{"id":"https://openalex.org/W2165696776","doi":"https://doi.org/10.1186/1471-2105-15-s5-s3","title":"timeClip: pathway analysis for time course data without replicates","display_name":"timeClip: pathway analysis for time course data without replicates","publication_year":2014,"publication_date":"2014-05-01","ids":{"openalex":"https://openalex.org/W2165696776","doi":"https://doi.org/10.1186/1471-2105-15-s5-s3","mag":"2165696776","pmid":"https://pubmed.ncbi.nlm.nih.gov/25077979"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-15-s5-s3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-s5-s3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-S5-S3","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/10.1186/1471-2105-15-S5-S3","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5058895507","display_name":"Paolo Martini","orcid":"https://orcid.org/0000-0002-0146-1031"},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Paolo Martini","raw_affiliation_strings":["Department of Biology, University of Padova, Padova, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Biology, University of Padova, Padova, Italy","institution_ids":["https://openalex.org/I138689650"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070887609","display_name":"Gabriele Sales","orcid":"https://orcid.org/0000-0003-2078-5661"},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Gabriele Sales","raw_affiliation_strings":["Department of Biology, University of Padova, Padova, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Biology, University of Padova, Padova, Italy","institution_ids":["https://openalex.org/I138689650"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091476817","display_name":"Enrica Calura","orcid":"https://orcid.org/0000-0001-8463-2432"},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Enrica Calura","raw_affiliation_strings":["Department of Biology, University of Padova, Padova, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Biology, University of Padova, Padova, Italy","institution_ids":["https://openalex.org/I138689650"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011190061","display_name":"Stefano Cagnin","orcid":"https://orcid.org/0000-0001-7271-4625"},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Stefano Cagnin","raw_affiliation_strings":["Department of Biology, University of Padova, Padova, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Biology, University of Padova, Padova, Italy","institution_ids":["https://openalex.org/I138689650"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065068163","display_name":"Monica Chiogna","orcid":"https://orcid.org/0000-0002-7238-3739"},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Monica Chiogna","raw_affiliation_strings":["Department of Statistics, University of Padova, Padova, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Statistics, University of Padova, Padova, Italy","institution_ids":["https://openalex.org/I138689650"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082717632","display_name":"Chiara Romualdi","orcid":"https://orcid.org/0000-0003-4792-9047"},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Chiara Romualdi","raw_affiliation_strings":["Department of Biology, University of Padova, Padova, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Biology, University of Padova, Padova, Italy","institution_ids":["https://openalex.org/I138689650"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5058895507"],"corresponding_institution_ids":["https://openalex.org/I138689650"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.5686,"has_fulltext":true,"cited_by_count":19,"citation_normalized_percentile":{"value":0.83150672,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"15","issue":"S5","first_page":"S3","last_page":"S3"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9984999895095825,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9984999895095825,"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/T11041","display_name":"Ubiquitin and proteasome pathways","score":0.9975000023841858,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9918000102043152,"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/computer-science","display_name":"Computer science","score":0.5820785760879517},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5166080594062805},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3866465091705322},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3686513900756836},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.35266757011413574}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5820785760879517},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5166080594062805},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3866465091705322},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3686513900756836},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.35266757011413574}],"mesh":[{"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009132","descriptor_name":"Muscles","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009132","descriptor_name":"Muscles","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009132","descriptor_name":"Muscles","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012038","descriptor_name":"Regeneration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012038","descriptor_name":"Regeneration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012038","descriptor_name":"Regeneration","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},{"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":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058570","descriptor_name":"TOR Serine-Threonine Kinases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D058570","descriptor_name":"TOR Serine-Threonine Kinases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D058570","descriptor_name":"TOR Serine-Threonine Kinases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D058570","descriptor_name":"TOR Serine-Threonine Kinases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D058570","descriptor_name":"TOR Serine-Threonine Kinases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D058570","descriptor_name":"TOR