Relevant bibliographies by topics / Transcriptome data / Dissertations / Theses
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Dissertations / Theses on the topic 'Transcriptome data'

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Published: 4 June 2021
Last updated: 4 February 2022

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1

Liu, Zhe. "Machine annotation of genome and transcriptome data." Thesis, University of Edinburgh, 2015. http://hdl.handle.net/1842/17626.

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One of the key research topics of post-genome study is annotation of the gene with regards to specific function and biological processes. This can help us to understand the precise role that a gene or a group of genes carries. In this thesis, I developed techniques to automatically annotate genes on single gene and a group of genes levels. It is shown that these techniques improve our understanding of biological systems/diseases, and will aid drug discovery. In the first project, I attempted to achieve precise annotation for single genes. In the second and third projects, I performed annotatio
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2

Östman, Josephine. "The fertile ovary transcriptome and proteome." Thesis, Uppsala universitet, Institutionen för kvinnors och barns hälsa, 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-447785.

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The Human Protein Atlas is an open-source database containing information about protein expression and location in the human cells,tissues and organs. The aim is to map all the proteins in humans using various biotechnology techniques such as antibody-based imaging, andRNA sequencing etc. Based on previous transcriptome analysis, 173 genes were shown to have an elevated expression in ovary compared to all other major tissue types in the human body. There is however no information regarding the expression in ovary during the reproductive years versus the post-menopausal years. In this thesis, t
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3

Mangul, Serghei. "Algorithms for Transcriptome Quantification and Reconstruction from RNA-Seq Data." Digital Archive @ GSU, 2012. http://digitalarchive.gsu.edu/cs_diss/71.

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Massively parallel whole transcriptome sequencing and its ability to generate full transcriptome data at the single transcript level provides a powerful tool with multiple interrelated applications, including transcriptome reconstruction, gene/isoform expression estimation, also known as transcriptome quantification. As a result, whole transcriptome sequencing has become the technology of choice for performing transcriptome analysis, rapidly replacing array-based technologies. The most commonly used transcriptome sequencing protocol, referred to as RNA-Seq, generates short (single or paired) s
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4

Calviello, Lorenzo. "Detecting and quantifying the translated transcriptome with Ribo-seq data." Doctoral thesis, Humboldt-Universität zu Berlin, 2018. http://dx.doi.org/10.18452/18974.

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Die Untersuchung der posttranskriptionellen Genregulation erfordert eine eingehende Kenntnis vieler molekularer Prozesse, die auf RNA wirken, von der Prozessierung im Nukleus bis zur Translation und der Degradation im Zytoplasma. Mit dem Aufkommen von RNA-seq-Technologien können wir nun jeden dieser Schritte mit hohem Durchsatz und Auflösung verfolgen. Ribosome Profiling (Ribo-seq) ist eine RNA-seq-Technik, die darauf abzielt, die präzise Position von Millionen translatierender Ribosomen zu detektieren, was sich als ein wesentliches Instrument für die Untersuchung der Genregulation erweist.
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5

Xu, Guorong. "Computational Pipeline for Human Transcriptome Quantification Using RNA-seq Data." ScholarWorks@UNO, 2011. http://scholarworks.uno.edu/td/343.

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The main theme of this thesis research is concerned with developing a computational pipeline for processing Next-generation RNA sequencing (RNA-seq) data. RNA-seq experiments generate tens of millions of short reads for each DNA/RNA sample. The alignment of a large volume of short reads to a reference genome is a key step in NGS data analysis. Although storing alignment information in the Sequence Alignment/Map (SAM) or Binary SAM (BAM) format is now standard, biomedical researchers still have difficulty accessing useful information. In order to assist biomedical researchers to conveniently ac
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6

Hu, Yin. "A NOVEL COMPUTATIONAL FRAMEWORK FOR TRANSCRIPTOME ANALYSIS WITH RNA-SEQ DATA." UKnowledge, 2013. http://uknowledge.uky.edu/cs_etds/17.

