Compton CWR, Heuer C, Thomsen PT, Carpenter TE, Phyn CVC, McDougall S. Invited review: a systematic literature review and meta-analysis of mortality and culling in dairy cattle. J Dairy Sci. 2017;100(1):1–16.
Article
CAS
PubMed
Google Scholar
DAFM. AIM bovine statistics report, 2018, https://www.agriculture.gov.ie/media/migration/animalhealthwelfare/animalidentificationandmovement/AIMBovineStatisticsReport2018100519.pdf, Accessed 16 Mar 2020.
Google Scholar
Zhang H, Wang Y, Chang Y, Luo H, Brito LF, Dong Y, et al. Mortality-culling rates of dairy calves and replacement heifers and its risk factors in Holstein Cattle. Animals. 2019;9(10):730.
Article
PubMed Central
Google Scholar
Murray GM, More SJ, Clegg TA, Earley B, O’Neill RG, Johnston D, et al. Risk factors associated with exposure to bovine respiratory disease pathogens during the peri-weaning period in dairy bull calves. BMC Vet Res. 2018;14:53.
Article
PubMed
PubMed Central
CAS
Google Scholar
Conneely M, Berry DP, Murphy JP, Lorenz I, Doherty ML, Kennedy E. Effects of milk feeding volume and frequency on body weight and health of dairy heifer calves. Livest Sci. 2014;161:90–4.
Article
Google Scholar
Todd CG, McGee M, Tiernan K, Crosson P, O’Riordan E, McClure J, et al. An observational study on passive immunity in Irish suckler beef and dairy calves: tests for failure of passive transfer of immunity and associations with health and performance. Prev Vet Med. 2018;159:182–95.
Article
CAS
PubMed
Google Scholar
Johnston D, Kenny DA, McGee M, Waters SM, Kelly AK, Earley B. Electronic feeding behavioural data as indicators of health status in dairy calves. Irish J Agric Food Res. 2016;55(2):159–68.
Article
Google Scholar
Dubrovsky SA, Van Eenennaam AL, Karle BM, Rossitto PV, Lehenbauer TW, Aly SS. Epidemiology of bovine respiratory disease (BRD) in preweaned calves on California dairies: the BRD 10K study. J Dairy Sci. 2019;102(8):7306–19.
Article
CAS
PubMed
Google Scholar
Cramer MC, Ollivett TL. Growth of preweaned, group-housed dairy calves diagnosed with respiratory disease using clinical respiratory scoring and thoracic ultrasound—a cohort study. J Dairy Sci. 2019;102(5):4322–31.
Article
CAS
PubMed
Google Scholar
Karle BM, Maier GU, Love WJ, Dubrovsky SA, Williams DR, Anderson RJ, et al. Regional management practices and prevalence of bovine respiratory disease in California’s preweaned dairy calves. J Dairy Sci. 2019;102(8):7583–96.
Article
CAS
PubMed
Google Scholar
Taylor JD, Fulton RW, Lehenbauer TW, Step DL, Confer AW. The epidemiology of bovine respiratory disease: what is the evidence for preventive measures? Can Vet J. 2010;51(12):1351–9.
PubMed
PubMed Central
Google Scholar
McGuirk SM, Peek SF. Timely diagnosis of dairy calf respiratory disease using a standardized scoring system. Anim Health Res Rev. 2014;15(2):145–7.
Article
PubMed
Google Scholar
Caswell JL. Failure of respiratory defenses in the pathogenesis of bacterial pneumonia of cattle. Vet Pathol Online. 2014;51(2):393–409.
Article
CAS
Google Scholar
Johnston D, Earley B, Cormican P, Murray G, Kenny DA, Waters SM, et al. Illumina MiSeq 16S amplicon sequence analysis of bovine respiratory disease associated bacteria in lung and mediastinal lymph node tissue. BMC Vet Res. 2017;13(1):118.
Article
PubMed
PubMed Central
CAS
Google Scholar
Griffin D, Chengappa MM, Kuszak J, McVey DS. Bacterial pathogens of the bovine respiratory disease complex. Vet Clin North Am Food Anim. 2010;26(2):381–94.
Article
Google Scholar
Valarcher J-F, Taylor G. Bovine respiratory syncytial virus infection. Vet Res. 2007;38(2):153–80.
Article
CAS
PubMed
Google Scholar
Pardon B, Callens J, Maris J, Allais L, Van Praet W, Deprez P, et al. Pathogen-specific risk factors in acute outbreaks of respiratory disease in calves. J Dairy Sci. 2020;103(3):2556–66.
