{"id":"https://openalex.org/W4385686233","doi":"https://doi.org/10.4049/jimmunol.210.supp.161.09","title":"Targeted proteomics-driven computational modeling of the mouse macrophage toll-like receptor signaling pathway","display_name":"Targeted proteomics-driven computational modeling of the mouse macrophage toll-like receptor signaling pathway","publication_year":2023,"publication_date":"2023-05-01","ids":{"openalex":"https://openalex.org/W4385686233","doi":"https://doi.org/10.4049/jimmunol.210.supp.161.09"},"language":"en","primary_location":{"id":"doi:10.4049/jimmunol.210.supp.161.09","doi":"https://doi.org/10.4049/jimmunol.210.supp.161.09","is_oa":true,"landing_page_url":"https://doi.org/10.4049/jimmunol.210.supp.161.09","pdf_url":"https://journals.aai.org/jimmunol/article-pdf/210/1_Supplement/161.09/1633548/161_09.pdf","source":{"id":"https://openalex.org/S38008053","display_name":"The Journal of Immunology","issn_l":"0022-1767","issn":["0022-1767","1550-6606"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-b","doyens","jufo-2","ki-jl-2","medline","norway-2","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4320800377","host_organization_name":"American Association of Immunologists","host_organization_lineage":["https://openalex.org/P4320800377"],"host_organization_lineage_names":["American Association of Immunologists"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The Journal of Immunology","raw_type":"journal-article"},"volume":null,"type":"conference-abstract","is_traditional":false,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://journals.aai.org/jimmunol/article-pdf/210/1_Supplement/161.09/1633548/161_09.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5071916749","display_name":"Nathan P. Manes","orcid":"https://orcid.org/0000-0001-6701-3314","observed_orcids":["https://orcid.org/0000-0001-6701-3314"]},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210134534","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210134534"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nathan Paul Manes","raw_affiliation_strings":["NIAID, NIH","1NIAID, NIH"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NIAID, NIH","institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I4210134534"]},{"raw_affiliation_string":"1NIAID, NIH","institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I4210134534"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103421156","display_name":"Anthony A. Armstrong","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210134534","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210134534"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anthony A Armstrong","raw_affiliation_strings":["NIAID, NIH","1NIAID, NIH"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NIAID, NIH","institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I4210134534"]},{"raw_affiliation_string":"1NIAID, NIH","institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I4210134534"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041569902","display_name":"Iain D. C. Fraser","orcid":"https://orcid.org/0000-0003-2272-3907","observed_orcids":["https://orcid.org/0000-0003-2272-3907"]},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210134534","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210134534"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Iain D C Fraser","raw_affiliation_strings":["NIAID, NIH","1NIAID, NIH"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NIAID, NIH","institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I4210134534"]},{"raw_affiliation_string":"1NIAID, NIH","institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I4210134534"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088777789","display_name":"Ronald N. Germain","orcid":"https://orcid.org/0000-0003-1495-9143","observed_orcids":["https://orcid.org/0000-0003-1495-9143"]},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210134534","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210134534"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ronald Germain","raw_affiliation_strings":["NIAID, NIH","1NIAID, NIH"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NIAID, NIH","institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I4210134534"]},{"raw_affiliation_string":"1NIAID, NIH","institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I4210134534"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059988994","display_name":"Martin Meier\u2010Schellersheim","orcid":"https://orcid.org/0000-0002-8754-6377","observed_orcids":["https://orcid.org/0000-0002-8754-6377"]},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210134534","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210134534"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Martin