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Relevant bibliographies by topics / Single cell mRNA sequencing / Dissertations / Theses

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Dissertations / Theses on the topic 'Single cell mRNA sequencing'

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Published: 25 January 2025

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1

Johnson, Travis Steele. "Integrative approaches to single cell RNA sequencing analysis." The Ohio State University, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=osu1586960661272666.

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2

Borgström, Erik. "Technologies for Single Cell Genome Analysis." Doctoral thesis, KTH, Genteknologi, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-181059.

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During the last decade high throughput DNA sequencing of single cells has evolved from an idea to one of the most high profile fields of research. Much of this development has been possible due to the dramatic reduction in costs for massively parallel sequencing. The four papers included in this thesis describe or evaluate technological advancements for high throughput DNA sequencing of single cells and single molecules. As the sequencing technologies improve, more samples are analyzed in parallel. In paper 1, an automated procedure for preparation of samples prior to massively parallel sequen

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3

La, Forest Divonne Sébastien De. "Caractérisation constitutive et en condition d'infection bactérienne des populations hémocytaires par une approche intégrative cytologiques, transcriptomiques et fonctionnelles chez l'huitre creuse Crassostrea (Magallana) gigas." Electronic Thesis or Diss., Perpignan, 2024. http://www.theses.fr/2024PERP0025.

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L'huître du Pacifique, Crassostrea (Magallana) gigas, est un mollusque bivalve d'une importance écologique et économique majeure, et constitue désormais une espèce modèle émergente dans l'étude de l'immunité innée des bivalves. Ces dernières années, les élevages d'huîtres ont été confrontés à des épisodes de mortalités massives, exacerbés par le changement climatique et les activités anthropiques. Ces mortalités, bien que multifactorielles, partagent un point commun : la capacité des pathogènes (virus et bactéries) à échapper aux défenses immunitaires des huîtres, entraînant des septicémies so

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4

Raoux, Corentin. "Review and Analysis of single-cell RNA sequencing cell-type identification and annotation tools." Thesis, KTH, Skolan för kemi, bioteknologi och hälsa (CBH), 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-297852.

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Single-cell RNA-sequencing makes possible to study the gene expression at the level of individual cells. However, one of the main challenges of the single-cell RNA-sequencing analysis today, is the identification and annotation of cell types. The current method consists in manually checking the expression of genes using top differentially expressed genes and comparing them with related cell-type markers available in scientific publications. It is therefore time-consuming and labour intensive. Nevertheless, in the last two years,numerous automatic cell-type identification and annotation tools w

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5

Kindblom, Marie, and Hakim Ezeddin Al. "Phylogenetic fatemapping: estimating allelic dropout probability in single cell genomic sequencing." Thesis, KTH, Skolan för datavetenskap och kommunikation (CSC), 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-186453.

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Single-cell genomic sequencing is a rapidly developing field that will play a vital role in human biology and science in the future. As of now, next-generation sequencing is accelerating in speed and decreasing in cost more quickly than Moore's law. Studies have shown that all cells in the human body have with very high probability a unique genomic signature, due to the somatic evolution which have accumulated mutations starting from the zygotic state. The possible reconstruction of phylogenetic lineage trees would be of vital importance to several fields in medicine, such as the stem cell res

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6

Henao, Diaz Emanuela. "Towards single-cell exome sequencing with spatial resolution in tissue sections." Thesis, KTH, Skolan för bioteknologi (BIO), 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-150564.

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7

Evrony, Gilad David. "Single-cell Sequencing Studies of Somatic Mutation in the Human Brain." Thesis, Harvard University, 2013. http://dissertations.umi.com/gsas.harvard:10747.

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A major unanswered question in neuroscience is whether there exists genomic variability between individual neurons of the brain, contributing to functional diversity or to an unexplained burden of neurologic disease. To address this question, we developed methods to amplify genomes of single neurons from human brains, achieving >80% genome coverage of single-cells and allowing study of a wide-range of somatic mutation types.

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8

Ke, Rongqin. "Detection and Sequencing of Amplified Single Molecules." Doctoral thesis, Uppsala universitet, Molekylära verktyg, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-183141.

