{"id":"https://openalex.org/W2167778314","doi":"https://doi.org/10.1093/bioinformatics/btg257","title":"Modes and clustering for time-warped gene expression profile data","display_name":"Modes and clustering for time-warped gene expression profile data","publication_year":2003,"publication_date":"2003-10-10","ids":{"openalex":"https://openalex.org/W2167778314","doi":"https://doi.org/10.1093/bioinformatics/btg257","mag":"2167778314","pmid":"https://pubmed.ncbi.nlm.nih.gov/14555627"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btg257","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg257","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/19/15/1937/48904438/bioinformatics_19_15_1937.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/19/15/1937/48904438/bioinformatics_19_15_1937.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100625387","display_name":"Xueli Liu","orcid":"https://orcid.org/0000-0002-6094-0681"},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Xueli Liu","raw_affiliation_strings":["Department of Human Genetics, UCLA School of Medicine, Los Angeles, CA 90095, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Human Genetics, UCLA School of Medicine, Los Angeles, CA 90095, USA","institution_ids":["https://openalex.org/I161318765"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5050634491","display_name":"Hans\u2010Georg M\u00fcller","orcid":"https://orcid.org/0000-0002-6396-2552"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Hans-Georg M\u00fcller","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5100625387"],"corresponding_institution_ids":["https://openalex.org/I161318765"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.9166,"has_fulltext":false,"cited_by_count":38,"citation_normalized_percentile":{"value":0.73062216,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"19","issue":"15","first_page":"1937","last_page":"1944"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.8518999814987183,"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/T10885","display_name":"Gene expression and cancer classification","score":0.8518999814987183,"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/T12205","display_name":"Time Series Analysis and Forecasting","score":0.024700000882148743,"subfield":{"id":"https://openalex.org/subfields/1711","display_name":"Signal Processing"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11901","display_name":"Bayesian Methods and Mixture Models","score":0.014499999582767487,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.6527770161628723},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.6518889665603638},{"id":"https://openalex.org/keywords/dynamic-time-warping","display_name":"Dynamic time warping","score":0.6176623702049255},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.528180718421936},{"id":"https://openalex.org/keywords/sample","display_name":"Sample (material)","score":0.4411121904850006},{"id":"https://openalex.org/keywords/image-warping","display_name":"Image warping","score":0.42660826444625854},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.4124220013618469},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3838043808937073},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2222868800163269}],"concepts":[{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.6527770161628723},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.6518889665603638},{"id":"https://openalex.org/C88516994","wikidata":"https://www.wikidata.org/wiki/Q1268863","display_name":"Dynamic time warping","level":2,"score":0.6176623702049255},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.528180718421936},{"id":"https://openalex.org/C198531522","wikidata":"https://www.wikidata.org/wiki/Q485146","display_name":"Sample (material)","level":2,"score":0.4411121904850006},{"id":"https://openalex.org/C157202957","wikidata":"https://www.wikidata.org/wiki/Q1659609","display_name":"Image warping","level":2,"score":0.42660826444625854},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.4124220013618469},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3838043808937073},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2222868800163269},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"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/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000222","descriptor_name":"Adaptation, Physiological","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000222","descriptor_name":"Adaptation, Physiological","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000222","descriptor_name":"Adaptation, Physiological","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000375","descriptor_name":"Aging","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000375","descriptor_name":"Aging","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000375","descriptor_name":"Aging","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"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":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004330","descriptor_name":"Drosophila","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004330","descriptor_name":"Drosophila","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004330","descriptor_name":"Drosophila","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004330","descriptor_name":"Drosophila","qualifier_ui":"Q000254","qualifier_name":"growth & development","is_major_topic":false},{"descriptor_ui":"D004330","descriptor_name":"Drosophila","qualifier_ui":"Q000254","qualifier_name":"growth & development","is_major_topic":false},{"descriptor_ui":"D004330","descriptor_name":"Drosophila","qualifier_ui":"Q000254","qualifier_name":"growth & development","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D008018","descriptor_name":"Life Cycle Stages","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008018","descriptor_name":"Life Cycle Stages","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008018","descriptor_name":"Life Cycle Stages","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019992","descriptor_name":"Databases as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019992","descriptor_name":"Databases as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019992","descriptor_name":"Databases as Topic","qualifier_ui":null,"qualifier_name":null,"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}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btg257","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg257","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/19/15/1937/48904438/bioinformatics_19_15_1937.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:14555627","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/14555627","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":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.197.9866","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.197.9866","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://anson.ucdavis.edu/~mueller/Bioinfo03_warping.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.369.4157","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.369.4157","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://anson.ucdavis.edu/~mueller/bio2002-523revisednew.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.614.1948","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.614.1948","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/content/19/15/1937.full.pdf","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btg257","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg257","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/19/15/1937/48904438/bioinformatics_19_15_1937.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":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":18,"referenced_works":["https://openalex.org/W1964716164","https://openalex.org/W2008986601","https://openalex.org/W2021420689","https://openalex.org/W2022686119","https://openalex.org/W2053819132","https://openalex.org/W2064796257","https://openalex.org/W2065304595","https://openalex.org/W2067191022","https://openalex.org/W2074886232","https://openalex.org/W2103453943","https://openalex.org/W2105581244","https://openalex.org/W2128160875","https://openalex.org/W2132585078","https://openalex.org/W2135187880","https://openalex.org/W2141652419","https://openalex.org/W2150926065","https://openalex.org/W2164500538","https://openalex.org/W2164835120"],"related_works":["https://openalex.org/W1670332068","https://openalex.org/W2095618524","https://openalex.org/W2735770592","https://openalex.org/W2347413598","https://openalex.org/W1918542373","https://openalex.org/W71572444","https://openalex.org/W1997383766","https://openalex.org/W2154472250","https://openalex.org/W2350336482","https://openalex.org/W2229352698"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,120,153,184],"study":[2],"of":[3,6,17,27,61,71,79,83,106,109,126,129,162,173,179,196,202],"the":[4,15,25,42,59,72,80,124,146,160,171,193,209],"dynamics":[5,26],"regulatory":[7,47],"processes":[8,48],"has":[9],"led":[10],"to":[11,39,55,96,103,133,148,189],"increased":[12],"interest":[13],"for":[14,159,164,176],"analysis":[16],"temporal":[18,81],"gene":[19,50,62,84,181,197],"expression":[20,29,63,73,110,135,182],"level":[21],"data.":[22,45,183],"To":[23],"address":[24],"regulation,":[28],"data":[30,136,166],"are":[31],"collected":[32],"repeatedly":[33],"over":[34],"time.":[35],"It":[36],"is":[37,53,94,156],"difficult":[38],"statistically":[40],"represent":[41],"resulting":[43],"high-dimensional":[44],"When":[46],"determine":[49],"expression,":[51,198],"time-warping":[52,144],"likely":[54],"be":[56,187],"present,":[57],"i.e.":[58],"sample":[60,108,116,178],"trajectories":[64,195],"reflects":[65],"variation":[66],"not":[67],"only":[68],"in":[69,77,117,208],"terms":[70,78],"amplitudes,":[74],"but":[75],"also":[76],"structure":[82],"expression.":[85],"RESULTS:":[86],"A":[87],"non-parametric":[88],"time-synchronized":[89],"iterative":[90],"mean":[91],"updating":[92],"technique":[93],"proposed":[95,121,154],"find":[97],"an":[98,139],"overall":[99],"representation":[100],"that":[101,141],"corresponds":[102],"a":[104,107,114,177],"mode":[105,174],"profiles,":[111],"viewed":[112],"as":[113,206],"random":[115,143],"function":[118],"space.":[119],"algorithm":[122,155,185],"explores":[123],"application":[125],"previous":[127],"work":[128],"Hall":[130],"and":[131,137],"Heckman":[132],"genome-wide":[134],"provides":[138],"extension":[140],"includes":[142],"with":[145,167],"aim":[147],"synchronize":[149],"timescales":[150],"across":[151],"genes.":[152],"universally":[157],"applicable":[158],"construction":[161,172],"modes":[163],"functional":[165],"time-warping.":[168],"We":[169],"demonstrate":[170],"functions":[175],"Drosophila":[180],"can":[186],"applied":[188],"define":[190],"clusters":[191],"among":[192],"observed":[194],"without":[199],"any":[200],"kind":[201],"prior":[203],"non-time-warped":[204],"clustering,":[205],"illustrated":[207],"numerical":[210],"example.":[211]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":2}],"updated_date":"2026-06-16T07:32:37.131356","created_date":"2025-10-10T00:00:00"}