{"id":"https://openalex.org/W2417242574","doi":"https://doi.org/10.1385/1-59259-850-1:439","title":"In Silico and Wet-Bench Identification of Nuclear Matrix Attachment Regions","display_name":"In Silico and Wet-Bench Identification of Nuclear Matrix Attachment Regions","publication_year":2005,"publication_date":"2005-07-21","ids":{"openalex":"https://openalex.org/W2417242574","doi":"https://doi.org/10.1385/1-59259-850-1:439","mag":"2417242574","pmid":"https://pubmed.ncbi.nlm.nih.gov/16028699"},"language":"en","primary_location":{"id":"doi:10.1385/1-59259-850-1:439","doi":"https://doi.org/10.1385/1-59259-850-1:439","is_oa":false,"landing_page_url":"https://doi.org/10.1385/1-59259-850-1:439","pdf_url":null,"source":{"id":"https://openalex.org/S4306463399","display_name":"Humana Press eBooks","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/P4310315801","host_organization_name":"Humana Press","host_organization_lineage":["https://openalex.org/P4310315801","https://openalex.org/P4310319900"],"host_organization_lineage_names":["Humana Press","Springer Science+Business Media"],"type":"ebook platform"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Hypertension","raw_type":"book-chapter"},"volume":{"id":"https://openalex.org/W4251630725","display_name":"Hypertension"},"type":"book-chapter","indexed_in":["crossref","pubmed"],"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/A5045463023","display_name":"Stephen A. Krawetz","orcid":"https://orcid.org/0000-0002-7113-2364","observed_orcids":["https://orcid.org/0000-0002-7113-2364"]},"institutions":[{"id":"https://openalex.org/I185443292","display_name":"Wayne State University","ror":"https://ror.org/01070mq45","country_code":"US","type":"education","lineage":["https://openalex.org/I185443292"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Stephen A. Krawetz","raw_affiliation_strings":["Department of Obstetrics and Gynecology, Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA","Departments of Obstetrics and Gynecology and Computer Sciences, Center for Molecular Medicine and Genetics, Center for Scientific Computing, Wayne State University, Detroit, MI"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Obstetrics and Gynecology, Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA","institution_ids":["https://openalex.org/I185443292"]},{"raw_affiliation_string":"Departments of Obstetrics and Gynecology and Computer Sciences, Center for Molecular Medicine and Genetics, Center for Scientific Computing, Wayne State University, Detroit, MI","institution_ids":["https://openalex.org/I185443292"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006190733","display_name":"Sorin Dr\u0103ghici","orcid":"https://orcid.org/0000-0002-0786-8377","observed_orcids":["https://orcid.org/0000-0002-0786-8377"]},"institutions":[{"id":"https://openalex.org/I185443292","display_name":"Wayne State University","ror":"https://ror.org/01070mq45","country_code":"US","type":"education","lineage":["https://openalex.org/I185443292"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sorin Draghici","raw_affiliation_strings":["Department of Computer Sciences, Center for Scientific Computing, Wayne State University, Detroit, MI"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Sciences, Center for Scientific Computing, Wayne State University, Detroit, MI","institution_ids":["https://openalex.org/I185443292"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012153471","display_name":"Robert J. Goodrich","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I185443292","display_name":"Wayne State University","ror":"https://ror.org/01070mq45","country_code":"US","type":"education","lineage":["https://openalex.org/I185443292"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert Goodrich","raw_affiliation_strings":["Department of Obstetrics and Gynecology, Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Obstetrics and Gynecology, Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI","institution_ids":["https://openalex.org/I185443292"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004947640","display_name":"Zhandong Liu","orcid":"https://orcid.org/0000-0002-7608-0831","observed_orcids":["https://orcid.org/0000-0002-7608-0831","https://orcid.org/0000-0002-5310-8272"]},"institutions":[{"id":"https://openalex.org/I185443292","display_name":"Wayne State University","ror":"https://ror.org/01070mq45","country_code":"US","type":"education","lineage":["https://openalex.org/I185443292"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhandong Liu","raw_affiliation_strings":["Department of Computer Sciences, Wayne State University, Detroit, MI"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Sciences, Wayne State University, Detroit, MI","institution_ids":["https://openalex.org/I185443292"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5077140220","display_name":"Garry Charles Ostermeier","orcid":"https://orcid.org/0000-0002-3951-512X","observed_orcids":["https://orcid.org/0000-0002-3951-512X"]},"institutions":[{"id":"https://openalex.org/I185443292","display_name":"Wayne State University","ror":"https://ror.org/01070mq45","country_code":"US","type":"education","lineage":["https://openalex.org/I185443292"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"G. Charles Ostermeier","raw_affiliation_strings":["Department of Computer Sciences, Wayne State University, Detroit, MI"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Sciences, Wayne State University, Detroit, MI","institution_ids":["https://openalex.org/I185443292"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I185443292"],"apc_list":null,"apc_paid":null,"fwci":3.7292,"has_fulltext":false,"cited_by_count":13,"citation_normalized_percentile":{"value":0.93196544,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"108","issue":null,"first_page":"439","last_page":"458"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9994999766349792,"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":0.9994999766349792,"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/T11841","display_name":"Nuclear Structure and Function","score":9.999999747378752e-05,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":9.999999747378752e-05,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/matrix-attachment-regions","display_name":"matrix attachment regions","score":0.9589999914169312},{"id":"https://openalex.org/keywords/chromatin-looping","display_name":"chromatin looping","score":0.9259999990463257},{"id":"https://openalex.org/keywords/nuclear-matrix","display_name":"nuclear matrix","score":0.5249999761581421},{"id":"https://openalex.org/keywords/chromatin-organization","display_name":"chromatin organization","score":0.49799999594688416},{"id":"https://openalex.org/keywords/replication-origins","display_name":"origin of replication","score":0.7080000042915344},{"id":"https://openalex.org/keywords/transcription-factor-binding-sites","display_name":"transcription factor binding sites","score":0.8080000281333923},{"id":"https://openalex.org/keywords/gene-expression-regulation","display_name":"gene expression regulation","score":0.8169999718666077},{"id":"https://openalex.org/keywords/in-silico-identification","display_name":"in silico identification","score":0.6729999780654907}],"concepts":[{"id":"https://openalex.org/C56262557","wikidata":"https://www.wikidata.org/wiki/Q3931949","display_name":"Scaffold/matrix attachment region","level":5,"score":0.8247905969619751},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.7476978302001953},{"id":"https://openalex.org/C105686024","wikidata":"https://www.wikidata.org/wiki/Q906755","display_name":"Nuclear matrix","level":4,"score":0.7202423810958862},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.6975300312042236},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.555791974067688},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4851308763027191},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4613402485847473},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4512816369533539},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4382416009902954},{"id":"https://openalex.org/C93946551","wikidata":"https://www.wikidata.org/wiki/Q5113914","display_name":"Chromosome conformation capture","level":5,"score":0.41676396131515503},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.3863086998462677},{"id":"https://openalex.org/C167227067","wikidata":"https://www.wikidata.org/wiki/Q5113739","display_name":"Chromatin remodeling","level":4,"score":0.16200760006904602},{"id":"https://openalex.org/C111936080","wikidata":"https://www.wikidata.org/wiki/Q913367","display_name":"Enhancer","level":4,"score":0.15553772449493408}],"mesh":[{"descriptor_ui":"D000199","descriptor_name":"Actins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006367","descriptor_name":"HeLa Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015530","descriptor_name":"Nuclear