{"id":"https://openalex.org/W2524253479","doi":null,"title":"Computational Study of Transcriptional Regulation- From Sequence To Expression","display_name":"Computational Study of Transcriptional Regulation- From Sequence To Expression","publication_year":2013,"publication_date":"2013-01-01","ids":{"openalex":"https://openalex.org/W2524253479","mag":"2524253479"},"language":"en","primary_location":{"id":"pmh:oai:CiteSeerX.psu:10.1.1.363.406","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.363.406","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://reports-archive.adm.cs.cmu.edu/anon/lane/CMU-CB-13-101.pdf","raw_type":"text"},"volume":null,"type":"article","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":null,"display_name":"Shan Zhong","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Shan Zhong","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":null,"display_name":"Roni Rosenfeld","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Roni Rosenfeld","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.0,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"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":0.9818999767303467,"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":0.9818999767303467,"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":0.011300000362098217,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.0008999999845400453,"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/transcriptional-regulation","display_name":"transcriptional regulation","score":0.9990000128746033},{"id":"https://openalex.org/keywords/cis-regulatory-elements","display_name":"cis-regulatory elements","score":0.8949999809265137},{"id":"https://openalex.org/keywords/trans-acting-factors","display_name":"trans-acting factors","score":0.8949999809265137},{"id":"https://openalex.org/keywords/dna-binding-site-prediction","display_name":"DNA binding site prediction","score":0.7599999904632568},{"id":"https://openalex.org/keywords/gene-expression","display_name":"gene expression","score":0.8769999742507935},{"id":"https://openalex.org/keywords/eukaryotic-transcription","display_name":"eukaryotic transcription","score":0.9010000228881836},{"id":"https://openalex.org/keywords/spatiotemporal-gene-regulation","display_name":"spatiotemporal gene regulation","score":0.7860000133514404}],"concepts":[{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5587627291679382},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.539574384689331},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4821493327617645},{"id":"https://openalex.org/C27153228","wikidata":"https://www.wikidata.org/wiki/Q3787274","display_name":"Transcriptional regulation","level":4,"score":0.43744656443595886},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.41859710216522217},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3845561444759369},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.35967952013015747},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.32870322465896606},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.24505341053009033},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"pmh:oai:CiteSeerX.psu:10.1.1.363.406","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.363.406","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://reports-archive.adm.cs.cmu.edu/anon/lane/CMU-CB-13-101.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":193,"referenced_works":["https://openalex.org/W250876507","https://openalex.org/W1550637999","https://openalex.org/W1592870802","https://openalex.org/W1963778673","https://openalex.org/W1964031474","https://openalex.org/W1964719993","https://openalex.org/W1964963969","https://openalex.org/W1966354073","https://openalex.org/W1969415039","https://openalex.org/W1970156673","https://openalex.org/W1974939794","https://openalex.org/W1975036436","https://openalex.org/W1977620504","https://openalex.org/W1981509058","https://openalex.org/W1988294855","https://openalex.org/W1989080074","https://openalex.org/W1990157223","https://openalex.org/W1994122295","https://openalex.org/W1994383643","https://openalex.org/W1996212302","https://openalex.org/W1997956266","https://openalex.org/W1998000