{"id":"https://openalex.org/W2032189074","doi":"https://doi.org/10.1186/1471-2105-10-15","title":"Robust discovery of periodically expressed genes using the laplace periodogram","display_name":"Robust discovery of periodically expressed genes using the laplace periodogram","publication_year":2009,"publication_date":"2009-01-11","ids":{"openalex":"https://openalex.org/W2032189074","doi":"https://doi.org/10.1186/1471-2105-10-15","mag":"2032189074","pmid":"https://pubmed.ncbi.nlm.nih.gov/19134222"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-10-15","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-15","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-15","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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 Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-15","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5010459950","display_name":"Kuo\u2010ching Liang","orcid":"https://orcid.org/0000-0002-3020-4202"},"institutions":[{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kuo-ching Liang","raw_affiliation_strings":["Department of Electrical Engineering, Columbia University, New York, NY 10027, USA. kl2171@columbia.edu","Department of Electrical Engineering, Columbia University, New York, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering, Columbia University, New York, NY 10027, USA. kl2171@columbia.edu","institution_ids":["https://openalex.org/I78577930"]},{"raw_affiliation_string":"Department of Electrical Engineering, Columbia University, New York, USA","institution_ids":["https://openalex.org/I78577930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100382658","display_name":"Xiaodong Wang","orcid":"https://orcid.org/0000-0002-2945-9240"},"institutions":[{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Xiaodong Wang","raw_affiliation_strings":["Department of Electrical Engineering, Columbia University, New York, NY, 10027, USA","Department of Electrical Engineering, Columbia University, New York, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering, Columbia University, New York, NY, 10027, USA","institution_ids":["https://openalex.org/I78577930"]},{"raw_affiliation_string":"Department of Electrical Engineering, Columbia University, New York, USA","institution_ids":["https://openalex.org/I78577930"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5090385435","display_name":"Ta\u2010Hsin Li","orcid":"https://orcid.org/0000-0003-1769-9500"},"institutions":[{"id":"https://openalex.org/I1341412227","display_name":"IBM (United States)","ror":"https://ror.org/05hh8d621","country_code":"US","type":"company","lineage":["https://openalex.org/I1341412227"]},{"id":"https://openalex.org/I4210114115","display_name":"IBM Research - Thomas J. Watson Research Center","ror":"https://ror.org/0265w5591","country_code":"US","type":"facility","lineage":["https://openalex.org/I1341412227","https://openalex.org/I4210114115"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ta-Hsin Li","raw_affiliation_strings":["IBM T J Watson Research Center, Department of Mathematical Sciences, Yorktown Heights, NY, 10598, USA","IBM T. J. Watson Research Center, Department of Mathematical Sciences, Yorktown Heights, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IBM T J Watson Research Center, Department of Mathematical Sciences, Yorktown Heights, NY, 10598, USA","institution_ids":["https://openalex.org/I4210114115","https://openalex.org/I1341412227"]},{"raw_affiliation_string":"IBM T. J. Watson Research Center, Department of Mathematical Sciences, Yorktown Heights, USA","institution_ids":["https://openalex.org/I1341412227"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5100382658"],"corresponding_institution_ids":["https://openalex.org/I78577930"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.2324,"has_fulltext":true,"cited_by_count":18,"citation_normalized_percentile":{"value":0.7807822,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"10","issue":"1","first_page":"15","last_page":"15"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.2037000060081482,"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":0.2037000060081482,"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/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.08699999749660492,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.07199999690055847,"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/periodogram","display_name":"Periodogram","score":0.6797988414764404},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5704902410507202},{"id":"https://openalex.org/keywords/laplace-transform","display_name":"Laplace transform","score":0.5511823892593384},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5316256880760193},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.47309377789497375},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.434894859790802},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3577588200569153},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.34421586990356445},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.2785605192184448},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.26148080825805664},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.22652703523635864}],"concepts":[{"id":"https://openalex.org/C197680801","wikidata":"https://www.wikidata.org/wiki/Q587619","display_name":"Periodogram","level":2,"score":0.6797988414764404},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5704902410507202},{"id":"https://openalex.org/C97937538","wikidata":"https://www.wikidata.org/wiki/Q199691","display_name":"Laplace