{"id":"https://openalex.org/W2590141933","doi":null,"title":"Understanding human genome regulation through entropic graph-based regularization and submodular optimization","display_name":"Understanding human genome regulation through entropic graph-based regularization and submodular optimization","publication_year":2016,"publication_date":"2016-07-14","ids":{"openalex":"https://openalex.org/W2590141933","mag":"2590141933"},"language":"en","primary_location":{"id":"pmh:oai:digital.lib.washington.edu:1773/36547","doi":null,"is_oa":true,"landing_page_url":"http://hdl.handle.net/1773/36547","pdf_url":"https://digital.lib.washington.edu:443/researchworks/bitstream/1773/36547/1/Libbrecht_washington_0250E_16078.pdf","source":{"id":"https://openalex.org/S4306401128","display_name":"ResearchWorks at the University of Washington (University of Washington)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I201448701","host_organization_name":"University of Washington","host_organization_lineage":["https://openalex.org/I201448701"],"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":"Thesis"},"volume":null,"type":"dissertation","is_traditional":true,"indexed_in":[],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://digital.lib.washington.edu:443/researchworks/bitstream/1773/36547/1/Libbrecht_washington_0250E_16078.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5016115107","display_name":"Maxwell W. Libbrecht","orcid":"https://orcid.org/0000-0003-2502-0262","observed_orcids":["https://orcid.org/0000-0003-2502-0262"]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Maxwell W. Libbrecht","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0003-2502-0262","affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5016115107"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":1,"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":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.38350000977516174,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"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"}},"topics":[{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.38350000977516174,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.3174000084400177,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.09950000047683716,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"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"}}],"keywords":[{"id":"https://openalex.org/keywords/entropy-regularization","display_name":"entropy regularization","score":0.7250000238418579},{"id":"https://openalex.org/keywords/graph-regularization","display_name":"graph regularization","score":0.8379999995231628},{"id":"https://openalex.org/keywords/submodular-optimization","display_name":"submodular optimization","score":0.9900000095367432},{"id":"https://openalex.org/keywords/gene-regulatory-networks","display_name":"gene regulatory networks","score":0.671999990940094},{"id":"https://openalex.org/keywords/network-inference","display_name":"network inference","score":0.38100001215934753}],"concepts":[{"id":"https://openalex.org/C178621042","wikidata":"https://www.wikidata.org/wiki/Q7631710","display_name":"Submodular set function","level":2,"score":0.7670748233795166},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4700393080711365},{"id":"https://openalex.org/C2776135515","wikidata":"https://www.wikidata.org/wiki/Q17143721","display_name":"Regularization (linguistics)","level":2,"score":0.4441305696964264},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.43245095014572144},{"id":"https://openalex.org/C197077220","wikidata":"https://www.wikidata.org/wiki/Q720988","display_name":"Human genome","level":4,"score":0.42484280467033386},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4119333028793335},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.41140714287757874},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.38870301842689514},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.37227964401245117},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3574954867362976},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3343111574649811},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.285115510225296},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2613736391067505},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.24407464265823364},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.23366263508796692}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:digital.lib.washington.edu:1773/36547","doi":null,"is_oa":true,"landing_page_url":"http://hdl.handle.net/1773/36547","pdf_url":"https://digital.lib.washington.edu:443/researchworks/bitstream/1773/36547/1/Libbrecht_washington_0250E_16078.pdf","source":{"id":"https://openalex.org/S4306401128","display_name":"ResearchWorks at the University of Washington (University of Washington)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I201448701","host_organization_name":"University