Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 20 of 78 for “"Single-cell RNA-seq"”.
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Single cell RNA-seq analysis uncovers transcription regulation mechanisms in mouse germline cells
Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2025-08-01
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Using single-cell RNA-seq to assess the effect of common genetic variants on gene expression during development
… similar approaches have been applied to RNA sequencing (RNA-seq) data to find variants associated with expression level, called expression quantitative trait loci (eQTL). Recent advances in experimental techniques have provided an unprecedented opportunity to measure gene expression at …
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Comparison of dispersion metrics for estimating transcriptional noise in single-cell RNA-seq data and applications to cardiomyocyte biology
… burst frequency, amplitude, and variability. Single-cell RNA sequencing data analysis often focuses on comparing transcription levels. However, these analyses capture only a portion of the wealth of information conveyed by transcription. The quantification and analysis of transcriptional …
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Dynast: Inclusive and efficient quantification of metabolically labeled transcripts in single cells
Single cell RNA velocity, defined as the time derivative of gene expression, is a powerful concept that can predict the future transcriptional state of the cell. Traditionally, RNA velocity estimations relied on the distinction between spliced and unspliced mRNA in single cell RNA-seq (scRNA-seq) …
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Computational Analysis of Gene Expression Regulation from Cross Species Comparison to Single Cell Resolution
… conserved co-expression genes. Last, we analyzed single-cell RNA-seq data from monocytes to attempt to understand regulatory mechanism of innate immune system under low-grade inflammation. We identified novel subpopulations of cells treated with lipopolysaccharide (LPS), that show distinct …
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Regulation of Lung Mesenchymal Cells By Epithelial Wnt Ligands
<p>The mesenchyme comprises of heterogeneous cell populations that support neighboring structures and are integral to intercellular signaling. Despite such importance, mesenchymal cells are poorly defined morphologically and molecularly. Their signaling regulation is not well understood, lagging …
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A genome-wide, single-cell analysis of vascular smooth muscle cell plasticity
Vascular smooth muscle cells (VSMCs) possess a remarkable capacity to change phenotype in response to injury or inflammation. In healthy arteries, VSMCs exist in a contractile state, but upon vascular inflammation or injury, they can switch into an activated state, in which they downregulate the …
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TimiGP: A Computational Framework to Determine the Tumor Immune Microenvironment Associated with Prognosis and Immunotherapy Response
… designed to address this challenge. Leveraging single-cell RNA-seq (scRNA-seq) and bulk gene expression data alongside clinical information, TimiGP constructs a cell-cell interaction network that elucidates the relationship between immune cell function and relevant clinical outcomes, such as …
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LINEAGE TRACING REVEALS PAEP AS A CHEMOTHERAPY-INDUCED METASTATIC DRIVER AND EXPOSES METABOLIC VULNERABILITIES OF CIRCULATING TUMOR CELLS IN BREAST CANCER
… metastasis‐derived circulating tumor cells (CTCs), with the goal of revealing actionable vulnerabilities. I adapted a human TNBC (MDA‐MB‐231) xenograft to a clinically relevant AC regimen that produced stable disease, mirroring chemoresistant residual disease in patients. …
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Epithelial Tubular Fusion, Measuring Interconnection, and the Quest for Solving the Continuity Problem
… Although it has been well-studied how epithelial cells form tubules, it is not well understood how tubules and related epithelial micro-tissues such as spheroids and organoids interconnect with each other to form functional networks. Currently available model systems that spontaneously undergo …
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Inference of single cell profiles from histology stains with the Single-Cell omics from Histology Analysis Framework (SCHAF)
… biology involves an intricate balance between cell-intrinsic processes and interactions between cells organized in specific spatial patterns, which can be respectively captured by single-cell profiling methods, such as single-cell RNA-seq (scRNA-seq), and histology imaging data, such as …
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Applications of Machine Learning in Source Attribution and Gene Function Prediction
… source of bacterial pathogen using whole genome sequencing data, and (2) the functional annotation of genes using single- cell RNA sequencing data. This work proposes the development of a bioinformatics pipeline tailored for identifying genomic variants, including gene presence/absence and single …
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Knowledge-Guided Machine Learning for Single-Cell Regulatory Genomics
… elements coordinate gene regulation, and single-cell sequencing now enables these programs to be studied at high resolution. However, single-cell RNA-seq and ATAC-seq data are sparse and high-dimensional, making it difficult for existing methods to reliably infer TF activity and …
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THE TRANSCRIPTIONAL PROGRAM OF GOLGI BIOGENESIS
… functional stacks in a substantial cohort of cells within 10-18 hours. The structural and functional recovery of the Golgi allowed us to study transcriptomic changes associated with Golgi regeneration. Indeed, Single-cell RNA-seq of cells rebuilding the Golgi revealed coordinated induction of …
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Identification of SPINK2 as biomarker of primary chemoresistance in acute myeloid leukemia and its biochemical role in normal bone marrow.
… scaturisce da un’abnorme proliferazione delle cellule del sistema ematopoietico, chiamate blasti. Un ristretto gruppo di pazienti affetti da LAM non risponde alla terapia di induzione primaria, volta a ridurre il numero di blasti al di sotto del 5% nel midollo osseo, e sono per questo detti …
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Interpreting Deep Learning for cell differentiation. Supervised and Unsupervised models viewed through the lens of information and perturbation theory.
… the models, by identifying relevant genes for cell differentiation. We then continue to explore the rules and mechanisms behind the models from a theoretical perspective. Using information theory to explain the learning process and applying perturbation theory to transform the results into a …
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Single-cell analyses of tumor-infiltrating immune cells
… the presence of specific biomarkers that may be cellular, protein-based, or genomic in nature. Specifically, the discovery of cell-based biomarkers via the study of patient biopsies and other related samples remains a key problem due to the limited numbers of cells involved, and current …
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LINKING HISTONE LACTYLATION TO THE EPIGENETIC REPROGRAMMING OF CD4+ T REGULATORY LYMPHOCYTES IN THE TUMOR ECOSYSTEM
Tumor infiltrating regulatory T cells (TI-Tregs) exhibit a complex interplay with various cell types, including tumor cells, immune cells, and stromal cells thereby promoting tumor growth and invasion. TI-Treg are transcriptionally and epigenetically adapted to the hostile tumor microenvironment …
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Utilising Single-Cell Technology to Investigate Gene Regulation
Since the inception of single-cell sequencing in 2009, experimental and computational technologies have enabled the accurate quantification of gene expression on a cell-by-cell basis. By capturing the transcriptome of thousands of single cells within complex tissues, ranging from organoids to …
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Defining cell state regulators in cancers using single-cell analysis and CRISPR-Cas9 screening
… higher levels of plasticity. Development of single-cell profiling has had a particular impact for elucidating the composition of cell states occurring within individual tumours, and offers high-dimensional data which can be utilised for unsupervised signature extraction. The aim of this …
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