{"id":"https://openalex.org/W21723742","doi":null,"title":"BIOPHYSICAL MODELS OF TRANSCRIPTIONAL REGULATION FROM SEQUENCE DATA","display_name":"BIOPHYSICAL MODELS OF TRANSCRIPTIONAL REGULATION FROM SEQUENCE DATA","publication_year":2008,"publication_date":"2008-01-01","ids":{"openalex":"https://openalex.org/W21723742","mag":"21723742"},"language":"en","primary_location":{"id":"pmh:oai:repository.cshl.edu:31365","doi":null,"is_oa":false,"landing_page_url":"https://repository.cshl.edu/id/eprint/31365/","pdf_url":null,"source":{"id":"https://openalex.org/S4306402288","display_name":"Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"Thesis"},"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/A5069407651","display_name":"Justin B. Kinney","orcid":"https://orcid.org/0000-0003-1897-3778","observed_orcids":["https://orcid.org/0000-0003-1897-3778"]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Justin B. Kinney","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0003-1897-3778","affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5069407651"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.7202000021934509,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.7202000021934509,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.12700000405311584,"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.05990000069141388,"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/transcriptional-regulation","display_name":"transcriptional regulation","score":0.9980000257492065},{"id":"https://openalex.org/keywords/dna-sequence-data","display_name":"DNA sequence data","score":0.5099999904632568},{"id":"https://openalex.org/keywords/experimental-noise","display_name":"experimental noise","score":0.6690000295639038},{"id":"https://openalex.org/keywords/mutual-information","display_name":"mutual information","score":0.6480000019073486},{"id":"https://openalex.org/keywords/microarray-data","display_name":"microarray data","score":0.6959999799728394},{"id":"https://openalex.org/keywords/transcription-factors","display_name":"transcription factors","score":0.8790000081062317},{"id":"https://openalex.org/keywords/protein-dna-interactions","display_name":"protein-DNA interactions","score":0.7559999823570251},{"id":"https://openalex.org/keywords/protein-protein-interaction","display_name":"protein-protein interaction","score":0.9900000095367432},{"id":"https://openalex.org/keywords/c-reactive-protein","display_name":"C-reactive protein","score":0.7919999957084656},{"id":"https://openalex.org/keywords/lacz-promoter","display_name":"lacZ promoter","score":0.9900000095367432},{"id":"https://openalex.org/keywords/escherichia-coli","display_name":"Escherichia coli","score":0.7419999837875366},{"id":"https://openalex.org/keywords/biophysical-modeling","display_name":"biophysical model","score":0.5410000085830688}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5502106547355652},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.5451395511627197},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5375563502311707},{"id":"https://openalex.org/C75553542","wikidata":"https://www.wikidata.org/wiki/Q178161","display_name":"A priori and a posteriori","level":2,"score":0.5008032321929932},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.48470354080200195},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.4835924506187439},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.47879037261009216},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.42156532406806946},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.41906440258026123},{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.4161224663257599},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.37162935733795166},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.315280020236969},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.28320759534835815},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.23788166046142578},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.23756659030914307},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2009783685207367},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.19116085767745972},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:repository.cshl.edu:31365","doi":null,"is_oa":false,"landing_page_url":"https://repository.cshl.edu