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The advance of high-throughput sequencing technologies and their application on mRNA transcriptome sequencing (RNA-seq) have enabled comprehensive and unbiased profiling of the landscape of transcription in a cell. In order to address the current limitation of analyzing accuracy and scalability in transcriptome analysis, a novel computational framework has been developed on large-scale RNA-seq datasets with no dependence on transcript annotations. Directly from raw reads, a probabilistic approach is first applied to infer the best transcript fragment alignments from paired-end reads. Empowered
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7

Bécavin, Christophe. "Dimensionaly reduction and pathway network analysis of transcriptome data : application to T-cell characterization." Paris, Ecole normale supérieure, 2010. http://www.theses.fr/2010ENSUBS02.

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8

Kelso, Janet. "The development and application of informatics-based systems for the analysis of the human transcriptome." Thesis, University of the Western Cape, 2003. http://etd.uwc.ac.za/index.php?module=etd&action=viewtitle&id=gen8Srv25Nme4_5101_1185442672.

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<p>Despite the fact that the sequence of the human genome is now complete it has become clear that the elucidation of the transcriptome is more complicated than previously expected. There is mounting evidence for unexpected and previously underestimated phenomena such as alternative splicing in the transcriptome. As a result, the identification of novel transcripts arising from the genome continues. Furthermore, as the volume of transcript data grows it is becoming increasingly difficult to integrate expression information which is from different sources, is stored in disparate locations, and
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9

Johnson, Kristen. "Software for Estimation of Human Transcriptome Isoform Expression Using RNA-Seq Data." ScholarWorks@UNO, 2012. http://scholarworks.uno.edu/td/1448.

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The goal of this thesis research was to develop software to be used with RNA-Seq data for transcriptome quantification that was capable of handling multireads and quantifying isoforms on a more global level. Current software available for these purposes uses various forms of parameter alteration in order to work with multireads. Many still analyze isoforms per gene or per researcher determined clusters as well. By doing so, the effects of multireads are diminished or possibly wrongly represented. To address this issue, two programs, GWIE and ChromIE, were developed based on a simple iterative
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10

Windhorst, Anita Cornelia [Verfasser]. "Transcriptome analysis in preterm infants developing bronchopulmonary dysplasia : data processing and statistical analysis of microarray data / Anita Cornelia Windhorst." Gießen : Universitätsbibliothek, 2015. http://d-nb.info/1078220395/34.

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11

Hernandez-Ferrer, Carles 1987. "Bioinformatic tools for exposome data analysis : application to human molecular signatures of ultraviolet light effects." Doctoral thesis, Universitat Pompeu Fabra, 2017. http://hdl.handle.net/10803/572046.

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Las enfermedades complejas se encuentran entre las más comunes y son causadas por una combinación de factores genéticos y ambientales (contaminación ambiental, estilo de vida, etc). Entre las enfermedades complejas que se pueden destacar se encuentran la obesidad, el asma, la hipertensión o la diabetes. Diversos estudios científicos sugieren que el hecho de padecer enfermedades complejas está condicionado a la aparición o acumulación de determinados factores ambientales. Asimismo, se ha descrito que los factores ambientales son unos de los principales contribuyentes a la carga mundial de morbi
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12

Zenke-Philippi, Carola Anna Luise [Verfasser]. "Prediction of hybrid performance in maize with transcriptome data / Carola Anna Luise Zenke-Philippi." Gießen : Universitätsbibliothek, 2017. http://d-nb.info/1136569898/34.

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13

Jeanmougin, Marine. "Statistical methods for robust analysis of transcriptome data by integration of biological prior knowledge." Thesis, Evry-Val d'Essonne, 2012. http://www.theses.fr/2012EVRY0029/document.

