{"id":"https://openalex.org/W4402941219","doi":"https://doi.org/10.1186/s12859-024-05938-9","title":"Using flux theory in dynamic omics data sets to identify differentially changing signals using DPoP","display_name":"Using flux theory in dynamic omics data sets to identify differentially changing signals using DPoP","publication_year":2024,"publication_date":"2024-09-27","ids":{"openalex":"https://openalex.org/W4402941219","doi":"https://doi.org/10.1186/s12859-024-05938-9","pmid":"https://pubmed.ncbi.nlm.nih.gov/39333869"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-024-05938-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05938-9","pdf_url":"https://link.springer.com/content/pdf/10.1186/s12859-024-05938-9.pdf","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","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://link.springer.com/content/pdf/10.1186/s12859-024-05938-9.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5085824292","display_name":"Harley Edwards","orcid":"https://orcid.org/0000-0003-4110-1687"},"institutions":[{"id":"https://openalex.org/I79272384","display_name":"University of Maryland, Baltimore County","ror":"https://ror.org/02qskvh78","country_code":"US","type":"education","lineage":["https://openalex.org/I79272384"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Harley Edwards","raw_affiliation_strings":["Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA","institution_ids":["https://openalex.org/I79272384"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5106156736","display_name":"Joseph Zavorskas","orcid":null},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joseph Zavorskas","raw_affiliation_strings":["Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, CT, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, CT, USA","institution_ids":["https://openalex.org/I140172145"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086356649","display_name":"Walker Huso","orcid":null},"institutions":[{"id":"https://openalex.org/I79272384","display_name":"University of Maryland, Baltimore County","ror":"https://ror.org/02qskvh78","country_code":"US","type":"education","lineage":["https://openalex.org/I79272384"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Walker Huso","raw_affiliation_strings":["Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA","institution_ids":["https://openalex.org/I79272384"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041499956","display_name":"Alexander G. Doan","orcid":"https://orcid.org/0009-0008-6972-1865"},"institutions":[{"id":"https://openalex.org/I79272384","display_name":"University of Maryland, Baltimore County","ror":"https://ror.org/02qskvh78","country_code":"US","type":"education","lineage":["https://openalex.org/I79272384"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alexander G. Doan","raw_affiliation_strings":["Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA","institution_ids":["https://openalex.org/I79272384"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5106060051","display_name":"Caton Silbiger","orcid":null},"institutions":[{"id":"https://openalex.org/I79272384","display_name":"University of Maryland, Baltimore County","ror":"https://ror.org/02qskvh78","country_code":"US","type":"education","lineage":["https://openalex.org/I79272384"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Caton Silbiger","raw_affiliation_strings":["Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA","institution_ids":["https://openalex.org/I79272384"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049668338","display_name":"Steven D. Harris","orcid":"https://orcid.org/0000-0001-5196-1977"},"institutions":[{"id":"https://openalex.org/I173911158","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78","country_code":"US","type":"education","lineage":["https://openalex.org/I173911158"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Steven Harris","raw_affiliation_strings":["Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, IA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, IA, USA","institution_ids":["https://openalex.org/I173911158"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031675415","display_name":"Ranjan Srivastava","orcid":"https://orcid.org/0000-0003-4309-605X"},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ranjan Srivastava","raw_affiliation_strings":["Department of Biomedical Engineering, University of Connecticut, Storrs, CT, USA","Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, CT, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, University of Connecticut, Storrs, CT, USA","institution_ids":["https://openalex.org/I140172145"]},{"raw_affiliation_string":"Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, CT, USA","institution_ids":["https://openalex.org/I140172145"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5020773993","display_name":"Mark R. Marten","orcid":"https://orcid.org/0000-0002-1863-8956"},"institutions":[{"id":"https://openalex.org/I79272384","display_name":"University of Maryland, Baltimore