Meier-Schellersheim","raw_affiliation_strings":["NIAID, NIH","1NIAID, NIH"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NIAID, NIH","institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I4210134534"]},{"raw_affiliation_string":"1NIAID, NIH","institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I4210134534"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5084246364","display_name":"Aleksandra Nita\u2010Lazar","orcid":"https://orcid.org/0000-0002-8523-605X","observed_orcids":["https://orcid.org/0000-0002-8523-605X"]},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210134534","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210134534"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Aleksandra Nita-Lazar","raw_affiliation_strings":["NIAID, NIH","1NIAID, NIH"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NIAID, NIH","institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I4210134534"]},{"raw_affiliation_string":"1NIAID, NIH","institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I4210134534"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3500,"currency":"USD","value_usd":3500},"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"210","issue":"Supplement_1","first_page":"161.09","last_page":"161.09"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10371","display_name":"Immune Response and Inflammation","score":0.9077000021934509,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10371","display_name":"Immune Response and Inflammation","score":0.9077000021934509,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.04050000011920929,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.008700000122189522,"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/tlr4-signaling","display_name":"TLR4 signaling","score":0.9139999747276306},{"id":"https://openalex.org/keywords/macrophages","display_name":"macrophages","score":0.9629999995231628},{"id":"https://openalex.org/keywords/pathway-modeling","display_name":"pathway modeling","score":0.6309999823570251},{"id":"https://openalex.org/keywords/phosphoproteomics","display_name":"phosphoproteomics","score":0.8489999771118164},{"id":"https://openalex.org/keywords/lipopolysaccharide-stimulation","display_name":"lipopolysaccharide stimulation","score":0.6110000014305115},{"id":"https://openalex.org/keywords/erk1-phosphorylation","display_name":"ERK1 phosphorylation","score":0.949999988079071},{"id":"https://openalex.org/keywords/protein-complex-structure-prediction","display_name":"protein complex structure prediction","score":0.7509999871253967},{"id":"https://openalex.org/keywords/sepsis","display_name":"sepsis","score":0.7549999952316284},{"id":"https://openalex.org/keywords/rule-based-modeling","display_name":"rule-based models","score":0.5260000228881836},{"id":"https://openalex.org/keywords/parameter-space-exploration","display_name":"parameter space exploration","score":0.5899999737739563}],"concepts":[{"id":"https://openalex.org/C2776070231","wikidata":"https://www.wikidata.org/wiki/Q14914098","display_name":"TLR4","level":3,"score":0.6476197838783264},{"id":"https://openalex.org/C62478195","wikidata":"https://www.wikidata.org/wiki/Q828130","display_name":"Signal transduction","level":2,"score":0.5852416753768921},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5539186596870422},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.5236691832542419},{"id":"https://openalex.org/C11960822","wikidata":"https://www.wikidata.org/wiki/Q242736","display_name":"Phosphorylation","level":2,"score":0.5166816711425781},{"id":"https://openalex.org/C2776709828","wikidata":"https://www.wikidata.org/wiki/Q408004","display_name":"Toll-like receptor","level":4,"score":0.466835618019104},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.4667181372642517},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.41868138313293457},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4159157872200012},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3890872001647949},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.2271517813205719},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.22596442699432373},{"id":"https://openalex.org/C136449434","wikidata":"https://www.wikidata.org/wiki/Q428253","display_name":"Innate immune system","level":3,"score":0.2031981348991394}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.4049/jimmunol.210.supp.161.09","doi":"https://doi.org/10.4049/jimmunol.210.supp.161.09","is_oa":true,"landing_page_url":"https://doi.org/10.4049/jimmunol.210.supp.161.09","pdf_url":"https://journals.aai.org/jimmunol/article-pdf/210/1_Supplement/161.09/1633548/161_09.pdf","source":{"id":"https://openalex.org/S38008053","display_name":"The Journal of