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Au cours de la dernière décennie, les progrès en Biologie Moléculaire ont accéléré le développement de techniques d'investigation à haut-débit. En particulier, l'étude du transcriptome a permis des avancées majeures dans la recherche médicale. Dans cette thèse, nous nous intéressons au développement de méthodes statistiques dédiées au traitement et à l'analyse de données transcriptomiques à grande échelle. Nous abordons le problème de sélection de signatures de gènes à partir de méthodes d'analyse de l'expression différentielle et proposons une étude de comparaison de différentes approches, ba
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Zenke-Philippi, Carola [Verfasser]. "Prediction of hybrid performance in maize with transcriptome data / Carola Anna Luise Zenke-Philippi." Gießen : Universitätsbibliothek, 2017. http://d-nb.info/1136569898/34.

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15

Nascimento, Leandro Costa do. "Análise de expressão gênica diferencial entre diversas bibliotecas de soja." [s.n.], 2010. http://repositorio.unicamp.br/jspui/handle/REPOSIP/316766.

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Orientador: Gonçalo Amarante Guimarães Pereira<br>Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia<br>Made available in DSpace on 2018-08-17T20:48:34Z (GMT). No. of bitstreams: 1 Nascimento_LeandroCostado_M.pdf: 1292421 bytes, checksum: e05cfc27d3bf5ae000bfe8b621a750c8 (MD5) Previous issue date: 2010<br>Resumo: A soja é uma das principais commodities da economia internacional, sendo sua produção mundial de cerca de 220 milhões de toneladas por safra. Além de ser um alimento rico em proteínas e usado para a fabricação de óleo vegetal, a planta vem ganhando vis
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16

Hindle, Matthew Morritt. "An integrated approach to enhancing functional annotation of sequences for data analysis of a transcriptome." Thesis, University of Nottingham, 2012. http://eprints.nottingham.ac.uk/12580/.

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Given the ever increasing quantity of sequence data, functional annotation of new gene sequences persists as being a significant challenge for bioinformatics. This is a particular problem for transcriptomics studies in crop plants where large genomes and evolutionarily distant model organisms, means that identifying the function of a given gene used on a microarray, is often a non-trivial task. Information pertinent to gene annotations is spread across technically and semantically heterogeneous biological databases. Combining and exploiting these data in a consistent way has the potential to i
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17

Schissler, Alfred Grant, and Alfred Grant Schissler. "Contributions to Gene Set Analysis of Correlated, Paired-Sample Transcriptome Data to Enable Precision Medicine." Diss., The University of Arizona, 2017. http://hdl.handle.net/10150/624283.

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This dissertation serves as a unifying document for three related articles developed during my dissertation research. The projects involve the development of single-subject transcriptome (i.e. gene expression data) methodology for precision medicine and related applications. Traditional statistical approaches are largely unavailable in this setting due to prohibitive sample size and lack of independent replication. This leads one to rely on informatic devices including knowledgebase integration (e.g., gene set annotations) and external data sources (e.g., estimation of inter-gene correlation).
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18

Lim, Raymond. "Wide-scale comparison of transcriptome data and the role of microRNA in major depression and suicide." Thesis, University of British Columbia, 2011. http://hdl.handle.net/2429/38065.

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The first chapter of this thesis addresses a common problem in genomics experiments: interpreting a resulting "hit list" of interesting genes. We present work on an approach for summarizing and exploring "hit lists" that makes use of the large amount of gene expression data in public repositories such as the Gene Expression Omnibus. We compare the query list with datasets that we have analyzed for differential expression of genes. Studies that have similarities to the given hit list yield additional insights, help contextualize studies, and serve as a basis for future meta-analysis. A conce
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19

Guérin, Émilie. "Intégration de données pour l'analyse de transcriptome : mise en œuvre par l'entrepôt GEDAW (Gene Expression Data Warehouse)." Rennes 1, 2005. http://www.theses.fr/2005REN1S169.