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Improved analytical methods provide new opportunities for both biological research and medical applications. This thesis describes several novel molecular techniques for nucleic acid and protein analysis based on detection or sequencing of amplified single molecules (ASMs). ASMs were generated from padlock probe assay and proximity ligation assay (PLA) through a series of molecular processes. In Paper I, a simple colorimetric readout strategy for detection of ASMs generated from padlock probe assay was used for highly sensitive detection of RNA virus, showing the potential of using padlock pro

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Tu, Ang A. (Ang Andy). "Recovery of T cell receptor variable sequences from 3' barcoded single-cell RNA sequencing libraries." Thesis, Massachusetts Institute of Technology, 2020. https://hdl.handle.net/1721.1/127888.

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Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biological Engineering, May, 2020<br>Cataloged from PDF version of thesis.<br>Includes bibliographical references (pages 107-112).<br>Heterogeneity of the immune system has increasingly necessitated the use of high-resolution techniques, including flow cytometry, RNA-seq, and mass spectrometry, to decipher the immune underpinnings of various diseases such as cancer and autoimmune disorders. In recent years, high-throughput single-cell RNA sequencing (scRNA-seq) has gained popularity among immunologists due to its ability to e

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10

Lefebvre, Keely. "Resolving the Taxonomy and Phylogenetics of Benthic Diatoms from Single Cell Sequencing." Thesis, Université d'Ottawa / University of Ottawa, 2016. http://hdl.handle.net/10393/34553.

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Benthic diatoms are often used as indicators of water quality and past environmental conditions. This depends entirely on a reliable taxonomic system. With the advent of DNA techniques, genetic analyses can now be used in tandem with traditional microscopy in order to improve taxonomy and determine evolutionary relationships. This thesis examined a speciose genus of diatoms Neidium (> 300 species) and, using sequence data from molecular markers as well as traditional morphological analyses, investigated phylogenetic relationships. Fresh benthic samples from aquatic ecosystems in Eastern North

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11

Ziegenhain, Christoph [Verfasser], and Wolfgang [Akademischer Betreuer] Enard. "Improving & applying single-cell RNA sequencing / Christoph Ziegenhain ; Betreuer: Wolfgang Enard." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2017. http://d-nb.info/1151818372/34.

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Vieth, Beate [Verfasser], and Wolfgang [Akademischer Betreuer] Enard. "Statistical power analysis for single-cell RNA-sequencing / Beate Vieth ; Betreuer: Wolfgang Enard." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2020. http://d-nb.info/1225683033/34.

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13

Ross, Edith. "Inferring tumour evolution from single-cell and multi-sample data." Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/274604.

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Tumour development has long been recognised as an evolutionary process during which cells accumulate mutations and evolve into a mix of genetically distinct cell subpopulations. The resulting genetic intra-tumour heterogeneity poses a major challenge to cancer therapy, as it increases the chance of drug resistance. To study tumour evolution in more detail, reliable approaches to infer the life histories of tumours are needed. This dissertation focuses on computational methods for inferring trees of tumour evolution from single-cell and multi-sample sequencing data. Recent advances in single-ce

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Svensson, Valentine. "Probabilistic modelling of cellular development from single-cell gene expression." Thesis, University of Cambridge, 2017. https://www.repository.cam.ac.uk/handle/1810/267937.

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The recent technology of single-cell RNA sequencing can be used to investigate molecular, transcriptional, changes in cells as they develop. I reviewed the literature on the technology, and made a large scale quantitative comparison of the different implementations of single cell RNA sequencing to identify their technical limitations. I investigate how to model transcriptional changes during cellular development. The general forms of expression changes with respect to development leads to nonparametric regression models, in the forms of Gaussian Processes. I used Gaussian process models to inv

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Subramanian, Parimalam Sangamithirai. "Dissecting gene expression of single cells ｗith reduced perturbation". Doctoral thesis, Kyoto University, 2021. http://hdl.handle.net/2433/263616.

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Kinchen, James. "Intestinal stromal cell types in health and inflammatory bowel disease uncovered by single-cell transcriptomics." Thesis, University of Oxford, 2017. http://ora.ox.ac.uk/objects/uuid:1bf9d8f0-6d09-46f5-9d1e-3c9e0b826618.

