{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/120529"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/120529","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"A fully interpretable approach to sequence-to-expression modeling","abstract":"Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2025-05-01","abstract_html":"Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2025-05-01","abstract_has_math":false,"creators":["Bhogale, Shounak Girish"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"Biophysics & Quant Biology","degree_department":null,"school":null,"contributors":["Sinha, Saurabh","Zhao, Dave","Shukla, Diwakar","Maslov, Sergei"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2023,"date_issued":"2023-05","date_published":"2023-05","updated_at":"2026-07-22T22:24:57Z","subjects":["Grn","Sequence-to-expression Modeling"],"languages":["en","eng"],"rights":["Copyright 2023 Shounak Bhogale"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://hdl.handle.net/2142/120529","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Sinha, Saurabh","Zhao, Dave","Shukla, Diwakar","Maslov, Sergei"]},{"key":"dc:creator","label":"Author","values":["Bhogale, Shounak Girish"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2023-05","2023-04-26"]},{"key":"dc:type","label":"Dc Type","values":["text","Thesis"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Biophysics & Quant Biology"]},{"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":["Grn","Sequence-to-expression Modeling"]}]},{"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 2023 Shounak Bhogale"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://hdl.handle.net/2142/120529"]}]},{"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 2025-05-01","The student, Shounak Bhogale, accepted the attached license on 2023-04-22 at 03:08.","The student, Shounak Bhogale, submitted this Dissertation for approval on 2023-04-22 at 03:14.","This Dissertation was approved for publication on 2023-04-26 at 08:35.","DSpace SAF Submission Ingestion Package generated from Vireo submission #19045 on 2023-09-01 at 17:21:00","Gene expression regulation is a complex process where many regulatory elements such as transcription factors, enhancers, promoters, histone modifications work in tandem. In this thesis we focus our attention primarily on the interplay between two of the most important elements – transcription factors and enhancers. The binding of TFs to enhancers plays crucial role in modulating the gene expression. First, we present a thermodynamics-based sequence-to- expression model to study Drosophila mesodermal differentiation program. This model suggests indirect interaction between a transcription factor and DNA as a plausible mechanism for a transcription factor having dual regulatory roles (as an activator and a repressor) based on its environment. In the second part we discuss a neural network-based sequence-to-expression model to study neuronal stem cell differentiation program. The model learns the effect of transcription factors on gene expression across multiple cell types. It can also be used as a tool for de novo motif discovery or to improve the known motifs based on new data."]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["A fully interpretable approach to sequence-to-expression modeling"]}]}],"canonical_facts":{"dc:contributor":["Sinha, Saurabh","Zhao, Dave","Shukla, Diwakar","Maslov, Sergei"],"dc:creator":["Bhogale, Shounak Girish"],"dc:date":["2023-05","2023-04-26"],"dc:description":["Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2025-05-01","The student, Shounak Bhogale, accepted the attached license on 2023-04-22 at 03:08.","The student, Shounak Bhogale, submitted this Dissertation for approval on 2023-04-22 at 03:14.","This Dissertation was approved for publication on 2023-04-26 at 08:35.","DSpace SAF Submission Ingestion Package generated from Vireo submission #19045 on 2023-09-01 at 17:21:00","Gene expression regulation is a complex process where many regulatory elements such as transcription factors, enhancers, promoters, histone modifications work in tandem. 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