{"id":"https://openalex.org/W3109509290","doi":"https://doi.org/10.3390/data5040111","title":"In Silico Estimation of the Abundance and Phylogenetic Significance of the Composite Oct4-Sox2 Binding Motifs within a Wide Range of Species","display_name":"In Silico Estimation of the Abundance and Phylogenetic Significance of the Composite Oct4-Sox2 Binding Motifs within a Wide Range of Species","publication_year":2020,"publication_date":"2020-11-29","ids":{"openalex":"https://openalex.org/W3109509290","doi":"https://doi.org/10.3390/data5040111","mag":"3109509290"},"language":"en","primary_location":{"id":"doi:10.3390/data5040111","is_oa":true,"landing_page_url":"https://doi.org/10.3390/data5040111","pdf_url":"https://www.mdpi.com/2306-5729/5/4/111/pdf","source":{"id":"https://openalex.org/S4210226510","display_name":"Data","issn_l":"2306-5729","issn":["2306-5729"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Data","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.mdpi.com/2306-5729/5/4/111/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5026220838","display_name":"Arman Kulyyassov","orcid":"https://orcid.org/0000-0002-7932-5689"},"institutions":[{"id":"https://openalex.org/I4210101002","display_name":"National Center for Biotechnology","ror":"https://ror.org/00xhcc696","country_code":"KZ","type":"facility","lineage":["https://openalex.org/I4210101002"]}],"countries":["KZ"],"is_corresponding":true,"raw_author_name":"Arman Kulyyassov","raw_affiliation_strings":["Republican State Enterprise \u201cNational Center for Biotechnology\u201d, 13/5 Kurgalzhynskoye Road, Nur-Sultan 010000, Kazakhstan","Republican State Enterprise \"National Center for Biotechnology\", 13/5 Kurgalzhynskoye Road, Nur-Sultan 010000, Kazakhstan"],"raw_orcid":"https://orcid.org/0000-0002-7932-5689","affiliations":[{"raw_affiliation_string":"Republican State Enterprise \u201cNational Center for Biotechnology\u201d, 13/5 Kurgalzhynskoye Road, Nur-Sultan 010000, Kazakhstan","institution_ids":["https://openalex.org/I4210101002"]},{"raw_affiliation_string":"Republican State Enterprise \"National Center for Biotechnology\", 13/5 Kurgalzhynskoye Road, Nur-Sultan 010000, Kazakhstan","institution_ids":["https://openalex.org/I4210101002"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5040963956","display_name":"Ruslan Kalendar","orcid":"https://orcid.org/0000-0003-3986-2460"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]},{"id":"https://openalex.org/I60559429","display_name":"Nazarbayev University","ror":"https://ror.org/052bx8q98","country_code":"KZ","type":"education","lineage":["https://openalex.org/I60559429"]}],"countries":["FI","KZ"],"is_corresponding":true,"raw_author_name":"Ruslan Kalendar","raw_affiliation_strings":["Department of Agricultural Sciences, University of Helsinki, FI-00014 Helsinki, Finland","National Laboratory Astana, Nazarbayev University, Nur-Sultan 010000, Kazakhstan"],"raw_orcid":"https://orcid.org/0000-0003-3986-2460","affiliations":[{"raw_affiliation_string":"Department of Agricultural Sciences, University of Helsinki, FI-00014 Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]},{"raw_affiliation_string":"National Laboratory Astana, Nazarbayev University, Nur-Sultan 010000, Kazakhstan","institution_ids":["https://openalex.org/I60559429"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5026220838","https://openalex.org/A5040963956"],"corresponding_institution_ids":["https://openalex.org/I133731052","https://openalex.org/I4210101002","https://openalex.org/I60559429"],"apc_list":{"value":1600,"currency":"CHF","value_usd":1732},"apc_paid":{"value":1600,"currency":"CHF","value_usd":1732},"fwci":0.4637,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.76379139,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":95},"biblio":{"volume":"5","issue":"4","first_page":"111","last_page":"111"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9987999796867371,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9987999796867371,"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":0.9983999729156494,"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/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9979000091552734,"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/genome","display_name":"Genome","score":0.7614185810089111},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.7469805479049683},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.606663703918457},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.5674329400062561},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.5481089949607849},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.5176694393157959},{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.48736101388931274},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.45936980843544006},{"id":"https://openalex.org/keywords/sequence-motif","display_name":"Sequence