of Washington","host_organization_lineage":["https://openalex.org/I201448701"],"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":"Thesis"},{"id":"mag:2590141933","doi":null,"is_oa":false,"landing_page_url":"https://digital.lib.washington.edu:443/researchworks/handle/1773/36547","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"pmh:oai:digital.lib.washington.edu:1773/36547","doi":null,"is_oa":true,"landing_page_url":"http://hdl.handle.net/1773/36547","pdf_url":"https://digital.lib.washington.edu:443/researchworks/bitstream/1773/36547/1/Libbrecht_washington_0250E_16078.pdf","source":{"id":"https://openalex.org/S4306401128","display_name":"ResearchWorks at the University of Washington (University of Washington)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I201448701","host_organization_name":"University of Washington","host_organization_lineage":["https://openalex.org/I201448701"],"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":"Thesis"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2590141933.pdf","grobid_xml":"https://content.openalex.org/works/W2590141933.grobid-xml"},"referenced_works_count":138,"referenced_works":["https://openalex.org/W389907844","https://openalex.org/W612917828","https://openalex.org/W1492009297","https://openalex.org/W1498671329","https://openalex.org/W1510073064","https://openalex.org/W1550136613","https://openalex.org/W1554663460","https://openalex.org/W1554944419","https://openalex.org/W1595665778","https://openalex.org/W1596429464","https://openalex.org/W1630959083","https://openalex.org/W1680189815","https://openalex.org/W1709989312","https://openalex.org/W1730959447","https://openalex.org/W1898824936","https://openalex.org/W1964940342","https://openalex.org/W1968931043","https://openalex.org/W1971578941","https://openalex.org/W1971723950","https://openalex.org/W1976526581","https://openalex.org/W1977690815","https://openalex.org/W1979969525","https://openalex.org/W1983439231","https://openalex.org/W1984985727","https://openalex.org/W1996423252","https://openalex.org/W1999966058","https://openalex.org/W2014594785","https://openalex.org/W2015052645","https://openalex.org/W2017966952","https://openalex.org/W2019251848","https://openalex.org/W2022633023","https://openalex.org/W2027694180","https://openalex.org/W2029873987","https://openalex.org/W2037589637","https://openalex.org/W2037789405","https://openalex.org/W2038774969","https://openalex.org/W2044826047","https://openalex.org/W2049250303","https://openalex.org/W2055043387","https://openalex.org/W2062296203","https://openalex.org/W2064537118","https://openalex.org/W2067811518","https://openalex.org/W2068315875","https://openalex.org/W2070021921","https://openalex.org/W2073026107","https://openalex.org/W2073727170","https://openalex.org/W2076154138","https://openalex.org/W2078526277","https://openalex.org/W2084160423","https://openalex.org/W2085277871","https://openalex.org/W2085648025","https://openalex.org/W2087347434","https://openalex.org/W2090037139","https://openalex.org/W2095724929","https://openalex.org/W2095758845","https://openalex.org/W2095791120","https://openalex.org/W2096863518","https://openalex.org/W2097353028","https://openalex.org/W2097482982","https://openalex.org/W2098071274","https://openalex.org/W2098549100","https://openalex.org/W2099048402","https://openalex.org/W2099351601","https://openalex.org/W2100847260","https://openalex.org/W2101546138","https://openalex.org/W2105924780","https://openalex.org/W2107008379","https://openalex.org/W2108211735","https://openalex.org/W2109949710","https://openalex.org/W2114281975","https://openalex.org/W2120340025","https://openalex.org/W2121948489","https://openalex.org/W2123676422","https://openalex.org/W2124166542","https://openalex.org/W2124351063","https://openalex.org/W2125631472","https://openalex.org/W2125653933","https://openalex.org/W2127081697","https://openalex.org/W2129448726","https://openalex.org/W2129560785","https://openalex.org/W2130416704","https://openalex.org/W2131070718","https://openalex.org/W2131116802","https://openalex.org/W2131824593","https://openalex.org/W2132085065","https://openalex.org/W2133075481","https://openalex.org/W2133828198","https://openalex.org/W2134767644","https://openalex.org/W2135046866","https://openalex.org/W2135993011","https://openalex.org/W2137476312","https://openalex.org/W2137995988","https://openalex.org/W2140600399","https://openalex.org/W2141757539","https://openalex.org/W2142410561","https://openalex.org/W2143996311","https://openalex.org/W2144933361","https://openalex.org/W2146339031","https://openalex.org/W2147461734","https://openalex.org/W2149118429","https://openalex.org/W2151554678","https://openalex.org/W2153153865","https://openalex.org/W2154368244","https://openalex.org/W2156125289","https://openalex.org/W2158557760","https://openalex.org/W2158714788","https://openalex.org/W2159080219","https://openalex.org/W2160995259","https://openalex.org/W2161444669","https://openalex.org/W2162362951","https://openalex.org/W2162587106","https://openalex.org/W2166473218","https://openalex.org/W2166647372","https://openalex.org/W2166699767","https://openalex.org/W2168602111","https://openalex.org/W2169600004","https://openalex.org/W2170079803","https://openalex.org/W2170735271","https://openalex.org/W2171808845","https://openalex.org/W2187089797","https://openalex.org/W2250289728","https://openalex.org/W2251590347","https://openalex.org/W2263717697","https://openalex.org/W2340149117","https://openalex.org/W2567948266","https://openalex.org/W2611370172","https://openalex.org/W2963251648","https://openalex.org/W2971788173","https://openalex.org/W3118655244","https://openalex.org/W3119651796","https://openalex.org/W3145992521","https://openalex.org/W4230875896","https://openalex.org/W4298856955","https://openalex.org/W4300414009","https://openalex.org/W6959622252","https://openalex.org/W7098286111","https://openalex.org/W7098463221","https://openalex.org/W7099666281"],"related_works":["https://openalex.org/W6926564329","https://openalex.org/W7030147929","https://openalex.org/W2131539061","https://openalex.org/W6962023031","https://openalex.org/W7029354986","https://openalex.org/W2558917096","https://openalex.org/W2612812069","https://openalex.org/W1513074964","https://openalex.org/W1169270235","https://openalex.org/W1503774166"],"abstract_inverted_index":{"I":[0,25,72,109,138,144,182,250],"am":[1],"interested":[2],"in":[3,30,50,55,117,214,248,258,279,283,296],"developing":[4],"computational":[5,294],"methods":[6,147,201,289],"to":[7,52,85,155,244,255,268,293],"improve":[8],"understanding":[9],"of":[10,33,39,58,62,114,135,151,159,170,186,196,205,272,281,306],"human":[11,119],"genome":[12,297],"regulation.":[13],"This":[14,229,263],"thesis":[15],"is":[16,48,175,216,223],"organized":[17],"around":[18],"two":[19],"novel":[20],"machine":[21],"learning":[22],"methods.":[23,307],"First,":[24],"present":[26,145,183],"a":[27,40,45,70,74,111,132,168,189,193,235,252],"new":[28,133,146],"method":[29,75,190,264],"the":[31,124,149,156,203,303],"field":[32,150,204],"posterior":[34,79],"regularization.":[35],"The":[36],"genomic":[37,90,197],"neighborhood":[38],"gene":[41],"influences":[42],"its":[43],"activity,":[44],"behavior":[46],"that":[47,81,199],"attributable":[49],"part":[51],"domain-scale":[53],"regulation,":[54],"which":[56,137],"regions":[57],"hundreds":[59],"or":[60],"thousands":[61],"kilobases":[63],"known":[64,127],"as":[65,69,164,234],"domains":[66,116],"are":[67,290],"regulated":[68],"unit.":[71],"developed":[73],"called":[76],"entropic":[77],"graph-based":[78],"regularization":[80],"makes":[82],"it":[83],"possible":[84],"jointly":[86],"model":[87,113,236],"all":[88],"available":[89],"data":[91,261],"sets,":[92],"including":[93],"chromatin":[94,100,115],"state":[95],"information":[96,102],"from":[97,103,148,202],"ChIP-seq":[98,165],"and":[99,130,166,219,222,285,299],"conformation":[101],"3C-based":[104],"assays.":[105],"Using":[106],"this":[107],"approach,":[108],"produced":[110],"comprehensive":[112],"eight":[118],"cell":[120,180],"types,":[121],"thereby":[122],"revealing":[123],"relationships":[125],"among":[126],"domain":[128,136],"types":[129],"identifying":[131],"category":[134],"term":[139],"\"specific":[140],"expression":[141],"domains.\"":[142],"Second,":[143],"submodular":[152,184,206,239,266],"optimization.":[153,207],"Due":[154],"high":[157],"cost":[158],"sequencing-based":[160],"genomics":[161],"assays":[162,174,187,198],"such":[163],"DNase-seq,":[167],"panel":[169,195],"at":[171],"most":[172],"3-10":[173],"usually":[176],"performed":[177],"on":[178],"each":[179],"type.":[181],"selection":[185],"(SSA),":[188],"for":[191,237,302],"choosing":[192],"diverse":[194],"leverages":[200],"SSA":[208],"performs":[209],"better":[210,276],"than":[211],"alternative":[212],"strategies":[213],"practice,":[215],"computationally":[217],"efficient":[218],"extremely":[220],"flexible,":[221],"theoretically":[224],"optimal":[225],"under":[226],"certain":[227],"assumptions.":[228],"application":[230],"may":[231],"also":[232],"serve":[233],"how":[238],"optimization":[240,267],"can":[241],"be":[242],"applied":[243,251],"other":[245],"discrete":[246],"problems":[247,295],"biology.":[249],"similar":[253],"technique":[254],"remove":[256],"redundancy":[257,284],"protein":[259,273],"sequence":[260],"sets.":[262],"applies":[265],"choose":[269],"representative":[270],"sets":[271],"sequences,":[274],"achieving":[275],"results":[277],"both":[278],"terms":[280],"reduction":[282],"functional":[286],"diversity.":[287],"These":[288],"widely":[291],"applicable":[292],"biology":[298],"provide":[300],"opportunities":[301],"further":[304],"development":[305]},"counts_by_year":[{"year":2023,"cited_by_count":1}],"updated_date":"2026-11-07T11:25:07.637180","created_date":"2017-03-03T00:00:00"}