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Colonic stromal cells provide critical structural support but also regulate immunity, tolerance and inflammatory responses in the mucosa. Substantial variability and plasticity of mucosal stromal cells has been reported but a paucity of distinct marker genes exist to identify distinct cell states. Here single-cell RNA-sequencing is used to document heterogeneity and subtype specific markers of individual colonic stromal cells in human and mouse. Marker-free transcriptional clustering of fibroblast-like cells derived from healthy human tissue reveals distinct populations corresponding to myofib

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Chwastek, Damian. "Elucidating the Contribution of Stroke-Induced Changes to Neural Stem and Progenitor Cells Associated with a Neuronal Fate." Thesis, Université d'Ottawa / University of Ottawa, 2021. http://hdl.handle.net/10393/41839.

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Following stroke there is a robust increase in the proliferation of neural stem and progenitor cells (NSPCs) that ectopically migrate from the subventricular zone (SVZ) to surround the site of damage induced by stroke (infarct). Previous in vivo studies by our lab and others have shown that a majority of migrating NSPCs when labelled prior to stroke become astrocytes surrounding the infarct. In contrast, our lab has shown that the majority of NSPCs when labelled after stroke become neurons surrounding the infarct. This thesis aims to elucidate the contributions of intrinsic changes that can al

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Reiser, Anita [Verfasser], and Joachim [Akademischer Betreuer] Rädler. "Single-cell time courses of mRNA transport and translation kinetics / Anita Reiser ; Betreuer: Joachim Rädler." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2019. http://d-nb.info/1214593194/34.

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CAPRIOLI, CHIARA. "INTEGRATED SINGLE-CELL MUTATION, GENE EXPRESSION AND ISOFORM ANALYSIS TO DECONVOLVE ACUTE MYELOID LEUKEMIA HETEROGENEITY." Doctoral thesis, Università degli Studi di Milano, 2022. https://hdl.handle.net/2434/946325.

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Acute myeloid leukemia (AML) is an aggressive cancer arising from the hematopoietic stem cell (HSC). As other tumor types, AMLs are characterized by multiple and interconnected levels of intra-tumor heterogeneity, including genetic (DNA mutations), phenotypic (transcriptional patterns) and ecological (interactions with host immune-cells) diversity. Emerging evidence suggest that intra-tumor heterogeneity impacts directly on leukemogenesis, disease prognosis and sensitivity/resistance to available treatments. How the different layers of intra-tumoral heterogeneity interact with each other and s

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20

Ma, Sai. "Microfluidics for Genetic and Epigenetic Analysis." Diss., Virginia Tech, 2017. http://hdl.handle.net/10919/78187.

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Microfluidics has revolutionized how molecular biology studies are conducted. It permits profiling of genomic and epigenomic features for a wide range of applications. Microfluidics has been proven to be highly complementary to NGS technology with its unique capabilities for handling small volumes of samples and providing platforms for automation, integration, and multiplexing. In this thesis, we focus on three projects (diffusion-based PCR, MID-RRBS, and SurfaceChIP-seq), which improved the sensitivities of conventional assays by coupling with microfluidic technology. MID-RRBS and SurfaceChI

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21

MAHMOUD, NADY ABDELMOEZ ATTA. "On-chip Electrophoretic Fractionation of Cytoplasmic and Nuclear RNA from Single Cells." Kyoto University, 2019. http://hdl.handle.net/2433/244546.

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22

Hu, Bo. "Analysis of cellular drivers of zebrafish heart regeneration by single-cell RNA sequencing and high-throughput lineage tracing." Doctoral thesis, Humboldt-Universität zu Berlin, 2021. http://dx.doi.org/10.18452/23324.

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Das Herz eines Zebrafishs ist bemerkenswert, da es sich nach einer Verletzung vollständig regenerieren kann. Der Regenerationsprozess wird von Fibrose begleitet - der Bildung von überschüssigem Gewebe der extrazellulären Matrix (ECM). Anders als bei Säugetieren ist die Fibrose im Zebrafish nur transient. Viele Signalwege wurden identifiziert, die an der Herzregeneration beteiligt sind. Allerdings sind die Zelltypen, insbesondere Nicht-Kardiomyozyten, die für die Regulation des Regenerationsprozesses verantwortlich sind, weitgehend unbekannt. In dieser Arbeit haben wir systematisch alle Zelltyp

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Cherbonneau, Francois. "Development of new engineering methodologies for cell sequencing landscape : unbiased mRNA sampling of living cells by TRanscriptomic Analysis Captured in Extracellular vesicles (TRACE)." Thesis, Université de Paris (2019-....), 2021. https://wo.app.u-paris.fr/cgi-bin/WebObjects/TheseWeb.woa/wa/show?t=4387&f=28882.