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L'intégration de données en bioinformatique est devenue essentielle à l'exploitation des masses de données engendrées par les avancées de la génomique. D'autre part, l'interprétation des données générées par les technologies d'étude de transcriptome nécessite une confrontation de données complémentaires sur les gènes étudiés ainsi que des moyens d'analyses puissants. Dans ce contexte, nous avons développé une approche d'intégration dédiée à l'analyse de transcriptome. GEDAW (Gene Expression DAta Warehouse) est un entrepôt de données orienté objet qui intègre une variété de sources et de standa
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20

Isik, Zerrin, Tulin Ersahin, Volkan Atalay, Cevdet Aykanat, and Rengul Cetin-Atalay. "A signal transduction score flow algorithm for cyclic cellular pathway analysis, which combines transcriptome and ChIP-seq data." Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2014. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-138982.

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Determination of cell signalling behaviour is crucial for understanding the physiological response to a specific stimulus or drug treatment. Current approaches for large-scale data analysis do not effectively incorporate critical topological information provided by the signalling network. We herein describe a novel model- and data-driven hybrid approach, or signal transduction score flow algorithm, which allows quantitative visualization of cyclic cell signalling pathways that lead to ultimate cell responses such as survival, migration or death. This score flow algorithm translates signalling
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21

Isik, Zerrin, Tulin Ersahin, Volkan Atalay, Cevdet Aykanat, and Rengul Cetin-Atalay. "A signal transduction score flow algorithm for cyclic cellular pathway analysis, which combines transcriptome and ChIP-seq data." Royal Society of Chemistry, 2012. https://tud.qucosa.de/id/qucosa%3A27799.

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Determination of cell signalling behaviour is crucial for understanding the physiological response to a specific stimulus or drug treatment. Current approaches for large-scale data analysis do not effectively incorporate critical topological information provided by the signalling network. We herein describe a novel model- and data-driven hybrid approach, or signal transduction score flow algorithm, which allows quantitative visualization of cyclic cell signalling pathways that lead to ultimate cell responses such as survival, migration or death. This score flow algorithm translates signalling
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22

Rubanova, Natalia. "MasterPATH : network analysis of functional genomics screening data." Thesis, Sorbonne Paris Cité, 2018. http://www.theses.fr/2018USPCC109/document.

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Dans ce travail nous avons élaboré une nouvelle méthode de l'analyse de réseau à définir des membres possibles des voies moléculaires qui sont important pour ce phénotype en utilisant la « hit-liste » des expériences « omics » qui travaille dans le réseau intégré (le réseau comprend des interactions protéine-protéine, de transcription, l’acide ribonucléique micro-l’acide ribonucléique messager et celles métaboliques). La méthode tire des sous-réseaux qui sont construit des voies de quatre types les plus courtes (qui ne se composent des interactions protéine-protéine, ayant au minimum une inter
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23

Calviello, Lorenzo [Verfasser], Uwe [Gutachter] Ohler, Markus [Gutachter] Landthaler, and Nils [Gutachter] Blüthgen. "Detecting and quantifying the translated transcriptome with Ribo-seq data / Lorenzo Calviello ; Gutachter: Uwe Ohler, Markus Landthaler, Nils Blüthgen." Berlin : Humboldt-Universität zu Berlin, 2018. http://d-nb.info/1185496300/34.

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24

Garcia, Maxime. "Découverte de biomarqueurs prédictifs en cancer du sein par intégration transcriptome-interactome." Thesis, Aix-Marseille, 2013. http://www.theses.fr/2013AIXM4109/document.

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L’arrivée des technologies à haut-débit pour mesurer l’expression des gènes a permis l’utilisation de signatures génomiques pour prédire des conditions cliniques ou la survie du patient. Cependant de telles signatures ont des limitations, comme la dépendance au jeu de données d’entrainement et le manque de généralisation. Nous proposons un nouvel algorithme, Integration Transcriptome-Interactome (ITI) (Garcia et al.) pour extraire une signature generalisable prédisant la rechute métastatique dans le cancer du sein par superimposition d’un très large jeu de données d’interaction protèine-protèi
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25

Huang, Yan. "NOVEL COMPUTATIONAL METHODS FOR TRANSCRIPT RECONSTRUCTION AND QUANTIFICATION USING RNA-SEQ DATA." UKnowledge, 2015. http://uknowledge.uky.edu/cs_etds/28.