Immunology","issn_l":"0022-1767","issn":["0022-1767","1550-6606"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-b","doyens","jufo-2","ki-jl-2","medline","norway-2","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4320800377","host_organization_name":"American Association of Immunologists","host_organization_lineage":["https://openalex.org/P4320800377"],"host_organization_lineage_names":["American Association of Immunologists"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The Journal of Immunology","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.4049/jimmunol.210.supp.161.09","doi":"https://doi.org/10.4049/jimmunol.210.supp.161.09","is_oa":true,"landing_page_url":"https://doi.org/10.4049/jimmunol.210.supp.161.09","pdf_url":"https://journals.aai.org/jimmunol/article-pdf/210/1_Supplement/161.09/1633548/161_09.pdf","source":{"id":"https://openalex.org/S38008053","display_name":"The Journal of Immunology","issn_l":"0022-1767","issn":["0022-1767","1550-6606"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-b","doyens","jufo-2","ki-jl-2","medline","norway-2","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4320800377","host_organization_name":"American Association of Immunologists","host_organization_lineage":["https://openalex.org/P4320800377"],"host_organization_lineage_names":["American Association of Immunologists"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The Journal of Immunology","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.504800021648407,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4385686233.pdf","grobid_xml":"https://content.openalex.org/works/W4385686233.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W3175458097","https://openalex.org/W4290975569","https://openalex.org/W2739472610","https://openalex.org/W4313356043","https://openalex.org/W4416466294","https://openalex.org/W4385686635","https://openalex.org/W2077020648","https://openalex.org/W2915111519","https://openalex.org/W2494438678","https://openalex.org/W3086415127"],"abstract_inverted_index":{"Abstract":[0],"The":[1,158,176],"Toll-like":[2],"receptor":[3],"(TLR)":[4],"signaling":[5],"pathway":[6,60,123,138,174],"is":[7,28,179],"crucial":[8],"for":[9,82,172],"the":[10,56,100,189,207,215,227],"initiation":[11],"of":[12,18,55,104,152,206,219,231],"effective":[13],"immune":[14],"responses.":[15],"Computational":[16],"modeling":[17,47],"biological":[19],"pathways":[20],"can":[21],"test":[22],"mechanistic":[23],"hypotheses":[24],"about":[25],"how":[26],"regulation":[27],"achieved":[29],"and":[30,45,70,79,98,102,108,126,163,193],"why":[31],"it":[32],"sometimes":[33],"fails,":[34],"causing":[35],"disease":[36],"(e.g.,":[37,140],"sepsis).":[38],"In":[39],"this":[40],"investigation,":[41],"mass":[42],"spectrometry":[43],"(LC-MS)":[44],"computational":[46,194],"are":[48,167,196],"being":[49,168,180,197],"integrated":[50,198],"to":[51,88,96,112,120,133,146,182,199],"develop":[52],"a":[53,201],"model":[54,205],"TLR4":[57,59,137,173],"pathway.":[58,209],"proteins":[61,131],"within":[62],"mouse":[63],"macrophages":[64],"were":[65,110,156],"quantitated":[66],"using":[67],"targeted":[68],"LC-MS":[69],"stable-isotope":[71],"labeled":[72],"internal":[73],"(phospho)peptide":[74],"standards":[75],"(136":[76],"unmodified":[77],"peptides":[78],"29":[80],"phosphopeptides":[81],"54":[83],"(phospho)proteins).":[84],"AlphaFold-Multimer":[85],"was":[86,94,118,212,224],"used":[87,95,111,119,169],"predict":[89],"protein":[90],"complex":[91],"structures,":[92,101],"Rosetta":[93],"idealize":[97],"relax":[99],"Simulation":[103],"Diffusional":[105],"Association":[106],"(SDA)":[107],"TransComp":[109],"estimate":[113],"protein-protein":[114,153,164],"association":[115,154,165],"rates.":[116],"Simmune":[117],"perform":[121],"rule-based":[122],"modeling,":[124],"simulation,":[125],"training.":[127],"LPS":[128],"stimulation":[129],"altered":[130],"known":[132],"be":[134],"affected":[135],"by":[136,214,226],"activation":[139],"phosphorylated":[141],"ERK1":[142],"increased":[143],"from":[144],"30,000":[145],"250,000":[147],"copies":[148],"per":[149],"cell).":[150],"Hundreds":[151],"rates":[155,166],"predicted.":[157],"(phospho)protein":[159],"absolute":[160],"abundance":[161],"values":[162],"as":[170],"parameters":[171],"models.":[175],"parameter":[177,184],"space":[178],"explored":[181],"identify":[183],"sets":[185],"that":[186],"accurately":[187],"reproduce":[188],"experimental":[190],"data.":[191],"Experimental":[192],"techniques":[195],"generate":[200],"strongly":[202],"data":[203],"driven":[204],"TLR":[208],"This":[210,222],"work":[211,223],"supported":[213,225],"Intramural":[216,228],"Research":[217,229],"Program":[218,230],"NIAID,":[220,232],"NIH.":[221,233]},"counts_by_year":[{"year":2024,"cited_by_count":1}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2023-08-10T00:00:00"}