{"id":"https://openalex.org/W2065409326","doi":"https://doi.org/10.1186/1752-0509-5-s2-s8","title":"Novel Markov model of induced pluripotency predicts gene expression changes in reprogramming","display_name":"Novel Markov model of induced pluripotency predicts gene expression changes in reprogramming","publication_year":2011,"publication_date":"2011-12-01","ids":{"openalex":"https://openalex.org/W2065409326","doi":"https://doi.org/10.1186/1752-0509-5-s2-s8","mag":"2065409326","pmid":"https://pubmed.ncbi.nlm.nih.gov/22784579"},"language":"en","primary_location":{"id":"doi:10.1186/1752-0509-5-s2-s8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-5-s2-s8","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-5-S2-S8","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-5-S2-S8","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5108139208","display_name":"Zhirui Hu","orcid":"https://orcid.org/0000-0001-6352-4854"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhirui Hu","raw_affiliation_strings":["MOE Key Laboratory of Bioinformatics and Bioinformatics Div, TNLIST /Department of Automation, Tsinghua University, Beijing 100084, China","MOE Key Laboratory of Bioinformatics and Bioinformatics Div, TNLIST/Department of Automation, Tsinghua University, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"MOE Key Laboratory of Bioinformatics and Bioinformatics Div, TNLIST /Department of Automation, Tsinghua University, Beijing 100084, China","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"MOE Key Laboratory of Bioinformatics and Bioinformatics Div, TNLIST/Department of Automation, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108578958","display_name":"Minping Qian","orcid":null},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Minping Qian","raw_affiliation_strings":["School of Mathematics, Peking University, Beijing, 100871, China","School of Mathematics, Peking University, Beijing, CHINA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Mathematics, Peking University, Beijing, 100871, China","institution_ids":["https://openalex.org/I20231570"]},{"raw_affiliation_string":"School of Mathematics, Peking University, Beijing, CHINA","institution_ids":["https://openalex.org/I20231570"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5058814283","display_name":"Michael Q. Zhang","orcid":"https://orcid.org/0000-0002-7022-6115"},"institutions":[{"id":"https://openalex.org/I162577319","display_name":"The University of Texas at Dallas","ror":"https://ror.org/049emcs32","country_code":"US","type":"education","lineage":["https://openalex.org/I162577319"]},{"id":"https://openalex.org/I4210155419","display_name":"Center for Systems Biology","ror":"https://ror.org/05r3dyn47","country_code":"US","type":"facility","lineage":["https://openalex.org/I136199984","https://openalex.org/I4210087915","https://openalex.org/I4210155419","https://openalex.org/I48633490"]},{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN","US"],"is_corresponding":true,"raw_author_name":"Michael Q Zhang","raw_affiliation_strings":["Department of Molecular and Cell Biology, Center for Systems Biology, The University of Texas at Dallas, 800 West Campbell Road, RL11, Richardson, TX, 75080-3021, USA","MOE Key Laboratory of Bioinformatics and Bioinformatics Div, TNLIST /Department of Automation, Tsinghua University, Beijing, 100084, China","Department of Molecular and Cell Biology, Center for Systems Biology, The University of Texas at Dallas, Richardson, USA","MOE Key Laboratory of Bioinformatics and Bioinformatics Div, TNLIST /Department of Automation, Tsinghua University, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular and Cell Biology, Center for Systems Biology, The University of Texas at Dallas, 800 West Campbell Road, RL11, Richardson, TX, 75080-3021, USA","institution_ids":["https://openalex.org/I162577319"]},{"raw_affiliation_string":"MOE Key Laboratory of Bioinformatics and Bioinformatics Div, TNLIST /Department of Automation, Tsinghua University, Beijing, 100084, China","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"Department of Molecular and Cell Biology, Center for Systems Biology, The University of Texas at Dallas, Richardson, USA","institution_ids":["https://openalex.org/I162577319","https://openalex.org/I4210155419"]},{"raw_affiliation_string":"MOE Key Laboratory of Bioinformatics and Bioinformatics Div, TNLIST /Department of Automation, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5058814283"],"corresponding_institution_ids":["https://openalex.org/I162577319","https://openalex.org/I4210155419","https://openalex.org/I99065089"],"apc_list":{"value":2290,"currency":"USD","value_usd":2290},"apc_paid":{"value":2290,"currency":"USD","value_usd":2290},"fwci":0.0,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.09538553,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"5","issue":"S2","first_page":"S8","last_page":"S8"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10505","display_name":"Pluripotent Stem Cells Research","score":0.9771999716758728,"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/T10505","display_name":"Pluripotent Stem Cells Research","score":0.9771999716758728,"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/T10364","display_name":"Reproductive Biology and Fertility","score":0.008500000461935997,"subfield":{"id":"https://openalex.org/subfields/2739","display_name":"Public