Matrix","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016133","descriptor_name":"Polymerase Chain Reaction","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1385/1-59259-850-1:439","doi":"https://doi.org/10.1385/1-59259-850-1:439","is_oa":false,"landing_page_url":"https://doi.org/10.1385/1-59259-850-1:439","pdf_url":null,"source":{"id":"https://openalex.org/S4306463399","display_name":"Humana Press eBooks","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/P4310315801","host_organization_name":"Humana Press","host_organization_lineage":["https://openalex.org/P4310315801","https://openalex.org/P4310319900"],"host_organization_lineage_names":["Humana Press","Springer Science+Business Media"],"type":"ebook platform"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Hypertension","raw_type":"book-chapter"},{"id":"pmid:16028699","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16028699","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Methods in molecular medicine","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"sustainable_development_goals_aurora":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":3,"referenced_works":["https://openalex.org/W1964149125","https://openalex.org/W1984594229","https://openalex.org/W2055307610"],"related_works":["https://openalex.org/W2075220753","https://openalex.org/W2124773748","https://openalex.org/W2016733318","https://openalex.org/W2001354824","https://openalex.org/W1994928481","https://openalex.org/W2019310739","https://openalex.org/W2520694393","https://openalex.org/W2090980177","https://openalex.org/W1492579595","https://openalex.org/W2069949654"],"abstract_inverted_index":{"Chromatin":[0],"loops":[1],"are":[2,8,175,223],"tethered":[3],"at":[4],"discrete":[5],"regions":[6,15,64,241],"that":[7,37,46,89,120,148,184,202,222],"approx":[9,131],"100-1000":[10],"bp":[11],"in":[12,53,145,172,219,229],"length.":[13],"These":[14],"of":[16,29,69,95,102,112,129,152,167,208,217,242],"attachment":[17,44,63],"serve":[18,47,66],"as":[19,48,67,150],"specific":[20],"sequence":[21],"landmarks,":[22],"anchoring":[23],"the":[24,27,30,55,93,96,100,103,130,141,164,180,195,218,234],"DNA":[25],"to":[26,118,126,139,178,192,239],"fibers":[28],"chromosomal":[31,77],"scaffold.":[32],"It":[33],"has":[34],"been":[35],"estimated":[36],"our":[38,146],"genome":[39,147,169],"contains":[40],"70,000":[41],"nuclear":[42,51,104],"matrix":[43,62,243],"sites":[45],"a":[49,159,205,227],"dynamic":[50],"organizer":[52],"both":[54],"interphase":[56],"and":[57,199,226],"metaphase":[58],"cell.":[59],"Approximately":[60],"30,000-40,000":[61],"(MARs)":[65],"origins":[68],"replication.":[70],"MARs":[71,125],"can":[72],"also":[73],"be":[74],"associated":[75],"with":[76,81,99],"segments":[78],"densely":[79],"populated":[80],"transcription":[82,88],"factor-binding":[83],"sites.":[84],"This":[85,136,188],"may":[86],"facilitate":[87],"is":[90,116,137,190],"initiated":[91],"within":[92],"region":[94],"chromosome":[97],"coincident":[98],"surface":[101],"matrix.":[105],"Assuming":[106],"an":[107],"average":[108],"somatic":[109],"loop":[110],"size":[111],"100":[113],"kb,":[114],"it":[115],"reasonable":[117],"propose":[119],"each":[121,128,157],"cell":[122],"utilizes":[123],"30,000":[124,142],"anchor":[127],"20,000":[132],"active":[133],"genic":[134],"domains.":[135],"sufficient":[138],"encompass":[140],"functional":[143],"genes":[144],"exist":[149],"members":[151],"single":[153,160],"or":[154],"multigenic":[155],"families,":[156],"constituting":[158],"chromatin":[161],"domain.":[162],"With":[163],"sequencing":[165],"phase":[166],"various":[168],"projects":[170],"complete,":[171],"silico":[173,220],"tools":[174],"being":[176],"developed":[177],"identify":[179],"long-range":[181],"control":[182],"elements":[183],"modulate":[185],"gene":[186,209],"expression.":[187],"information":[189],"necessary":[191],"specifically":[193],"target":[194],"time-intensive":[196],"wet-bench":[197],"verification":[198],"expression":[200],"experiments":[201],"will":[203],"provide":[204],"unified":[206],"understanding":[207],"regulation.":[210],"In":[211],"this":[212],"chapter":[213],"we":[214],"review":[215],"some":[216],"strategies":[221],"currently":[224],"available":[225],"new":[228],"vivo":[230],"method":[231],"based":[232],"on":[233],"real-time":[235],"polymerase":[236],"chain":[237],"reaction,":[238],"assess":[240],"association.":[244]},"counts_by_year":[{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2016-06-24T00:00:00"}