{"id":"https://openalex.org/W100038328","doi":null,"title":"Quantifying Gene Regulatory Networks","display_name":"Quantifying Gene Regulatory Networks","publication_year":2014,"publication_date":"2014-01-01","ids":{"openalex":"https://openalex.org/W100038328","mag":"100038328"},"language":"en","primary_location":{"id":"pmh:oai:dukespace.lib.duke.edu:10161/8676","doi":null,"is_oa":false,"landing_page_url":"http://hdl.handle.net/10161/8676","pdf_url":null,"source":{"id":"https://openalex.org/S4306400687","display_name":"DukeSpace (Duke University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I170897317","host_organization_name":"Duke University","host_organization_lineage":["https://openalex.org/I170897317"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Dissertation"},"volume":null,"type":"dissertation","is_traditional":true,"indexed_in":[],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5000763951","display_name":"Shangying Wang","orcid":"https://orcid.org/0000-0003-3876-7680","observed_orcids":["https://orcid.org/0000-0003-3876-7680"]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Shangying Wang","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0003-3876-7680","affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5000763951"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":2,"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":0.9976000189781189,"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":0.9976000189781189,"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/T11513","display_name":"stochastic dynamics and bifurcation","score":0.0007999999797903001,"subfield":{"id":"https://openalex.org/subfields/3109","display_name":"Statistical and Nonlinear Physics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.00019999999494757503,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/gene-regulatory-networks","display_name":"gene regulatory networks","score":0.925000011920929},{"id":"https://openalex.org/keywords/stochastic-gene-expression","display_name":"stochastic gene expression","score":0.9679999947547913},{"id":"https://openalex.org/keywords/promoter-accessibility","display_name":"promoter accessibility","score":0.8320000171661377},{"id":"https://openalex.org/keywords/markov-processes","display_name":"Markov processes","score":0.7139999866485596},{"id":"https://openalex.org/keywords/master-equation","display_name":"master equation","score":0.996999979019165},{"id":"https://openalex.org/keywords/feedback-regulation","display_name":"feedback regulation","score":0.9210000038146973},{"id":"https://openalex.org/keywords/protein-fluctuations","display_name":"protein fluctuations","score":0.9620000123977661},{"id":"https://openalex.org/keywords/alternative-splicing","display_name":"alternative splicing","score":0.9929999709129333},{"id":"https://openalex.org/keywords/exon-skipping","display_name":"exon skipping","score":0.9869999885559082},{"id":"https://openalex.org/keywords/intron-retention","display_name":"intron retention","score":0.9990000128746033},{"id":"https://openalex.org/keywords/transcriptional-noise","display_name":"transcriptional noise","score":0.4580000042915344},{"id":"https://openalex.org/keywords/single-cell-gene-expression","display_name":"single-cell gene expression","score":0.38600000739097595},{"id":"https://openalex.org/keywords/neural-development","display_name":"neural development","score":0.34299999475479126},{"id":"https://openalex.org/keywords/neural-circuit-remodeling","display_name":"neural circuit remodeling","score":0.3720000088214874},{"id":"https://openalex.org/keywords/activity-dependent-gene-expression","display_name":"activity-dependent gene expression","score":0.5789999961853027},{"id":"https://openalex.org/keywords/time-varying-stimuli","display_name":"time-varying stimuli","score":0.5789999961853027}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5059463381767273},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.4682786464691162},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.42944222688674927},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3896785378456116},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3408879339694977},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.3380464017391205},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3205695152282715},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.29790663719177246},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.17090001702308655}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:dukespace.lib.duke.edu:10161/8676","doi":null,"is_oa":false,"landing_page_url":"http://hdl.handle.net/10161/8676","pdf_url":null,"source":{"id":"https://openalex.org/S4306400687","display_name":"DukeSpace (Duke University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I170897317","host_organization_name":"Duke