{"id":"https://openalex.org/W2988646204","doi":"https://doi.org/10.1093/bioinformatics/btz838","title":"Estimating chain length for time delays in dynamical systems using profile likelihood","display_name":"Estimating chain length for time delays in dynamical systems using profile likelihood","publication_year":2019,"publication_date":"2019-11-13","ids":{"openalex":"https://openalex.org/W2988646204","doi":"https://doi.org/10.1093/bioinformatics/btz838","mag":"2988646204","pmid":"https://pubmed.ncbi.nlm.nih.gov/32176768"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz838","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz838","pdf_url":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5053049078","display_name":"Adrian L. Hauber","orcid":"https://orcid.org/0000-0002-3053-5124"},"institutions":[{"id":"https://openalex.org/I161046081","display_name":"University of Freiburg","ror":"https://ror.org/0245cg223","country_code":"DE","type":"education","lineage":["https://openalex.org/I161046081"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Adrian L Hauber","raw_affiliation_strings":["Institute of Physics, University of Freiburg , Freiburg 79104, Germany"],"raw_orcid":"https://orcid.org/0000-0002-3053-5124","affiliations":[{"raw_affiliation_string":"Institute of Physics, University of Freiburg , Freiburg 79104, Germany","institution_ids":["https://openalex.org/I161046081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070152986","display_name":"Raphael Engesser","orcid":null},"institutions":[{"id":"https://openalex.org/I161046081","display_name":"University of Freiburg","ror":"https://ror.org/0245cg223","country_code":"DE","type":"education","lineage":["https://openalex.org/I161046081"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Raphael Engesser","raw_affiliation_strings":["Institute of Physics, University of Freiburg , Freiburg 79104, Germany","Signalling Research Centres BIOSS and CIBSS, University of Freiburg , Freiburg 79104, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Physics, University of Freiburg , Freiburg 79104, Germany","institution_ids":["https://openalex.org/I161046081"]},{"raw_affiliation_string":"Signalling Research Centres BIOSS and CIBSS, University of Freiburg , Freiburg 79104, Germany","institution_ids":["https://openalex.org/I161046081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111900042","display_name":"Joep Vanlier","orcid":null},"institutions":[{"id":"https://openalex.org/I161046081","display_name":"University of Freiburg","ror":"https://ror.org/0245cg223","country_code":"DE","type":"education","lineage":["https://openalex.org/I161046081"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Joep Vanlier","raw_affiliation_strings":["Institute of Physics, University of Freiburg , Freiburg 79104, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Physics, University of Freiburg , Freiburg 79104, Germany","institution_ids":["https://openalex.org/I161046081"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5052831097","display_name":"Jens Timmer","orcid":"https://orcid.org/0000-0003-4517-1383"},"institutions":[{"id":"https://openalex.org/I161046081","display_name":"University of Freiburg","ror":"https://ror.org/0245cg223","country_code":"DE","type":"education","lineage":["https://openalex.org/I161046081"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Jens Timmer","raw_affiliation_strings":["Institute of Physics, University of Freiburg , Freiburg 79104, Germany","Signalling Research Centres BIOSS and CIBSS, University of Freiburg , Freiburg 79104, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Physics, University of Freiburg , Freiburg 79104, Germany","institution_ids":["https://openalex.org/I161046081"]},{"raw_affiliation_string":"Signalling Research Centres BIOSS and CIBSS, University of Freiburg , Freiburg 79104, Germany","institution_ids":["https://openalex.org/I161046081"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5053049078"],"corresponding_institution_ids":["https://openalex.org/I161046081"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.11229276,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"36","issue":"6","first_page":"1848","last_page":"1854"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.942799985408783,"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":0.942799985408783,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.01510000042617321,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.014399999752640724,"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/identifiability","display_name":"Identifiability","score":0.8348150253295898},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7156052589416504},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.5620579719543457},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5472648739814758},{"id":"https://openalex.org/keywords/bayesian-information-criterion","display_name":"Bayesian information criterion","score":0.47477126121520996},{"id":"https://openalex.org/keywords/series","display_name":"Series (stratigraphy)","score":0.47392281889915466},{"id":"https://openalex.org/keywords/chain","display_name":"Chain (unit)","score":0.46340131759643555},{"id":"https://openalex.org/keywords/maximum-likelihood","display_name":"Maximum likelihood","score":0.44371411204338074},{"id":"https://openalex.org/keywords/cls-upper-limits","display_name":"CLs upper limits","score":0.41907066106796265},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.32503560185432434},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.2431837022304535},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.23201927542686462},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.17899063229560852},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.16829046607017517}],"concepts":[{"id":"https://openalex.org/C122770356","wikidata":"https://www.wikidata.org/wiki/Q1656753","display_name":"Identifiability","level":2,"score":0.8348150253295898},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7156052589416504},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.5620579719543457},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5472648739814758},{"id":"https://openalex.org/C168136583","wikidata":"https://www.wikidata.org/wiki/Q1988242","display_name":"Bayesian