{"id":"https://openalex.org/W298724625","doi":null,"title":"Studying Nucleosome Positioning, DNA Methylation, and Other Epigenetic Factors Using Genomic Approaches","display_name":"Studying Nucleosome Positioning, DNA Methylation, and Other Epigenetic Factors Using Genomic Approaches","publication_year":2012,"publication_date":"2012-01-01","ids":{"openalex":"https://openalex.org/W298724625","mag":"298724625"},"language":"en","primary_location":{"id":"pmh:oai:escholarship.org/ark:/13030/qt5qg1h83p","doi":null,"is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/5qg1h83p","pdf_url":"https://escholarship.org/uc/item/5qg1h83p","source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"etd"},"volume":null,"type":"dissertation","is_traditional":true,"indexed_in":[],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://escholarship.org/uc/item/5qg1h83p","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5034027813","display_name":"Ramakrishna K. Chodavarapu","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Ramakrishna K. Chodavarapu","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5034027813"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"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/T10269","display_name":"Epigenetics and DNA Methylation","score":0.9463000297546387,"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/T10269","display_name":"Epigenetics and DNA Methylation","score":0.9463000297546387,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.044199999421834946,"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":0.0017000000225380063,"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/nucleosome-positioning","display_name":"nucleosome positioning","score":0.9330000281333923},{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":1.0},{"id":"https://openalex.org/keywords/epigenomics","display_name":"epigenomics","score":0.8610000014305115},{"id":"https://openalex.org/keywords/histone-modifications","display_name":"histone modifications","score":0.8790000081062317},{"id":"https://openalex.org/keywords/exon-intron-boundaries","display_name":"exon-intron boundaries","score":0.8830000162124634},{"id":"https://openalex.org/keywords/hybrid-rice","display_name":"hybrid rice","score":0.7350000143051147},{"id":"https://openalex.org/keywords/rice-ecotypes","display_name":"rice ecotypes","score":0.7250000238418579},{"id":"https://openalex.org/keywords/single-nucleotide-polymorphisms","display_name":"single nucleotide polymorphisms","score":0.8270000219345093},{"id":"https://openalex.org/keywords/differentially-methylated-regions","display_name":"differentially methylated regions","score":0.7160000205039978},{"id":"https://openalex.org/keywords/gene-expression","display_name":"gene expression","score":0.5189999938011169},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-seq","score":0.9409999847412109},{"id":"https://openalex.org/keywords/epigenetic-inheritance","display_name":"epigenetic inheritance","score":0.6359999775886536}],"concepts":[{"id":"https://openalex.org/C121912465","wikidata":"https://www.wikidata.org/wiki/Q3589153","display_name":"Epigenomics","level":5,"score":0.8774746656417847},{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.7909644842147827},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6866078972816467},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.6355823278427124},{"id":"https://openalex.org/C41091548","wikidata":"https://www.wikidata.org/wiki/Q26939","display_name":"Epigenetics","level":3,"score":0.615234375},{"id":"https://openalex.org/C84772758","wikidata":"https://www.wikidata.org/wiki/Q271794","display_name":"Nucleosome","level":4,"score":0.542437732219696},{"id":"https://openalex.org/C163002167","wikidata":"https://www.wikidata.org/wiki/Q7277124","display_name":"RNA-Directed DNA Methylation","level":5,"score":0.5090815424919128},{"id":"https://openalex.org/C64927066","wikidata":"https://www.wikidata.org/wiki/Q36293","display_name":"Histone","level":3,"score":0.4005281627178192},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.35240811109542847},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3013060390949249},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.17552149295806885}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:escholarship.org/ark:/13030/qt5qg1h83p","doi":null,"is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/5qg1h83p","pdf_url":"https://escholarship.org/uc/item/5qg1h83p","source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"etd"},{"id":"mag:298724625","doi":null,"is_oa":false,"landing_page_url":"https://escholarship.org/content/qt5qg1h83p/qt5qg1h83p.pdf?t=mntaj7","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":{"id":"pmh:oai:escholarship.org/ark:/13030/qt5qg1h83p","doi":null,"is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/5qg1h83p","pdf_url":"https://escholarship.org/uc/item/5qg1h83p","source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"etd"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G1181485187","display_name":"Predoctoral