University","host_organization_lineage":["https://openalex.org/I170897317"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Dissertation"},{"id":"mag:100038328","doi":null,"is_oa":false,"landing_page_url":"https://dukespace.lib.duke.edu/dspace/handle/10161/8676","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":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":105,"referenced_works":["https://openalex.org/W144423133","https://openalex.org/W1590222219","https://openalex.org/W1968569455","https://openalex.org/W1970070519","https://openalex.org/W1972064898","https://openalex.org/W1975437957","https://openalex.org/W1978329448","https://openalex.org/W1981836110","https://openalex.org/W1986043841","https://openalex.org/W1988163167","https://openalex.org/W1991095439","https://openalex.org/W1991425207","https://openalex.org/W1993743396","https://openalex.org/W1994231988","https://openalex.org/W1999777663","https://openalex.org/W2000418014","https://openalex.org/W2002504696","https://openalex.org/W2003605043","https://openalex.org/W2009312009","https://openalex.org/W2010173857","https://openalex.org/W2011920499","https://openalex.org/W2014517533","https://openalex.org/W2016027614","https://openalex.org/W2016773845","https://openalex.org/W2017270642","https://openalex.org/W2017886758","https://openalex.org/W2018045523","https://openalex.org/W2018625617","https://openalex.org/W2019028138","https://openalex.org/W2022851859","https://openalex.org/W2022959246","https://openalex.org/W2027862889","https://openalex.org/W2032619610","https://openalex.org/W2036853573","https://openalex.org/W2044692345","https://openalex.org/W2046930479","https://openalex.org/W2047300623","https://openalex.org/W2050066317","https://openalex.org/W2052418876","https://openalex.org/W2053460598","https://openalex.org/W2059043977","https://openalex.org/W2059053384","https://openalex.org/W2060383308","https://openalex.org/W2063674195","https://openalex.org/W2064371703","https://openalex.org/W2069725730","https://openalex.org/W2070444361","https://openalex.org/W2071601513","https://openalex.org/W2074097219","https://openalex.org/W2075527287","https://openalex.org/W2077046573","https://openalex.org/W2077336113","https://openalex.org/W2081704409","https://openalex.org/W2083381199","https://openalex.org/W2087859143","https://openalex.org/W2088844778","https://openalex.org/W2091198609","https://openalex.org/W2092879602","https://openalex.org/W2093131463","https://openalex.org/W2094179288","https://openalex.org/W2095535075","https://openalex.org/W2097242011","https://openalex.org/W2097842145","https://openalex.org/W2097851712","https://openalex.org/W2098335118","https://openalex.org/W2098622547","https://openalex.org/W2101531288","https://openalex.org/W2102406695","https://openalex.org/W2102643936","https://openalex.org/W2103018966","https://openalex.org/W2103354991","https://openalex.org/W2104146201","https://openalex.org/W2105057212","https://openalex.org/W2106085645","https://openalex.org/W2108915709","https://openalex.org/W2109732750","https://openalex.org/W2111167674","https://openalex.org/W2114870653","https://openalex.org/W2115530456","https://openalex.org/W2117383597","https://openalex.org/W2119176236","https://openalex.org/W2120599553","https://openalex.org/W2122575917","https://openalex.org/W2127013070","https://openalex.org/W2132980978","https://openalex.org/W2133083344","https://openalex.org/W2133403209","https://openalex.org/W2133667940","https://openalex.org/W2133968430","https://openalex.org/W2138458807","https://openalex.org/W2141998004","https://openalex.org/W2143368326","https://openalex.org/W2144148386","https://openalex.org/W2146470265","https://openalex.org/W2153265394","https://openalex.org/W2155804510","https://openalex.org/W2157727502","https://openalex.org/W2158469604","https://openalex.org/W2159579373","https://openalex.org/W2166797651","https://openalex.org/W2167244112","https://openalex.org/W2171280873","https://openalex.org/W2171327609","https://openalex.org/W7097514665","https://openalex.org/W7100804310"],"related_works":["https://openalex.org/W1993927835","https://openalex.org/W7052896499","https://openalex.org/W7098585656","https://openalex.org/W7097796339","https://openalex.org/W3094784860","https://openalex.org/W2141688036","https://openalex.org/W2122121413","https://openalex.org/W303371926","https://openalex.org/W2024498258","https://openalex.org/W846913356"],"abstract_inverted_index":{"\\\\abstract":[0],"Transcription":[1],"and":[2,39,51,78,87,167,211,300,386,399,418,422,475],"translation":[3],"describe":[4,150],"the":[5,32,35,47,85,119,173,177,181,208,214,275,281,292,308,315,332,351,368,376,383,394,406,410,413,425,430,433,436,448,454,464,486,497],"flow":[6],"of":[7,34,37,49,89,121,176,180,183,213,241,267,277,283,295,310,318,334,371,389,396,409,412,424,435,444,457,466,488],"genetic":[8],"information":[9],"from":[10,