{"id":"https://openalex.org/W2564089750","doi":"https://doi.org/10.1093/bioinformatics/btw709","title":"Agent-based re-engineering of ErbB signaling: a modeling pipeline for integrative systems\u00a0biology","display_name":"Agent-based re-engineering of ErbB signaling: a modeling pipeline for integrative systems\u00a0biology","publication_year":2016,"publication_date":"2016-11-08","ids":{"openalex":"https://openalex.org/W2564089750","doi":"https://doi.org/10.1093/bioinformatics/btw709","mag":"2564089750","pmid":"https://pubmed.ncbi.nlm.nih.gov/27998938"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw709","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw709","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/A5051736757","display_name":"Arya A. Das","orcid":"https://orcid.org/0009-0000-6423-0663"},"institutions":[{"id":"https://openalex.org/I146682468","display_name":"National Institute for Interdisciplinary Science and Technology","ror":"https://ror.org/05bkc5375","country_code":"IN","type":"facility","lineage":["https://openalex.org/I146682468","https://openalex.org/I2799351866","https://openalex.org/I4210134808","https://openalex.org/I66760702"]},{"id":"https://openalex.org/I66760702","display_name":"Council of Scientific and Industrial Research","ror":"https://ror.org/021wm7p51","country_code":"IN","type":"government","lineage":["https://openalex.org/I2799351866","https://openalex.org/I4210134808","https://openalex.org/I66760702"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Arya A Das","raw_affiliation_strings":["Computational Modeling and Simulation Unit, Council of Scientific and Industrial Research-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram, Kerala, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Modeling and Simulation Unit, Council of Scientific and Industrial Research-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram, Kerala, India","institution_ids":["https://openalex.org/I146682468","https://openalex.org/I66760702"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089472821","display_name":"T Ajayakumar Darsana","orcid":null},"institutions":[{"id":"https://openalex.org/I146682468","display_name":"National Institute for Interdisciplinary Science and Technology","ror":"https://ror.org/05bkc5375","country_code":"IN","type":"facility","lineage":["https://openalex.org/I146682468","https://openalex.org/I2799351866","https://openalex.org/I4210134808","https://openalex.org/I66760702"]},{"id":"https://openalex.org/I66760702","display_name":"Council of Scientific and Industrial Research","ror":"https://ror.org/021wm7p51","country_code":"IN","type":"government","lineage":["https://openalex.org/I2799351866","https://openalex.org/I4210134808","https://openalex.org/I66760702"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"T Ajayakumar Darsana","raw_affiliation_strings":["Computational Modeling and Simulation Unit, Council of Scientific and Industrial Research-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram, Kerala, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Modeling and Simulation Unit, Council of Scientific and Industrial Research-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram, Kerala, India","institution_ids":["https://openalex.org/I146682468","https://openalex.org/I66760702"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5036074252","display_name":"Elizabeth Jacob","orcid":"https://orcid.org/0000-0001-8099-0902"},"institutions":[{"id":"https://openalex.org/I146682468","display_name":"National Institute for Interdisciplinary Science and Technology","ror":"https://ror.org/05bkc5375","country_code":"IN","type":"facility","lineage":["https://openalex.org/I146682468","https://openalex.org/I2799351866","https://openalex.org/I4210134808","https://openalex.org/I66760702"]},{"id":"https://openalex.org/I66760702","display_name":"Council of Scientific and Industrial Research","ror":"https://ror.org/021wm7p51","country_code":"IN","type":"government","lineage":["https://openalex.org/I2799351866","https://openalex.org/I4210134808","https://openalex.org/I66760702"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Elizabeth Jacob","raw_affiliation_strings":["Computational Modeling and Simulation Unit, Council of Scientific and Industrial Research-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram, Kerala, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Modeling and Simulation Unit, Council of Scientific and Industrial Research-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram, Kerala, India","institution_ids":["https://openalex.org/I146682468","https://openalex.org/I66760702"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5036074252"],"corresponding_institution_ids":["https://openalex.org/I146682468","https://openalex.org/I66760702"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.3482,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.69974425,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"33","issue":"5","first_page":"726","last_page":"732"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.32850000262260437,"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":0.32850000262260437,"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/T11829","display_name":"Mathematical Biology Tumor Growth","score":0.22290000319480896,"subfield":{"id":"https://openalex.org/subfields/2611","display_name":"Modeling and Simulation"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10755","display_name":"HER2/EGFR in Cancer Research","score":0.10000000149011612,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7274852395057678},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.6793546676635742},{"id":"https://openalex.org/keywords/reverse-engineering","display_name":"Reverse engineering","score":0.5799357891082764},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.5747754573822021},{"id":"https://openalex.org/keywords/formalism","display_name":"Formalism (music)","score":0.49541914463043213},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.4940066933631897},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.427612841129303},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3754175305366516},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.33133965730667114},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3233509063720703},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.15730175375938416},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.14319342374801636},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1264573037624359}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7274852395057678},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.6793546676635742},{"id":"https://openalex.org/C207850805","wikidata":"https://www.wikidata.org/wiki/Q269608","display_name":"Reverse