745","https://openalex.org/W1998300401","https://openalex.org/W2003616516","https://openalex.org/W2006617902","https://openalex.org/W2008051478","https://openalex.org/W2009001778","https://openalex.org/W2009576540","https://openalex.org/W2012114217","https://openalex.org/W2014529296","https://openalex.org/W2016344207","https://openalex.org/W2025129963","https://openalex.org/W2025722611","https://openalex.org/W2026328081","https://openalex.org/W2027287962","https://openalex.org/W2027458139","https://openalex.org/W2030216833","https://openalex.org/W2032609519","https://openalex.org/W2033396645","https://openalex.org/W2034145535","https://openalex.org/W2035188041","https://openalex.org/W2036131961","https://openalex.org/W2036145288","https://openalex.org/W2037787140","https://openalex.org/W2037992536","https://openalex.org/W2038282326","https://openalex.org/W2039176012","https://openalex.org/W2040686597","https://openalex.org/W2041877620","https://openalex.org/W2042392223","https://openalex.org/W2044937161","https://openalex.org/W2045299822","https://openalex.org/W2045362835","https://openalex.org/W2046624631","https://openalex.org/W2046853446","https://openalex.org/W2047708521","https://openalex.org/W2048263136","https://openalex.org/W2048695823","https://openalex.org/W2048822761","https://openalex.org/W2049101886","https://openalex.org/W2049339208","https://openalex.org/W2049481764","https://openalex.org/W2059667789","https://openalex.org/W2059699217","https://openalex.org/W2059774006","https://openalex.org/W2062155001","https://openalex.org/W2062553575","https://openalex.org/W2063978378","https://openalex.org/W2066011773","https://openalex.org/W2067339099","https://openalex.org/W2067387842","https://openalex.org/W2069013709","https://openalex.org/W2069645361","https://openalex.org/W2073850887","https://openalex.org/W2074324848","https://openalex.org/W2076439598","https://openalex.org/W2077606580","https://openalex.org/W2078034709","https://openalex.org/W2078059415","https://openalex.org/W2080498142","https://openalex.org/W2081468394","https://openalex.org/W2081592065","https://openalex.org/W2083835304","https://openalex.org/W2084831115","https://openalex.org/W2084908610","https://openalex.org/W2085442947","https://openalex.org/W2086745302","https://openalex.org/W2087676315","https://openalex.org/W2089515936","https://openalex.org/W2089783852","https://openalex.org/W2091176739","https://openalex.org/W2093255871","https://openalex.org/W2095005830","https://openalex.org/W2095532403","https://openalex.org/W2095718954","https://openalex.org/W2095791120","https://openalex.org/W2097117811","https://openalex.org/W2097175728","https://openalex.org/W2098115340","https://openalex.org/W2101142880","https://openalex.org/W2102904139","https://openalex.org/W2103941911","https://openalex.org/W2104748610","https://openalex.org/W2105025553","https://openalex.org/W2105924780","https://openalex.org/W2108539079","https://openalex.org/W2108675631","https://openalex.org/W2109502519","https://openalex.org/W2109521384","https://openalex.org/W2110503722","https://openalex.org/W2111840226","https://openalex.org/W2112019511","https://openalex.org/W2114324579","https://openalex.org/W2114715558","https://openalex.org/W2115248104","https://openalex.org/W2115428292","https://openalex.org/W2116194650","https://openalex.org/W2116735936","https://openalex.org/W2118628540","https://openalex.org/W2119559540","https://openalex.org/W2119804413","https://openalex.org/W2120391288","https://openalex.org/W2121607820","https://openalex.org/W2121967239","https://openalex.org/W2122056961","https://openalex.org/W2122342005","https://openalex.org/W2124112735","https://openalex.org/W2124201592","https://openalex.org/W2124716054","https://openalex.org/W2125598804","https://openalex.org/W2125631472","https://openalex.org/W2126558916","https://openalex.org/W2129795133","https://openalex.org/W2129905922","https://openalex.org/W2131918846","https://openalex.org/W2132872450","https://openalex.org/W2133009404","https://openalex.org/W2133036743","https://openalex.org/W2134459829","https://openalex.org/W2135030836","https://openalex.org/W2135517348","https://openalex.org/W2137543617","https://openalex.