County","ror":"https://ror.org/02qskvh78","country_code":"US","type":"education","lineage":["https://openalex.org/I79272384"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mark R. Marten","raw_affiliation_strings":["Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA. marten@umbc.edu"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA. marten@umbc.edu","institution_ids":["https://openalex.org/I79272384"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5085824292"],"corresponding_institution_ids":["https://openalex.org/I79272384"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.2185,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.57032139,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"25","issue":"1","first_page":"312","last_page":"312"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.3357999920845032,"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":0.3357999920845032,"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":0.20489999651908875,"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/T10885","display_name":"Gene expression and cancer classification","score":0.12359999865293503,"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/computational-biology","display_name":"Computational biology","score":0.5580847263336182},{"id":"https://openalex.org/keywords/omics","display_name":"Omics","score":0.5083393454551697},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5066960453987122},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4972844421863556},{"id":"https://openalex.org/keywords/proteomics","display_name":"Proteomics","score":0.4645518958568573},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.4359193444252014},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3535677194595337},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.26863086223602295},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.16610091924667358},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.08772340416908264},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.0702071487903595}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5580847263336182},{"id":"https://openalex.org/C157585117","wikidata":"https://www.wikidata.org/wiki/Q158666","display_name":"Omics","level":2,"score":0.5083393454551697},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5066960453987122},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4972844421863556},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.4645518958568573},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.4359193444252014},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3535677194595337},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.26863086223602295},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.16610091924667358},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.08772340416908264},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0702071487903595}],"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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001233","descriptor_name":"Aspergillus nidulans","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001233","descriptor_name":"Aspergillus nidulans","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001233","descriptor_name":"Aspergillus nidulans","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001233","descriptor_name":"Aspergillus nidulans","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001233","descriptor_name":"Aspergillus nidulans","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D001233","descriptor_name":"Aspergillus nidulans","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D001233","descriptor_name":"Aspergillus nidulans","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D001233","descriptor_name":"Aspergillus nidulans","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-024-05938-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05938-9","pdf_url":"https://link.springer.com/content/pdf/10.1186/s12859-024-05938-9.pdf","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:39333869","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39333869","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:pubmedcentral.nih.gov:11437665","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11437665","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11437665/pdf/12859_2024_Article_5938.pdf","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:d26deb736ab64e25bf183ecfb8936f79","is_oa":true,"landing_page_url":"https://doaj.org/article/d26deb736ab64e25bf183ecfb8936f79","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 25, Iss 1, Pp 1-20 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-024-05938-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05938-9","pdf_url":"https://link.springer.com/content/pdf/10.1186/s12859-024-05938-9.pdf","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","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/G8604981005","display_name":null,"funder_award_id":"2006189","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320309204","display_name":"University