transform","level":2,"score":0.5511823892593384},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5316256880760193},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.47309377789497375},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.434894859790802},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3577588200569153},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.34421586990356445},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.2785605192184448},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.26148080825805664},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.22652703523635864},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000235","qualifier_name":"genetics","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":4,"locations":[{"id":"doi:10.1186/1471-2105-10-15","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-15","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-15","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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 Bioinformatics","raw_type":"journal-article"},{"id":"pmid:19134222","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19134222","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 bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:91458b3cd085482cb3d33a1667c4c5c7","is_oa":false,"landing_page_url":"https://doaj.org/article/91458b3cd085482cb3d33a1667c4c5c7","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 Bioinformatics, Vol 10, Iss 1, p 15 (2009)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2650682","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2650682","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 Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-10-15","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-15","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-15","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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 Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/16","display_name":"Peace, Justice and strong institutions","score":0.6600000262260437}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2032189074.pdf","grobid_xml":"https://content.openalex.org/works/W2032189074.grobid-xml"},"referenced_works_count":43,"referenced_works":["https://openalex.org/W1483505747","https://openalex.org/W1514245537","https://openalex.org/W1964636649","https://openalex.org/W1969289662","https://openalex.org/W1974618482","https://openalex.org/W1986316936","https://openalex.org/W1987144436","https://openalex.org/W2008107402","https://openalex.org/W2013607137","https://openalex.org/W2016076879","https://openalex.org/W2029124387","https://openalex.org/W2040870891","https://openalex.org/W2041687729","https://openalex.org/W2073506826","https://openalex.org/W2090159240","https://openalex.org/W2102794349","https://openalex.org/W2103274883","https://openalex.org/W2103453943","https://openalex.org/W2105712639","https://openalex.org/W2112047656","https://openalex.org/W2116687437","https://openalex.org/W2122135124","https://openalex.org/W2123902215","https://openalex.org/W2132585078","https://openalex.org/W2134314273","https://openalex.org/W2137786672","https://openalex.org/W2137810258","https://openalex.org/W2140884902","https://openalex.org/W2140971281","https://openalex.org/W2142460132","https://openalex.org/W2142894222","https://openalex.org/W2146078808","https://openalex.org/W2148541040","https://openalex.org/W2149866115","https://openalex.org/W2150375898","https://openalex.org/W2155120241","https://openalex.org/W2489822048","https://openalex.org/W2798766386","https://openalex.org/W2997000181","https://openalex.org/W4236956086","https://openalex.org/W4292963524","https://openalex.org/W4297440291","https://openalex.org/W6641170335"],"related_works":["https://openalex.org/W2057009832","https://openalex.org/W2780156044","https://openalex.org/W2408114858","https://openalex.org/W2073741588","https://openalex.org/W3148881609","https://openalex.org/W2350962908","https://openalex.org/W1508605967","https://openalex.org/W2177793333","https://openalex.org/W2490267035","https://openalex.org/W2581535539"],"abstract_inverted_index":{"BACKGROUND:":[0],"Time-course":[1,103],"gene":[2,67,104],"expression":[3,68,105],"analysis":[4],"has":[5],"become":[6],"important":[7,28],"in":[8,69,134],"recent":[9],"developments":[10],"due":[11,110],"to":[12,33,59,79,82,94,111,142],"the":[13,35,40,49,54,70,86,112,124,129,151],"increasingly":[14],"available":[15,125],"experimental":[16],"data.":[17],"The":[18,74,137],"detection":[19,64,130],"of":[20,65,72,114,131,153],"genes":[21],"that":[22,159],"are":[23,100,107,160],"periodically":[24],"expressed":[25],"is":[26,77,140],"an":[27],"step":[29],"which":[30,52],"allows":[31],"us":[32],"study":[34],"regulatory":[36],"mechanisms":[37],"associated":[38],"with":[39,148],"cell":[41],"cycle.":[42],"RESULTS:":[43],"In":[44],"this":[45],"work,":[46],"we":[47],"present":[48],"Laplace":[50,75,138],"periodogram":[51,76,139],"employs":[53],"least":[55],"absolute":[56],"deviation":[57],"criterion":[58],"provide":[60],"a":[61],"more":[62],"robust":[63],"periodic":[66],"presence":[71,152],"outliers.":[73,120],"shown":[78,141],"perform":[80,143],"comparably":[81],"existing":[83,96],"methods":[84,97],"for":[85,145,157],"Sacharomyces":[87],"cerevisiae":[88],"and":[89,93,117,127,149,155],"Arabidopsis":[90],"time-course":[91],"datasets,":[92],"outperform":[95],"when":[98],"outliers":[99],"present.":[101],"CONCLUSION:":[102],"data":[106,126,147,158],"often":[108],"noisy":[109],"limitations":[113],"current":[115],"technology,":[116],"may":[118],"include":[119],"These":[121],"artifacts":[122],"corrupt":[123],"make":[128],"periodicity":[132],"difficult":[133],"many":[135],"cases.":[136],"well":[144],"both":[146],"without":[150],"outliers,":[154],"also":[156],"non-uniformly":[161],"sampled.":[162]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":5}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}