Article
CAS
PubMed
PubMed Central
Google Scholar
Neibergs HL, Seabury CM, Wojtowicz AJ, Wang Z, Scraggs E, Kiser JN, et al. Susceptibility loci revealed for bovine respiratory disease complex in pre-weaned Holstein calves. BMC Genomics. 2014;15:1164.
Article
PubMed
PubMed Central
CAS
Google Scholar
Snowder GD, Van Vleck LD, Cundiff LV, Bennett GL. Bovine respiratory disease in feedlot cattle: environmental, genetic, and economic factors. J Anim Sci. 2006;84(8):1999–2008.
Article
CAS
PubMed
Google Scholar
Quick AE, Ollivett TL, Kirkpatrick BW, Weigel KA. Genomic analysis of bovine respiratory disease and lung consolidation in preweaned Holstein calves using clinical scoring and lung ultrasound. J Dairy Sci. 2020;103(2):1632–41.
Article
CAS
PubMed
Google Scholar
Edwards TA. Control methods for bovine respiratory disease for feedlot cattle. Vet Clin North Am Food Anim. 2010;26(2):273–84.
Article
CAS
Google Scholar
Johnston D, Earley B, McCabe MS, Lemon K, Duffy C, McMenamy M, et al. Experimental challenge with bovine respiratory syncytial virus in dairy calves: bronchial lymph node transcriptome response. Sci Rep. 2019;9(1):14736.
Article
PubMed
PubMed Central
CAS
Google Scholar
Tizioto PC, Kim J, Seabury CM, Schnabel RD, Gershwin LJ, Van Eenennaam AL, et al. Immunological response to single pathogen challenge with agents of the bovine respiratory disease complex: an RNA-sequence analysis of the bronchial lymph node transcriptome. PLoS One. 2015;10(6):e0131459.
Article
PubMed
PubMed Central
CAS
Google Scholar
Behura SK, Tizioto PC, Kim J, Grupioni NV, Seabury CM, Schnabel RD, et al. Tissue tropism in host transcriptional response to members of the bovine respiratory disease complex. Sci Rep. 2017;7:17938.
Article
PubMed
PubMed Central
CAS
Google Scholar
Lipkin E, Strillacci MG, Eitam H, Yishay M, Schiavini F, Soller M, et al. The use of kosher Phenotyping for mapping QTL affecting susceptibility to bovine respiratory disease. PLoS One. 2016;11(4):e0153423.
Article
PubMed
PubMed Central
CAS
Google Scholar
Keele JW, Kuehn LA, McDaneld TG, Tait RG Jr, Jones SA, Smith TPL, et al. Genomewide association study of lung lesions in cattle using sample pooling. J Anim Sci. 2015;93(3):956–64.
Article
CAS
PubMed
Google Scholar
Johnston D, Mukiibi R, Waters SM, Surlis C, McClure JC, McClure MC, et al. Genome wide association study of passive immunity and disease traits in beef-suckler and dairy calves on Irish farms. Sci Rep. 2020;10(1):1–0.
Article
CAS
Google Scholar
Buenrostro JD, Wu B, Chang HY, Greenleaf WJ. ATAC-seq: a method for assaying chromatin accessibility genome-wide. Curr Protoc Mol Biol. 2015;109:21.9.1–9.
Google Scholar
Yan F, Powell DR, Curtis DJ, Wong NC. From reads to insight: a hitchhiker’s guide to ATAC-seq data analysis. Genome Biol. 2020;21(1):22.
Article
PubMed
PubMed Central
Google Scholar
Hulsen T, de Vlieg J, Alkema W. BioVenn - a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams. BMC Genomics. 2008;9(1):488.
Article
PubMed
PubMed Central
CAS
Google Scholar
Sun Y, Miao N, Sun T. Detect accessible chromatin using ATAC-sequencing, from principle to applications. Hereditas. 2019;156:29.
Article
PubMed
PubMed Central
Google Scholar
Corces MR, Trevino AE, Hamilton EG, Greenside PG, Sinnott-Armstrong NA, Vesuna S, et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods. 2017;14(10):959–62.
Article
CAS
PubMed
PubMed Central
Google Scholar
Durham AL, Adcock IM. Basic science: epigenetic programming and the respiratory system. Breathe. 2013;9(4):278–88.
Article
Google Scholar
Silmon de Monerri NC, Kim K. Pathogens hijack the epigenome: a new twist on host-pathogen interactions. Am J Pathol. 2014;184(4):897–911.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fang L, Liu S, Liu M, Kang X, Lin S, Li B, et al. Functional annotation of the cattle genome through systematic discovery and characterization of chromatin states and butyrate-induced variations. BMC Biol. 2019;17(1):68.
