{"id":"https://openalex.org/W2971279876","doi":"https://doi.org/10.1109/tcbb.2019.2937033","title":"Modeling Cell Communication with Time-Dependent Signaling Hypergraphs","display_name":"Modeling Cell Communication with Time-Dependent Signaling Hypergraphs","publication_year":2019,"publication_date":"2019-08-26","ids":{"openalex":"https://openalex.org/W2971279876","doi":"https://doi.org/10.1109/tcbb.2019.2937033","mag":"2971279876","pmid":"https://pubmed.ncbi.nlm.nih.gov/31449029"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2019.2937033","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2019.2937033","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-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/A5053277299","display_name":"Michael R. Schwob","orcid":"https://orcid.org/0000-0001-6367-2013"},"institutions":[{"id":"https://openalex.org/I133999245","display_name":"University of Nevada, Las Vegas","ror":"https://ror.org/0406gha72","country_code":"US","type":"education","lineage":["https://openalex.org/I133999245"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Michael R. Schwob","raw_affiliation_strings":["University of Nevada, Las Vegas, Las Vegas, NV, USA"],"affiliations":[{"raw_affiliation_string":"University of Nevada, Las Vegas, Las Vegas, NV, USA","institution_ids":["https://openalex.org/I133999245"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021549646","display_name":"Justin Zhan","orcid":"https://orcid.org/0000-0001-8991-5669"},"institutions":[{"id":"https://openalex.org/I78715868","display_name":"University of Arkansas at Fayetteville","ror":"https://ror.org/05jbt9m15","country_code":"US","type":"education","lineage":["https://openalex.org/I78715868"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Justin Zhan","raw_affiliation_strings":["University of Arkansas, Fayetteville, AR, USA"],"affiliations":[{"raw_affiliation_string":"University of Arkansas, Fayetteville, AR, USA","institution_ids":["https://openalex.org/I78715868"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5112525229","display_name":"Aeren Dempsey","orcid":null},"institutions":[{"id":"https://openalex.org/I133999245","display_name":"University of Nevada, Las Vegas","ror":"https://ror.org/0406gha72","country_code":"US","type":"education","lineage":["https://openalex.org/I133999245"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Aeren Dempsey","raw_affiliation_strings":["University of Nevada, Las Vegas, Las Vegas, NV, USA"],"affiliations":[{"raw_affiliation_string":"University of Nevada, Las Vegas, Las Vegas, NV, USA","institution_ids":["https://openalex.org/I133999245"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5053277299"],"corresponding_institution_ids":["https://openalex.org/I133999245"],"apc_list":null,"apc_paid":null,"fwci":1.2786,"has_fulltext":false,"cited_by_count":22,"citation_normalized_percentile":{"value":0.80039558,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":98},"biblio":{"volume":"18","issue":"3","first_page":"1151","last_page":"1163"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9993000030517578,"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":0.9993000030517578,"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/T10621","display_name":"Gene Regulatory Network Analysis","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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9962999820709229,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.6392501592636108},{"id":"https://openalex.org/keywords/cell-signaling","display_name":"Cell signaling","score":0.6097440719604492},{"id":"https://openalex.org/keywords/dependency","display_name":"Dependency (UML)","score":0.5187094807624817},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.5166726112365723},{"id":"https://openalex.org/keywords/signal-transduction","display_name":"Signal transduction","score":0.5053830146789551},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4944925010204315},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.2931184768676758},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2666352391242981},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.09069141745567322}],"concepts":[{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.6392501592636108},{"id":"https://openalex.org/C150555746","wikidata":"https://www.wikidata.org/wiki/Q210973","display_name":"Cell signaling","level":3,"score":0.6097440719604492},{"id":"https://openalex.org/C19768560","wikidata":"https://www.wikidata.org/wiki/Q320727","display_name":"Dependency (UML)","level":2,"score":0.5187094807624817},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.5166726112365723},{"id":"https://openalex.org/C62478195","wikidata":"https://www.wikidata.org/wiki/Q828130","display_name":"Signal transduction","level":2,"score":0.5053830146789551},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4944925010204315},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.2931184768676758},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2666352391242981},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.09069141745567322},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"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":"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":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2019.2937033","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2019.2937033","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31449029","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31449029","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1480113724","display_name":null,"funder_award_id":"1710716","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G1942964926","display_name":null,"funder_award_id":"W911NF1710088","funder_id":"https://openalex.org/F4320306078","funder_display_name":"U.S. Department of