This thesis describes the conception, design, and development of novel computational tools, theoretical models, and experimental techniques applied to the dissection of molecular factors underlying phenotypic variation. The first part of my work is focused on finding rare genetic variants in pooled DNA samples, leading to the development of a novel set of algorithms, SNPseeker and SPLINTER, applied to next-generation sequencing data. The second part of my work describes the creation of a reporter system for DNA methylation for the purpose of dissecting the genetic contribution of tissue-specific patterns of DNA methylation across the genome. Finally the last part of my work is focused on understanding the basis of stochastic variation in gene expression with a focus on modeling and dissecting the relationship between single-cell protein variance and mean at a genome-wide scale.
","abstract_html":"<p>This thesis describes the conception, design, and development of novel computational tools, theoretical models, and experimental techniques applied to the dissection of molecular factors underlying phenotypic variation. The first part of my work is focused on finding rare genetic variants in pooled DNA samples, leading to the development of a novel set of algorithms, SNPseeker and SPLINTER, applied to next-generation sequencing data. The second part of my work describes the creation of a reporter system for DNA methylation for the purpose of dissecting the genetic contribution of tissue-specific patterns of DNA methylation across the genome. Finally the last part of my work is focused on understanding the basis of stochastic variation in gene expression with a focus on modeling and dissecting the relationship between single-cell protein variance and mean at a genome-wide scale.</p>","abstract_has_math":false,"creators":["Vallania, Francesco"],"institution":null,"degree_name":"Doctor of Philosophy (PhD)","degree_level":"Dissertation","degree_discipline":"Biology and Biomedical Sciences: Computational and Systems Biology","degree_department":null,"school":null,"contributors":["Robi D Mitra"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2013,"date_issued":"2013-12-18T08:00:00Z","date_published":"2013-12-18T08:00:00Z","updated_at":"2026-07-24T06:12:48Z","subjects":["DNA methylation","Epigenetics","Genomics","Rare Variants","Stochastic Expression","Systems Biology","Computational Biology"],"languages":["English (en)"],"rights":[],"rights_urls":[],"identifier_entries":[{"key":"dc:identifier.doi","label":"DOI","values":["https://doi.org/10.7936/K79S1P12"],"render_values":[{"text":"https://doi.org/10.7936/K79S1P12","href":"https://doi.org/10.7936/K79S1P12","code":true}]}]},"links":{"outbound_url":"https://openscholarship.wustl.edu/etd/1201","outbound_label":"Repository record","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Robi D Mitra"]},{"key":"dc:creator","label":"Author","values":["Vallania, Francesco"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.available","label":"Dc Date Available","values":["2016-01-16T08:00:00Z"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Biology and Biomedical Sciences: Computational and Systems Biology"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Dissertation"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Doctor of Philosophy (PhD)"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["DNA methylation","Epigenetics","Genomics","Rare Variants","Stochastic Expression","Systems Biology","Computational Biology"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["English (en)"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://openscholarship.wustl.edu/etd/1201"]},{"key":"dc:identifier.doi","label":"DOI","values":["https://doi.org/10.7936/K79S1P12"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["This thesis describes the conception, design, and development of novel computational tools, theoretical models, and experimental techniques applied to the dissection of molecular factors underlying phenotypic variation. The first part of my work is focused on finding rare genetic variants in pooled DNA samples, leading to the development of a novel set of algorithms, SNPseeker and SPLINTER, applied to next-generation sequencing data. The second part of my work describes the creation of a reporter system for DNA methylation for the purpose of dissecting the genetic contribution of tissue-specific patterns of DNA methylation across the genome. Finally the last part of my work is focused on understanding the basis of stochastic variation in gene expression with a focus on modeling and dissecting the relationship between single-cell protein variance and mean at a genome-wide scale.
"]},{"key":"dc:title","label":"Title","values":["On the Origin of Phenotypic Variation: Novel Technologies to Dissect Molecular Determinants of Phenotype"]}]}],"canonical_facts":{"dc:contributor":["Robi D Mitra"],"dc:creator":["Vallania, Francesco"],"dc:date.available":["2016-01-16T08:00:00Z"],"dc:description.abstract":["This thesis describes the conception, design, and development of novel computational tools, theoretical models, and experimental techniques applied to the dissection of molecular factors underlying phenotypic variation. The first part of my work is focused on finding rare genetic variants in pooled DNA samples, leading to the development of a novel set of algorithms, SNPseeker and SPLINTER, applied to next-generation sequencing data. The second part of my work describes the creation of a reporter system for DNA methylation for the purpose of dissecting the genetic contribution of tissue-specific patterns of DNA methylation across the genome. Finally the last part of my work is focused on understanding the basis of stochastic variation in gene expression with a focus on modeling and dissecting the relationship between single-cell protein variance and mean at a genome-wide scale.
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