Article
PubMed
PubMed Central
CAS
Google Scholar
Ming H, Sun J, Pasquariello R, Herrick JR, Yuan Y, Gutierrez E, et al. The landscape of accessible chromatin in bovine oocytes and early embryos. Reprod Fertil Dev. 2019;32(2):125.
Article
Google Scholar
Foissac S, Djebali S, Munyard K, Vialaneix N, Rau A, Muret K, et al. Multi-species annotation of transcriptome and chromatin structure in domesticated animals. BMC Biol. 2019;17(1):108.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang Z, Tu K, Xia L, Luo K, Luo W, Tang J, et al. The open chromatin landscape of non–small cell lung carcinoma. Cancer Res. 2019;79(19):4840–54.
Article
CAS
PubMed
Google Scholar
Chen K, Kolls JK. T cell-mediated host immune defenses in the lung. Annu Rev Immunol. 2013;31:605–33.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gershwin LJ. Immunology of bovine respiratory syncytial virus infection of cattle. Comp Immunol Microbiol Infect Dis. 2012;35(3):253–7.
Article
PubMed
Google Scholar
Gashev AA. Basic mechanisms controlling lymph transport in the mesenteric lymphatic net. Ann N Y Acad Sci. 2010;1207(Suppl 1):E16–20.
Article
PubMed
PubMed Central
Google Scholar
Gallagher MD, Chen-Plotkin AS. The post-GWAS era: from association to function. Am J Hum Genet. 2018;102(5):717–30.
Article
CAS
PubMed
PubMed Central
Google Scholar
Belyaeva OV, Adams MK, Popov KM, Kedishvili NY. Generation of retinaldehyde for retinoic acid biosynthesis. Biomolecules. 2020;10(1):5.
Article
CAS
Google Scholar
Eisfeld A-K, Marcucci G, Liyanarachchi S, Döhner K, Schwind S, Maharry K, et al. Heritable polymorphism predisposes to high BAALC expression in acute myeloid leukemia. Proc Natl Acad Sci U S A. 2012;109(17):6668–73.
Article
CAS
PubMed
PubMed Central
Google Scholar
Paris AJ, Snapir Z, Christopherson CD, Kwok SY, Lee UE, Ghiassi-Nejad Z, et al. A polymorphism that delays fibrosis in hepatitis C promotes alternative splicing of AZIN1, reducing fibrogenesis. Hepatology. 2011;54(6):2198–207.
Article
CAS
PubMed
Google Scholar
Pasdeloup D, McElwee M, Beilstein F, Labetoulle M, Rixon FJ. Herpesvirus tegument protein pUL37 interacts with Dystonin/BPAG1 to promote capsid transport on microtubules during egress. J Virol. 2013;87(5):2857–67.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bishop JA, Cowan ML, Shum CH, Westra WH. MAML2 rearrangements in variant forms of mucoepidermoid carcinoma: ancillary diagnostic testing for the ciliated and warthin-like variants. Am J Surg Pathol. 2018;42(1):130–6.
PubMed
PubMed Central
Google Scholar
Langmead B, Trapnell C, Pop M, Salzberg S. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10(3):R25.
Article
PubMed
PubMed Central
CAS
Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25(16):2078–9.
Article
PubMed
PubMed Central
CAS
Google Scholar
Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137-R.
Article
CAS
Google Scholar
Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26(6):841–2.
Article
CAS
PubMed
PubMed Central
Google Scholar
Stark R, Brown G. DiffBind: differential binding analysis of ChIP-Seq peak data. http://bioconductor.org/packages/release/bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf. 2011.
Google Scholar
Ross-Innes CS, Stark R, Teschendorff AE, Holmes KA, Ali HR, Dunning MJ, et al. Differential oestrogen receptor binding is associated with clinical outcome in breast cancer. Nature. 2012;481(7381):389–93.
Article
CAS
PubMed
PubMed Central
Google Scholar
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550.
Article
PubMed
PubMed Central
CAS
Google Scholar
Robinson MD, McCarthy DJ, Smyth GK. EdgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26(1):139–40.
Article
CAS
PubMed
Google Scholar
Yu G, Wang L-G, Han Y, He Q-Y. ClusterProfiler: an R package for comparing biological themes among gene clusters. OMICS. 2012;16(5):284–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Huang DW, Sherman BT, Lempicki RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 2009;37(1):1–13.
Article
CAS
Google Scholar
Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4(1):44–57.
Article
CAS
Google Scholar
Kanehisa M, Goto S. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 2000;28:27–30.
Article
CAS
PubMed
PubMed Central
Google Scholar
Krämer A, Green J, Pollard J, Tugendreich S. Causal analysis approaches in ingenuity pathway analysis. Bioinformatics. 2014;30(4):523–30.
Article
PubMed
CAS
Google Scholar