{"id":"https://openalex.org/W2748875147","doi":"https://doi.org/10.1145/3107411.3107420","title":"Circadian Rhythms in <i>Neurospora</i> Exhibit Biologically Relevant Driven and Damped Harmonic Oscillations","display_name":"Circadian Rhythms in <i>Neurospora</i> Exhibit Biologically Relevant Driven and Damped Harmonic Oscillations","publication_year":2017,"publication_date":"2017-08-20","ids":{"openalex":"https://openalex.org/W2748875147","doi":"https://doi.org/10.1145/3107411.3107420","mag":"2748875147","pmid":"https://pubmed.ncbi.nlm.nih.gov/31844846"},"language":"en","primary_location":{"id":"doi:10.1145/3107411.3107420","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3107411.3107420","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5091591204","display_name":"Hannah De los Santos","orcid":"https://orcid.org/0000-0003-2543-3286"},"institutions":[{"id":"https://openalex.org/I165799507","display_name":"Rensselaer Polytechnic Institute","ror":"https://ror.org/01rtyzb94","country_code":"US","type":"education","lineage":["https://openalex.org/I165799507"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Hannah De los Santos","raw_affiliation_strings":["Rensselaer Polytechnic Institute, Troy, NY, USA"],"affiliations":[{"raw_affiliation_string":"Rensselaer Polytechnic Institute, Troy, NY, USA","institution_ids":["https://openalex.org/I165799507"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026265263","display_name":"Emily Collins","orcid":null},"institutions":[{"id":"https://openalex.org/I165799507","display_name":"Rensselaer Polytechnic Institute","ror":"https://ror.org/01rtyzb94","country_code":"US","type":"education","lineage":["https://openalex.org/I165799507"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Emily J. Collins","raw_affiliation_strings":["Rensselaer Polytechnic Institute, Troy, NY, USA"],"affiliations":[{"raw_affiliation_string":"Rensselaer Polytechnic Institute, Troy, NY, USA","institution_ids":["https://openalex.org/I165799507"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016869041","display_name":"Jennifer Hurley","orcid":"https://orcid.org/0000-0002-1085-9391"},"institutions":[{"id":"https://openalex.org/I165799507","display_name":"Rensselaer Polytechnic Institute","ror":"https://ror.org/01rtyzb94","country_code":"US","type":"education","lineage":["https://openalex.org/I165799507"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jennifer M. Hurley","raw_affiliation_strings":["Rensselaer Polytechnic Institute, Troy, NY, USA"],"affiliations":[{"raw_affiliation_string":"Rensselaer Polytechnic Institute, Troy, NY, USA","institution_ids":["https://openalex.org/I165799507"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5048876983","display_name":"Kristin P. Bennett","orcid":"https://orcid.org/0000-0002-8782-105X"},"institutions":[{"id":"https://openalex.org/I165799507","display_name":"Rensselaer Polytechnic Institute","ror":"https://ror.org/01rtyzb94","country_code":"US","type":"education","lineage":["https://openalex.org/I165799507"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kristin P. Bennett","raw_affiliation_strings":["Rensselaer Polytechnic Institute, Troy, NY, USA"],"affiliations":[{"raw_affiliation_string":"Rensselaer Polytechnic Institute, Troy, NY, USA","institution_ids":["https://openalex.org/I165799507"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5091591204"],"corresponding_institution_ids":["https://openalex.org/I165799507"],"apc_list":null,"apc_paid":null,"fwci":0.8124,"has_fulltext":false,"cited_by_count":16,"citation_normalized_percentile":{"value":0.67470989,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"2017","issue":null,"first_page":"455","last_page":"463"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10342","display_name":"Circadian rhythm and melatonin","score":0.9991999864578247,"subfield":{"id":"https://openalex.org/subfields/2807","display_name":"Endocrine and Autonomic Systems"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10342","display_name":"Circadian rhythm and melatonin","score":0.9991999864578247,"subfield":{"id":"https://openalex.org/subfields/2807","display_name":"Endocrine and