{"id":"https://openalex.org/W2171832486","doi":"https://doi.org/10.1093/bioinformatics/btl017","title":"Polynomial model approach for resynchronization analysis of cell-cycle gene expression data","display_name":"Polynomial model approach for resynchronization analysis of cell-cycle gene expression data","publication_year":2006,"publication_date":"2006-01-24","ids":{"openalex":"https://openalex.org/W2171832486","doi":"https://doi.org/10.1093/bioinformatics/btl017","mag":"2171832486","pmid":"https://pubmed.ncbi.nlm.nih.gov/16434439"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btl017","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl017","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/8/959/48841185/bioinformatics_22_8_959.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/22/8/959/48841185/bioinformatics_22_8_959.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101449042","display_name":"Peng Qiu","orcid":"https://orcid.org/0009-0007-0332-4165"},"institutions":[{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Peng Qiu","raw_affiliation_strings":["Department of Electrical and Computer Engineering, University of Maryland 1 \u00a0 1 \u00a0 \u00a0 College Park, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, University of Maryland 1 \u00a0 1 \u00a0 \u00a0 College Park, USA","institution_ids":["https://openalex.org/I66946132"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051587486","display_name":"Z. Jane Wang","orcid":"https://orcid.org/0000-0002-3791-0249"},"institutions":[{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Z. Jane Wang","raw_affiliation_strings":["Department of Electrical and Computer Engineering, University of British Columbia 2 \u00a0 2 \u00a0 \u00a0 Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, University of British Columbia 2 \u00a0 2 \u00a0 \u00a0 Canada","institution_ids":["https://openalex.org/I141945490"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5032395820","display_name":"K. J. Ray Liu","orcid":"https://orcid.org/0000-0001-5469-5811"},"institutions":[{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"K. J. Ray Liu","raw_affiliation_strings":["Department of Electrical and Computer Engineering, University of Maryland 1 \u00a0 1 \u00a0 \u00a0 College Park, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, University of Maryland 1 \u00a0 1 \u00a0 \u00a0 College Park, USA","institution_ids":["https://openalex.org/I66946132"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5101449042"],"corresponding_institution_ids":["https://openalex.org/I66946132"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":0.8888,"has_fulltext":true,"cited_by_count":14,"citation_normalized_percentile":{"value":0.71963126,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"22","issue":"8","first_page":"959","last_page":"966"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.40389999747276306,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.40389999747276306,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.27390000224113464,"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/T10885","display_name":"Gene expression and cancer classification","score":0.1720000058412552,"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/computational-biology","display_name":"Computational biology","score":0.5930666923522949},{"id":"https://openalex.org/keywords/microarray-analysis-techniques","display_name":"Microarray analysis techniques","score":0.5865741968154907},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.572148323059082},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5342511534690857},{"id":"https://openalex.org/keywords/cell-cycle","display_name":"Cell cycle","score":0.5166821479797363},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5015177726745605},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.47796177864074707},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.4690449833869934},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.44870486855506897},{"id":"https://openalex.org/keywords/functional-genomics","display_name":"Functional genomics","score":0.4215487837791443},{"id":"https://openalex.org/keywords/microarray","display_name":"Microarray","score":0.4172508418560028},{"id":"https://openalex.org/keywords/gene-expression-profiling","display_name":"Gene expression profiling","score":0.41717153787612915},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.4024292826652527},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3554595708847046},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2894425094127655},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.28170618414878845}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5930666923522949},{"id":"https://openalex.org/C8415881","wikidata":"https://www.wikidata.org/wiki/Q6839217","display_name":"Microarray analysis techniques","level":4,"score":0.5865741968154907},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.572148323059082},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5342511534690857},{"id":"https://openalex.org/C29537977","wikidata":"https://www.wikidata.org/wiki/Q188941","display_name":"Cell cycle","level":3,"score":0.5166821479797363},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5015177726745605},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.47796177864074707},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.4690449833869934},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.44870486855506897},{"id":"https://openalex.org/C161078062","wikidata":"https://www.wikidata.org/wiki/Q1068690","display_name":"Functional