of Maryland, Baltimore County","ror":"https://ror.org/02qskvh78"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4402941219.pdf"},"referenced_works_count":28,"referenced_works":["https://openalex.org/W1483337923","https://openalex.org/W1599740911","https://openalex.org/W1983736629","https://openalex.org/W1984415302","https://openalex.org/W2024713199","https://openalex.org/W2031028006","https://openalex.org/W2110065044","https://openalex.org/W2121211805","https://openalex.org/W2133210805","https://openalex.org/W2141407136","https://openalex.org/W2145860152","https://openalex.org/W2160697532","https://openalex.org/W2179438025","https://openalex.org/W2766437506","https://openalex.org/W2995671733","https://openalex.org/W3000652702","https://openalex.org/W3004671862","https://openalex.org/W3006800618","https://openalex.org/W3008401039","https://openalex.org/W3021135130","https://openalex.org/W3028228569","https://openalex.org/W3094030353","https://openalex.org/W3114526652","https://openalex.org/W3121873626","https://openalex.org/W3139170447","https://openalex.org/W3174219818","https://openalex.org/W3194520274","https://openalex.org/W4308834893"],"related_works":["https://openalex.org/W1488408180","https://openalex.org/W177137871","https://openalex.org/W4292302930","https://openalex.org/W4386960635","https://openalex.org/W2360290178","https://openalex.org/W2035260723","https://openalex.org/W1979675584","https://openalex.org/W3195112886","https://openalex.org/W2590543013","https://openalex.org/W4389089607"],"abstract_inverted_index":{"BACKGROUND:":[0],"Derivative":[1,142],"profiling":[2,77,172,283,300],"is":[3,32,38,57,107,117,192,195,245],"a":[4,33,39,58,108,160,223,246],"novel":[5],"approach":[6,17],"to":[7,22,80,103,237,254,280,284,293],"identify":[8],"differential":[9],"signals":[10],"from":[11],"dynamic":[12,24,45,239],"omics":[13,25,35,46,52,55,144,273],"data":[14,264,286],"sets.":[15],"This":[16,27,115,130],"applies":[18],"variable":[19],"step-size":[20],"differentiation":[21],"time":[23,238,262],"data.":[26],"work":[28,271],"assumes":[29],"that":[30,37,50,61,105,159,193,250],"there":[31,106],"general":[34],"derivative":[36,76,171,282],"useful":[40],"and":[41,95,121,214,241,257],"descriptive":[42],"feature":[43],"of":[44,75,188,222,299],"experiments.":[47],"We":[48],"assert":[49],"this":[51,235,270],"derivative,":[53],"or":[54,67,228],"flux,":[56],"valuable":[59],"descriptor":[60],"can":[62,162,251],"be":[63,252],"used":[64],"instead":[65],"of,":[66],"with,":[68],"fold":[69,91,202],"change":[70,92,203],"calculations.":[71],"RESULTS:":[72],"The":[73,186,266],"results":[74,173],"are":[78],"compared":[79],"established":[81],"methods":[82],"such":[83],"as":[84,209,211],"Multivariate":[85],"Adaptive":[86],"Regression":[87],"Splines,":[88],"significance":[89],"versus":[90],"analysis":[93,102,191],"(Volcano),":[94],"an":[96,136],"adjusted":[97],"ratio":[98],"over":[99,226],"intensity":[100],"(M/A)":[101],"find":[104],"statistically":[109],"significant":[110],"similarity":[111],"between":[112],"the":[113,141,156,165,170,189,296],"results.":[114],"comparison":[116],"repeated":[118],"for":[119],"transcriptomic":[120,240],"phosphoproteomic":[122,242],"expression":[123],"profiles":[124],"previously":[125],"characterized":[126],"in":[127,135,155,169,179,261,269,302],"Aspergillus":[128],"nidulans.":[129],"method":[131,236],"has":[132,152],"been":[133,153],"packaged":[134],"open-source,":[137],"GUI-based":[138],"MATLAB":[139],"app,":[140],"Profiling":[143],"Package":[145],"(DPoP).":[146],"Gene":[147],"Ontology":[148],"(GO)":[149],"term":[150],"enrichment":[151],"included":[154],"app":[157,267],"so":[158],"user":[161],"automatically/programmatically":[163],"describe":[164],"over/under-represented":[166],"GO":[167,183],"terms":[168],"using":[174],"domain":[175],"specific":[176,182],"knowledge":[177],"found":[178],"their":[180,285],"organism's":[181],"database":[184],"file.":[185],"advantage":[187],"DPoP":[190],"it":[194,198,205,215,244],"computationally":[196],"inexpensive,":[197],"does":[199],"not":[200],"require":[201],"calculations,":[204],"describes":[206],"both":[207],"instantaneous":[208],"well":[210],"overall":[212],"behavior,":[213],"achieves":[216],"statistical":[217],"confidence":[218],"with":[219,275],"signal":[220],"trajectories":[221],"single":[224],"bio-replicate":[225],"four":[227],"more":[229],"points.":[230],"CONCLUSIONS:":[231],"While":[232],"we":[233],"apply":[234,281],"datasets,":[243],"numerically":[247],"generalizable":[248],"technique":[249],"applied":[253],"any":[255,258],"organism":[256],"field":[259],"interested":[260],"series":[263],"analysis.":[265],"described":[268],"enables":[272],"researchers":[274],"no":[276],"computer":[277],"science":[278],"background":[279],"sets,":[287],"while":[288],"also":[289],"allowing":[290],"multidisciplined":[291],"users":[292],"build":[294],"on":[295],"nascent":[297],"idea":[298],"derivatives":[301],"omics.":[303]},"counts_by_year":[{"year":2024,"cited_by_count":1}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}