Health, Environmental and Occupational Health"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10878","display_name":"CRISPR and Genetic Engineering","score":0.0013000000035390258,"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/reprogramming","display_name":"Reprogramming","score":0.9724348783493042},{"id":"https://openalex.org/keywords/induced-pluripotent-stem-cell","display_name":"Induced pluripotent stem cell","score":0.8005044460296631},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6380823850631714},{"id":"https://openalex.org/keywords/somatic-cell","display_name":"Somatic cell","score":0.5805287957191467},{"id":"https://openalex.org/keywords/gene-knockdown","display_name":"Gene knockdown","score":0.5244384407997131},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.469078004360199},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4592447578907013},{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":0.43213361501693726},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.42666566371917725},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.42285674810409546},{"id":"https://openalex.org/keywords/regulation-of-gene-expression","display_name":"Regulation of gene expression","score":0.41658732295036316},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3950313925743103},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3882068693637848},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.336056113243103},{"id":"https://openalex.org/keywords/embryonic-stem-cell","display_name":"Embryonic stem cell","score":0.20167824625968933}],"concepts":[{"id":"https://openalex.org/C77255625","wikidata":"https://www.wikidata.org/wiki/Q402093","display_name":"Reprogramming","level":3,"score":0.9724348783493042},{"id":"https://openalex.org/C107459253","wikidata":"https://www.wikidata.org/wiki/Q674925","display_name":"Induced pluripotent stem cell","level":4,"score":0.8005044460296631},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6380823850631714},{"id":"https://openalex.org/C134305767","wikidata":"https://www.wikidata.org/wiki/Q725508","display_name":"Somatic cell","level":3,"score":0.5805287957191467},{"id":"https://openalex.org/C173396325","wikidata":"https://www.wikidata.org/wiki/Q1501275","display_name":"Gene knockdown","level":3,"score":0.5244384407997131},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.469078004360199},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4592447578907013},{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.43213361501693726},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.42666566371917725},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.42285674810409546},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.41658732295036316},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3950313925743103},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3882068693637848},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.336056113243103},{"id":"https://openalex.org/C145103041","wikidata":"https://www.wikidata.org/wiki/Q1151519","display_name":"Embryonic stem cell","level":3,"score":0.20167824625968933}],"mesh":[{"descriptor_ui":"D002453","descriptor_name":"Cell Cycle","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002453","descriptor_name":"Cell Cycle","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002453","descriptor_name":"Cell Cycle","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002454","descriptor_name":"Cell Differentiation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002454","descriptor_name":"Cell Differentiation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002454","descriptor_name":"Cell Differentiation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","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":"D006801","descriptor_name":"Humans","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":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D044127","descriptor_name":"Epigenesis, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D044127","descriptor_name":"Epigenesis, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D044127","descriptor_name":"Epigenesis, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053595","descriptor_name":"Embryonic Stem Cells","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D053595","descriptor_name":"Embryonic Stem Cells","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D053595","descriptor_name":"Embryonic Stem Cells","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D053595","descriptor_name":"Embryonic Stem Cells","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D053595","descriptor_name":"Embryonic Stem Cells","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D053595","descriptor_name":"Embryonic Stem Cells","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D057026","descriptor_name":"Induced Pluripotent Stem Cells","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D057026","descriptor_name":"Induced Pluripotent Stem Cells","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D057026","descriptor_name":"Induced Pluripotent Stem Cells","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D065150","descriptor_name":"Cellular Reprogramming","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D065150","descriptor_name":"Cellular