Defense"},{"id":"https://openalex.org/G6499355239","display_name":null,"funder_award_id":"1625677","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7447493799","display_name":null,"funder_award_id":"W911NF1810246","funder_id":"https://openalex.org/F4320306078","funder_display_name":"U.S. Department of Defense"},{"id":"https://openalex.org/G8619485319","display_name":null,"funder_award_id":"75585-NS-RI","funder_id":"https://openalex.org/F4320306078","funder_display_name":"U.S. Department of Defense"},{"id":"https://openalex.org/G8644965492","display_name":null,"funder_award_id":"W911NF1810437","funder_id":"https://openalex.org/F4320306078","funder_display_name":"U.S. Department of Defense"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306078","display_name":"U.S. Department of Defense","ror":"https://ror.org/0447fe631"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":77,"referenced_works":["https://openalex.org/W137936598","https://openalex.org/W1494578976","https://openalex.org/W1525912444","https://openalex.org/W1558016752","https://openalex.org/W1807981783","https://openalex.org/W1969709265","https://openalex.org/W1970516489","https://openalex.org/W1973661008","https://openalex.org/W1973897738","https://openalex.org/W1980917656","https://openalex.org/W1986365650","https://openalex.org/W1987916269","https://openalex.org/W1989229844","https://openalex.org/W1989277387","https://openalex.org/W1990198677","https://openalex.org/W1997966434","https://openalex.org/W2010571055","https://openalex.org/W2035669429","https://openalex.org/W2046783872","https://openalex.org/W2047197934","https://openalex.org/W2051159649","https://openalex.org/W2056388892","https://openalex.org/W2057748277","https://openalex.org/W2069157810","https://openalex.org/W2071273959","https://openalex.org/W2073307618","https://openalex.org/W2081554709","https://openalex.org/W2082049134","https://openalex.org/W2083786039","https://openalex.org/W2085543001","https://openalex.org/W2089338760","https://openalex.org/W2096766502","https://openalex.org/W2102894828","https://openalex.org/W2104509220","https://openalex.org/W2107648723","https://openalex.org/W2110861948","https://openalex.org/W2111823238","https://openalex.org/W2119517032","https://openalex.org/W2120901716","https://openalex.org/W2122516422","https://openalex.org/W2125403403","https://openalex.org/W2129557999","https://openalex.org/W2130965298","https://openalex.org/W2133667940","https://openalex.org/W2142203996","https://openalex.org/W2146918064","https://openalex.org/W2166236009","https://openalex.org/W2167913971","https://openalex.org/W2197121351","https://openalex.org/W2269895670","https://openalex.org/W2299844414","https://openalex.org/W2403714621","https://openalex.org/W2415993698","https://openalex.org/W2463826254","https://openalex.org/W2524699965","https://openalex.org/W2553390933","https://openalex.org/W2564037751","https://openalex.org/W2577823455","https://openalex.org/W2607843552","https://openalex.org/W2612379539","https://openalex.org/W2618370510","https://openalex.org/W2625693911","https://openalex.org/W2730110879","https://openalex.org/W2735584150","https://openalex.org/W2743219614","https://openalex.org/W2766916839","https://openalex.org/W2767397323","https://openalex.org/W2770057757","https://openalex.org/W2773997834","https://openalex.org/W2803606270","https://openalex.org/W2808549270","https://openalex.org/W2884259470","https://openalex.org/W4233698560","https://openalex.org/W4245562979","https://openalex.org/W6633400222","https://openalex.org/W6713476953","https://openalex.org/W6732276043"],"related_works":["https://openalex.org/W2068787210","https://openalex.org/W4390006811","https://openalex.org/W3203208080","https://openalex.org/W3092591054","https://openalex.org/W1504782610","https://openalex.org/W2106363574","https://openalex.org/W2969388149","https://openalex.org/W2130108353","https://openalex.org/W2008572054","https://openalex.org/W1897115642"],"abstract_inverted_index":{"Signaling":[0,51],"pathways":[1,27,52,123,143,152,173],"describe":[2],"a":[3,8,132],"group":[4],"of":[5,93,105,117,160,171,178],"molecules":[6],"in":[7,120],"cell":[9,17,21,24,47,67,106],"that":[10,128],"collaborate":[11],"to":[12,77,101,138,156],"control":[13],"one":[14],"or":[15,23],"more":[16,78,139],"functions,":[18],"such":[19,82],"as":[20,56,83],"division":[22],"death.":[25],"The":[26,146,165],"communicate":[28],"by":[29],"sending":[30],"signals":[31],"between":[32],"molecules,":[33],"and":[34,45,69,86,174],"this":[35,113],"process":[36],"is":[37,43,49,124,144],"repeated":[38],"until":[39],"the":[40,46,91,103,115,130,157,168,176],"terminal":[41],"molecule":[42],"activated":[44],"function":[48],"executed.":[50],"are":[53,153],"often":[54],"represented":[55],"directed":[57,72],"graphs,":[58],"which":[59],"does":[60],"not":[61],"provide":[62],"enough":[63],"information":[64],"when":[65],"modeling":[66,121],"functions":[68],"reactions.":[70],"Recently,":[71],"hypergraphs":[73,137,161],"have":[74],"been":[75],"proposed":[76],"accurately":[79],"represent":[80],"reactions":[81],"protein":[84],"activation":[85],"interaction.":[87],"To":[88],"further":[89],"improve":[90,102],"representation":[92,104,170],"signaling":[94,107,122,142,151,172,180],"pathways,":[95],"time":[96,118],"dependency":[97,119],"must":[98],"be":[99],"considered":[100],"at":[108],"any":[109],"given":[110],"time.":[111],"In":[112],"paper,":[114],"importance":[116],"presented.":[125],"An":[126],"algorithm":[127],"finds":[129],"shortest":[131,147],"priori":[133],"path":[134],"using":[135],"time-dependent":[136,148,179],"robustly":[140],"model":[141],"adopted.":[145],"hyperpaths":[149],"representing":[150,162],"an":[154],"improvement":[155],"recent":[158],"adoption":[159,177],"these":[163],"pathways.":[164],"results":[166],"display":[167],"improved":[169],"motivate":[175],"hypergraphs.":[181]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
