{"id":"https://openalex.org/W2775388002","doi":"https://doi.org/10.1109/bibm.2017.8218034","title":"Development of an informatics analytics workflow for DAP-seq data exploration and validation for auxin response factors in maize","display_name":"Development of an informatics analytics workflow for DAP-seq data exploration and validation for auxin response factors in maize","publication_year":2017,"publication_date":"2017-11-01","ids":{"openalex":"https://openalex.org/W2775388002","doi":"https://doi.org/10.1109/bibm.2017.8218034","mag":"2775388002"},"language":"en","primary_location":{"id":"doi:10.1109/bibm.2017.8218034","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2017.8218034","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"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/A5045752323","display_name":"Sidharth Sen","orcid":"https://orcid.org/0000-0002-9196-204X"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sidharth Sen","raw_affiliation_strings":["Informatics Institute University of Missouri, Columbia, MO, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Informatics Institute University of Missouri, Columbia, MO, USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015253816","display_name":"Mary Galli","orcid":"https://orcid.org/0000-0001-7413-9409"},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mary Galli","raw_affiliation_strings":["Waksman Institute of Microbiology, Rutgers University, New Brunswick, NJ, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Waksman Institute of Microbiology, Rutgers University, New Brunswick, NJ, USA","institution_ids":["https://openalex.org/I102322142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086607445","display_name":"Andrea Gallavotti","orcid":"https://orcid.org/0000-0002-1901-2971"},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Andrea Gallavotti","raw_affiliation_strings":["Dept. of Plant Biology and Pathology, Rutgers University, New Brunswick, NJ, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept. of Plant Biology and Pathology, Rutgers University, New Brunswick, NJ, USA","institution_ids":["https://openalex.org/I102322142"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5071079252","display_name":"Trupti Joshi","orcid":"https://orcid.org/0000-0001-8944-4924"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Trupti Joshi","raw_affiliation_strings":["Dept. of HMI, University of Missouri, Columbia, MO, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept. of HMI, University of Missouri, Columbia, MO, USA","institution_ids":["https://openalex.org/I76835614"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"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":"2300","last_page":"2301"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10184","display_name":"Plant Molecular Biology Research","score":0.9972000122070312,"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"}},"topics":[{"id":"https://openalex.org/T10184","display_name":"Plant Molecular Biology Research","score":0.9972000122070312,"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"}},{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9968000054359436,"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/T11468","display_name":"Genetic Mapping and Diversity in Plants and Animals","score":0.9944999814033508,"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/workflow","display_name":"Workflow","score":0.6620914340019226},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5987406969070435},{"id":"https://openalex.org/keywords/informatics","display_name":"Informatics","score":0.5430648922920227},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.5169017314910889},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.46302762627601624},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.45886629819869995},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.4162346124649048},{"id":"https://openalex.org/keywords/health-informatics-tools","display_name":"Health informatics