{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T21:03:52Z","timestamp":1792789432364,"version":"4.5.0"},"reference-count":51,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2025,5,1]],"date-time":"2025-05-01T00:00:00Z","timestamp":1746057600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2025,5,1]],"date-time":"2025-05-01T00:00:00Z","timestamp":1746057600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2024,6,21]],"date-time":"2024-06-21T00:00:00Z","timestamp":1718928000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/100006031","name":"United States - Israel Binational Agricultural Research and Development Fund","doi-asserted-by":"publisher","award":["8042-31000-112-00-D"],"award-info":[{"award-number":["8042-31000-112-00-D"]}],"id":[{"id":"10.13039\/100006031","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000199","name":"U.S. Department of Agriculture","doi-asserted-by":"publisher","award":["8042-31310-114-00-D"],"award-info":[{"award-number":["8042-31310-114-00-D"]}],"id":[{"id":"10.13039\/100000199","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001269","name":"BARD","doi-asserted-by":"publisher","award":["US-4997-17"],"award-info":[{"award-number":["US-4997-17"]}],"id":[{"id":"10.13039\/501100001269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100005825","name":"National Institute of Food and Agriculture","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100005825","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Journal of Advanced Research"],"published-print":{"date-parts":[[2025,5]]},"DOI":"10.1016\/j.jare.2024.06.020","type":"journal-article","created":{"date-parts":[[2024,6,24]],"date-time":"2024-06-24T20:19:58Z","timestamp":1719260398000},"page":"67-80","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":4,"special_numbering":"C","title":["Transcriptomic profiling of gastrointestinal tracts in dairy cattle during lactation reveals molecular adaptations for milk synthesis"],"prefix":"10.1016","volume":"71","author":[{"given":"Yahui","family":"Gao","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"George E.","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Li","family":"Ma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lingzhao","family":"Fang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cong-jun","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"suffix":"VI","given":"Ransom L.","family":"Baldwin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.jare.2024.06.020_b0005","doi-asserted-by":"crossref","DOI":"10.1038\/sdata.2018.227","article-title":"Global distribution data for cattle, buffaloes, horses, sheep, goats, pigs, chickens and ducks in 2010","volume":"5","author":"Gilbert","year":"2018","journal-title":"Sci Data"},{"issue":"11","key":"10.1016\/j.jare.2024.06.020_b0010","doi-asserted-by":"crossref","first-page":"5335","DOI":"10.3168\/jds.2009-2461","article-title":"Invited review: milk protein polymorphisms in cattle: effect on animal breeding and human nutrition","volume":"92","author":"Caroli","year":"2009","journal-title":"J Dairy Sci"},{"key":"10.1016\/j.jare.2024.06.020_b0015","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1146\/annurev-animal-021815-111422","article-title":"Genomic Selection in Dairy Cattle: The USDA Experience","volume":"5","author":"Wiggans","year":"2017","journal-title":"Annu Rev Anim Biosci"},{"key":"10.1016\/j.jare.2024.06.020_b0020","doi-asserted-by":"crossref","first-page":"118","DOI":"10.3389\/fgene.2015.00118","article-title":"Go with the flow-biology and genetics of the lactation cycle","volume":"6","author":"Strucken","year":"2015","journal-title":"Front Genet"},{"key":"10.1016\/j.jare.2024.06.020_b0025","first-page":"215","article-title":"Systems biology and animal nutrition: insights from the dairy cow during growth and the lactation cycle","author":"Loor","year":"2011","journal-title":"In"},{"key":"10.1016\/j.jare.2024.06.020_b0030","series-title":"Nutrient Requirements of Dairy Cattle: Seventh Revised Edition, 2001","author":"Council","year":"2001"},{"key":"10.1016\/j.jare.2024.06.020_b0035","unstructured":"NRC: Nutrient Requirements of Dairy Cattle, 7th rev. ed. edn. Washington DC: Natl. Acas. Sci.; 2001."