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The advent of RNA-seq technologies provides an unprecedented opportunity to precisely profile the mRNA transcriptome of a specific cell population. It helps reveal the characteristics of the cell under the particular condition such as a disease. It is now possible to discover mRNA transcripts not cataloged in existing database, in addition to assessing the identities and quantities of the known transcripts in a given sample or cell. However, the sequence reads obtained from an RNA-seq experiment is only a short fragment of the original transcript. How to recapitulate the mRNA transcriptome fro
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26

Torkler, Phillipp [Verfasser], and Johannes [Akademischer Betreuer] Söding. "STAMMP : A statistical model and processing pipeline for PAR-CLIP data reveals transcriptome maps of mRNP biogenesis factors / Phillipp Torkler. Betreuer: Johannes Söding." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2015. http://d-nb.info/1072376628/34.

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27

Pantano, Rubiño Lorena. "Full characterization of the small RNA transcriptome using novel computational methods for high-throughput sequencing data: study of miRNA variability in eukaryote organisms." Doctoral thesis, Universitat Pompeu Fabra, 2011. http://hdl.handle.net/10803/53576.

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In this thesis we have developed a user-friendly tool, SeqBuster, for the analysis of small RNA (sRNA) data generated by next generation sequencing strategies, with special emphasis on deep characterization of miRNA variants (isomiRs). We tested the tool using public datasets, revealing an unexpected amount of isomiRs in the total miRNA profile in different species. In addition, we detected all known classes of non-miRNA sRNAs and new sRNAs with a still unassigned function. Furthermore, we studied the implication of miRNAs and isomiRs in human brain development and aging and in Huntingt
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28

Junior, Milton Yutaka Nishiyama. "Desenvolvimento da plataforma CaneRegNet para anotação funcional e análises do transcriptoma da cana-de-açúcar." Universidade de São Paulo, 2015. http://www.teses.usp.br/teses/disponiveis/95/95131/tde-28032016-154802/.

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A identificação de genes alvos, vias de sinalização e vias metabólicas para melhoramento de cana-de-açúcar associados a características de interesse, ainda são pouco conhecidos e estudados. Alguns estudos do transcriptoma através de plataformas de microarranjo têm buscado identificar listas de genes, para experimentos tecido- específico ou submetidos a condições de estresse bióticos e abióticos. Estudos pontuais destes dados tem sido associados a vias metabólicas ou vias de sinalização já descritas na literatura, de forma a identificar alterações relacionadas a padrões de expressão gênica. Por
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29

Shi, Xu. "Bayesian Modeling for Isoform Identification and Phenotype-specific Transcript Assembly." Diss., Virginia Tech, 2017. http://hdl.handle.net/10919/79772.

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The rapid development of biotechnology has enabled researchers to collect high-throughput data for studying various biological processes at the genomic level, transcriptomic level, and proteomic level. Due to the large noise in the data and the high complexity of diseases (such as cancer), it is a challenging task for researchers to extract biologically meaningful information that can help reveal the underlying molecular mechanisms. The challenges call for more efforts in developing efficient and effective computational methods to analyze the data at different levels so as to understand the bi
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30

Ribichich, Karina Fabiana. "Análise de seqüências expressas durante a fase de esporulação do fungo aquático Blastocladiella emersonii." Universidade de São Paulo, 2004. http://www.teses.usp.br/teses/disponiveis/46/46131/tde-19092016-180402/.

