{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,22]],"date-time":"2026-10-22T22:15:56Z","timestamp":1792707356251,"version":"4.5.0"},"reference-count":55,"publisher":"Public Library of Science (PLoS)","issue":"6","license":[{"start":{"date-parts":[[2015,6,29]],"date-time":"2015-06-29T00:00:00Z","timestamp":1435536000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0131459","type":"journal-article","created":{"date-parts":[[2015,6,29]],"date-time":"2015-06-29T14:11:58Z","timestamp":1435587118000},"page":"e0131459","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":69,"title":["Immunological Response to Single Pathogen Challenge with Agents of the Bovine Respiratory Disease Complex: An RNA-Sequence Analysis of the Bronchial Lymph Node Transcriptome"],"prefix":"10.1371","volume":"10","author":[{"given":"Polyana C.","family":"Tizioto","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"JaeWoo","family":"Kim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher M.","family":"Seabury","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert D.","family":"Schnabel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laurel J.","family":"Gershwin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alison L.","family":"Van Eenennaam","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rachel","family":"Toaff-Rosenstein","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Holly L.","family":"Neibergs","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"name":"Bovine Respiratory Disease Complex Coordinated Agricultural Project Research Team","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeremy F.","family":"Taylor","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2015,6,29]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1016\/j.cvfa.2010.03.005","article-title":"Control methods for bovine respiratory disease for feedlot cattle","volume":"26","author":"TA Edwards","year":"2010","journal-title":"Vet Clin North Am Food Anim Pract"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1017\/S1466252309990090","article-title":"Overview of the North American beef cattle industry and the incidence of bovine respiratory disease (BRD)","volume":"10","author":"DG Miles","year":"2009","journal-title":"Anim Health Res Rev"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1016\/j.cvfa.2010.04.007","article-title":"Bovine herpesvirus type 1 (BHV-1) is an important cofactor in the bovine respiratory disease complex","volume":"26","author":"C Jones","year":"2010","journal-title":"Vet Clin North Am Food Anim Pract"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1177\/104063870601800104","article-title":"Diseases and pathogens associated with mortality in Ontario beef feedlots","volume":"18","author":"MI Gagea","year":"2006","journal-title":"J Vet Diagn Invest"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1016\/S0749-0720(15)30005-0","article-title":"The immunology of the bovine respiratory disease complex","volume":"17","author":"JA Ellis","year":"2001","journal-title":"Vet Clin North Am Food Anim Pract"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1017\/S1466252307001375","article-title":"Mannheimia haemolytica and bovine respiratory disease","volume":"8","author":"JA Rice","year":"2007","journal-title":"Anim Health Res Rev"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1177\/104063870802000105","article-title":"Respiratory disease associated with bovine coronavirus infection in cattle herds in Southern Italy","volume":"20","author":"N Decaro","year":"2008","journal-title":"J Vet Diagn Invest"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"480","DOI":"10.1111\/j.1751-0813.2003.tb13367.x","article-title":"The medicine and epidemiology of bovine respiratory disease in feedlots","volume":"81","author":"PM Cusack","year":"2003","journal-title":"Aust Vet J"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"1999","DOI":"10.2527\/jas.2006-046","article-title":"Bovine respiratory disease in feedlot cattle: Environmental, genetic, and economic factors","volume":"84","author":"GD Snowder","year":"2006","journal-title":"J Anim Sci"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1016\/j.cell.2013.10.058","article-title":"Leveraging cross-species transcription factor binding site patterns: from diabetes risk loci to disease mechanisms","volume":"156","author":"M Claussnitzer","year":"2014","journal-title":"Cell"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"1427","DOI":"10.1161\/ATVBAHA.112.300112","article-title":"A systems biology framework identifies molecular underpinnings of coronary heart disease","volume":"33","author":"T Huan","year":"2013","journal-title":"Arterioscler Thromb Vasc Biol"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1038\/nrg3575","article-title":"Systems genetics approaches to understand complex traits","volume":"15","author":"M Civelek","year":"2014","journal-title":"Nat Rev Genet"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1016\/j.cvfa.2007.10.003","article-title":"Disease management of dairy calves and heifers","volume":"24","author":"SM McGuirk","year":"2008","journal-title":"Vet Clin North Am Food Anim Pract"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"1225","DOI":"10.1016\/S0264-410X(98)80123-0","article-title":"A bovine model of vaccine enhanced respiratory syncytial virus","volume":"16","author":"LJ Gershwin","year":"1998","journal-title":"Vaccine"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/0007-1935(92)90064-8","article-title":"Pulmonary function changes and clinical