{"id":"https://openalex.org/W6959666607","doi":"https://doi.org/10.13016/rhk0-gyx2","title":"Algorithmic approaches for investigating DNA Methylation in tumor evolution and heterogeneity","display_name":"Algorithmic approaches for investigating DNA Methylation in tumor evolution and heterogeneity","publication_year":2024,"publication_date":"2024-01-01","ids":{"openalex":"https://openalex.org/W6959666607","doi":"https://doi.org/10.13016/rhk0-gyx2"},"language":"en","primary_location":{"id":"pmh:oai:drum.lib.umd.edu:1903/33784","is_oa":false,"landing_page_url":"https://drum.lib.umd.edu/bitstreams/26eaa968-a1df-4679-a45d-22ddf4c8c80b/download","pdf_url":null,"source":{"id":"https://openalex.org/S4306401518","display_name":"University Libraries (University of Maryland)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I66946132","host_organization_name":"University of Maryland, College Park","host_organization_lineage":["https://openalex.org/I66946132"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Dissertation"},"type":"other","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.13016/rhk0-gyx2","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Li, Xuan","orcid":null},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Li, Xuan","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":true,"primary_topic":{"id":"https://openalex.org/T13168","display_name":"Plant Ecology and Taxonomy Studies","score":0.2011999934911728,"subfield":{"id":"https://openalex.org/subfields/1105","display_name":"Ecology, Evolution, Behavior and Systematics"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T13168","display_name":"Plant Ecology and Taxonomy Studies","score":0.2011999934911728,"subfield":{"id":"https://openalex.org/subfields/1105","display_name":"Ecology, Evolution, Behavior and Systematics"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10012","display_name":"Genetic diversity and population structure","score":0.12160000205039978,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12115","display_name":"Genetic and Environmental Crop Studies","score":0.07639999687671661,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":0.7369999885559082},{"id":"https://openalex.org/keywords/epigenetics","display_name":"Epigenetics","score":0.6895999908447266},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5181000232696533},{"id":"https://openalex.org/keywords/methylation","display_name":"Methylation","score":0.4503999948501587},{"id":"https://openalex.org/keywords/epigenomics","display_name":"Epigenomics","score":0.413100004196167},{"id":"https://openalex.org/keywords/cancer","display_name":"Cancer","score":0.38760000467300415},{"id":"https://openalex.org/keywords/cpg-site","display_name":"CpG site","score":0.36899998784065247}],"concepts":[{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.7369999885559082},{"id":"https://openalex.org/C41091548","wikidata":"https://www.wikidata.org/wiki/Q26939","display_name":"Epigenetics","level":3,"score":0.6895999908447266},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6432999968528748},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6414999961853027},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5181000232696533},{"id":"https://openalex.org/C33288867","wikidata":"https://www.wikidata.org/wiki/Q518328","display_name":"Methylation","level":3,"score":0.4503999948501587},{"id":"https://openalex.org/C121912465","wikidata":"https://www.wikidata.org/wiki/Q3589153","display_name":"Epigenomics","level":5,"score":0.413100004196167},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.39879998564720154},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.38760000467300415},{"id":"https://openalex.org/C140173407","wikidata":"https://www.wikidata.org/wiki/Q1138358","display_name":"CpG site","level":5,"score":0.36899998784065247},{"id":"https://openalex.org/C3018028425","wikidata":"https://www.wikidata.org/wiki/Q15917291","display_name":"Tumor heterogeneity","level":3,"score":0.3440999984741211},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.34150001406669617},{"id":"https://openalex.org/C2779256057","wikidata":"https://www.wikidata.org/wiki/Q16909647","display_name":"Tumor progression","level":3,"score":0.33090001344680786},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.31450000405311584},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.31189998984336853},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3084999918937683},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.29440000653266907},{"id":"https://openalex.org/C2776817793","wikidata":"https://www.wikidata.org/wiki/Q6553369","display_name":"Lineage (genetic)","level":3,"score":0.28060001134872437},{"id":"https://openalex.org/C113968399","wikidata":"https://www.wikidata.org/wiki/Q7559241","display_name":"Somatic evolution in cancer","level":3,"score":0.26440000534057617},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.26330000162124634}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:drum.lib.umd.edu:1903/33784","is_oa":false,"landing_page_url":"https://drum.lib.umd.edu/bitstreams/26eaa968-a1df-4679-a45d-22ddf4c8c80b/download","pdf_url":null,"source":{"id":"https://openalex.org/S4306401518","display_name":"University Libraries (University of Maryland)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I66946132","host_organization_name":"University of Maryland, College Park","host_organization_lineage":["https://openalex.org/I66946132"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Dissertation"},{"id":"doi:10.13016/rhk0-gyx2","is_oa":true,"landing_page_url":"https://doi.org/10.13016/rhk0-gyx2","pdf_url":null,"source":{"id":"https://openalex.org/S4306402644","display_name":"Digital