Development of bioinformatic tools to analyze eukaryotic genomes and pangenomes
Esta tesis se presentó para obtener el grado de Doctor en Biología Evolutiva y Ecología en la Universidad de Montpellier.
- Autores:
-
González García, Laura Natalia
- Tipo de recurso:
- Doctoral thesis
- Fecha de publicación:
- 2024
- Institución:
- Universidad de los Andes
- Repositorio:
- Séneca: repositorio Uniandes
- Idioma:
- eng
fra
- OAI Identifier:
- oai:repositorio.uniandes.edu.co:1992/75356
- Acceso en línea:
- https://hdl.handle.net/1992/75356
- Palabra clave:
- Genomics
Comparative genomics
Genome assembly
Transposable elements
Leishmania
Coffea
Ingeniería
Biología
Microbiología
- Rights
- openAccess
- License
- Attribution-NonCommercial-NoDerivatives 4.0 International
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Development of bioinformatic tools to analyze eukaryotic genomes and pangenomes |
| title |
Development of bioinformatic tools to analyze eukaryotic genomes and pangenomes |
| spellingShingle |
Development of bioinformatic tools to analyze eukaryotic genomes and pangenomes Genomics Comparative genomics Genome assembly Transposable elements Leishmania Coffea Ingeniería Biología Microbiología |
| title_short |
Development of bioinformatic tools to analyze eukaryotic genomes and pangenomes |
| title_full |
Development of bioinformatic tools to analyze eukaryotic genomes and pangenomes |
| title_fullStr |
Development of bioinformatic tools to analyze eukaryotic genomes and pangenomes |
| title_full_unstemmed |
Development of bioinformatic tools to analyze eukaryotic genomes and pangenomes |
| title_sort |
Development of bioinformatic tools to analyze eukaryotic genomes and pangenomes |
| dc.creator.fl_str_mv |
González García, Laura Natalia |
| dc.contributor.advisor.none.fl_str_mv |
Guyot, Romain Duitama Castellanos, Jorge Alexander |
| dc.contributor.author.none.fl_str_mv |
González García, Laura Natalia |
| dc.contributor.jury.none.fl_str_mv |
Mirouze, Marie van Sluys, Marie Anne López Kleine, Liliana Riaño Pachón, Diego Mauricio Fiston Lavier, Anna Sophie Garcés Pernett, Kelly Johany |
| dc.contributor.researchgroup.none.fl_str_mv |
Facultad de Ingeniería::TICSw: Tecnologías de Información y Construcción de Software |
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Genomics Comparative genomics Genome assembly Transposable elements Leishmania Coffea |
| topic |
Genomics Comparative genomics Genome assembly Transposable elements Leishmania Coffea Ingeniería Biología Microbiología |
| dc.subject.themes.none.fl_str_mv |
Ingeniería Biología Microbiología |
| description |
Esta tesis se presentó para obtener el grado de Doctor en Biología Evolutiva y Ecología en la Universidad de Montpellier. |
| publishDate |
2024 |
| dc.date.issued.none.fl_str_mv |
2024-11-27 |
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2025-01-13T14:23:14Z |
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2025-01-13T14:23:14Z |
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Trabajo de grado - Doctorado |
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info:eu-repo/semantics/doctoralThesis |
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https://hdl.handle.net/1992/75356 |
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instname:Universidad de los Andes |
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reponame:Repositorio Institucional Séneca |
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https://hdl.handle.net/1992/75356 |
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eng fra |
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eng fra |
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Attribution-NonCommercial-NoDerivatives 4.0 International |
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http://creativecommons.org/licenses/by-nc-nd/4.0/ |
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info:eu-repo/semantics/openAccess |
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openAccess |
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297 páginas |
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application/pdf |
| dc.publisher.none.fl_str_mv |
Universidad de los Andes |
| dc.publisher.program.none.fl_str_mv |
Doctorado en Ingeniería |
| dc.publisher.faculty.none.fl_str_mv |
Facultad de Ingeniería |
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Universidad de los Andes |
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Universidad de los Andes |
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Guyot, RomainDuitama Castellanos, Jorge Alexandervirtual::21985-1González García, Laura NataliaMirouze, Marievan Sluys, Marie AnneLópez Kleine, LilianaRiaño Pachón, Diego MauricioFiston Lavier, Anna SophieGarcés Pernett, Kelly JohanyFacultad de Ingeniería::TICSw: Tecnologías de Información y Construcción de Software2025-01-13T14:23:14Z2025-01-13T14:23:14Z2024-11-27https://hdl.handle.net/1992/75356instname:Universidad de los Andesreponame:Repositorio Institucional Sénecarepourl:https://repositorio.uniandes.edu.co/Esta tesis se presentó para obtener el grado de Doctor en Biología Evolutiva y Ecología en la Universidad de Montpellier.Pangenomes represent the entire genetic diversity of a species offering insights into genomic diversity, evolution, and functional variation. This thesis addresses three key bottlenecks in pangenome reconstruction through the development of algorithms. i) A genome assembler based on the overlapping layout consensus algorithm to assemble genomes using long-reads. ii) An alignment-free method to annotate transposable elements. iii) An algorithm for the identification of orthologs and the reconstruction of gene-based pangenomes. These tools were used to explore their applications in two contrasting case studies of clinical and agricultural importance in Colombia: Leishmania parasites and Coffea species. This work demonstrates the potential of analyzing large-scale genomic data with efficient bioinformatic approaches to understand human pathogen and wild and cultivated plant diversity and evolution.Ministerio de Ciencia , Tecnología e Innovación - ColombiaAgropolis Foundation - FranciaInstitut de Recherche pour le Développement - FranciaDoctoradoBioinformáticaBiología Computacional297 páginasapplication/pdfengfraUniversidad de los AndesDoctorado en IngenieríaFacultad de IngenieríaAttribution-NonCommercial-NoDerivatives 4.0 Internationalhttp://creativecommons.org/licenses/by-nc-nd/4.0/info:eu-repo/semantics/openAccesshttp://purl.org/coar/access_right/c_abf2Development of bioinformatic tools to analyze eukaryotic genomes and pangenomesTrabajo de grado - Doctoradoinfo:eu-repo/semantics/doctoralThesisinfo:eu-repo/semantics/acceptedVersionhttp://purl.org/coar/resource_type/c_db06Texthttps://purl.org/redcol/resource_type/TDGenomicsComparative genomicsGenome assemblyTransposable 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