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L’Hétérogénéité cellulaire et les expressions génétiques fluctuantes dans un microenvironnement spécifique restent mal comprises. Ainsi, afin d’apporter un début de réponse à toutes ces questions, beaucoup de paradigmes scientifiques ont été développés, permettant de toujours repousser plus loin les limites du possible. Ainsi, l'objectif de ce premier projet de thèse fut de développer une méthode innovante pour l'analyse épigénétique multiplexée de cellules à une résolution cellulaire unique. En reliant la protéine transposon Tn5 à des anticorps ciblant des facteurs épigénétiques clés, il pour

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24

El, Bardisy Shaheer [Verfasser]. "Development of a High-Throughput Single-Cell Sequencing Platform for the Discovery of Shared-Antigen and Neoepitope-Specific T-Cell Receptors / Shaheer El Bardisy." Mainz : Universitätsbibliothek Mainz, 2020. http://d-nb.info/1211519929/34.

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25

Tatsuoka, Hisato. "Single-cell Transcriptome Analysis Dissects the Replicating Process of Pancreatic Beta Cells in Partial Pancreatectomy Model." Doctoral thesis, Kyoto University, 2021. http://hdl.handle.net/2433/263543.

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Lu, Sijia. "Label-Free Optical Imaging of Chromophores and Genome Analysis at the Single Cell Level." Thesis, Harvard University, 2012. http://dissertations.umi.com/gsas.harvard:10563.

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Since the emergence of biology as a quantitative science in the past century, a lot of biological discoveries have been driven by milestone technical advances such as X-ray crystallography, fluorescence microscopy and high-throughput sequencing. Fluorescence microscopy is widely used to explore the nanoscale cellular world because of its superb sensitivity and spatial resolution. However, many species (e.g. lipids, small proteins) are non-fluorescent and are difficult to label without disturbing their native functions. In the first part of the dissertation, we explore using three different con

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Vuong, Nhung. "Molecular Mechanisms by Which Estrogen Causes Ovarian Epithelial Cell Dysplasia." Thesis, Université d'Ottawa / University of Ottawa, 2018. http://hdl.handle.net/10393/37286.

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The initiating events of ovarian cancer remain unknown, but an established risk factor is use of estrogen therapy by post-menopausal women where there is a positive correlation between duration of use and risk for disease. Mouse models of ovarian cancer have shown that exposure to exogenous 17β-estradiol (E2) accelerates tumour onset so this study aims to investigate the E2 signalling mechanisms responsible for sensitizing ovarian epithelial cells to transformation. By developing model systems that are responsive to E2 manipulation, we showed that E2 induces the formation of epithelial dysplas

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Hu, Bo [Verfasser]. "Analysis of cellular drivers of zebrafish heart regeneration by single-cell RNA sequencing and high-throughput lineage tracing / Bo Hu." Berlin : Humboldt-Universität zu Berlin, 2021. http://nbn-resolving.de/urn:nbn:de:kobv:11-110-18452/24021-9.

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29

Sarma, Mimosa. "Microfluidic platforms for Transcriptomics and Epigenomics." Diss., Virginia Tech, 2019. http://hdl.handle.net/10919/90294.

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A cell, the building block of all life, stores a plethora of information in its genome, epigenome, and transcriptome which needs to be analyzed via various Omic studies. The heterogeneity in a seemingly similar group of cells is an important factor to consider and it could lead us to better understand processes such as cancer development and resistance to treatment, fetal development, and immune response. There is an ever growing demand to be able to develop more sensitive, accurate and robust ways to study Omic information and to analyze subtle biological variation between samples even with l

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Ferraioli, Anna. "Comparison of cell types across life cycle stages of the hydrozoan Clytia hemisphaerica." Electronic Thesis or Diss., Sorbonne université, 2022. http://www.theses.fr/2022SORUS497.