Repository at the University of Maryland (University of Maryland College Park)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I66946132","host_organization_name":"University of Maryland, College Park","host_organization_lineage":["https://openalex.org/I66946132"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"thesis"}],"best_oa_location":{"id":"doi:10.13016/rhk0-gyx2","is_oa":true,"landing_page_url":"https://doi.org/10.13016/rhk0-gyx2","pdf_url":null,"source":{"id":"https://openalex.org/S4306402644","display_name":"Digital Repository at the University of Maryland (University of Maryland College Park)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I66946132","host_organization_name":"University of Maryland, College Park","host_organization_lineage":["https://openalex.org/I66946132"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"thesis"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Intratumor":[0],"heterogeneity":[1,77,98],"and":[2,18,42,78,97,123,126,136,153,176,244,265,284,315,336,380,387,398],"tumor":[3,53,79,95,131,133,140,172,178,190,268,375],"diversity":[4],"of":[5,13,29,44,94,144,149,195,302,311,334,343,352],"cancer":[6,15,30,108,353,378],"impose":[7],"significant":[8],"challenges":[9,301,347],"on":[10,65],"the":[11,26,38,66,92,145,164,186,193,201,261,276,300,308,332,344,350,369,384,392,403],"prospect":[12],"personalized":[14,377],"diagnosis,":[16],"treatment,":[17,379],"prognostics.":[19],"While":[20],"many":[21],"studies":[22],"seek":[23],"to":[24,50,74,87,102,169,207,247,258,280,298,340],"understand":[25],"complex":[27,146,395],"dynamics":[28],"with":[31,292],"theoretically":[32],"well-suited":[33],"biomarkers":[34],"like":[35,62],"DNA":[36,63,89,118],"mutations,":[37],"relative":[39],"molecular":[40,396],"rigidity":[41],"sparsity":[43],"mutation":[45,56],"make":[46],"it":[47],"often":[48],"challenging":[49],"reconstruct":[51,177],"reliable":[52,245,267],"lineage":[54],"using":[55],"profiles":[57,310],"in":[58,91,106,139,204,210,320,328,348,362,374,402],"practice.":[59],"Epigenetic":[60],"markers":[61],"methylation,":[64],"other":[67],"hand,":[68],"serve":[69],"as":[70,236],"a":[71,242],"promising":[72],"alternative":[73],"elucidate":[75],"intratumor":[76],"diversity.":[80],"However,":[81],"systematic":[82],"research":[83,373],"leveraging":[84],"algorithmic":[85,238,335],"approaches":[86,339],"investigate":[88],"methylation":[90,119,182,197,212,255,309,363],"context":[93],"evolution":[96,191],"remains":[99],"limited.":[100],"Aimed":[101],"address":[103],"critical":[104],"gaps":[105],"computational":[107,114,167,357,385],"research,":[109],"this":[110,329,366],"dissertation":[111,330],"presents":[112,224],"novel":[113,356],"frameworks":[115,386],"for":[116,142,188,217,371],"analyzing":[117],"at":[120],"both":[121],"single-cell":[122,181,196,211,254,279],"bulk":[124,281,303,321],"levels":[125],"offers":[127],"insights":[128,401],"into":[129],"methylation-based":[130],"heterogeneity,":[132],"evolutionary":[134],"dynamics,":[135],"cellular":[137],"composition":[138,319],"samples":[141,216,257],"characterization":[143],"epigenetic":[147],"landscape":[148],"tumors.":[150],"Chapter":[151,154,205,222,273],"2":[152,206],"3":[155],"introduce":[156],"Sgootr":[157,184],"(Single-cell":[158],"Genomic":[159],"methylatiOn":[160],"tumOr":[161],"Tree":[162],"Reconstruction),":[163],"first":[165],"distance-based":[166],"method":[168],"jointly":[170],"select":[171,249],"lineage-informative":[173,269],"CpG":[174,250,270],"sites":[175,251],"lineages":[179],"from":[180,278],"data.":[183],"lays":[185],"groundwork":[187],"understanding":[189,349],"through":[192],"lens":[194],"profiles.":[198],"Motivated":[199],"by":[200,306],"need":[202],"highlighted":[203],"overcome":[208],"imbalances":[209],"data":[213,337,364,397],"across":[214,252],"patient":[215,220,256,263],"interpretable":[218],"comparative":[219],"analysis,":[221,365],"4":[223],"FALAFL":[225,240],"(FAir":[226],"muLti-sAmple":[227],"Feature":[228],"seLection).":[229],"With":[230,355],"integer":[231],"linear":[232],"programming":[233],"(ILP)":[234],"serving":[235],"its":[237],"backbone,":[239],"provides":[241],"fast":[243],"solution":[246],"fairly":[248],"different":[253],"optimally":[259],"represent":[260],"entire":[262],"cohort":[264],"identify":[266],"sites.":[271],"Finally,":[272],"5":[274],"shifts":[275],"scope":[277],"tissue":[282,304],"contexts":[283],"introduces":[285],"Qombucha":[286],"(Quadratic":[287],"prOgraMming":[288],"Based":[289],"tUmor":[290],"deConvolution":[291],"cell":[293,317],"HierArchy),":[294],"which":[295],"is":[296],"designed":[297],"tackle":[299,341],"analysis":[305],"inferring":[307],"progenitor":[312],"brain":[313],"cells":[314],"determining":[316],"type":[318],"glioblastoma":[322],"(GBM)":[323],"samples.":[324],"The":[325],"work":[326,367],"presented":[327,389],"demonstrates":[331],"power":[333],"science":[338],"some":[342],"most":[345],"pressing":[346],"complexity":[351],"epigenomics.":[354],"tools":[358],"addressing":[359],"current":[360],"limitations":[361],"paves":[368],"way":[370],"further":[372],"evolution,":[376],"biomarker":[381],"discovery.":[382],"Overall,":[383],"findings":[388],"here":[390],"bridge":[391],"gap":[393],"between":[394],"clinically":[399],"meaningful":[400],"battle":[404],"against":[405],"cancer.":[406]},"counts_by_year":[],"updated_date":"2025-11-06T06:51:31.235846","created_date":"2025-10-10T00:00:00"}