motif","score":0.4571017026901245},{"id":"https://openalex.org/keywords/comparative-genomics","display_name":"Comparative genomics","score":0.43617355823516846},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.43352073431015015},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.338915079832077}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.7614185810089111},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7469805479049683},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.606663703918457},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.5674329400062561},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.5481089949607849},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.5176694393157959},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.48736101388931274},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.45936980843544006},{"id":"https://openalex.org/C117745874","wikidata":"https://www.wikidata.org/wiki/Q901612","display_name":"Sequence motif","level":3,"score":0.4571017026901245},{"id":"https://openalex.org/C105176652","wikidata":"https://www.wikidata.org/wiki/Q1147112","display_name":"Comparative genomics","level":5,"score":0.43617355823516846},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.43352073431015015},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.338915079832077}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.3390/data5040111","is_oa":true,"landing_page_url":"https://doi.org/10.3390/data5040111","pdf_url":"https://www.mdpi.com/2306-5729/5/4/111/pdf","source":{"id":"https://openalex.org/S4210226510","display_name":"Data","issn_l":"2306-5729","issn":["2306-5729"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Data","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:e37490991d344ca19759e079b445ee51","is_oa":true,"landing_page_url":"https://doaj.org/article/e37490991d344ca19759e079b445ee51","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Data, Vol 5, Iss 4, p 111 (2020)","raw_type":"article"},{"id":"pmh:oai:helda.helsinki.fi:10138/322680","is_oa":true,"landing_page_url":"http://hdl.handle.net/10138/322680","pdf_url":null,"source":{"id":"https://openalex.org/S4210213322","display_name":"Ty\u00f6v\u00e4entutkimus Vuosikirja","issn_l":"0784-1272","issn":["0784-1272","1459-7780"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"http://purl.org/eprint/entityType/JournalArticle"},{"id":"pmh:oai:helda.helsinki.fi:10138/323128","is_oa":true,"landing_page_url":"https://www.mdpi.com/2306-5729/5/4/111","pdf_url":null,"source":{"id":"https://openalex.org/S4210213322","display_name":"Ty\u00f6v\u00e4entutkimus Vuosikirja","issn_l":"0784-1272","issn":["0784-1272","1459-7780"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"pmh:oai:mdpi.com:/2306-5729/5/4/111/","is_oa":true,"landing_page_url":"https://dx.doi.org/10.3390/data5040111","pdf_url":null,"source":{"id":"https://openalex.org/S4306400947","display_name":"MDPI (MDPI AG)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210097602","host_organization_name":"Multidisciplinary Digital Publishing Institute (Switzerland)","host_organization_lineage":["https://openalex.org/I4210097602"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Data; Volume 5; Issue 4; Pages: 111","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.3390/data5040111","is_oa":true,"landing_page_url":"https://doi.org/10.3390/data5040111","pdf_url":"https://www.mdpi.com/2306-5729/5/4/111/pdf","source":{"id":"https://openalex.org/S4210226510","display_name":"Data","issn_l":"2306-5729","issn":["2306-5729"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Data","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land","score":0.5600000023841858}],"awards":[{"id":"https://openalex.org/G6351110504","display_name":null,"funder_award_id":"AP05132131","funder_id":"https://openalex.org/F4320322726","funder_display_name":"Ministry