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L'Hydrozoaire Clytia hemisphaerica présente un cycle de vie triphasique, typique des hydrozoaires, comprenant une colonie de polypes à propagation végétative et une forme nageant librement, la méduse qui est se reproduisent de façon sexuée. Les méduses mâles et femelles se reproduisent quotidiennement, déclenchées par la lumière et environ un jour après la fécondation, une larve planula ciliée se forme. Après trois jours, la planula se fixe sur le substrat et se métamorphose pour donner naissance à un polype fondateur de la colonie, destiné pour l’alimentation, le gastrozooïde. La colonie se p

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STEINFELDER, ROBERT SEBASTIAN. "Development and implementation of novel applications of massively parallel sequencing in precision medicine." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2016. http://hdl.handle.net/10281/114589.

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Next-generation sequencing (NGS) based on “sequencing by synthesis”, such as Illumina’s MiSeq, NextSeq500 or HiSeq instruments has reached a state where consistency, throughput and quality make it a mature technology to use for cancer genome research, such as single-cell sequencing or in clinical diagnostics. Within the scope of this thesis, we designed and tested three protocols to mobilise high-throughput sequencing for precision medicine to provide optimal solutions for doctors to help with understanding, diagnosing and determining states of human cancer cells. Targeted re-sequencing of cli

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32

Kuut, Gunnar [Verfasser], and Veit [Akademischer Betreuer] Hornung. "Using RNA barcoding and sequencing to study cellular differentiation on a single-cell and population level / Gunnar Kuut ; Betreuer: Veit Hornung." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2021. http://d-nb.info/123801707X/34.

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Reddy, Devulapally Praneeth [Verfasser]. "High-throughput sequencing of human B cell receptor repertoires at single-cell level with preservation of the native antibody heavy and light chain pairs / Praneeth Reddy Devulapally." Berlin : Freie Universität Berlin, 2017. http://d-nb.info/1143596021/34.

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34

Muench, David. "Gfi1-controlled transcriptional circuits in normal and malignant hematopoiesis." University of Cincinnati / OhioLINK, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1553250015825734.

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Genga, Ryan M. "Towards Understanding the Molecular Basis of Human Endoderm Development Using CRISPR-Effector and Single-Cell Technologies." eScholarship@UMMS, 2019. https://escholarship.umassmed.edu/gsbs_diss/1008.

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The definitive endoderm gives rise to several specialized organs, including the thymus. Improper development of the definite endoderm or its derivatives can lead to human disease; in the case of the thymus, immunodeficiency or autoimmune disorders. Human pluripotent stem cells (hPSCs) have emerged as a system to model human development, as study of their differentiation allows for elucidation of the molecular basis of cell fate decisions, under both healthy and impaired conditions. Here, we first developed a CRISPR-effector system to control endogenous gene expression in hPSCs, a novel approac

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Chen, Huiyi. "System-Wide Studies of Gene Expression in Escherichia coli by Fluorescence Microscopy and High Throughput Sequencing." Thesis, Harvard University, 2011. http://dissertations.umi.com/gsas.harvard:10044.

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Gene expression is a fundamental process in the cell and is made up of two parts – the information flow from DNA to RNA, and from RNA to protein. Here, we examined specific sub-processes in Escherichia coli gene expression using newly available tools that permit genome-wide analysis. We begin our studies measuring mRNA and protein abundances in single cells by single-molecule fluorescence microscopy, and then focus our attention to studying RNA generation and degradation by high throughput sequencing. The details of the dynamics of gene expression can be observed from fluctuations in mRNA and

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Lavagi, Ilaria Verfasser], and Eckhard [Akademischer Betreuer] [Wolf. "Analysis of blastomere of bovine embryos during genome activation by evaluation of single-cell RNA sequencing data / Ilaria Lavagi ; Betreuer: Eckhard Wolf." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2018. http://d-nb.info/1167160541/34.

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Lee, Jiyoung. "Computational Analysis of Gene Expression Regulation from Cross Species Comparison to Single Cell Resolution." Diss., Virginia Tech, 2020. http://hdl.handle.net/10919/99878.