Autonomic Systems"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11268","display_name":"Light effects on plants","score":0.9972000122070312,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12813","display_name":"Plant and Biological Electrophysiology Studies","score":0.9675999879837036,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/circadian-rhythm","display_name":"Circadian rhythm","score":0.8210554718971252},{"id":"https://openalex.org/keywords/amplitude","display_name":"Amplitude","score":0.7394341826438904},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.572418212890625},{"id":"https://openalex.org/keywords/neurospora-crassa","display_name":"Neurospora crassa","score":0.5587989091873169},{"id":"https://openalex.org/keywords/harmonic-oscillator","display_name":"Harmonic oscillator","score":0.5416832566261292},{"id":"https://openalex.org/keywords/circadian-clock","display_name":"Circadian clock","score":0.50008225440979},{"id":"https://openalex.org/keywords/harmonic","display_name":"Harmonic","score":0.4527979791164398},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.41611990332603455},{"id":"https://openalex.org/keywords/chronobiology","display_name":"Chronobiology","score":0.41001415252685547},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.3217236399650574},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.28931641578674316},{"id":"https://openalex.org/keywords/neuroscience","display_name":"Neuroscience","score":0.20243334770202637},{"id":"https://openalex.org/keywords/acoustics","display_name":"Acoustics","score":0.15650221705436707},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.15581977367401123},{"id":"https://openalex.org/keywords/quantum-mechanics","display_name":"Quantum mechanics","score":0.1554945409297943}],"concepts":[{"id":"https://openalex.org/C121446783","wikidata":"https://www.wikidata.org/wiki/Q208353","display_name":"Circadian rhythm","level":2,"score":0.8210554718971252},{"id":"https://openalex.org/C180205008","wikidata":"https://www.wikidata.org/wiki/Q159190","display_name":"Amplitude","level":2,"score":0.7394341826438904},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.572418212890625},{"id":"https://openalex.org/C2776739539","wikidata":"https://www.wikidata.org/wiki/Q133459","display_name":"Neurospora crassa","level":4,"score":0.5587989091873169},{"id":"https://openalex.org/C40934718","wikidata":"https://www.wikidata.org/wiki/Q190070","display_name":"Harmonic oscillator","level":2,"score":0.5416832566261292},{"id":"https://openalex.org/C38606739","wikidata":"https://www.wikidata.org/wiki/Q5121352","display_name":"Circadian clock","level":3,"score":0.50008225440979},{"id":"https://openalex.org/C127934551","wikidata":"https://www.wikidata.org/wiki/Q1148098","display_name":"Harmonic","level":2,"score":0.4527979791164398},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.41611990332603455},{"id":"https://openalex.org/C187765855","wikidata":"https://www.wikidata.org/wiki/Q506874","display_name":"Chronobiology","level":3,"score":0.41001415252685547},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3217236399650574},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.28931641578674316},{"id":"https://openalex.org/C169760540","wikidata":"https://www.wikidata.org/wiki/Q207011","display_name":"Neuroscience","level":1,"score":0.20243334770202637},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.15650221705436707},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.15581977367401123},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.1554945409297943},{"id":"https://openalex.org/C143065580","wikidata":"https://www.wikidata.org/wiki/Q3285695","display_name":"Mutant","level":3,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1145/3107411.3107420","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3107411.3107420","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics","raw_type":"proceedings-article"},{"id":"pmid:31844846","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31844846","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":"ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine","raw_type":null},{"id":"pmh:oai:europepmc.org:5868624","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6913202","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1844279810","display_name":null,"funder_award_id":"1331023","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4344210073","display_name":null,"funder_award_id":"U01 