNA sequencing, RNA sequencing, and expression analysis (collectively called <i>omics</i>); however, researchers and physicians are overwhelmed by the quantities of big data from these assays and cannot interpret this information accurately without specialized tools. To address this problem, I have created software methods and tools called <i>OCCAM</i> (OmiC data Cancer Analytic Model) and DIPSC (Differential Pathway Signature Correlation) for automatically extracting knowled

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