Training Program in Genetic Mechanisms","funder_award_id":"T32GM007104","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G7439169801","display_name":"Understanding the Rice Epigenome: From Genes to Genomes","funder_award_id":"0701745","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G9000078557","display_name":null,"funder_award_id":"GM60398","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G9000212802","display_name":null,"funder_award_id":"GM42143","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306082","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90"},{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320311350","display_name":"Life Sciences Research Foundation","ror":"https://ror.org/0195dxj21"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W298724625.pdf","grobid_xml":"https://content.openalex.org/works/W298724625.grobid-xml"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W1558207160","https://openalex.org/W1964188377","https://openalex.org/W1964271596","https://openalex.org/W1971400148","https://openalex.org/W1986849101","https://openalex.org/W1989568035","https://openalex.org/W1994288562","https://openalex.org/W1999478182","https://openalex.org/W1999491723","https://openalex.org/W2004206635","https://openalex.org/W2016597274","https://openalex.org/W2017198614","https://openalex.org/W2026177649","https://openalex.org/W2026343134","https://openalex.org/W2028839461","https://openalex.org/W2029873987","https://openalex.org/W2036806870","https://openalex.org/W2040528706","https://openalex.org/W2045389794","https://openalex.org/W2059979506","https://openalex.org/W2063679723","https://openalex.org/W2072152932","https://openalex.org/W2079514282","https://openalex.org/W2089417246","https://openalex.org/W2097065948","https://openalex.org/W2106448802","https://openalex.org/W2107337799","https://openalex.org/W2110776599","https://openalex.org/W2114752404","https://openalex.org/W2124985265","https://openalex.org/W2126606466","https://openalex.org/W2135173446","https://openalex.org/W2144792857","https://openalex.org/W2154109129","https://openalex.org/W2155453721","https://openalex.org/W2158009361","https://openalex.org/W2161655813","https://openalex.org/W2170671616"],"related_works":["https://openalex.org/W2765894397","https://openalex.org/W1985624299","https://openalex.org/W2077562677","https://openalex.org/W2125893498","https://openalex.org/W2043515750","https://openalex.org/W2225434408","https://openalex.org/W4287448603","https://openalex.org/W4230684349","https://openalex.org/W7099291644","https://openalex.org/W2288359971"],"abstract_inverted_index":{"Epigenomics":[0],"is":[1],"the":[2,6,20,107,114,126,129,141,144,154,157,160,170],"genome-wide":[3],"study":[4,80],"of":[5,48,54,81,98,103,109,143,151],"factors":[7,26],"that":[8],"cause":[9],"changes":[10],"to":[11,19],"gene":[12],"expression,":[13],"but":[14],"are":[15,27,38],"not":[16],"directly":[17],"related":[18,96],"primary":[21],"DNA":[22,28,49,55,110,122,145],"sequence.":[23],"Among":[24],"these":[25,175],"methylation,":[29],"nucleosome":[30],"positioning,":[31],"and":[32,51,68,84,106,128,156,159],"histone":[33],"modifications.":[34],"Two":[35],"epigenomic":[36],"projects":[37],"described":[39],"here.":[40],"The":[41,75,163],"first":[42],"describes":[43,62,77,140],"a":[44,101,166],"ten":[45],"base":[46],"periodicity":[47],"methylation":[50,56,111,123,146],"an":[52,78],"enrichment":[53],"over":[57,66],"nucleosomal":[58],"DNA.":[59],"It":[60,138],"also":[61,139],"nucleosomes":[63],"being":[64,69],"enriched":[65],"exons":[67],"placed":[70],"preferentially":[71],"at":[72,100,119,135],"intron-exon":[73],"boundaries.":[74],"other":[76],"integrative":[79],"BS-seq,":[82],"RNA-seq,":[83],"siRNA-seq":[85],"data":[86],"in":[87,174],"rice":[88,99],"hybrids.":[89],"SNPs":[90],"were":[91,131],"found":[92],"between":[93,113,125,153],"two":[94,161,176],"closely":[95],"subspeicies":[97],"rate":[102],"1/253":[104],"bp":[105],"frequency":[108],"differences":[112,124,147],"ecotypes":[115],"was":[116],"much":[117,132],"higher":[118],"nearly":[120,136],"8%.":[121],"parents":[127,155],"hybrids":[130,158],"more":[133],"muted,":[134],"1%.":[137],"impact":[142],"on":[148,169],"differential":[149],"expression":[150],"genes":[152],"ecotypes.":[162],"dissertation":[164],"includes":[165],"brief":[167],"discussion":[168],"main":[171],"methods":[172],"employed":[173],"studies":[177],"as":[178],"well.":[179]},"counts_by_year":[],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2016-06-24T00:00:00"}