},{"issue":"5","key":"10.1016\/j.jare.2024.06.020_b0040","doi-asserted-by":"crossref","first-page":"2106","DOI":"10.3168\/jds.2008-1897","article-title":"Liver phosphorus content in Holstein-Friesian cows during the transition period","volume":"92","author":"Grunberg","year":"2009","journal-title":"J Dairy Sci"},{"issue":"1","key":"10.1016\/j.jare.2024.06.020_b0045","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1186\/s12864-016-2938-1","article-title":"Transcriptomics of liver and muscle in Holstein cows genetically divergent for fertility highlight differences in nutrient partitioning and inflammation processes","volume":"17","author":"Moran","year":"2016","journal-title":"BMC Genomics"},{"issue":"7","key":"10.1016\/j.jare.2024.06.020_b0050","doi-asserted-by":"crossref","first-page":"8152","DOI":"10.3168\/jds.2020-19302","article-title":"Effect of overconditioning on the hepatic global gene expression pattern of dairy cows at the end of pregnancy","volume":"104","author":"Pascottini","year":"2021","journal-title":"J Dairy Sci"},{"key":"10.1016\/j.jare.2024.06.020_b0055","doi-asserted-by":"crossref","unstructured":"Veshkini A, H MH, Vogel L, Delosiere M, Viala D, Dejean S, Troscher A, Ceciliani F, Sauerwein H, Bonnet M: Liver proteome profiling in dairy cows during the transition from gestation to lactation: effects of supplementation with essential fatty acids and conjugated linoleic acids as explored by PLS-DA. J Proteomics 2022;252:104436.","DOI":"10.1016\/j.jprot.2021.104436"},{"issue":"3","key":"10.1016\/j.jare.2024.06.020_b0060","doi-asserted-by":"crossref","first-page":"507","DOI":"10.3168\/jds.S0022-0302(02)74102-7","article-title":"Role of prolactin, growth hormone and insulin-like growth factor 1 in mammary gland involution in the dairy cow","volume":"85","author":"Accorsi","year":"2002","journal-title":"J Dairy Sci"},{"issue":"1","key":"10.1016\/j.jare.2024.06.020_b0065","doi-asserted-by":"crossref","first-page":"165","DOI":"10.3168\/jds.S0022-0302(07)72618-8","article-title":"Effect of continuous milking and bovine somatotropin supplementation on mammary epithelial cell turnover","volume":"90","author":"Annen","year":"2007","journal-title":"J Dairy Sci"},{"issue":"10","key":"10.1016\/j.jare.2024.06.020_b0070","doi-asserted-by":"crossref","first-page":"4922","DOI":"10.3168\/jds.2010-4116","article-title":"Effect of dry period management on mammary gland function and its endocrine regulation in dairy cows","volume":"94","author":"Bernier-Dodier","year":"2011","journal-title":"J Dairy Sci"},{"issue":"1","key":"10.1016\/j.jare.2024.06.020_b0075","doi-asserted-by":"crossref","first-page":"604","DOI":"10.1080\/09712119.2017.1368524","article-title":"Characteristics of mammary secretions from Holstein cows at approximately 10 days before parturition: with or without intramammary infection","volume":"46","author":"Watanabe","year":"2017","journal-title":"J Appl Anim Res"},{"issue":"8","key":"10.1016\/j.jare.2024.06.020_b0080","doi-asserted-by":"crossref","first-page":"6701","DOI":"10.3168\/jds.2019-16377","article-title":"Invited review: accelerating mammary gland involution after drying-off in dairy cattle","volume":"102","author":"Zhao","year":"2019","journal-title":"J Dairy Sci"},{"issue":"3","key":"10.1016\/j.jare.2024.06.020_b0085","doi-asserted-by":"crossref","first-page":"2631","DOI":"10.3168\/jds.2017-13212","article-title":"Changes in gene expression in the rumen and colon epithelia during the