engineering","level":2,"score":0.5799357891082764},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.5747754573822021},{"id":"https://openalex.org/C73301696","wikidata":"https://www.wikidata.org/wiki/Q5469984","display_name":"Formalism (music)","level":3,"score":0.49541914463043213},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.4940066933631897},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.427612841129303},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3754175305366516},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.33133965730667114},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3233509063720703},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.15730175375938416},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.14319342374801636},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1264573037624359},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C558565934","wikidata":"https://www.wikidata.org/wiki/Q2743","display_name":"Musical","level":2,"score":0.0},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","level":1,"score":0.0},{"id":"https://openalex.org/C153349607","wikidata":"https://www.wikidata.org/wiki/Q36649","display_name":"Visual arts","level":1,"score":0.0},{"id":"https://openalex.org/C142362112","wikidata":"https://www.wikidata.org/wiki/Q735","display_name":"Art","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":"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":"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":"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},{"descriptor_ui":"D066246","descriptor_name":"ErbB Receptors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D066246","descriptor_name":"ErbB Receptors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D066246","descriptor_name":"ErbB Receptors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btw709","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw709","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:27998938","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27998938","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":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":26,"referenced_works":["https://openalex.org/W1964321121","https://openalex.org/W1969996736","https://openalex.org/W1990808537","https://openalex.org/W1995457482","https://openalex.org/W2001620484","https://openalex.org/W2041844855","https://openalex.org/W2045628158","https://openalex.org/W2057485245","https://openalex.org/W2075161553","https://openalex.org/W2078112275","https://openalex.org/W2083540678","https://openalex.org/W2092578710","https://openalex.org/W2093868559","https://openalex.org/W2096595244","https://openalex.org/W2121490181","https://openalex.org/W2125857415","https://openalex.org/W2126841263","https://openalex.org/W2133068979","https://openalex.org/W2138321569","https://openalex.org/W2141708465","https://openalex.org/W2150701033","https://openalex.org/W2154601808","https://openalex.org/W2154731971","https://openalex.org/W2155418451","https://openalex.org/W2163493106","https://openalex.org/W3011439212"],"related_works":["https://openalex.org/W2363831530","https://openalex.org/W4307821979","https://openalex.org/W2150019175","https://openalex.org/W2139769766","https://openalex.org/W1679963423","https://openalex.org/W2003230381","https://openalex.org/W2149918584","https://openalex.org/W3013063242","https://openalex.org/W2169348520","https://openalex.org/W2031656933"],"abstract_inverted_index":{"Motivation:":[0],"Experiments":[1],"in":[2,35,144,217,254],"systems":[3,105],"biology":[4,234],"are":[5,264],"generally":[6],"supported":[7],"by":[8,20,118],"a":[9,73,109],"computational":[10],"model":[11,136,162],"which":[12,213],"quantitatively":[13,138],"estimates":[14],"the":[15,18,22,26,38,47,50,79,88,93,115,126,160,165,175,184,197,204,208,229,243],"parameters":[16],"of":[17,49,78,141,167,199,206,211,231],"system":[19],"finding":[21],"best":[23],"fit":[24],"to":[25,32,45,58,66,71,98,128,170],"experiment.":[27],"Mathematical":[28],"models":[29],"have":[30,56],"proved":[31],"be":[33],"successful":[34],"reverse":[36,119,200],"engineering":[37],"system.":[39],"The":[40,53,154],"data":[41,116,212,263],"generated":[42],"is":[43,60,63],"interpreted":[44],"understand":[46],"dynamics":[48],"underlying":[51],"phenomena.":[52],"question":[54],"we":[55],"sought":[57],"answer":[59],"that":[61,112,137,163],"-":[62],"it":[64,123],"possible":[65],"use":[67,77],"an":[68,100],"agent-based":[69],"approach":[70,90],"re-engineer":[72],"biological":[74],"process,":[75],"making":[76],"available":[80,253,265],"knowledge":[81],"from":[82,92,114,159],"experimental":[83],"and":[84,121,146,235,239],"modelling":[85,102,110,236],"efforts?":[86],"Can":[87],"bottom-up":[89],"benefit":[91],"top-down":[94],"exercise":[95],"so":[96],"as":[97],"create":[99],"integrated":[101],"formalism":[103],"for":[104,124,151,174],"biology?":[106],"We":[107,190],"propose":[108],"pipeline":[111,155],"learns":[113],"given":[117],"engineering,":[120,201],"uses":[122],"re-engineering":[125,193],"system,":[127],"carry":[129],"out":[130],"in-silico":[131],"experiments.":[132],"Results:":[133],"A":[134],"mathematical":[135],"predicts":[139],"co-expression":[140],"EGFR-HER2":[142,188],"receptors":[143],"activation":[145],"trafficking":[147],"has":[148],"been":[149],"taken":[150],"this":[152],"study.":[153],"architecture":[156],"takes":[157],"cues":[158],"population":[161],"gives":[164],"rates":[166],"biochemical":[168],"reactions,":[169],"formulate":[171],"knowledge-based":[172],"rules":[173],"particle":[176],"model.":[177],"Agent-based":[178],"simulations":[179],"using":[180,196],"these":[181],"rules,":[182],"support":[183],"existing":[185],"facts":[186],"on":[187,242],"dynamics.":[189],"conclude":[191],"that,":[192],"models,":[194],"built":[195],"results":[198],"opens":[202],"up":[203],"possibility":[205],"harnessing":[207],"power":[209],"pack":[210],"now":[214],"lies":[215],"scattered":[216],"literature.":[218],"Virtual":[219],"experiments":[220],"could":[221],"then":[222],"become":[223],"more":[224],"realistic":[225],"when":[226],"empowered":[227],"with":[228],"findings":[230],"empirical":[232],"cell":[233],"studies.":[237],"Availability":[238],"Implementation:":[240],"Implemented":[241],"Agent":[244],"Modelling":[245],"Framework":[246],"developed":[247],"in-house.":[248],"C":[249],"++":[250],"code":[251],"templates":[252],"Supplementary":[255,260,262],"material":[256],".":[257],"Contact:":[258],"liz.csir@gmail.com.":[259],"information:":[261],"at":[266],"Bioinformatics":[267],"online.":[268]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":2}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}