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Blastocladiella emersonii é um fungo aquático da classe dos quitridiomicetos, notável pelas mudanças morfogenéticas que ocorrem durante o seu ciclo de vida. Neste trabalho isolamos 8.495 seqüências expressas (ESTs) deste fungo, que representam 3.226 seqüências únicas putativas. Destas seqüências, 37% foram classificadas segundo o processo biológico onde estariam envolvidas, de acordo com o sistema de anotação do Gene Ontology (GO). Analisamos os perfis de expressão in silico das ESTs usando estatística Bayesiana e os resultados obtidos foram validados por Northern blot para sete perfis de expr
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31

Metzner, Ernst Michael [Verfasser], Patrick [Akademischer Betreuer] Schweizer, Ralph [Akademischer Betreuer] Hückelhoven, and Karin D. [Akademischer Betreuer] Breunig. "Barley infected by powdery mildew : host transcriptome and proteome changes and the integration of both data sets / Ernst Michael Metzner. Betreuer: Patrick Schweizer ; Ralph Hückelhoven ; Karin D. Breunig." Halle, Saale : Universitäts- und Landesbibliothek Sachsen-Anhalt, 2012. http://d-nb.info/1025352505/34.

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32

Sadacca, Benjamin. "Pharmacogenomic and High-Throughput Data Analysis to Overcome Triple Negative Breast Cancers Drug Resistance." Thesis, Université Paris-Saclay (ComUE), 2017. http://www.theses.fr/2017SACLS538/document.

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Devant le grand nombre de tumeurs du sein triple négatif résistant aux traitements, il est essentiel de comprendre les mécanismes de résistance et de trouver de nouvelles molécules efficaces. En premier lieu, nous analysons deux ensembles de données pharmacogénomiques à grande échelle. Nous proposons une nouvelle classification basée sur des profils transcriptomiques de lignées cellulaires, selon un processus de sélection de gènes basé sur des réseaux biologiques. Notre classification moléculaire montre une plus grande homogénéité dans la réponse aux médicaments que lorsque l’on regroupe les l
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33

Oerton, Erin. "Understanding disease and disease relationships using transcriptomic data." Thesis, University of Cambridge, 2019. https://www.repository.cam.ac.uk/handle/1810/289128.

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As the volume of transcriptomic data continues to increase, so too does its potential to deepen our understanding of disease; for example, by revealing gene expression patterns shared between diseases. However, key questions remain around the strength of the transcriptomic signal of disease and the identification of meaningful commonalities between datasets, which are addressed in this thesis as follows. The first chapter, Concordance of Microarray Studies of Parkinson's Disease, examines the agreement between differential expression signatures across 33 studies of Parkinson's disease. Compari
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Parikh, Jignesh Rajesh. "Interrogating signaling pathways using transcriptomic and proteomic data." Thesis, Boston University, 2012. https://hdl.handle.net/2144/32042.

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Thesis (Ph.D.)--Boston University<br>PLEASE NOTE: Boston University Libraries did not receive an Authorization To Manage form for this thesis or dissertation. It is therefore not openly accessible, though it may be available by request. If you are the author or principal advisor of this work and would like to request open access for it, please contact us at open-help@bu.edu. Thank you.<br>Information from the cell surface is propagated to the nucleus via interconnected signaling pathways that regulate transcription factors, thereby controlling cellular processes, such as migration, proliferati
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Coudret, Raphaël. "Stochastic modelling using large data sets : applications in ecology and genetics." Phd thesis, Université Sciences et Technologies - Bordeaux I, 2013. http://tel.archives-ouvertes.fr/tel-00865867.

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There are two main parts in this thesis. The first one concerns valvometry, which is here the study of the distance between both parts of the shell of an oyster, over time. The health status of oysters can be characterized using valvometry in order to obtain insights about the quality of their environment. We consider that a renewal process with four states underlies the behaviour of the studied oysters. Such a hidden process can be retrieved from a valvometric signal by assuming that some probability density function linked with this signal, is bimodal. We then compare several estimators whic
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Hie, Brian. "Stitching and sketching large-scale single-cell transcriptomic data." Thesis, Massachusetts Institute of Technology, 2019. https://hdl.handle.net/1721.1/121734.

