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.
Results
Showing 1 to 19 of 19 for “"pseudotime"”.
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Understanding tumor cell plasticity in spatial transcriptomics with graph attention networks and walk-based pseudotime analysis
Tumor cell plasticity in cancer is a key driver in tumor progression, heterogeneity, metastasis, and treatment resistance. Tumor cells change states from the conventionally easier to treat epithelial state to the more resistant mesenchymal state. Understanding the transition dynamics of these …
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Decoding Dynamic Gene Regulation in Hair Cell Development and Regeneration
… of gene-regulatory relationships across pseudotime-ordered single-cell trajectories. I first show that combining supervised deep learning with joint probability matrices of pseudotime-lagged trajectories allows the neural network to overcome important limitations of ordinary Granger …
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Heterogeneity in vascular smooth muscle cell gene expression and its association with clonal proliferation in models of vascular disease
… showed contractile marker downregulation over pseudotime, corresponding to increased expression of Sca1 and proliferation marker Ki67. Moreover, Ki67+Sca1+ VSMCs were identified post-CL via flow cytometry, indicating that Sca1+ VSMCs indeed expand in disease. Investigation of candidate genes …
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Investigating the coordination of germline stem cell fate by ecdysone signaling and BMP signaling in the Drosophila ovary
… Network Inference and Cluster (SCENIC), pseudotime analysis, and single cell velocity (scVelo) to help identify other potential common targets of ecdysone signaling and BMP signaling. Our results suggest that ecdysone signaling and BMP signaling converge on a common point of regulation to …
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Understanding transcriptional regulation through computational analysis of single-cell transcriptomics
… predictor of gene interactions using pseudotime-ordered single-cell expression data. In addition, I have obtained novel biological insights by analysing single-cell RNAseq data from the epiblast stem cells reprogramming and the leukaemia systems. Three different driver genes, namely …
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Single-cell transcriptomics identifies key components in metabolic pathways of drug perturbed activated CD4+ T cells
… cell populations. Then, I characterise distinct pseudotime trajectories representing the progression from naïve to effector memory cells at each time point. With linear models, I identify the immune-related disease genes regulated by both drug effects and the effector status of cells. Leveraging …
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A Higher Order Accurate Finite Element Method for Viscous Compressible Flows
… solved using an approximate Newton method with a pseudotime term. The resulting linear system is solved using the Generalized Minimum Residual algorithm with block diagonal preconditioning. The exact solutions of Ringleb flow and Couette flow are used to quantitatively establish the spatial …
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Simulation of nonisothermal and time-dependent viscoelastic flows
… variations on the stress in the fluid. The pseudotime method developed by Crochet and Naghdi (1978) and by Sarti (1977) is used to obtain thermodynamically consistent constitutive equations for the internal energy, the stress, and the heat flux vector. Fourier"s Jaw is assumed for the …
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Scalable Machine Learning Methods For The Analysis Of Single-Cell Transcriptomics And Multiomics Data
… for our methods, such as improving downstream pseudotime analyses using batch correction and identifying immune response biomarkers to an H1N1 vaccine.
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Biophysical dynamical priors in machine learning
… of single-cell resolution quantities such as pseudotime. Finally, Chapter 6 presents a conclusion on all the work conducted along with directions for future work.
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Understanding Development of Human Immunity One Cell at a Time
… a novel strategy to leverage scVDJ-seq data in pseudotime trajectory inference. The application of Dandelion improved the alignment of human thymic development trajectories of double positive T cells to mature single-positive CD4/CD8 T cells, and provided novel insights into the origins of human …
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Gene-regulatory circuitry of disease risk and progression
… developing methods for building disease-driven pseudotime trajectories and mapping transcriptomic changes along paths to neuronal senescence driven by DNA damage accumulation.
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Algorithms for regulatory network inference and experiment planning in systems biology
… are moderate. Techniques that do not require pseudotime-ordered cells are generally more accurate. Based on these results, I present recommendations to end users of GRN inference methods. BEELINE will aid the development of gene regulatory network inference algorithms. (iv) Based on the …
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Not Black and White: BMP Signaling Drives Melanocyte Differentiation Downstream of Stem Cell Activation
… in their differentiating progeny. ScRNA-seq and pseudotime analysis of Bmpr1a null cells indicated a block in the differentiation program just downstream of the early McCP stage, and I detected further signs of melanocyte immaturity using immunofluorescence and electron microscopy analyses. …
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Exploring the transcriptomic landscape of the Drosophila melanogaster embryonic salivary gland.
… machinery far earlier than previously reported. Pseudotime analysis enabled the identification of temporally controlled expression of transcription factors and adhesion molecules in time with morphogenetic movement of the tissue.
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Trophoblast specification and differentiation potential in early human and non-human primate embryogenesis
… development, I generated a continuous pseudotime trajectory of human trophoblast development from zygote to mid-gestation using publicly available single cell RNA sequencing datasets. The results from this analysis showed that core transcription factors controlling trophectoderm, …
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UNVEILING HUMAN NATURAL KILLER CELLS ONTOGENESIS IN HOMEOSTATIC CONDITIONS AND DURING THE IMMUNE RECONSTITUTION AFTER HAPLOIDENTICAL HEMATOPOIETIC STEM CELL TRANSPLANTATION
… a transcriptomic point of view and to perform a pseudotime trajectory analysis that could infer differentiation trajectories based on transcriptional similarities. Last, a consistent part of this study was carried out on HSCT patients, a unique setting reported as a reliable model to study the …
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Cellular and Molecular Mechanisms Governing Intramuscular Fat Development and Growth in Cattle
… SVF. Gene set variation analysis (GSVA) and pseudotime trajectory analysis showed that C1 and C3 represented more differentiated APCs, characterized by elevated expression of adipogenesis-related genes such as PPARG, ADAM12, and PPARGC1A. Together, the findings from the second study reveal …
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Bayesian modelling and sampling strategies for ordering and clustering problems with a focus on next-generation sequencing data
This thesis presents novel methods for ordering and clustering problems. The first two parts focus on the development of models and sampling strategies specifically tailored for next-generation sequencing data. Most high-throughput measurements for single-cell data are destructive, resulting in the …