genomics","level":5,"score":0.4215487837791443},{"id":"https://openalex.org/C186836561","wikidata":"https://www.wikidata.org/wiki/Q1931516","display_name":"Microarray","level":4,"score":0.4172508418560028},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.41717153787612915},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.4024292826652527},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3554595708847046},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2894425094127655},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.28170618414878845},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009716","descriptor_name":"Numerical Analysis, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009716","descriptor_name":"Numerical Analysis, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009716","descriptor_name":"Numerical Analysis, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010507","descriptor_name":"Periodicity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010507","descriptor_name":"Periodicity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010507","descriptor_name":"Periodicity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D018797","descriptor_name":"Cell Cycle Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D018797","descriptor_name":"Cell Cycle Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D018797","descriptor_name":"Cell Cycle Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","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":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btl017","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl017","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/8/959/48841185/bioinformatics_22_8_959.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:16434439","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16434439","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":"Bioinformatics (Oxford, England)","raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btl017","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl017","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/8/959/48841185/bioinformatics_22_8_959.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2171832486.pdf","grobid_xml":"https://content.openalex.org/works/W2171832486.grobid-xml"},"referenced_works_count":16,"referenced_works":["https://openalex.org/W1971947347","https://openalex.org/W2076204760","https://openalex.org/W2098521923","https://openalex.org/W2103453943","https://openalex.org/W2105712639","https://openalex.org/W2122135124","https://openalex.org/W2126602684","https://openalex.org/W2142460132","https://openalex.org/W2142894222","https://openalex.org/W2145456195","https://openalex.org/W2159309601","https://openalex.org/W2163599171","https://openalex.org/W2168525657","https://openalex.org/W2970760985","https://openalex.org/W2997000181","https://openalex.org/W3133603318"],"related_works":["https://openalex.org/W2360935227","https://openalex.org/W2364993072","https://openalex.org/W2115576822","https://openalex.org/W2356429006","https://openalex.org/W2155595079","https://openalex.org/W2380568150","https://openalex.org/W2183420549","https://openalex.org/W2039699813","https://openalex.org/W2081507994","https://openalex.org/W1972696957"],"abstract_inverted_index":{"MOTIVATION:":[0],"Identification":[1],"of":[2,11,29,45,106],"genes":[3,32,155],"expressed":[4,76,135],"in":[5,23,73,130],"a":[6,20,50,84,93,104],"cell-cycle-specific":[7],"periodical":[8],"manner":[9],"is":[10,40,118,124,150],"great":[12],"interest":[13],"to":[14,63,127,132],"understand":[15],"cyclic":[16,154],"systems":[17],"which":[18],"play":[19],"critical":[21],"role":[22],"many":[24],"biological":[25],"processes.":[26],"However,":[27],"identification":[28],"cell-cycle":[30],"regulated":[31],"by":[33,42,97],"raw":[34],"microarray":[35,143],"gene":[36,100,159],"expression":[37,55,60,101,116,160],"data":[38,144,169],"directly":[39],"complicated":[41],"the":[43,54,66,71,99,128,147,164],"factor":[44],"synchronization":[46,94],"loss,":[47],"thus":[48],"remains":[49],"challenging":[51],"problem.":[52],"Decomposing":[53],"measurements":[56,102,129],"and":[57,69,123,141,156],"extracting":[58],"synchronized":[59],"will":[61],"allow":[62],"better":[64],"represent":[65],"single-cell":[67],"behavior":[68],"improve":[70],"accuracy":[72],"identifying":[74,88,153],"periodically":[75,134],"genes.":[77,90,136],"RESULTS:":[78],"In":[79],"this":[80],"paper,":[81],"we":[82],"propose":[83],"resynchronization-based":[85],"algorithm":[86],"for":[87,152],"cell-cycle-related":[89],"We":[91],"introduce":[92],"loss":[95],"model":[96],"modeling":[98],"as":[103],"superposition":[105],"different":[107,112],"cell":[108],"populations":[109],"growing":[110],"at":[111],"rates.":[113],"The":[114],"underlying":[115,158],"profile":[117],"then":[119],"reconstructed":[120],"through":[121],"resynchronization":[122],"further":[125],"fitted":[126],"order":[131],"identify":[133],"Results":[137],"from":[138],"both":[139],"simulations":[140],"real":[142],"show":[145],"that":[146],"proposed":[148],"scheme":[149],"promising":[151],"revealing":[157],"profiles.":[161],"AVAILABILITY:":[162],"Contact":[163],"authors.":[165],"SUPPLEMENTARY":[166],"INFORMATION:":[167],"Supplementary":[168],"are":[170],"available":[171],"at:":[172],"http://dsplab.eng.umd.edu/~genomics/syn/":[173]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