tools","score":0.41224798560142517},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4075673520565033},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.39579904079437256},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.36911338567733765},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3307892680168152},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.20793300867080688}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.6620914340019226},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5987406969070435},{"id":"https://openalex.org/C191630685","wikidata":"https://www.wikidata.org/wiki/Q4027615","display_name":"Informatics","level":2,"score":0.5430648922920227},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.5169017314910889},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.46302762627601624},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.45886629819869995},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.4162346124649048},{"id":"https://openalex.org/C167785021","wikidata":"https://www.wikidata.org/wiki/Q5691083","display_name":"Health informatics tools","level":3,"score":0.41224798560142517},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4075673520565033},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.39579904079437256},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.36911338567733765},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3307892680168152},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.20793300867080688},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm.2017.8218034","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2017.8218034","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":4,"referenced_works":["https://openalex.org/W1876346091","https://openalex.org/W2109897790","https://openalex.org/W2171808845","https://openalex.org/W2401562190"],"related_works":["https://openalex.org/W2463183163","https://openalex.org/W2017123803","https://openalex.org/W2974071312","https://openalex.org/W2320705913","https://openalex.org/W2955949264","https://openalex.org/W2005011662","https://openalex.org/W3174814859","https://openalex.org/W4311292698","https://openalex.org/W4309236105","https://openalex.org/W2979004191"],"abstract_inverted_index":{"DNA":[0],"affinity":[1],"purification":[2],"sequencing":[3],"(DAP-seq)":[4],"is":[5,29],"a":[6,107,134],"recently":[7],"developed":[8],"technique":[9],"for":[10,44,88],"transcription":[11,142],"factor":[12,143],"(TF)":[13],"binding":[14,55,77,144,166],"site":[15,145],"discovery":[16],"that":[17,30],"produces":[18],"datasets":[19,207],"like":[20],"ChIP-seq.":[21],"A":[22],"major":[23],"advantage":[24],"of":[25,66,79,123,133,136,160,175,187,219,225],"the":[26,42,64,67,158,164,171,205,223],"DAP-seq":[27,115,206],"method":[28,72],"it":[31],"uses":[32],"exogenously":[33],"expressed":[34],"TFs":[35,124],"to":[36,73,116,170,181,185,208],"directly":[37],"interrogate":[38],"genomic":[39,59,211],"DNA,":[40],"without":[41],"need":[43],"tagged":[45],"transgenic":[46],"lines":[47],"or":[48,90],"gene-specific":[49],"antibodies":[50],"while":[51],"still":[52],"capturing":[53],"TF":[54],"events":[56],"in":[57,100,110],"their":[58],"sequence":[60],"context.":[61],"To":[62],"assess":[63],"accuracy":[65,159,224],"DAP-seq,":[68],"we":[69,221],"utilized":[70],"this":[71,120,200],"generate":[74],"genome":[75],"wide":[76],"profiles":[78],"maize":[80],"AUXIN":[81],"RESPONSE":[82],"FACTORS":[83],"(ARFs).":[84],"ARFs":[85,178],"are":[86,179],"responsible":[87],"activating":[89],"repressing":[91],"auxin":[92],"response":[93],"genes":[94],"and":[95,102,141,173,195,230],"play":[96],"an":[97],"important":[98,121],"role":[99],"growth":[101],"developmental":[103],"processes.":[104],"This":[105],"provides":[106],"typical":[108],"scenario":[109],"which":[111],"researchers":[112],"would":[113],"use":[114],"better":[117],"understand":[118],"how":[119],"family":[122],"regulates":[125],"gene":[126],"expression.":[127],"The":[128],"informatics":[129],"analysis":[130],"workflow":[131,203],"consists":[132],"selection":[135],"highly":[137],"validated":[138],"read":[139],"aligners":[140],"prediction":[146],"bioinformatics":[147],"tools":[148],"supported":[149],"by":[150],"in-house":[151],"built":[152],"custom":[153],"python":[154],"scripts.":[155],"We":[156],"investigate":[157],"pattern":[161],"mining":[162],"underlying":[163],"ARF":[165],"signatures":[167],"with":[168,213,227],"respect":[169],"presence":[172],"position":[174],"conserved":[176],"motifs.":[177],"known":[180,228],"bind":[182],"as":[183,190],"dimers":[184],"pairs":[186],"TGTC":[188],"motifs":[189],"direct":[191],"repeats,":[192],"inverted":[193],"repeats":[194],"everted":[196],"repeats.":[197],"Based":[198],"on":[199],"knowledge,":[201],"our":[202,234],"mines":[204],"find":[209],"specific":[210],"regions":[212],"such":[214],"signatures.":[215],"After":[216],"each":[217],"round":[218],"mining,":[220],"validate":[222],"results":[226],"patterns":[229],"domain":[231],"knowledge":[232],"from":[233],"collaborators.":[235]},"counts_by_year":[],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}