EB022546","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306080","display_name":"Foundation for the National Institutes of Health","ror":"https://ror.org/00k86s890"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320334618","display_name":"Fonds de Recherche du Qu\u00e9bec - Sant\u00e9","ror":"https://ror.org/02eqrsj93"},{"id":"https://openalex.org/F4320337363","display_name":"National Institute of Biomedical Imaging and Bioengineering","ror":"https://ror.org/00372qc85"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":22,"referenced_works":["https://openalex.org/W31275902","https://openalex.org/W264578019","https://openalex.org/W1964504813","https://openalex.org/W1971575429","https://openalex.org/W1979385177","https://openalex.org/W2007885546","https://openalex.org/W2018598287","https://openalex.org/W2022734245","https://openalex.org/W2035476735","https://openalex.org/W2056395995","https://openalex.org/W2090209293","https://openalex.org/W2100311257","https://openalex.org/W2111220881","https://openalex.org/W2115688366","https://openalex.org/W2115742710","https://openalex.org/W2116107838","https://openalex.org/W2137917513","https://openalex.org/W2149811710","https://openalex.org/W2155450177","https://openalex.org/W2169784081","https://openalex.org/W2411520408","https://openalex.org/W2582743722"],"related_works":["https://openalex.org/W2071690264","https://openalex.org/W2050100795","https://openalex.org/W2140682486","https://openalex.org/W2092146436","https://openalex.org/W2411520408","https://openalex.org/W4285097245","https://openalex.org/W2090209293","https://openalex.org/W3136837454","https://openalex.org/W2477634377","https://openalex.org/W1577140614"],"abstract_inverted_index":{"Circadian":[0],"rhythms":[1],"are":[2,18],"endogenous":[3],"cycles":[4,17],"of":[5,133,156],"approximately":[6],"24":[7],"hours":[8,40],"reinforced":[9],"by":[10,102],"external":[11,46],"cues":[12],"such":[13],"as":[14,21,112],"light.":[15],"These":[16],"typically":[19],"modeled":[20],"harmonic":[22,59,71,84,136,161],"oscillators":[23,162],"with":[24,45,153],"fixed":[25,109],"amplitude":[26,110],"peaks.":[27],"Using":[28],"experimental":[29],"data":[30],"measuring":[31],"global":[32],"gene":[33,151],"transcription":[34],"in":[35,41,61,73],"<i>Neurospora":[36],"crassa</i>":[37],"over":[38],"48":[39],"the":[42,63,75,103],"dark":[43],"(i.e.":[44],"queues":[47],"removed),":[48],"we":[49,93],"demonstrate":[50],"that":[51,98,107,120],"many":[52],"circadian":[53,96,146,169],"genes":[54,97,126],"frequently":[55],"exhibit":[56,127],"either":[57],"damped":[58,123],"oscillations,":[60,72],"which":[62,74,87],"peak":[64,76],"amplitudes":[65,77],"decrease":[66],"each":[67,79],"day,":[68],"or":[69,124],"driven":[70,125],"increase":[78],"day.":[80],"By":[81],"fitting":[82],"extended":[83,134],"oscillator":[85,137],"models":[86,138],"include":[88],"a":[89,164],"damping":[90],"ratio":[91],"coefficient,":[92],"detected":[94],"additional":[95],"were":[99],"not":[100,142],"identified":[101,122],"current":[104],"standard":[105],"tools":[106],"use":[108],"waves":[111],"reference,":[113],"e.g.":[114],"JTK_CYCLE.":[115],"Functional":[116],"Catalogue":[117],"analysis":[118],"confirms":[119],"our":[121],"distinct":[128],"biological":[129,157],"functions.":[130],"The":[131],"application":[132],"damped/driven":[135],"thus":[139],"can":[140],"elucidate,":[141],"only":[143],"previously":[144],"unidentified":[145],"genes,":[147],"but":[148],"also":[149],"characterize":[150],"subsets":[152],"expression":[154],"patterns":[155],"relevance.":[158],"Thus,":[159],"expanded":[160],"provide":[163],"powerful":[165],"new":[166],"tool":[167],"for":[168],"system":[170],"biology.":[171]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":3}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2017-08-31T00:00:00"}