org/W2137683543","https://openalex.org/W2138522837","https://openalex.org/W2139025111","https://openalex.org/W2139617657","https://openalex.org/W2140952049","https://openalex.org/W2141224484","https://openalex.org/W2141408320","https://openalex.org/W2142410561","https://openalex.org/W2143310096","https://openalex.org/W2144665374","https://openalex.org/W2144738674","https://openalex.org/W2146894368","https://openalex.org/W2147213963","https://openalex.org/W2147946837","https://openalex.org/W2148101811","https://openalex.org/W2150076905","https://openalex.org/W2151686961","https://openalex.org/W2152482800","https://openalex.org/W2153726199","https://openalex.org/W2154383218","https://openalex.org/W2155718935","https://openalex.org/W2156643308","https://openalex.org/W2156733952","https://openalex.org/W2157758083","https://openalex.org/W2160894282","https://openalex.org/W2161197995","https://openalex.org/W2161523118","https://openalex.org/W2161849959","https://openalex.org/W2164814636","https://openalex.org/W2166277117","https://openalex.org/W2166429927","https://openalex.org/W2167499687","https://openalex.org/W2167827705","https://openalex.org/W2169950095","https://openalex.org/W2170037981","https://openalex.org/W2171030481","https://openalex.org/W2171111703","https://openalex.org/W2171369894","https://openalex.org/W2171407623","https://openalex.org/W2171808845","https://openalex.org/W2171941327","https://openalex.org/W2177510297","https://openalex.org/W2293652778","https://openalex.org/W2328176404","https://openalex.org/W2396024272","https://openalex.org/W2610493035","https://openalex.org/W7070664267","https://openalex.org/W7095841607","https://openalex.org/W7098463784","https://openalex.org/W7099666281","https://openalex.org/W7100282755"],"related_works":["https://openalex.org/W1627262848","https://openalex.org/W7097968211","https://openalex.org/W7099753738","https://openalex.org/W7001347304","https://openalex.org/W74189222","https://openalex.org/W1777042887","https://openalex.org/W1915321537","https://openalex.org/W2026234230","https://openalex.org/W7099123280","https://openalex.org/W6906823784"],"abstract_inverted_index":{"Transcription":[0,16,42],"is":[1,23,43,63,89],"the":[2,12,24,28,55,132,171],"process":[3,92],"during":[4],"which":[5,111],"RNA":[6],"molecules":[7],"are":[8,108],"synthesized":[9],"based":[10],"on":[11],"DNAs":[13],"in":[14,27,75,80,141,146],"cells.":[15],"leads":[17],"to":[18,35,82,128,167,170],"gene":[19],"expression,":[20],"and":[21,48,70,79,93,100,113,131,160],"it":[22],"first":[25],"step":[26],"flow":[29],"of":[30,57,68,121,157,173],"genetic":[31],"information":[32],"from":[33,144],"DNA":[34,174],"proteins":[36],"that":[37,54],"carry":[38],"out":[39],"biological":[40],"functions.":[41],"tightly":[44],"regulated":[45,109],"both":[46,97],"spatially":[47],"temporally":[49],"at":[50,139],"multiple":[51],"levels,":[52],"so":[53],"amount":[56],"mRNAs":[58],"produced":[59],"for":[60],"different":[61,66,76,83],"genes":[62,107],"controlled":[64],"across":[65],"kinds":[67],"cells":[69],"tissues,":[71],"as":[72,74],"well":[73],"developmental":[77],"stages":[78],"response":[81],"environmental":[84,129],"stimulus.":[85],"In":[86,150],"eukaryotes,":[87],"transcription":[88],"a":[90,118,155,165],"complicated":[91],"its":[94],"regulation":[95],"involves":[96],"cis-regulatory":[98],"elements":[99],"trans-acting":[101],"factors.":[102],"By":[103],"studying":[104],"spatiotemporally":[105],"what":[106],"by":[110],"cis-elements":[112],"trans-factors,":[114],"we":[115,123,126,153],"can":[116],"get":[117],"better":[119],"understanding":[120],"how":[122,125],"develop,":[124],"react":[127],"signals,":[130],"mechanisms":[133],"behind":[134],"diseases":[135],"like":[136],"cancer":[137],"that,":[138,162],"least":[140],"part,":[142],"result":[143],"failures":[145],"proper":[147],"transcriptional":[148],"regulation.":[149],"this":[151],"thesis,":[152],"present":[154],"suite":[156],"computational":[158],"methods":[159],"analyses":[161],"combined,":[163],"provide":[164],"solution":[166],"problems":[168],"related":[169],"identification":[172],"binding":[175]},"counts_by_year":[],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2025-10-27T00:00:00"}