Serine-Threonine Kinases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1186/1471-2105-15-s5-s3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-s5-s3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-S5-S3","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:25077979","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25077979","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:cris.unibo.it:11585/647104","is_oa":false,"landing_page_url":"http://hdl.handle.net/11585/647104","pdf_url":null,"source":{"id":"https://openalex.org/S4306402579","display_name":"Archivio istituzionale della ricerca (Alma Mater Studiorum Universit\u00e0 di Bologna)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210117483","host_organization_name":"Istituto di Ematologia di Bologna","host_organization_lineage":["https://openalex.org/I4210117483"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:europepmc.org:3076107","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4095003","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:iris.unibs.it:11379/533953","is_oa":false,"landing_page_url":"http://hdl.handle.net/11379/533953","pdf_url":null,"source":{"id":"https://openalex.org/S4306400804","display_name":"Institutional Research Information System (Universit\u00e0 degli Studi di Brescia)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I66752286","host_organization_name":"University of Milano-Bicocca","host_organization_lineage":["https://openalex.org/I66752286"],"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":"info:eu-repo/semantics/article"},{"id":"pmh:oai:www.research.unipd.it:11577/2831339","is_oa":true,"landing_page_url":"http://hdl.handle.net/11577/2831339","pdf_url":null,"source":{"id":"https://openalex.org/S4377196283","display_name":"Research Padua  Archive (University of Padua)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I138689650","host_organization_name":"University of Padua","host_organization_lineage":["https://openalex.org/I138689650"],"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":null,"raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-15-s5-s3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-s5-s3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-S5-S3","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":[],"awards":[{"id":"https://openalex.org/G2489103016","display_name":null,"funder_award_id":"RISIB","funder_id":"https://openalex.org/F4320326074","funder_display_name":"Regione del Veneto"},{"id":"https://openalex.org/G7924601289","display_name":null,"funder_award_id":"CARIPARO","funder_id":"https://openalex.org/F4320321966","funder_display_name":"Universit\u00e0 degli Studi di Padova"}],"funders":[{"id":"https://openalex.org/F4320321966","display_name":"Universit\u00e0 degli Studi di Padova","ror":"https://ror.org/00240q980"},{"id":"https://openalex.org/F4320326074","display_name":"Regione del Veneto","ror":"https://ror.org/03mm67z69"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2165696776.pdf","grobid_xml":"https://content.openalex.org/works/W2165696776.grobid-xml"},"referenced_works_count":64,"referenced_works":["https://openalex.org/W1533335653","https://openalex.org/W1546952499","https://openalex.org/W1790978987","https://openalex.org/W1963770435","https://openalex.org/W1967162333","https://openalex.org/W1973647162","https://openalex.org/W1973887944","https://openalex.org/W1977148017","https://openalex.org/W1980217160","https://openalex.org/W1983463159","https://openalex.org/W2025176940","https://openalex.org/W2026012474","https://openalex.org/W2026341138","https://openalex.org/W2029485495","https://openalex.org/W2037893131","https://openalex.org/W2063202299","https://openalex.org/W2064533818","https://openalex.org/W2069531683","https://openalex.org/W2075602427","https://openalex.org/W2080466236","https://openalex.org/W2087924310","https://openalex.org/W2097997980","https://openalex.org/W2101934336","https://openalex.org/W2102555672","https://openalex.org/W2106248311","https://openalex.org/W2110687686","https://openalex.org/W2112039060","https://openalex.org/W2113958470","https://openalex.org/W2116606180","https://openalex.org/W2117587325","https://openalex.org/W2118069309","https://openalex.org/W2119454933","https://openalex.org/W2120169559","https://openalex.org/W2120391288","https://openalex.org/W2127938920","https://openalex.org/W2130410032","https://openalex.org/W2130666470","https://openalex.org/W2134736660","https://openalex.org/W2135230352","https://openalex.org/W2135597559","https://openalex.org/W2135827569","https://openalex.org/W2141703917","https://openalex.org/W2149566602","https://openalex.org/W2153675946","https://openalex.org/W2154167701","https://openalex.org/W2154972152","https://openalex.org/W2155142785","https://openalex.org/W2156004795","https://openalex.org/W2157096644","https://openalex.org/W2157646380","https://openalex.org/W2159835316","https://openalex.org/W2161175828","https://openalex.org/W2163811214","https://openalex.org/W2165040702","https://openalex.org/W2167119716","https://openalex.org/W2184417913","https://openalex.org/W2949754388","https://openalex.org/W3021971632","https://openalex.org/W3104024536","https://openalex.org/W3104970456","https://openalex.org/W3186622552","https://openalex.org/W4255852734","https://openalex.org/W4292156489","https://openalex.org/W4388323202"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189","https://openalex.org/W2013243191","https://openalex.org/W2117258802"],"abstract_inverted_index":{"timeClip":[0,25],"represents":[1],"a":[2,27],"new":[3],"improvement":[4],"in":[5],"the":[6,37],"field":[7],"of":[8,39],"time-dependent":[9,21],"pathway":[10],"analysis.":[11],"It":[12],"allows":[13],"to":[14,35],"isolate":[15],"and":[16],"dissect":[17],"pathways":[18],"characterized":[19],"by":[20],"components.":[22],"Furthermore,":[23],"using":[24],"on":[26],"mouse":[28],"muscle":[29,40],"regeneration":[30,42],"dataset":[31],"we":[32],"were":[33],"able":[34],"characterize":[36],"process":[38],"fiber":[41],"with":[43],"its":[44],"correct":[45],"timing.":[46]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":2}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