of Education and Science of the Republic of Kazakhstan"}],"funders":[{"id":"https://openalex.org/F4320322726","display_name":"Ministry of Education and Science of the Republic of Kazakhstan","ror":"https://ror.org/03pj6ge82"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3109509290.pdf","grobid_xml":"https://content.openalex.org/works/W3109509290.grobid-xml"},"referenced_works_count":46,"referenced_works":["https://openalex.org/W1683181063","https://openalex.org/W1981059575","https://openalex.org/W1981253959","https://openalex.org/W1987390450","https://openalex.org/W1989769057","https://openalex.org/W1989858799","https://openalex.org/W2002499610","https://openalex.org/W2013246689","https://openalex.org/W2016015848","https://openalex.org/W2022584463","https://openalex.org/W2023116564","https://openalex.org/W2026129783","https://openalex.org/W2034463580","https://openalex.org/W2038831321","https://openalex.org/W2043765395","https://openalex.org/W2047182840","https://openalex.org/W2057764922","https://openalex.org/W2059699217","https://openalex.org/W2066364577","https://openalex.org/W2068098232","https://openalex.org/W2090567401","https://openalex.org/W2093906255","https://openalex.org/W2097220641","https://openalex.org/W2104287544","https://openalex.org/W2107575419","https://openalex.org/W2114405551","https://openalex.org/W2118290853","https://openalex.org/W2125987139","https://openalex.org/W2127799088","https://openalex.org/W2129148890","https://openalex.org/W2138977668","https://openalex.org/W2142046859","https://openalex.org/W2161889215","https://openalex.org/W2163421223","https://openalex.org/W2171609896","https://openalex.org/W2273958019","https://openalex.org/W2509683490","https://openalex.org/W2565944951","https://openalex.org/W2613127536","https://openalex.org/W2739634185","https://openalex.org/W2783784339","https://openalex.org/W2900648630","https://openalex.org/W2948363023","https://openalex.org/W2950620706","https://openalex.org/W2999168229","https://openalex.org/W3000371996"],"related_works":["https://openalex.org/W2036948647","https://openalex.org/W1565527690","https://openalex.org/W1493660383","https://openalex.org/W2759519215","https://openalex.org/W2353729507","https://openalex.org/W4318240630","https://openalex.org/W2350466590","https://openalex.org/W1542620732","https://openalex.org/W3031625301","https://openalex.org/W4386771068"],"abstract_inverted_index":{"High-throughput":[0],"sequencing":[1],"technologies":[2],"have":[3],"greatly":[4],"accelerated":[5],"the":[6,26,35,41,79,87,103],"progress":[7],"of":[8,17,28,37,46,89,96,105],"genomics,":[9],"transcriptomics,":[10],"and":[11,44,67,71,84,114],"metagenomics.":[12],"Currently,":[13],"a":[14,54],"large":[15],"amount":[16],"genomic":[18],"data":[19],"from":[20,122],"various":[21],"organisms":[22],"is":[23,30,49],"being":[24],"generated,":[25],"volume":[27],"which":[29,74],"increasing":[31],"every":[32],"year.":[33],"Therefore,":[34],"development":[36],"methods":[38],"that":[39,61],"allow":[40],"rapid":[42],"search":[43],"analysis":[45,95],"DNA":[47],"sequences":[48],"urgent.":[50],"Here,":[51],"we":[52],"present":[53],"novel":[55],"motif-based":[56],"high-throughput":[57],"sequence":[58],"scoring":[59],"method":[60],"generates":[62],"genome":[63,110],"information.":[64],"We":[65],"found":[66],"identified":[68],"Utf1-like,":[69,112],"Fgf4-like,":[70,113],"Hoxb1-like":[72,115],"motifs,":[73],"are":[75],"cis-regulatory":[76],"elements":[77],"for":[78],"pluripotency":[80],"transcription":[81],"factors":[82],"Sox2":[83],"Oct4":[85],"within":[86],"genomes":[88,121],"different":[90],"eukaryotic":[91],"organisms.":[92],"The":[93],"genome-wide":[94],"these":[97],"motifs":[98],"was":[99,118],"performed":[100],"to":[101],"understand":[102],"impact":[104],"their":[106],"diversification":[107],"on":[108],"mammalian":[109],"evolution.":[111],"motif":[116],"diversity":[117],"evaluated":[119],"across":[120],"multiple":[123],"species.":[124]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2020-12-07T00:00:00"}