information criterion","level":2,"score":0.47477126121520996},{"id":"https://openalex.org/C143724316","wikidata":"https://www.wikidata.org/wiki/Q312468","display_name":"Series (stratigraphy)","level":2,"score":0.47392281889915466},{"id":"https://openalex.org/C199185054","wikidata":"https://www.wikidata.org/wiki/Q552299","display_name":"Chain (unit)","level":2,"score":0.46340131759643555},{"id":"https://openalex.org/C49781872","wikidata":"https://www.wikidata.org/wiki/Q1045555","display_name":"Maximum likelihood","level":2,"score":0.44371411204338074},{"id":"https://openalex.org/C190729725","wikidata":"https://www.wikidata.org/wiki/Q5012817","display_name":"CLs upper limits","level":2,"score":0.41907066106796265},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32503560185432434},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.2431837022304535},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.23201927542686462},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.17899063229560852},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.16829046607017517},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C119767625","wikidata":"https://www.wikidata.org/wiki/Q618211","display_name":"Optometry","level":1,"score":0.0},{"id":"https://openalex.org/C1276947","wikidata":"https://www.wikidata.org/wiki/Q333","display_name":"Astronomy","level":1,"score":0.0},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","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":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btz838","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz838","pdf_url":null,"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:32176768","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32176768","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}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6800558654","display_name":null,"funder_award_id":"INST 35/1134-1 FUGG","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":25,"referenced_works":["https://openalex.org/W1494118823","https://openalex.org/W1972200266","https://openalex.org/W1994031807","https://openalex.org/W2016966551","https://openalex.org/W2042628558","https://openalex.org/W2045115006","https://openalex.org/W2062404235","https://openalex.org/W2071448055","https://openalex.org/W2086663631","https://openalex.org/W2094631910","https://openalex.org/W2117057692","https://openalex.org/W2129992593","https://openalex.org/W2131043603","https://openalex.org/W2131230954","https://openalex.org/W2136098137","https://openalex.org/W2143894094","https://openalex.org/W2168648059","https://openalex.org/W2169090274","https://openalex.org/W2179083909","https://openalex.org/W2483655230","https://openalex.org/W2515696031","https://openalex.org/W2762851762","https://openalex.org/W2934894223","https://openalex.org/W3102649939","https://openalex.org/W4299993032"],"related_works":["https://openalex.org/W2724847603","https://openalex.org/W2034041141","https://openalex.org/W2184661725","https://openalex.org/W2900187352","https://openalex.org/W2573470972","https://openalex.org/W2105626102","https://openalex.org/W2131038454","https://openalex.org/W112856298","https://openalex.org/W4236149988","https://openalex.org/W2090499145"],"abstract_inverted_index":{"MOTIVATION:":[0],"Apparent":[1],"time":[2],"delays":[3,35,43],"in":[4,36,116],"partly":[5],"observed,":[6],"biochemical":[7,37],"reaction":[8,18],"networks":[9],"can":[10],"be":[11],"modelled":[12],"by":[13],"lumping":[14],"a":[15,20,45,90,108,117,143,167],"more":[16,54],"complex":[17,48],"into":[19],"series":[21],"of":[22,47,72,79,145,152],"linear":[23,30],"reactions":[24,38],"often":[25,53],"referred":[26],"to":[27,74,96,103,112,123,172],"as":[28,135,137],"the":[29,57,70,76,83,105,113,125,150,163,180,184],"chain":[31,84],"trick.":[32],"Since":[33],"most":[34],"are":[39,195,205],"no":[40],"true,":[41],"hard":[42],"but":[44],"consequence":[46],"unobserved":[49],"processes,":[50],"this":[51,66,101],"approach":[52],"closely":[55],"represents":[56],"true":[58],"system":[59],"compared":[60,177],"with":[61,107,132,138,178],"delay":[62],"differential":[63],"equations.":[64],"In":[65],"paper,":[67],"we":[68],"address":[69],"question":[71],"how":[73],"select":[75],"optimal":[77],"number":[78],"additional":[80],"equations,":[81],"i.e.":[82],"length":[85],"(CL).":[86],"RESULTS:":[87],"We":[88,129],"derive":[89],"criterion":[91],"based":[92],"on":[93],"parameter":[94],"identifiability":[95],"infer":[97],"CLs":[98],"and":[99,148,156,175,190,199],"compare":[100],"method":[102,165],"choosing":[104,179],"model":[106,144,154,181],"CL":[109],"that":[110,162,182],"leads":[111],"best":[114],"fit":[115],"maximum":[118],"likelihood":[119],"sense,":[120],"which":[121],"corresponds":[122],"optimizing":[124],"Bayesian":[126],"information":[127],"criterion.":[128],"evaluate":[130],"performance":[131,169],"simulated":[133],"data":[134,141,157,176,191,204],"well":[136],"measured":[139],"biological":[140,173],"for":[142,193],"JAK2/STAT5":[146],"signalling":[147],"access":[149],"influence":[151],"different":[153],"structures":[155],"characteristics.":[158],"Our":[159],"analysis":[160],"revealed":[161],"proposed":[164],"features":[166],"superior":[168],"when":[170],"applied":[171],"models":[174],"maximizes":[183],"likelihood.":[185],"AVAILABILITY":[186],"AND":[187],"IMPLEMENTATION:":[188],"Models":[189],"used":[192],"simulations":[194],"available":[196,206],"at":[197,207],"https://github.com/Data2Dynamics/d2d":[198],"http://jeti.uni-freiburg.de/PNAS_Swameye_Data.":[200],"SUPPLEMENTARY":[201],"INFORMATION:":[202],"Supplementary":[203],"Bioinformatics":[208],"online.":[209]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}