322,367],"DNA":[11],"to":[12,14,99,104,137,154,189,195,217,232,238,259,375,429,468],"mRNA":[13,38,50,184],"protein.":[15],"Recent":[16],"studies":[17,83,490],"show":[18,301,403],"that":[19,112,246,302,404,471],"at":[20],"a":[21,101,151,160,164,169,202,341],"single":[22,55],"cell":[23,56],"level,":[24],"these":[25,61],"processes":[26],"are":[27,57,143,416],"stochastic,":[28],"which":[29,141,254,339],"results":[30],"in":[31,53,69,125,133,159,227,272,280,347,432,439,447,460,496],"variation":[33],"number":[36,48,182,193],"proteins":[40,352,470],"even":[41],"under":[42],"identical":[43],"environmental":[44],"conditions.":[45],"Because":[46],"protein":[52,261,303,319],"each":[54],"actually":[58],"very":[59],"small,":[60],"variations":[62],"can":[63],"be":[64,223,443],"crucial":[65],"for":[66,172,206,344,491],"cellular":[67],"function":[68,276],"diverse":[70],"contexts,":[71],"such":[72,244],"as":[73,163,221],"development,":[74],"stress":[75],"response,":[76],"immunological":[77],"nervous":[79,449,498],"system":[80],"function.":[81,482],"Most":[82],"examine":[84,130,190,331,485],"origin":[86],"effects":[88],"stochastic":[90,122,369],"gene":[91,107,123,157,234,284,326,378,440,494],"expression":[92,108,158,235,379,441,495],"using":[93,109],"computer":[94],"simulations.":[95],"My":[96],"goal":[97],"is":[98,236,250,340,361],"develop":[100],"theoretical":[102],"framework":[103],"study":[105],"activity-dependent":[106],"simplified":[110],"models":[111],"capture":[113],"essential":[114],"features.":[115],"I":[116,129,149,290,313,330,381,402,484],"have":[117,269,356],"examined":[118],"dynamics":[120],"regulation":[124,285,297],"three":[126],"contexts.":[127],"First,":[128],"how":[131,191,364],"fluctuations":[132,304,320,335],"promoter":[134],"accessibility":[135],"lead":[136],"\"bursty\"":[138],"transcription,":[139],"during":[140],"genes":[142,467],"turned":[144],"\"on\"":[145],"or":[146],"\"off\"":[147],"stochastically.":[148],"mathematical":[152],"formalism":[153],"represent":[155],"bursty":[156],"coarse-grained":[161],"manner":[162],"Markov":[165],"process":[166,216],"derive":[168],"master":[170],"equation":[171],"time":[174,196,218],"evolution":[175],"probability":[178],"distribution":[179],"molecules.":[185],"This":[186,199],"allows":[187],"us":[188],"transcript":[192,248],"responds":[194],"varying":[197,219],"stimuli.":[198],"model":[200],"forms":[201],"basic":[203],"building":[204],"block":[205],"understanding":[207],"signal":[209],"transmission":[210],"noise":[212,365,387],"transcription":[215],"inputs":[220],"would":[222],"sensed":[224],"by":[225,251,298,462],"cells":[226],"dynamic":[228],"environments.":[229],"In":[230],"addition":[231],"synthesis,":[233],"subject":[237],"additional":[239],"modes":[240],"regulation.":[242],"One":[243],"mechanism":[245],"controls":[247],"numbers":[249],"microRNAs":[252],"(miRNAs),":[253],"pair":[255],"with":[256],"target":[257],"mRNAs":[258,411],"repress":[260],"production":[262],"following":[263],"transcription.":[264],"Although":[265,350],"hundreds":[266],"miRNAs":[268,299],"been":[270,357],"identified":[271],"mammalian":[273],"genomes,":[274],"miRNA-based":[278],"repression":[279,324],"context":[282],"networks":[286],"still":[287],"remains":[288],"unclear.":[289],"explore":[291,382],"functional":[293,316,384],"roles":[294,385],"feedback":[296],"strongly":[305],"depend":[306],"on":[307,325,336,393],"mode":[309],"miRNA-mediated":[311,323],"repression.":[312],"discuss":[314],"implications":[317,487],"arising":[321,366],"regulatory":[327],"networks.":[328],"Finally,":[329,483],"impact":[333],"alternative":[337,354,372,390],"splicing,":[338,391],"major":[342],"source":[343],"proteomic":[345],"complexity":[346],"higher":[348,479],"eukaryotes.":[349],"regulating":[353],"splicing":[355,373,426],"extensively":[358],"studied,":[359],"little":[360],"known":[362],"about":[363],"nature":[370],"contributes":[374,428],"entire":[377],"process.":[380],"properties":[388],"focusing":[392],"case":[395],"exon":[397],"skipping":[398],"intron":[400],"retention.":[401],"while":[405],"overall":[407],"counts":[408],"two":[414],"isoforms":[415],"independent":[417],"Poisson":[419],"distributed,":[420],"diffusion":[421],"binding":[423],"factors":[427],"variance":[431],"abundance":[434],"isoforms.":[437],"Noise":[438],"may":[442],"particular":[445],"relevance":[446],"system.":[450,499],"Environmental":[451],"stimuli":[452],"drive":[453],"rapid":[455],"remodeling":[456],"neural":[458],"circuitry":[459],"part":[461],"inducing":[463],"activation":[465],"make":[469],"modify":[472],"neuronal":[473],"excitability":[474],"connectivity,":[476],"ultimately":[477],"influencing":[478],"order":[480],"brain":[481],"our":[489],"activity":[492],"dependent":[493]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2019,"cited_by_count":1}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2016-06-24T00:00:00"}
