Colombia | Trabajo de grado - Maestría

A computational methodology for the generation of genomic maps from fluoroscanning images

dc.contributorHernandez Ortiz, Juan Pablo
dc.contributorCrs-Tid Center for Research and Surveillance of Tropical and Infectious Diseases
dc.contributorCeballos Arroyo, Alberto Mario [0000-0002-4883-5440]
dc.contributor_zL4pEkAAAAJ
dc.creatorCeballos-Arroyo, Alberto Mario
dc.date.accessioned2023-01-31T15:49:30Z
dc.date.accessioned2023-06-07T00:08:28Z
dc.date.available2023-01-31T15:49:30Z
dc.date.available2023-06-07T00:08:28Z
dc.date.created2023-01-31T15:49:30Z
dc.date.issued2022
dc.identifierhttps://repositorio.unal.edu.co/handle/unal/83214
dc.identifierUniversidad Nacional de Colombia
dc.identifierRepositorio Institucional Universidad Nacional de Colombia
dc.identifierhttps://repositorio.unal.edu.co/
dc.identifier.urihttps://repositorioslatinoamericanos.uchile.cl/handle/2250/6651760
dc.description.abstractFluoroscanning is a novel system for quickly generating genomic maps. Unlike preceding systems like optical mapping and nanocoding, Fluoroscanning relies only on the intensity signals produced by dye fluorochromes when bound to DNA nucleotides, which we deem Fluoroscans. As part of this work, we wanted to develop and evaluated a fast digital image processing pipeline for extracting Fluoroscan signals from fluorescence microscopy images, to devise and implement a parallel and highly optimized algorithm for simulating the physical principles behind Fluoroscanning, and to guide laboratory experiments using such a tool in order to enable the generation of genomic maps through alignment algorithms. As a result of our work, we were able to set up a workflow in which real Fluoroscans extracted from digital images were used to adjust the parameters of a Monte Carlo simulation of Fluoroscanning which was then leveraged to guide further laboratory experiments and to generate a synthetic human-genome-scale dataset which will enable the development of signal alignment algorithms for genomic map generation.
dc.description.abstractEl Fluoroscanning es un sistema novedoso para la generación rápida de mapas genómicos. A diferencia de sistemas anteriores como el optical mapping y el nanocoding, el Fluoroscanning solo se basa en la intensidad de las señales (que llamamos Fluoroscans) producidas por fluorocromos de tinte cuando se adhieren a nucleótidos de ADN. Como parte de este trabajo, se desarrolla y se evalúa una serie de pasos que incluyen procesamiento de imágenes para extraer señales Fluoroscan de manera rápida a partir de imágenes de microscopía de fluorescencia, un algoritmo paralelo y altamente optimizado para simular los principios físicos detrás del Fluoroscanning y una metodología para guiar experimentos de laboratorio a partir de dicho algoritmo. Como resultado de nuestro trabajo, pudimos establecer un flujo de trabajo en el que Fluoroscans reales extraídos de imágenes digitales se utilizaron para ajustar los parámetros de las simulaciones, que a su vez fueron utilizadas para guiar experimentos de laboratorio y para generar un conjunto de datos sintético a escala genómica que permitirá ayudar al desarrollo de algoritmos de alineamiento de señales para la generación de mapas genómicos. (Texto tomado de la fuente)
dc.languageeng
dc.publisherUniversidad Nacional de Colombia
dc.publisherMedellín - Minas - Maestría en Ingeniería - Ingeniería de Sistemas
dc.publisherFacultad de Minas
dc.publisherMedellín, Colombia
dc.publisherUniversidad Nacional de Colombia - Sede Medellín
dc.relationRedCol
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dc.rightsReconocimiento 4.0 Internacional
dc.rightshttp://creativecommons.org/licenses/by/4.0/
dc.rightsinfo:eu-repo/semantics/openAccess
dc.titleA computational methodology for the generation of genomic maps from fluoroscanning images
dc.typeTrabajo de grado - Maestría


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