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Thesis: S.M., Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, 2019<br>Cataloged from PDF version of thesis.<br>Includes bibliographical references (pages 57-65).<br>Researchers are generating single-cell RNA sequencing (scRNA-seq) profiles of diverse biological systems [1]-[7] and every cell type in the human body [8] at an unprecedented scale, with scRNA-seq experiments regularly profiling gene expression in hundreds of thousands or even millions of cells [9]. Leveraging this data to gain unprecedented insight into biology and disease requires
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Xu, Huan. "Controlling false positive rate in network analysis of transcriptomic data." University of Cincinnati / OhioLINK, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=ucin156267322069819.

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38

Ranjbar, Niloufar. "Integration of Transcriptomic and Proteomic Data during Nucleus Lobulation of Granulocytes." Master's thesis, Alma Mater Studiorum - Università di Bologna, 2021.

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Nucleus is the origin of most phenotypic activities in a cell. Depending on the cell type, the nucleus can appear in different forms. Mature neutrophils are granulocytic white blood cells with lobulated nucleus that enables them to perform their specialized roles like cell migration in the immune system. Quantitative temporal profiles of human granulocytic cell ensembles of DNA transcripts and proteins, that were previously collected along the process of nuclear deformation, are examined in this thesis. The general aim is to screen the cellular changes during granulocytic differentiation accom
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Battke, Florian Verfasser], and Kay [Akademischer Betreuer] [Nieselt. "Computational Methods for High-Throughput Transcriptomic Data / Florian Battke ; Betreuer: Kay Nieselt." Tübingen : Universitätsbibliothek Tübingen, 2012. http://d-nb.info/1162843306/34.

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Nadeem, Malik-Sajjad-Ahmed. "Classification with a reject-option to improve transcriptomic data based decision support systems." Paris 13, 2011. http://www.theses.fr/2011PA132012.

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L’obésité et le cancer sont des maladies complexes multifactorielles. Les données de puces à ADN représentent une source importante de connaissances pour étudier ces maladies. Le choix d’une thérapie pour lutter contre l’obésité pourrait avoir un impact élevé sur sa prévalence, mais l’utilisation de modèles prédictifs dans ce cadre reste un domaine de recherche relativement inexploré. De telles méthodes sont utilisées pour l’aide au diagnostic avec un certain succès dans le domaine du cancer, mais elles nécessitent encore des améliorations. La majorité des études de puces à ADN sont basées sur
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Wu, Mei. "Detection of aberrant events in RNA for clinical diagnostics." Thesis, Uppsala universitet, Institutionen för biologisk grundutbildning, 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-448361.

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Rare diseases are estimated to affect 3.75% of the global population, which roughly translates to 300 million affected individuals. A large proportion of patients still do not have their diagnosis and current approaches such as chromosomal microarray (CMA), whole exome sequencing (WES), and whole genome sequencing (WGS) that targets DNA and the exome aims to resolve that very first step. RNA-seq serves as a powerful approach complementing the aforementioned methods that have reached a plateau in the diagnostic yield. RNA-seq can facilitate the finding of aberrant events that appear during tran
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Koban, Martin. "Machine learning models for quantifying phenotypic signatures of cancer cells based on transcriptomic and epigenomic data." Master's thesis, Vysoké učení technické v Brně. Fakulta elektrotechniky a komunikačních technologií, 2020. http://www.nusl.cz/ntk/nusl-433123.

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S rozvojom techník pre efektívnu akvizíciu genomických dát sa jednou z kľúčových vedeckých výziev stala interpretácia výsledkov týchto experimentov v zmysluplnom biologickom kontexte. Táto práca sa zameriava na využitie informácií ukrytých v dobre charakterizovaných transkriptomických a epigenomických dátach z verejne dostupných zdrojov pre účely takejto interpretácie. Najskôr je vytvorený integrovaný súbor dát generovaných metódami DNase-seq a ATAC-seq, ktoré kvantifikujú chromatínovú dostupnosť. Tieto údaje sú doplnené verejne dostupnými výsledkami techniky RNA-seq pre kvantitatívne hodnoten
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Chauhan, Ritika. "Bioinformatics of next generation sequencing approaches : using 454 and Illumina data to look at insect genomes and transcriptomes." Thesis, University of Exeter, 2013. http://hdl.handle.net/10871/10123.