dry period through lactation of dairy cows and effects of live yeast supplementation","volume":"101","author":"Bach","year":"2018","journal-title":"J Dairy Sci"},{"issue":"2","key":"10.1016\/j.jare.2024.06.020_b0090","doi-asserted-by":"crossref","first-page":"1866","DOI":"10.3168\/jds.2018-15243","article-title":"Symposium review: the importance of the ruminal epithelial barrier for a healthy and productive cow","volume":"102","author":"Aschenbach","year":"2019","journal-title":"J Dairy Sci"},{"key":"10.1016\/j.jare.2024.06.020_b0095","doi-asserted-by":"crossref","first-page":"214","DOI":"10.3389\/fvets.2019.00214","article-title":"Transcriptomic profiling of duodenal epithelium reveals temporally dynamic impacts of direct duodenal starch-infusion during dry period of dairy cattle","volume":"6","author":"Li","year":"2019","journal-title":"Front Vet Sci"},{"issue":"6","key":"10.1016\/j.jare.2024.06.020_b0100","doi-asserted-by":"crossref","first-page":"649","DOI":"10.1093\/jn\/120.6.649","article-title":"Changes in liver and gastrointestinal tract energy demands in response to physiological workload in ruminants","volume":"120","author":"Johnson","year":"1990","journal-title":"J Nutr"},{"issue":"3","key":"10.1016\/j.jare.2024.06.020_b0105","doi-asserted-by":"crossref","DOI":"10.1093\/jas\/skac044","article-title":"Limiting factors for milk production in dairy cows: perspectives from physiology and nutrition","volume":"100","author":"Gross","year":"2022","journal-title":"J Anim Sci"},{"issue":"7766","key":"10.1016\/j.jare.2024.06.020_b0110","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1038\/s41586-019-1338-5","article-title":"Gene expression across mammalian organ development","volume":"571","author":"Cardoso-Moreira","year":"2019","journal-title":"Nature"},{"issue":"11","key":"10.1016\/j.jare.2024.06.020_b0115","doi-asserted-by":"crossref","first-page":"1900","DOI":"10.1101\/gr.248997.119","article-title":"Dynamics of microRNA expression during mouse prenatal development","volume":"29","author":"Rahmanian","year":"2019","journal-title":"Genome Res"},{"key":"10.1016\/j.jare.2024.06.020_b0120","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.30860","article-title":"A high-resolution mRNA expression time course of embryonic development in zebrafish","volume":"6","author":"White","year":"2017","journal-title":"Elife"},{"issue":"1","key":"10.1016\/j.jare.2024.06.020_b0125","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1186\/s12915-021-01127-9","article-title":"Comprehensive transcriptome and methylome analysis delineates the biological basis of hair follicle development and wool-related traits in Merino sheep","volume":"19","author":"Zhao","year":"2021","journal-title":"BMC Biol"},{"key":"10.1016\/j.jare.2024.06.020_b0130","doi-asserted-by":"crossref","unstructured":"Shi L, Li H, Huang X, Shu Z, Li J, Wang L, Yan H, Wang L. Integrated analysis of transcriptome and metabolome revealed biological basis of sows from estrus to lactation. iScience 2023, 26(1).","DOI":"10.1016\/j.isci.2022.105825"},{"issue":"1","key":"10.1016\/j.jare.2024.06.020_b0135","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1186\/s12915-022-01269-4","article-title":"Transcriptional atlas analysis from multiple tissues reveals the expression specificity patterns in beef cattle","volume":"20","author":"Zhang","year":"2022","journal-title":"BMC Biol"},{"issue":"18","key":"10.1016\/j.jare.2024.06.020_b0140","doi-asserted-by":"crossref","first-page":"2598","DOI":"10.1093\/bioinformatics\/btu333","article-title":"Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series","volume":"30","author":"Nueda","year":"2014","journal-title":"Bioinformatics"},{"key":"10.1016\/j.jare.2024.06.020_b0145","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1186\/1471-2105-9-559","article-title":"WGCNA: an R