{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/117566"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/117566","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Development and application of machine learning tools for the advancement of energy crop genetic manipulation using the CRISPR/Cas technology","abstract":"Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2024-12-01","abstract_html":"Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2024-12-01","abstract_has_math":false,"creators":["Muller Paul, Hans"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"Informatics","degree_department":null,"school":null,"contributors":["Hudson, Mathew","Moose, Stephen","Marshall-Colon, Amy","Zhao, Sihai"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2022,"date_issued":"2022-12","date_published":"2022-12","updated_at":"2026-07-22T22:24:56Z","subjects":["Machine Learning","Crop Sciences","Crispr","Cas9","Sgrna","Algorithm","Genome-wide","Software Tool"],"languages":["en","eng"],"rights":["Copyright 2022 Hans Müller Paul"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://hdl.handle.net/2142/117566","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Hudson, Mathew","Moose, Stephen","Marshall-Colon, Amy","Zhao, Sihai"]},{"key":"dc:creator","label":"Author","values":["Muller Paul, Hans"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2022-12","2022-11-23"]},{"key":"dc:type","label":"Dc Type","values":["text","Thesis"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Informatics"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Dissertation"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Ph.D."]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["University of Illinois at Urbana-Champaign"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Machine Learning","Crop Sciences","Crispr","Cas9","Sgrna","Algorithm","Genome-wide","Software Tool"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en","eng"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2022 Hans Müller Paul"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://hdl.handle.net/2142/117566"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2024-12-01","The student, Hans Muller Paul, accepted the attached license on 2022-11-22 at 13:23.","The student, Hans Muller Paul, submitted this Dissertation for approval on 2022-11-22 at 13:34.","This Dissertation was approved for publication on 2022-11-23 at 08:47.","DSpace SAF Submission Ingestion Package generated from Vireo submission #18619 on 2023-04-12 at 11:35:13","Crop genomes, often highly complex and polyploid, are tailored to optimize specific traits by generations of breeding. Editing such genomes without disrupting decades worth of selective breeding is a challenging task. The CRISPR/Cas9 technology's ability to perform targeted mutations has made it a prime candidate for this purpose. The majority of software tools currently available for designing CRISPR/Cas9 guide sequences were developed for mammalian genomes, and focus specifically on the genome's coding regions. We have developed CROPSR | an open-source tool to design and evaluate gRNA sequences for CRISPR experiments. Advantages over competing tools include a genome-wide approach, which facilitates the design of CRISPR/Cas9 guide RNAs in non-coding regions of the genome, and accounts for polyploidy present in many crop genomes. Novel algorithms were developed to increase performance when evaluating crop genomes, but without sacrificing performance when evaluating mammalian genomes. Incorporating biophysical properties of the CRISPR nucleoprotein complex, particularly the secondary structure of the gRNA molecule, enabled a two-fold increase in the correlation between the predicted and experimental metrics for mutation efficiency. Additionally, software performance was optimized to reduce resource allocation and run time. The results presented in this work are the initial steps in a longer journey to improve the tools available editing crop genomes. CROPSR enables a significant reduction in the time needed to design a CRISPR/Cas9 mutation experiments in complex, polyploid genomes. The addition of biophysical characteristics of the CRISPR/Cas9 complex were considered to develop a novel approach for mutation performance evaluation, resulting in significant increases in predictive accuracy and enabling improving confidence in the generated guide sequences."]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["Development and application of machine learning tools for the advancement of energy crop genetic manipulation using the CRISPR/Cas technology"]}]}],"canonical_facts":{"dc:contributor":["Hudson, Mathew","Moose, Stephen","Marshall-Colon, Amy","Zhao, Sihai"],"dc:creator":["Muller Paul, Hans"],"dc:date":["2022-12","2022-11-23"],"dc:description":["Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2024-12-01","The student, Hans Muller Paul, accepted the attached license on 2022-11-22 at 13:23.","The student, Hans Muller Paul, submitted this Dissertation for approval on 2022-11-22 at 13:34.","This Dissertation was approved for publication on 2022-11-23 at 08:47.","DSpace SAF Submission Ingestion Package generated from Vireo submission #18619 on 2023-04-12 at 11:35:13","Crop genomes, often highly complex and polyploid, are tailored to optimize specific traits by generations of breeding. Editing such genomes without disrupting decades worth of selective breeding is a challenging task. The CRISPR/Cas9 technology's ability to perform targeted mutations has made it a prime candidate for this purpose. The majority of software tools currently available for designing CRISPR/Cas9 guide sequences were developed for mammalian genomes, and focus specifically on the genome's coding regions. We have developed CROPSR | an open-source tool to design and evaluate gRNA sequences for CRISPR experiments. Advantages over competing tools include a genome-wide approach, which facilitates the design of CRISPR/Cas9 guide RNAs in non-coding regions of the genome, and accounts for polyploidy present in many crop genomes. Novel algorithms were developed to increase performance when evaluating crop genomes, but without sacrificing performance when evaluating mammalian genomes. Incorporating biophysical properties of the CRISPR nucleoprotein complex, particularly the secondary structure of the gRNA molecule, enabled a two-fold increase in the correlation between the predicted and experimental metrics for mutation efficiency. Additionally, software performance was optimized to reduce resource allocation and run time. The results presented in this work are the initial steps in a longer journey to improve the tools available editing crop genomes. CROPSR enables a significant reduction in the time needed to design a CRISPR/Cas9 mutation experiments in complex, polyploid genomes. The addition of biophysical characteristics of the CRISPR/Cas9 complex were considered to develop a novel approach for mutation performance evaluation, resulting in significant increases in predictive accuracy and enabling improving confidence in the generated guide sequences."],"dc:format":["application/pdf"],"dc:identifier":["https://hdl.handle.net/2142/117566"],"dc:language":["en","eng"],"dc:rights":["Copyright 2022 Hans Müller Paul"],"dc:subject":["Machine Learning","Crop Sciences","Crispr","Cas9","Sgrna","Algorithm","Genome-wide","Software Tool"],"dc:title":["Development and application of machine learning tools for the advancement of energy crop genetic manipulation using the CRISPR/Cas technology"],"dc:type":["text","Thesis"],"thesis:degree_discipline":["Informatics"],"thesis:degree_level":["Dissertation"],"thesis:degree_name":["Ph.D."],"thesis:institution_name":["University of Illinois at Urbana-Champaign"]},"updated_at":"2026-07-22T22:24:56Z"}