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By providing a rapid and cost effective means of generating sequencing resources for almost any organism, ‘Next generation sequencing technologies’ (NGS) have great potential to help address numerous gene and genome level questions in molecular biology. Progress in NGS is exponentially increasing sequence throughput and large scale studies in the genomics/transcriptomics of non-model organisms are becoming a reality. Therefore the main focus of the work presented in this thesis is on the analysis of the large scale non-model insect datasets generated by NGS technologies and their potential to
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Wachter, Astrid [Verfasser], Tim [Akademischer Betreuer] [Gutachter] Beißbarth, and Edgar [Gutachter] Wingender. "Data Integration of High-Throughput Proteomic and Transcriptomic Data based on Public Database Knowledge / Astrid Wachter ; Gutachter: Tim Beißbarth, Edgar Wingender ; Betreuer: Tim Beißbarth." Göttingen : Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2017. http://d-nb.info/1132336767/34.

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Jäger, Günter Verfasser], and Kay [Akademischer Betreuer] [Nieselt. "Advanced Visual Analytics Approaches for the Integrative Study of Genomic and Transcriptomic Data / Günter Jäger ; Betreuer: Kay Nieselt." Tübingen : Universitätsbibliothek Tübingen, 2016. http://d-nb.info/1164168916/34.

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Jäger, Günter [Verfasser], and Kay [Akademischer Betreuer] Nieselt. "Advanced Visual Analytics Approaches for the Integrative Study of Genomic and Transcriptomic Data / Günter Jäger ; Betreuer: Kay Nieselt." Tübingen : Universitätsbibliothek Tübingen, 2016. http://d-nb.info/1164168916/34.

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Michna, Agata [Verfasser], and Horst [Akademischer Betreuer] Zitzelsberger. "Identification of gene association networks of the cellular radiation response from time-course transcriptomic data / Agata Michna ; Betreuer: Horst Zitzelsberger." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2017. http://d-nb.info/1128594005/34.

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Schmidt, Florian [Verfasser], and Marcel Holger [Akademischer Betreuer] Schulz. "Applications, challenges and new perspectives on the analysis of transcriptional regulation using epigenomic and transcriptomic data / Florian Schmidt ; Betreuer: Marcel Holger Schulz." Saarbrücken : Saarländische Universitäts- und Landesbibliothek, 2019. http://d-nb.info/1196090173/34.

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Schmidt, Florian Verfasser], and Marcel Holger [Akademischer Betreuer] [Schulz. "Applications, challenges and new perspectives on the analysis of transcriptional regulation using epigenomic and transcriptomic data / Florian Schmidt ; Betreuer: Marcel Holger Schulz." Saarbrücken : Saarländische Universitäts- und Landesbibliothek, 2019. http://nbn-resolving.de/urn:nbn:de:bsz:291--ds-287773.

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Czerwińska, Urszula. "Unsupervised deconvolution of bulk omics profiles : methodology and application to characterize the immune landscape in tumors Determining the optimal number of independent components for reproducible transcriptomic data analysis Application of independent component analysis to tumor transcriptomes reveals specific and reproducible immune-related signals A multiscale signalling network map of innate immune response in cancer reveals signatures of cell heterogeneity and functional polarization." Thesis, Sorbonne Paris Cité, 2018. http://www.theses.fr/2018USPCB075.

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Les tumeurs sont entourées d'un microenvironnement complexe comprenant des cellules tumorales, des fibroblastes et une diversité de cellules immunitaires. Avec le développement actuel des immunothérapies, la compréhension de la composition du microenvironnement tumoral est d'une importance critique pour effectuer un pronostic sur la progression tumorale et sa réponse au traitement. Cependant, nous manquons d'approches quantitatives fiables et validées pour caractériser le microenvironnement tumoral, facilitant ainsi le choix de la meilleure thérapie. Une partie de ce défi consiste à quantifier
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