package for weighted correlation network analysis","volume":"9","author":"Langfelder","year":"2008","journal-title":"BMC Bioinf"},{"issue":"23","key":"10.1016\/j.jare.2024.06.020_b0150","doi-asserted-by":"crossref","first-page":"3827","DOI":"10.1093\/bioinformatics\/btw780","article-title":"TimesVector: a vectorized clustering approach to the analysis of time series transcriptome data from multiple phenotypes","volume":"33","author":"Jung","year":"2017","journal-title":"Bioinformatics"},{"issue":"2","key":"10.1016\/j.jare.2024.06.020_b0155","doi-asserted-by":"crossref","DOI":"10.1016\/j.ygeno.2022.110296","article-title":"Functional annotation of regulatory elements in cattle genome reveals the roles of extracellular interaction and dynamic change of chromatin states in rumen development during weaning","volume":"114","author":"Gao","year":"2022","journal-title":"Genomics"},{"issue":"D1","key":"10.1016\/j.jare.2024.06.020_b0160","doi-asserted-by":"crossref","first-page":"D956","DOI":"10.1093\/nar\/gkab1116","article-title":"Bringing the animal QTLdb and CorrDB into the future: meeting new challenges and providing updated services","volume":"50","author":"Hu","year":"2022","journal-title":"Nucleic Acids Res"},{"issue":"11","key":"10.1016\/j.jare.2024.06.020_b0165","doi-asserted-by":"crossref","first-page":"2259","DOI":"10.3168\/jds.S0022-0302(99)75474-3","article-title":"ADSA foundation scholar award. Biology of dairy cows during the transition period: the final frontier?","volume":"82","author":"Drackley","year":"1999","journal-title":"J Dairy Sci"},{"key":"10.1016\/j.jare.2024.06.020_b0170","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.jare.2021.11.009","article-title":"Cross-tissue single-cell transcriptomic landscape reveals the key cell subtypes and their potential roles in the nutrient absorption and metabolism in dairy cattle","volume":"37","author":"Wu","year":"2022","journal-title":"J Adv Res"},{"issue":"15","key":"10.1016\/j.jare.2024.06.020_b0175","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"issue":"3","key":"10.1016\/j.jare.2024.06.020_b0180","doi-asserted-by":"crossref","DOI":"10.1093\/gigascience\/giaa021","article-title":"De novo assembly of the cattle reference genome with single-molecule sequencing","volume":"9","author":"Rosen","year":"2020","journal-title":"GigaScience"},{"issue":"8","key":"10.1016\/j.jare.2024.06.020_b0185","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1038\/s41587-019-0201-4","article-title":"Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype","volume":"37","author":"Kim","year":"2019","journal-title":"Nat Biotechnol"},{"issue":"16","key":"10.1016\/j.jare.2024.06.020_b0190","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"Genome project data processing S: the sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"issue":"3","key":"10.1016\/j.jare.2024.06.020_b0195","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1038\/nbt.3122","article-title":"StringTie enables improved reconstruction of a transcriptome from RNA-seq reads","volume":"33","author":"Pertea","year":"2015","journal-title":"Nat Biotechnol"},{"issue":"7","key":"10.1016\/j.jare.2024.06.020_b0200","doi-asserted-by":"crossref","first-page":"923","DOI":"10.1093\/bioinformatics\/btt656","article-title":"featureCounts: an efficient general purpose program for assigning sequence reads to genomic features","volume":"30","author":"Liao","year":"2014","journal-title":"Bioinformatics"},{"issue":"12","key":"10.1016\/j.jare.2024.06.020_b0205","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol"},{"issue":"7","key":"10.1016\/j.jare.2024.06.020_b0210","doi-asserted-by":"crossref","first-page":"e47","DOI":"10.1093\/nar\/gkv007","article-title":"limma powers differential expression analyses for RNA-sequencing and microarray