findings associated with chronic respiratory disease in calves","volume":"148","author":"DD Collie","year":"1992","journal-title":"Br Vet J"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1152\/physiolgenomics.00128.2012","article-title":"Characterization of the rat developmental liver transcriptome","volume":"45","author":"RH Chapple","year":"2013","journal-title":"Physiol Genomics"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"1105","DOI":"10.1093\/bioinformatics\/btp120","article-title":"TopHat: Discovering splice junctions with RNA-Seq","volume":"25","author":"C Trapnell","year":"2009","journal-title":"Bioinformatics"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1038\/nbt.1621","article-title":"Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation","volume":"28","author":"C Trapnell","year":"2010","journal-title":"Nat Biotechnol"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1038\/nbt.2450","article-title":"Differential analysis of gene regulation at transcript resolution with RNA-seq","volume":"31","author":"C Trapnell","year":"2013","journal-title":"Nat Biotechnol"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"P3","DOI":"10.1186\/gb-2003-4-5-p3","article-title":"DAVID: Database for annotation, visualization, and integrated discovery","volume":"4","author":"G Dennis Jr","year":"2003","journal-title":"Genome Biol"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"562","DOI":"10.1038\/nprot.2012.016","article-title":"Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks","volume":"7","author":"C Trapnell","year":"2012","journal-title":"Nat Protoc"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"470","DOI":"10.1038\/nature07509","article-title":"Alternative isoform regulation in human tissue transcriptomes","volume":"456","author":"ET Wang","year":"2008","journal-title":"Nature"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"1164","DOI":"10.1186\/1471-2164-15-1164","article-title":"Susceptibility loci revealed for bovine respiratory disease complex in pre-weaned holstein calves","volume":"15","author":"HL Neibergs","year":"2014","journal-title":"BMC Genomics"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"530","DOI":"10.1038\/415530a","article-title":"Gene expression profiling predicts clinical outcome of breast cancer","volume":"415","author":"LJ Van\u2019t Veer","year":"2002","journal-title":"Nature"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"1999","DOI":"10.1056\/NEJMoa021967","article-title":"A gene-expression signature as a predictor of survival in breast cancer","volume":"347","author":"MJ Van de Vijver","year":"2002","journal-title":"N Engl J Med"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1017\/S1466252307001326","article-title":"Immune evasion by pathogens of bovine respiratory disease complex","volume":"8","author":"S Srikumaran","year":"2007","journal-title":"Anim Health Res Rev"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"50","DOI":"10.1126\/science.272.5258.50","article-title":"The instructive role of innate immunity in the acquired immune response","volume":"272","author":"DT Fearon","year":"1996","journal-title":"Science"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"1099","DOI":"10.1038\/35074106","article-title":"The innate immune response to bacterial flagellin is mediated by Toll-like receptor 5","volume":"410","author":"F Hayashi","year":"2001","journal-title":"Nature"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"6758","DOI":"10.1038\/sj.onc.1209943","article-title":"NF-kappaB and the immune response","volume":"25","author":"MS Hayden","year":"2006","journal-title":"Oncogene"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1146\/annurev.cellbio.21.122303.115827","article-title":"Recognition and signaling by Toll-like receptors","volume":"22","author":"AP West","year":"2006","journal-title":"Annu Rev Cell Dev Biol"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"816","DOI":"10.1038\/sj.cdd.4401850","article-title":"TLR signaling","volume":"13","author":"T Kawai","year":"2006","journal-title":"Cell Death Differ"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"389","DOI":"10.1038\/nri2975","article-title":"Mitochondria in innate immune responses","volume":"11","author":"AP West","year":"2011","journal-title":"Nat Rev Immunol"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"860","DOI":"10.1189\/jlb.1006639","article-title":"Regulation of innate immunity by MAPK dual-specificity phosphatases: Knockout models reveal new tricks of old genes","volume":"81","author":"K Salojin","year":"2007","journal-title":"J Leukoc Biol"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1146\/annurev.immunol.24.021605.090737","article-title":"Transforming growth factor-beta regulation of immune responses","volume":"24","author":"MO Li","year":"2006","journal-title":"Annu Rev Immunol"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1146\/annurev.immunol.17.1.189","article-title":"Natural killer cells in antiviral defense: Function and regulation by innate cytokines","volume":"17","author":"CA Biron","year":"1999","journal-title":"Annu Rev Immunol"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1182\/blood-2010-08-265892","article-title":"Cytokine release from innate immune cells: association with diverse membrane trafficking pathways","volume":"118","author":"P Lacy","year":"2011","journal-title":"Blood"},{"key":"ref37","article-title":"Immunobiology: The immune system in health and disease. 