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 51 for “"Computational Pipeline"”.
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Computational Pipeline for Human Transcriptome Quantification Using RNA-seq Data
… 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 …
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DeepARG+ - A Computational Pipeline for the Prediction of Antibiotic Resistance
… such data, but there are a limited number of pipelines that enable the identification of novel ARGs belonging to diverse antibiotic classes at present. Therefore, there is a need for the development of computational pipelines that can identify these putative novel ARGs. Such pipelines should …
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Developing a Computational Pipeline for Detecting Multi-Functional Antibiotic Resistance Genes in Metagenomics Data
… in metagenomic data. In this study, we develop a computational pipeline to detect multi-functional ARGs in metagenomic data. The pipeline takes raw metagenomic data as the input and generates a list of potential multi-functional ARGs. A plot for each potential multi-functional ARG is also created, …
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Development of an Experimental and Computational Pipeline for Characterizing the Mechanical Properties and Micromechanical Environment within In Vitro 3D Printed Bone Tissue Engineered Scaffolds
… This study aims to develop an experimental and computational pipeline for mechanically characterizing 3D printed (3DP) scaffolds—Voronoi, IsoTruss, and Truncated Octahedron (TO) geometries—that will be the foundation for future studies to explore patient-specific mechanical biomarkers in these …
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RNA CoMPASS: RNA Comprehensive Multi-Processor Analysis System for Sequencing
… of this dissertation is to develop a distributed computational pipeline for processing next-generation RNA sequencing (RNA-seq) data. RNA-seq experiments generate hundreds of millions of short reads for each DNA/RNA sample. There are many existing bioinformatics tools developed for the analysis …
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Scalable Tools for High-throughput Viral Sequence Analysis
… thesis focuses on developing novel and improved computational methods for high-throughput analysis of large viral sequence datasets. I have developed a novel computational pipeline, Pipelign, to detect potentially unrelated sequences from groups of viral sequences during sequence alignment. …
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Predicting Transcatheter Aortic Valve Leaflet Thrombosis Risk Using Pre-Procedural Computed Tomography Angiogram and Computational Modeling
… pre-procedural CTA. This study presents a novel computational pipeline consisting of 1) pre-TAVR CTA reconstruction and reduced order modeling (ROM) simulations to automatically measure post-TAVR geometrical parameters, 2) a landmark-guided, intensity-based automated left ventricular segmentation …
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Computational Analysis of Viruses in Metagenomic Data
… In order to answer this question, we developed a computational pipeline, FastViromeExplorer. FastViromeExplorer leverages a pseudoalignment based approach, which is faster than the traditional alignment based approach to quickly align millions/billions of reads. Application of FastViromeExplorer …
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Subpixel multiframe registration for formation flying spacecraft
… noisy frames which have been generated by a computational pipeline designed to simulate observations that will be made by the VIrtual Super-resolution Optics with Reconfigurable Swarms (VISORS) Cubesat mission, set to be launched in 2023.
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Modeling the Performance and Resource Requirements for Gamma-Ray Telescope Signal Processing
… the buffering requirements of the data pipeline for the Advanced Particle-astrophysics Telescope gamma-ray telescope. Given the importance and stochastic arrivals of astronomical signals, it is crucial to ensure that each gamma-ray signal is fully buffered to prevent data loss. To …
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Convergence of regulatory mutations into oncogenic pathways across multiple tumor types
… functional impact. In this study, we develop a computational pipeline to identify non-coding mutational drivers across multiple tumor types. We describe the non-coding mutational profiles of 854 samples, spread across 15 tumor types, in the context of their respective tissue type-specific …
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Evolutionary Analysis of Large-Scale Genomic Changes
… the methanogens, and five mammalian orders. A computational pipeline was developed to construct distance-based gene order trees. The resulting gene order phylogeny was consistent and congruent with the sequence-based trees. It also resolved the controversial branches within these lineages. For …
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Interpreting Raman spectra using machine learning: towards a non-invasive method of characterizing single cells
… cell types. This thesis also presents a robust computational pipeline to preprocess Raman spectra, calibrate multi-modal data, and segment nuclei; an analysis of methods to increase the signal-to-noise ratio of Raman spectra; and an analysis of Raman spectral features important for predicting …
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Quantum Algorithms for Solving Differential Equations with Application to Computational Fluid Dynamics
… to transform the way solutions to large-scale computational fluid dynamics (CFD) problems are obtained. This requires the development of efficient quantum algorithms for differential equations that are classically intractable. By bridging quantum mechanics with classical numerical methods and …
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4D Ex Vivo Crispr/Cas9 Whole-Genome Screen to Identify Genes Regulating Lung Cancer Metastasis
… next generation sequencing. I created a computational pipeline to demultiplex samples and align reads to the library. I recovered genes previously implicated in lung cancer and metastasis enriched in the Primary and Metastasis samples. SPI1 was identified as the central node in network …
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Computational algorithm development for epigenomic analysis
Multiple computational algorithms were developed for analyzing ChIP-seq datasets of histone modifications. For basic ChIP-seq data processing, the problems of ambiguous short sequence read mapping and broad peak calling of diffuse ChIP-seq signals were solved by novel statistical methods. Their …
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Integration of metabolic modelling with machine learning to identify mechanisms underlying antibiotic killing
… of primary targets. Here we present a novel computational pipeline to expedite investigation of these effects: we combine computational modelling of metabolic networks with data from experimental screens on antibiotic susceptibility to identify metabolic vulnerabilities that can enhance …
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Computational Discovery of Microstructured Composites with Optimized Trade-Off between Strength and Toughness
… challenge. In this work, we propose a computational pipeline where microstructures with optimal strength and toughness trade-offs are automatically discovered and analyzed for intrinsic toughening mechanisms. Based on a fast physics-based simulator, it employs a competitive game …
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Coordination of cellular force-generation during Drosophila ventral furrow formation
… tissue contraction and folding. I developed a computational pipeline to identify and classify contraction events from live images of ventral furrow formation. Using this framework, I found heterogeneity in contraction events, both in terms of contraction intensity as well as apical area …
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Identification of common and unique stress responsive genes of Arabidopsis thaliana under different abiotic stress through RNA-Seq meta-analysis
… light and wounding. We developed a multi-step computational pipeline, which performs data downloading, preprocessing, read mapping, read counting and differential expression analyses for RNA-Seq data. We found that 5729 and 5062 genes are induced or repressed by only one type of abiotic …
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