Reprogramming","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D065150","descriptor_name":"Cellular Reprogramming","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1752-0509-5-s2-s8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-5-s2-s8","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-5-S2-S8","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},{"id":"pmid:22784579","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22784579","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,"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":"BMC systems biology","raw_type":null},{"id":"pmh:oai:doaj.org/article:7b22f8aae68a45a9b140bed494f53ae1","is_oa":false,"landing_page_url":"https://doaj.org/article/7b22f8aae68a45a9b140bed494f53ae1","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Systems Biology, Vol 5, Iss Suppl 2, p S8 (2011)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:3287488","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3287488","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Syst Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1752-0509-5-s2-s8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-5-s2-s8","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-5-S2-S8","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1140348878","display_name":null,"funder_award_id":"HG001696","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2012299116","display_name":null,"funder_award_id":"91019016","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8121044731","display_name":null,"funder_award_id":"31061160497","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2065409326.pdf","grobid_xml":"https://content.openalex.org/works/W2065409326.grobid-xml"},"referenced_works_count":22,"referenced_works":["https://openalex.org/W1966083128","https://openalex.org/W1968931043","https://openalex.org/W1969015262","https://openalex.org/W1973908442","https://openalex.org/W1974012180","https://openalex.org/W2009817296","https://openalex.org/W2012092587","https://openalex.org/W2016958167","https://openalex.org/W2017438799","https://openalex.org/W2017840637","https://openalex.org/W2019229253","https://openalex.org/W2038437697","https://openalex.org/W2076373434","https://openalex.org/W2078201066","https://openalex.org/W2108241558","https://openalex.org/W2125987139","https://openalex.org/W2133465414","https://openalex.org/W2135086442","https://openalex.org/W2149573463","https://openalex.org/W2151522898","https://openalex.org/W2158217645","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W3029540856","https://openalex.org/W2418603484","https://openalex.org/W4254937032","https://openalex.org/W2744405843","https://openalex.org/W2415743749","https://openalex.org/W3032669875","https://openalex.org/W2992250893","https://openalex.org/W3169544955","https://openalex.org/W3175545508","https://openalex.org/W4255292861"],"abstract_inverted_index":{"BACKGROUND:":[0],"Somatic":[1],"cells":[2,9,212],"can":[3],"be":[4,171],"reprogrammed":[5],"to":[6,213],"induced-pluripotent":[7],"stem":[8],"(iPSCs)":[10],"by":[11,38,115,174],"introducing":[12],"few":[13],"reprogramming":[14,41,55,78,105,133,144,147,162,169,204],"factors,":[15],"which":[16],"challenges":[17],"the":[18,28,39,69,77,87,103,110,119,131,146,200,207],"long":[19],"held":[20],"view":[21],"that":[22,82],"cell":[23],"differentiation":[24],"is":[25,33],"irreversible.":[26],"However,":[27],"mechanism":[29,202],"of":[30,43,68,89,91,97,112,161,188,203,209],"induced":[31],"pluripotency":[32],"still":[34],"unknown.":[35],"METHODS:":[36],"Inspired":[37],"phenomenological":[40],"model":[42,70,114,176,196],"Artyomov":[44],"et":[45],"al":[46],"(2010),":[47],"we":[48,108],"proposed":[49],"a":[50],"novel":[51],"Markov":[52,56],"model,":[53,58],"stepwise":[54],"(SRM)":[57],"with":[59,71,102,118,155],"simpler":[60],"gene":[61,122,137,165,189],"regulation":[62,190],"rules":[63,187],"and":[64,80,145,164,205],"explored":[65],"various":[66],"properties":[67],"Monte":[72],"Carlo":[73],"simulation.":[74],"We":[75],"calculated":[76],"rate":[79,148],"showed":[81],"it":[83,117],"would":[84],"increase":[85],"in":[86,130,143,192],"condition":[88],"knockdown":[90],"somatic":[92,211],"transcription":[93],"factors":[94,163],"or":[95],"inhibition":[96],"DNA":[98],"methylation":[99],"globally,":[100],"consistent":[101],"real":[104,120],"experiments.":[106],"Furthermore,":[107],"demonstrated":[109],"utility":[111],"our":[113,156,175,185],"testing":[116],"dynamic":[121],"expression":[123,138,166],"data":[124,139],"spanning":[125],"across":[126],"different":[127],"intermediate":[128],"stages":[129,142],"iPS":[132],"process.":[134],"RESULTS:":[135],"The":[136,159],"at":[140],"several":[141,150],"under":[149],"typically":[151],"experiment":[152],"conditions":[153],"coincided":[154],"simulation":[157],"results.":[158],"function":[160],"change":[167],"during":[168],"could":[170],"partly":[172],"explained":[173],"reasonably":[177],"well.":[178],"CONCLUSIONS:":[179],"This":[180,195],"lands":[181],"further":[182],"support":[183],"on":[184],"general":[186],"network":[191],"iPSC":[193],"reprogramming.":[194],"may":[197],"help":[198],"uncover":[199],"basic":[201],"improve":[206],"efficiency":[208],"converting":[210],"iPSCs.":[214]},"counts_by_year":[{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1}],"updated_date":"2026-07-27T08:26:11.824852","created_date":"2025-10-10T00:00:00"}