studies","volume":"43","author":"Ritchie","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"10.1016\/j.jare.2024.06.020_b0215","doi-asserted-by":"crossref","unstructured":"Camargo AP, Vasconcelos AA, Fiamenghi MB, Pereira GAG, Carazzolle MF.Tspex : a Tissue-Specificity Calculator for Gene Expression Data. 2020:1\u20137.","DOI":"10.21203\/rs.3.rs-51998\/v1"},{"issue":"2","key":"10.1016\/j.jare.2024.06.020_b0220","first-page":"205","article-title":"A benchmark of gene expression tissue-specificity metrics","volume":"18","author":"Kryuchkova-Mostacci","year":"2017","journal-title":"Brief Bioinform"},{"issue":"W1","key":"10.1016\/j.jare.2024.06.020_b0225","doi-asserted-by":"crossref","first-page":"W317","DOI":"10.1093\/nar\/gkab447","article-title":"KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis","volume":"49","author":"Bu","year":"2021","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"10.1016\/j.jare.2024.06.020_b0230","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1038\/nmeth.1906","article-title":"ChromHMM: automating chromatin-state discovery and characterization","volume":"9","author":"Ernst","year":"2012","journal-title":"Nat Methods"},{"issue":"7","key":"10.1016\/j.jare.2024.06.020_b0235","doi-asserted-by":"crossref","first-page":"773","DOI":"10.1038\/s41587-019-0114-2","article-title":"Determining cell type abundance and expression from bulk tissues with digital cytometry","volume":"37","author":"Newman","year":"2019","journal-title":"Nat Biotechnol"},{"issue":"7","key":"10.1016\/j.jare.2024.06.020_b0240","doi-asserted-by":"crossref","first-page":"1888","DOI":"10.1016\/j.cell.2019.05.031","article-title":"Comprehensive integration of single-cell data","volume":"177","author":"Stuart","year":"2019","journal-title":"Cell"},{"key":"10.1016\/j.jare.2024.06.020_b0245","doi-asserted-by":"crossref","unstructured":"Hunt SE, McLaren W, Gil L, Thormann A, Schuilenburg H, Sheppard D, Parton A, Armean IM, Trevanion SJ, Flicek P et al: Ensembl variation resources. Database (Oxford) 2018; 2018.","DOI":"10.1093\/database\/bay119"},{"key":"10.1016\/j.jare.2024.06.020_b0250","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gks1150","article-title":"Animal QTLdb: an improved database tool for livestock animal QTL\/association data dissemination in the post-genome era","volume":"41","author":"Hu","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"10.1016\/j.jare.2024.06.020_b0255","doi-asserted-by":"crossref","DOI":"10.1016\/j.gpb.2019.03.007","article-title":"BGVD: an integrated database for bovine sequencing variations and selective signatures","author":"Chen","year":"2020","journal-title":"Genom Proteom Bioinform"}],"container-title":["Journal of Advanced Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2090123224002571?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2090123224002571?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,11,8]],"date-time":"2025-11-08T10:53:56Z","timestamp":1762599236000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2090123224002571"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,5]]},"references-count":51,"alternative-id":["S2090123224002571"],"URL":"https:\/\/doi.org\/10.1016\/j.jare.2024.06.020","relation":{},"ISSN":["2090-1232"],"issn-type":[{"value":"2090-1232","type":"print"}],"subject":[],"published":{"date-parts":[[2025,5]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Transcriptomic profiling of gastrointestinal tracts in dairy cattle during lactation reveals molecular adaptations for milk synthesis","name":"articletitle","label":"Article Title"},{"value":"Journal of Advanced Research","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.jare.2024.06.020","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2024 The Authors. Published by Elsevier B.V. on behalf of Cairo University.","name":"copyright","label":"Copyright"}]}}