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Gene expression regulation is dynamic and specific to various factors such as developmental stages, environmental conditions, and stimulation of pathogens. Nowadays, a tremendous amount of transcriptome data sets are available from diverse species. This trend enables us to perform comparative transcriptome analysis that identifies conserved or diverged gene expression responses across species using transcriptome data. The goal of this dissertation is to develop and apply approaches of comparative transcriptomics to transfer knowledge from model species to non-model species with the hope that s

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Reinsborough, Calder. "Search for Novel DNA Modifications in Saccharomyces cerevisiae mtDNA using Single Molecule Real Time Sequencing and Effects of Mitochondrial Metabolic Dynamics on Gene Expression." Thesis, Icahn School of Medicine at Mount Sinai, 2014. http://pqdtopen.proquest.com/#viewpdf?dispub=1569125.

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<p> In the past five years, Single Molecule Real Time (SMRT) sequencing technology has been found to be a reliable indicator of certain epigenetic modifications in bacterial genomes. The genome of the model organism <i>Saccharomyces cerevisiae</i> has long been thought to be free of DNA level modification, but literature surrounding this subject is conflicting. Additionally, the mitochondria of <i>S. cerevisiae</i> control the transition between three distinct chronological life phases – exponential, postdiauxic, and stationary - as defined by their main metabolic processes. This study a

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Petrany, Michael J. "Consequences of Cell Fusion and Multinucleation for Skeletal Muscle Development and Disease." University of Cincinnati / OhioLINK, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1595847866440328.

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Wu, Zhiyuan [Verfasser], Lars [Akademischer Betreuer] Mägdefessel, Hendrik [Gutachter] Sager, and Lars [Gutachter] Mägdefessel. "Single-Cell RNA Sequencing Analysis Revealed Cellular Heterogeneity of Human Abdominal Aortic Aneurysm / Zhiyuan Wu ; Gutachter: Hendrik Sager, Lars Mägdefessel ; Betreuer: Lars Mägdefessel." München : Universitätsbibliothek der TU München, 2021. http://d-nb.info/1240384114/34.

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Hirabayashi, Shigeki. "APOBEC3B is preferentially expressed at the G2/M phase of cell cycle." Doctoral thesis, Kyoto University, 2021. http://hdl.handle.net/2433/264663.

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京都大学<br>新制・課程博士<br>博士(医学)<br>甲第23382号<br>医博第4751号<br>新制||医||1052(附属図書館)<br>京都大学大学院医学研究科医学専攻<br>(主査)教授伊藤貴浩, 教授滝田順子, 教授江藤浩之<br>学位規則第4条第1項該当<br>Doctor of Medical Science<br>Kyoto University<br>DFAM

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Teufel, Lotte. "Cyclins and their roles in cell cycle progression, transcriptional regulation and osmostress adaptation in Saccharomyces cerevisiae. A transcriptome-wide and single cell approach." Doctoral thesis, Humboldt-Universität zu Berlin, 2020. http://dx.doi.org/10.18452/21205.

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Der eukaryotische Zellzyklus ist ein streng regulierter Prozess, für dessen zeitlichen Ablauf unter anderem oszillierende Genexpression notwendig ist. Die Regulation und die zeitliche Koordination des Zellzyklus sind nach wie vor fundamentale Fragen der Zellbiologie. Spezifische Ereignisse, wie DNA Replikation und Zellkernteilung, können vier Zellzyklusphasen zugeordnet werden, welche durch Cyclin-abhängige Kinasen, Cycline und deren Inhibitoren reguliert werden. Während in Saccharomyces cerevisiae Cyclin-abhängige Kinasen (Cdc28, Pho85) über den gesamten Zellzyklus zu Verfügung stehen, wer

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Yuan, Xiao. "Graph neural networks for spatial gene expression analysis of the developing human heart." Thesis, Uppsala universitet, Institutionen för biologisk grundutbildning, 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-427330.

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Single-cell RNA sequencing and in situ sequencing were combined in a recent study of the developing human heart to explore the transcriptional landscape at three developmental stages. However, the method used in the study to create the spatial cellular maps has some limitations. It relies on image segmentation of the nuclei and cell types defined in advance by single-cell sequencing. In this study, we applied a new unsupervised approach based on graph neural networks on the in situ sequencing data of the human heart to find spatial gene expression patterns and detect novel cell and sub-cell ty

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Sivertsson, Åsa. "Detection and analysis of genetic alterations in normal skin and skin tumours." Doctoral thesis, KTH, Biotechnology, 2002. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-3432.