/id/eprint/31365/","pdf_url":null,"source":{"id":"https://openalex.org/S4306402288","display_name":"Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"Thesis"},{"id":"mag:21723742","doi":null,"is_oa":false,"landing_page_url":"https://www.princeton.edu/physics/graduate-program/theses/theses-from-2008/J.Kinneythesis.pdf","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":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":108,"referenced_works":["https://openalex.org/W201917955","https://openalex.org/W1182508228","https://openalex.org/W1482227507","https://openalex.org/W1498410508","https://openalex.org/W1502502335","https://openalex.org/W1506197483","https://openalex.org/W1544162067","https://openalex.org/W1562374859","https://openalex.org/W1584866863","https://openalex.org/W1593308984","https://openalex.org/W1658221551","https://openalex.org/W1930635754","https://openalex.org/W1975036436","https://openalex.org/W1980253661","https://openalex.org/W1986902849","https://openalex.org/W1986920519","https://openalex.org/W1989080074","https://openalex.org/W1991770658","https://openalex.org/W1992536060","https://openalex.org/W1994057432","https://openalex.org/W1994122295","https://openalex.org/W1998300401","https://openalex.org/W1999602995","https://openalex.org/W2001706442","https://openalex.org/W2001770641","https://openalex.org/W2001798854","https://openalex.org/W2002841189","https://openalex.org/W2007969038","https://openalex.org/W2010888033","https://openalex.org/W2011871011","https://openalex.org/W2014047578","https://openalex.org/W2018507982","https://openalex.org/W2022217979","https://openalex.org/W2022891974","https://openalex.org/W2025183920","https://openalex.org/W2032548898","https://openalex.org/W2034817839","https://openalex.org/W2038186289","https://openalex.org/W2038282326","https://openalex.org/W2046355391","https://openalex.org/W2048066878","https://openalex.org/W2048869777","https://openalex.org/W2049633694","https://openalex.org/W2053671774","https://openalex.org/W2054624670","https://openalex.org/W2055723458","https://openalex.org/W2056002855","https://openalex.org/W2058332274","https://openalex.org/W2058552632","https://openalex.org/W2059328257","https://openalex.org/W2059699217","https://openalex.org/W2065579185","https://openalex.org/W2073850887","https://openalex.org/W2079321730","https://openalex.org/W2079450159","https://openalex.org/W2080152736","https://openalex.org/W2080498142","https://openalex.org/W2082682118","https://openalex.org/W2084908610","https://openalex.org/W2087234479","https://openalex.org/W2091307684","https://openalex.org/W2092980609","https://openalex.org/W2095749144","https://openalex.org/W2096121210","https://openalex.org/W2097173970","https://openalex.org/W2099111195","https://openalex.org/W2108190672","https://openalex.org/W2109584604","https://openalex.org/W2110310164","https://openalex.org/W2112621436","https://openalex.org/W2118304741","https://openalex.org/W2118628540","https://openalex.org/W2121356022","https://openalex.org/W2122107930","https://openalex.org/W2122452605","https://openalex.org/W2125498357","https://openalex.org/W2125819516","https://openalex.org/W2126602684","https://openalex.org/W2128114769","https://openalex.org/W2129344046","https://openalex.org/W2129795133","https://openalex.org/W2130174998","https://openalex.org/W2133369691","https://openalex.org/W2136093058","https://openalex.org/W2141354959","https://openalex.org/W2142691347","https://openalex.org/W2144347639","https://openalex.org/W2144634347","https://openalex.org/W2144710927","https://openalex.org/W2146196741","https://openalex.org/W2146264532","https://openalex.org/W2147794131","https://openalex.org/W2147946837","https://openalex.org/W2149769193","https://openalex.org/W2150301908","https://openalex.org/W2151387592","https://openalex.org/W2151907070","https://openalex.org/W2159883877","https://openalex.org/W2161224111","https://openalex.org/W2162966913","https://openalex.org/W2165182519","https://openalex.org/W2165228646","https://openalex.org/W2166277117","https://openalex.org/W2171878324","https://openalex.org/W2582938705","https://openalex.org/W2593075177","https://openalex.org/W2887017701","https://openalex.org/W4242441490"],"related_works":["https://openalex.org/W2159933659","https://openalex.org/W2810602463","https://openalex.org/W2036122730","https://openalex.org/W2737890714","https://openalex.org/W7014682843","https://openalex.org/W2064464492","https://openalex.org/W4414453660","https://openalex.org/W1981779495","https://openalex.org/W2161013044","https://openalex.org/W2795970574"],"abstract_inverted_index":{"In":[0],"the":[1,18,65,78,85,109,146,212,243,265,276,281,307,334],"post-genomics":[2],"era,":[3],"DNA":[4,53,112,339],"sequence":[5,30,54,113,121,340],"itself":[6,341],"is":[7,62,72,123,145,180],"becoming":[8,34],"a":[9,48,126,152,230,259,344],"medium":[10],"by":[11,104,125,158,348],"which":[12,91,119,140,163,349],"to":[13,58,89,95,171,175,183,208,221,228,241,274,318,350],"probe":[14,242,351],"biological":[15,60],"phenomena.":[16],"With":[17],"advent":[19,335],"of":[20,37,51,69,87,111,132,138,148,167,215,268,280,309,336],"microarray":[21,201],"technology,":[22],"and":[23,97,245,322],"ultrahigh-":[24],"throughput":[25],"sequencing":[26,240],"more":[27],"recently,":[28],"large":[29,295],"data":[31,46,114,117,144,225,257,271,297,305],"sets":[32],"are":[33],"standard":[35],"products":[36],"day-to-day":[38],"research.":[39],"Yet":[40],"as":[41,100],"software":[42],"for":[43,76,108,118,211],"analyzing":[44],"such":[45,142],"proliferates,":[47],"fundamental":[49],"understanding":[50],"how":[52],"should":[55,315],"be":[56,172,316],"used":[57],"gain":[59],"insight":[61],"missing":[63],"from":[64,258,294],"literature.":[66],"The":[67,219],"focus":[68],"this":[70,156],"thesis":[71],"on":[73,198],"developing":[74],"tools":[75],"characterizing":[77,149],"biophysical":[79,133,165],"interactions":[80,247],"underlying":[81,248],"transcriptional":[82,249],"regulation":[83,250],"{":[84,115],"ability":[86,220],"cells":[88],"control":[90],"genes":[92],"they":[93],"transcribe":[94],"mRNA,":[96],"thus":[98],"express":[99],"protein.":[101],"We":[102,154,193,255,285,299,330],"begin":[103],"presenting":[105],"basic":[106],"principles":[107],"analysis":[110],"specically,":[116],"each":[120],"\ufffd":[122],"accompanied":[124],"(perhaps":[127],"very":[128,345],"noisy)":[129],"measurement":[130],"z":[131],"functionality.":[134],"A":[135],"salient":[136],"feature":[137],"experiments":[139],"produce":[141],"\ufffdz":[143,176,224,304],"di\ufffdculty":[147],"experimental":[150,232],"noise":[151],"priori.":[153],"overcome":[155],"obstacle":[157],"introducing":[159],"error-model-averaged":[160],"(EMA)":[161],"likelihood,":[162],"allows":[164],"models":[166,210],"arbitrary":[168],"functional":[169],"form":[170],"rigorously":[173],"t":[174],"data.":[177],"EMA":[178,195],"likelihood":[179],"closely":[181],"related":[182],"mutual":[184],"information,":[185],"but":[186],"its":[187],"probabilistic":[188],"interpretation":[189],"provides":[190],"some":[191],"advantages.":[192],"demonstrate":[194],"likelihood's":[196],"utility":[197],"previously":[199],"published":[200],"data,":[202],"using":[203],"Metropolis":[204],"Monte":[205],"Carlo":[206],"sampling":[207],"infer":[209,293,319],"DNA-binding":[213],"energy":[214,279],"transcription":[216,282],"factor":[217,283],"proteins.":[218],"properly":[222],"analyze":[223],"leads":[226],"us":[227],"propose":[229],"new":[231],"assay,":[233],"called":[234],"Sort-Seq.":[235],"This":[236],"technique":[237],"uses":[238],"ultra-high-throughput":[239],"protein-DNA":[244,321],"protein-protein":[246,323],"at":[251],"specific":[252],"genomic":[253],"loci.":[254],"present":[256],"proof-of-principle":[260],"Sort-":[261],"Seq":[262],"experiment":[263],"probing":[264,306],"lacZ":[266],"promoter":[267],"E.":[269],"coli,":[270],"we":[272],"use":[273],"characterize":[275],"sequence-dependent":[277],"binding":[278,308],"CRP.":[284],"then":[286],"discuss":[287],"what":[288],"one":[289,314],"can,":[290],"in":[291,326,352],"principle,":[292],"Sort-Seq":[296],"sets.":[298],"show":[300],"that,":[301,332],"with":[302,333],"enough":[303],"multiple":[310],"proteins":[311],"per":[312],"sequence,":[313],"able":[317],"both":[320],"interaction":[324],"energies":[325],"absolute":[327],"thermal":[328],"units.":[329],"conclude":[331],"ultra-highthroughput":[337],"sequencing,":[338],"might":[342],"provide":[343],"sensitive":[346],"means":[347],"vivo":[353],"biophysics.":[354]},"counts_by_year":[{"year":2014,"cited_by_count":1}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2016-06-24T00:00:00"}