5th edition","author":"CA Janeway Jr","year":"2001","journal-title":"New York: Garland Science"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"49","DOI":"10.2174\/1874285800802010049","article-title":"Toll-like receptors and viruses: Induction of innate antiviral immune responses","volume":"2","author":"A Xagorari","year":"2008","journal-title":"Open Microbiol J"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"675","DOI":"10.1038\/90609","article-title":"Toll-like receptors: Critical proteins linking innate and acquired immunity","volume":"2","author":"S Akira","year":"2001","journal-title":"Nat Immunol"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"64","DOI":"10.3109\/08916930903374634","article-title":"Immune pathology associated with altered actin cytoskeleton regulation","volume":"43","author":"DC Wickramarachchi","year":"2010","journal-title":"Autoimmunity"},{"key":"ref41","first-page":"30","article-title":"Changing the energy of an immune response","volume":"2","author":"MM Delmastro-Greenwood","year":"2013","journal-title":"Am J Clin Exp Immunol"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"685","DOI":"10.3233\/JAD-2012-111592","article-title":"Mitochondrial dysfunction and immune activation are detectable in early Alzheimer's disease blood","volume":"30","author":"K Lunnon","year":"2012","journal-title":"J Alzheimers Dis"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"308","DOI":"10.1186\/1743-422X-9-308","article-title":"Why are the neurodegenerative disease-related pathways overrepresented in primary HIV-infected peripheral blood mononuclear cells: A genome-wide perspective","volume":"9","author":"L Zhou","year":"2012","journal-title":"Virol J"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1093\/bioinformatics\/btt703","article-title":"Causal analysis approaches in Ingenuity Pathway Analysis","volume":"30","author":"A Kramer","year":"2014","journal-title":"Bioinformatics"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"1624","DOI":"10.1111\/j.1462-5822.2009.01353.x","article-title":"Lipopolysaccharide-induced innate immune responses in primary hepatocytes downregulates woodchuck hepatitis virus replication via interferon-independent pathways","volume":"11","author":"X Zhang","year":"2009","journal-title":"Cell Microbiol"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"888","DOI":"10.1111\/j.1365-2893.2008.01001.x","article-title":"Characterization of the innate immune signalling pathways in hepatocyte cell lines","volume":"15","author":"S Preiss","year":"2008","journal-title":"J Viral Hepat"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"2706","DOI":"10.4049\/jimmunol.178.5.2706","article-title":"Invariant NKT cells amplify the innate immune response to lipopolysaccharide","volume":"178","author":"NA Nagarajan","year":"2007","journal-title":"J Immunol"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"172","DOI":"10.1097\/MCP.0b013e3283455c0b","article-title":"Pulmonary infectious diseases in patients with primary immunodeficiency and those treated with biologic immunomodulating agents","volume":"17","author":"B Alvarez","year":"2011","journal-title":"Curr Opin Pulm Med"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"1037","DOI":"10.1136\/annrheumdis-2011-201270","article-title":"Anti-TNF treatment blocks the induction of T cell-dependent humoral responses","volume":"72","author":"GF Salinas","year":"2013","journal-title":"Ann Rheum Dis"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"10200","DOI":"10.1073\/pnas.0504754102","article-title":"Human ISG15 conjugation targets both IFN-induced and constitutively expressed proteins functioning in diverse cellular pathways","volume":"102","author":"C Zhao","year":"2005","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1016\/0014-4827(88)90123-1","article-title":"Evidence that transferrin supports cell proliferation by supplying iron for DNA synthesis","volume":"176","author":"J Laskey","year":"1988","journal-title":"Exp Cell Res"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"H558","DOI":"10.1152\/ajpheart.01275.2004","article-title":"Leukocyte-derived matrix metalloproteinase-9 mediates blood-brain barrier breakdown and is proinflammatory after transient focal cerebral ischemia","volume":"289","author":"JM Gidday","year":"2005","journal-title":"Am J Physiol Heart Circ Physiol"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"1357","DOI":"10.1016\/S0002-9440(10)63494-3","article-title":"Expression analysis of the T-cell-targeting chemokines CXCL9 and CXCL10 in mice and humans with endothelial infections caused by rickettsiae of the spotted fever group","volume":"163","author":"G Valbuena","year":"2003","journal-title":"Am J Pathol"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1186\/1471-2172-6-2","article-title":"Expression profile of immune response genes in patients with Severe Acute Respiratory Syndrome","volume":"6","author":"R Reghunathan","year":"2005","journal-title":"BMC Immunol"},{"key":"ref55","author":"S Sisson","year":"1914"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0131459","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,8,27]],"date-time":"2019-08-27T16:19:06Z","timestamp":1566922746000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0131459"}},"subtitle":[],"editor":[{"given":"Kevin","family":"Harrod","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2015,6,29]]},"references-count":55,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2015,6,29]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0131459","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,6,29]]}}}