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<p>The investigation of genetic alterations in cancer-relatedgenes is useful for research, prognostic and therapeuticpurposes. However, the genetic heterogeneity that often occursduring tumour progression can make correct analysischallenging. The objective of this work has been to develop,evaluate and apply techniques that are sufficiently sensitiveand specific to detect and analyse genetic alterations in skintumours as well as in normal skin.</p><p>Initially, a method based on laser-assisted microdissectionin combination with conventional dideoxy sequencing wasdeveloped and evaluated for the

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LUONGO, RAFFAELE. "TOWARDS PATIENT-SPECIFIC MODELS IN HIGH GRADE SEROUS OVARIAN CANCER (HGSOC): LINKING EPIGENETIC TRACING OF CELL OF ORIGIN WITH ACTIONABLE ORGANOID MODELS." Doctoral thesis, Università degli Studi di Milano, 2021. http://hdl.handle.net/2434/883835.

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Ovarian Cancer (OC) is a major cause of cancer-related mortality, due to the late-stage diagnosis and failure of surgery and chemotherapy to fully eradicate the disease, that is reflected in a high rate of tumor relapse after treatments. Patients with high-grade serous ovarian cancer (HGSOC), representing the largest majority of OC (~70%), have not experienced significant improvement in overall survival in last decades (1), pointing to the acute need to identify new predictive biomarkers and therapeutic targets for clinical settings. This unresolved emergency derives from our poor understandi

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Buchet, Samuel. "Vérification formelle et apprentissage logique pour la modélisation qualitative à partir de données single-cell." Thesis, Ecole centrale de Nantes, 2022. http://www.theses.fr/2022ECDN0011.

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La compréhension des mécanismes cellulaires à l’œuvre au sein des organismes vivants repose généralement sur l’étude de leur expression génétique. Cependant, les gènes sont impliqués dans des processus de régulation complexes et leur mesureest difficile à réaliser. Dans ce contexte, la modélisation qualitative des réseaux de régulation génétique vise à établir la fonction de chaque gène à partir de la modélisation discrète d’un réseau d’interaction dynamique. Dans cette thèse, nous avons pour objectif de mettre en place cette approche de modélisation à partir des données de séquençage single-c

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Bampalikis, Dimitrios. "Recognizing biological and technical differences in scRNAseq : A comparison of two protocols." Thesis, Uppsala universitet, Institutionen för biologisk grundutbildning, 2018. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-366169.

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Recent advances in sequencing technology have given access to information extracted on a single cell level. Single cell RNA sequencing enables for transcriptomes to be sequenced, allowing for studies within and between cell types. A recently developed protocol, based on Smart-seq2, and the Proximity ligation essay, allows for the detection of protein data from single cells, in parallel with RNA. The combination of the transcriptomic and proteomic data will enhance researchers’ ability to explore cell states. In this study, we are comparing a new pulldown protocol with the widely-used Smart-seq

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Sandberg, Julia. "Massively parallel analysis of cells and nucleic acids." Doctoral thesis, KTH, Genteknologi, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-45671.

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Recent proceedings in biotechnology have enabled completely new avenues in life science research to be explored. By allowing increased parallelization an ever-increasing complexity of cell samples or experiments can be investigated in shorter time and at a lower cost. This facilitates for example large-scale efforts to study cell heterogeneity at the single cell level, by analyzing cells in parallel that also can include global genomic analyses. The work presented in this thesis focuses on massively parallel analysis of cells or nucleic acid samples, demonstrating technology developments in th

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Weinberger, Michael. "Epicardial heterogeneity during zebrafish heart development." Thesis, University of Oxford, 2017. http://ora.ox.ac.uk/objects/uuid:3f26b933-5f17-4fe3-bd86-9211af69a558.

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The epicardium, a cell layer enveloping the heart muscle, drives embryonic heart development and heart repair in the adult zebrafish. Previous studies found the epicardium to consist of multiple cell populations with distinct phenotypes and functions. Here, I investigated epicardial heterogeneity in the developing zebrafish heart, focusing on the developmental gene program that is also reactivated during adult heart regeneration. Transcription factor 21 (Tcf21), T-box 18 (Tbx18) and Wilms' tumor suppressor 1b (Wt1b) are often used interchangeably to identify the zebrafish epicardium. Analyzing

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