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Genomics Insights: 1. doi:10.4137\/GEI.S9125.","DOI":"10.4137\/GEI.S9125"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"713","DOI":"10.1046\/j.1523-1755.1999.00299.x","article-title":"The Banff 97 working classification of renal allograft pathology","volume":"55","author":"LC Racusen","year":"1999","journal-title":"Kidney International"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"964","DOI":"10.1592\/phco.24.11.964.36143","article-title":"Pharmacoepidemiology I: A Review of Pharmacoepidemiologic Study Designs","volume":"24","author":"M Etminan","year":"2004","journal-title":"Pharmacotherapy: The Journal of Human Pharmacology and Drug Therapy"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"1388","DOI":"10.1097\/TP.0b013e3182003df6","article-title":"Whole Blood Biomarkers of Acute Cardiac Allograft Rejection: Double-Crossing the Biopsy","volume":"90","author":"Z Hollander","year":"2010","journal-title":"Transplantation"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"3162","DOI":"10.1093\/bioinformatics\/btm487","article-title":"MDQC: a new quality assessment method for microarrays based on quality control reports","volume":"23","author":"GV Cohen Freue","year":"2007","journal-title":"Bioinformatics"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1093\/bioinformatics\/19.2.185","article-title":"A comparison of normalization methods for high density oligonucleotide array data based on variance and bias","volume":"19","author":"BM Bolstad","year":"2003","journal-title":"Bioinformatics"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"943","DOI":"10.1093\/bioinformatics\/btl033","article-title":"A new summarization method for affymetrix probe level data","volume":"22","author":"S Hochreiter","year":"2006","journal-title":"Bioinformatics"},{"key":"ref30","unstructured":"Team RC (2012) R: A Language and Environment for Statistical Computing. Vienna, Austria. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.R-project.org\" xlink:type=\"simple\">http:\/\/www.R-project.org<\/ext-link>."},{"key":"ref31","doi-asserted-by":"crossref","first-page":"R80","DOI":"10.1186\/gb-2004-5-10-r80","article-title":"Bioconductor: open software development for computational biology and bioinformatics","volume":"5","author":"RC Gentleman","year":"2004","journal-title":"Genome biology"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v033.i01","article-title":"Regularization paths for generalized linear models via coordinate descent","volume":"33","author":"J Friedman","year":"2010","journal-title":"Journal of statistical software"},{"key":"ref33","doi-asserted-by":"crossref","unstructured":"Wickham H (2009) Ggplot2: elegant graphics for data analysis. New York: Springer. 212 p.","DOI":"10.1007\/978-0-387-98141-3"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"D991","DOI":"10.1093\/nar\/gks1193","article-title":"NCBI GEO: archive for functional genomics data sets\u2014update","volume":"41","author":"T Barrett","year":"2012","journal-title":"Nucleic Acids Research"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1111\/j.1467-9868.2005.00503.x","article-title":"Regularization and variable selection via the elastic net","volume":"67","author":"H Zou","year":"2005","journal-title":"Journal of the Royal Statistical Society: Series B (Statistical Methodology)"},{"key":"ref36","doi-asserted-by":"crossref","unstructured":"Smyth GK (2005) Limma: linear models for microarray data. In: Gentleman R, Carey V, Dudoit S, Irizarry R, Huber W, editors. Bioinformatics and Computational Biology Solutions Using R and Bioconductor. New York: Springer. pp. 397\u2013420.","DOI":"10.1007\/0-387-29362-0_23"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"5116","DOI":"10.1073\/pnas.091062498","article-title":"Significance analysis of microarrays applied to the ionizing radiation response","volume":"98","author":"VG Tusher","year":"2001","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1038\/nmeth.1830","article-title":"Gene expression deconvolution in linear space","volume":"9","author":"Y Zhong","year":"2012","journal-title":"Nat Meth"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"5376","DOI":"10.1182\/blood-2010-01-263855","article-title":"Gene enrichment profiles reveal T-cell development, differentiation, and lineage-specific transcription factors including ZBTB25 as a novel NF-AT repressor","volume":"115","author":"Y Benita","year":"2010","journal-title":"Blood"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"15545","DOI":"10.1073\/pnas.0506580102","article-title":"Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles","volume":"102","author":"A Subramanian","year":"2005","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing","volume":"57","author":"Y Benjamini","year":"1995","journal-title":"Journal of the Royal Statistical Society Series B (Methodological)"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"e1001538","DOI":"10.1371\/journal.pmed.1001538","article-title":"Detection of Tuberculosis in HIV-Infected and -Uninfected African Adults Using Whole Blood RNA Expression Signatures: A Case-Control Study","volume":"10","author":"M Kaforou","year":"2013","journal-title":"PLoS Med"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"104","DOI":"10.1309\/EK3C7CTDKNVPXVTN","article-title":"Automated Blood Cell Counts: State of the Art","volume":"130","author":"M Buttarello","year":"2008","journal-title":"American Journal of Clinical Pathology"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"687","DOI":"10.1093\/ajcp\/112.5.687","article-title":"Refrigerated storage improves the stability of the complete blood cell count and automated differential","volume":"112","author":"BL Wood","year":"1999","journal-title":"Am J Clin Pathol"},{"key":"ref45","first-page":"144","article-title":"Flow Cytometric Detection of Neutrophil-associated Immunoglobulin in Patients with or without Neutropenia and Establishment of the Reference Interval","volume":"41","author":"K Hwang","year":"2011","journal-title":"Ann Clin Lab Sci"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"1848","DOI":"10.1172\/JCI39922","article-title":"Development of a cross-platform biomarker signature to detect renal transplant tolerance in humans","volume":"120","author":"P Sagoo","year":"2010","journal-title":"Journal of Clinical Investigation"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"7503","DOI":"10.4049\/jimmunol.178.12.7503","article-title":"The Innate Immune System in Allograft Rejection and Tolerance","volume":"178","author":"DF LaRosa","year":"2007","journal-title":"J Immunol"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"1451","DOI":"10.1056\/NEJMra0902927","article-title":"Rejection of the Kidney Allograft","volume":"363","author":"BJ Nankivell","year":"2010","journal-title":"New England Journal of Medicine"},{"key":"ref49","doi-asserted-by":"crossref","unstructured":"Puttarajappa C, Shapiro R, Tan HP (2012) Antibody-Mediated Rejection in Kidney Transplantation: A Review. Journal of Transplantation 2012. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.hindawi.com\/journals\/jtran\/2012\/193724\/abs\/\" xlink:type=\"simple\">http:\/\/www.hindawi.com\/journals\/jtran\/2012\/193724\/abs\/<\/ext-link>. Accessed 2013 Apr 25.","DOI":"10.1155\/2012\/193724"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"6999","DOI":"10.4049\/jimmunol.1000929","article-title":"Platelets Contribute to Allograft Rejection through Glutamate Receptor Signaling","volume":"185","author":"AF Swaim","year":"2010","journal-title":"J Immunol"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1056\/NEJM199801153380304","article-title":"Interleukin-2\u2013Receptor Blockade with Daclizumab to Prevent Acute Rejection in Renal Transplantation","volume":"338","author":"F Vincenti","year":"1998","journal-title":"New England Journal of Medicine"}],"container-title":["PLoS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0095224","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,9]],"date-time":"2020-05-09T05:38:55Z","timestamp":1589002735000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0095224"}},"subtitle":[],"editor":[{"given":"Gualtiero I.","family":"Colombo","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2014,4,14]]},"references-count":51,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2014,4,14]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0095224","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,4,14]]}}}