ImmPort: Disseminating data to the public for the future of immunology

Immunologic Research

Volumn 58, Issue 2-3, 2014, Pages 234-239

  Bhattacharya, Sanchita ^a   Andorf, Sandra ^a   Gomes, Linda ^b   Dunn, Patrick ^b   Schaefer, Henry ^c   Pontius, Joan ^c   Berger, Patty ^b   Desborough, Vince ^b   Smith, Tom ^b   Campbell, John ^b   Thomson, Elizabeth ^b   Monteiro, Ruth ^b   Guimaraes, Patricia ^b   Walters, Bryan ^b   Wiser, Jeff ^b   Butte, Atul J ^a,d  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b Northrop Grumman Health IT Systems   (United States)

^c ESAC Inc   (United States)

^d LUCILE PACKARD CHILDREN S HOSPITAL   (United States)

Author keywords

Clinical trials; Flow cytometry; Informatics; Open access; Publicly available data

Indexed keywords

ACCESS TO INFORMATION; ARTICLE; BIOINFORMATICS; CLINICAL DATA REPOSITORY; DATA BASE; IMMUNOLOGY; INFORMATION PROCESSING; MEASUREMENT; MEDICAL RESEARCH; PRIORITY JOURNAL; REPRODUCIBILITY; COMPUTER PROGRAM; FACTUAL DATABASE; HUMAN; INTERNET; RESEARCH; TRENDS;

ALLERGY AND IMMUNOLOGY; DATABASES, FACTUAL; DATASETS AS TOPIC; HUMANS; INTERNET; RESEARCH; SOFTWARE;

EID: 84901459546     PISSN: 0257277X     EISSN: 15590755     Source Type: Journal    
DOI: 10.1007/s12026-014-8516-1     Document Type: Article

References (23)

1. Qian Y, Wei C, Eun-Hyung Lee F, Campbell J, Halliley J, Lee JA, et al. Elucidation of seventeen human peripheral blood B-cell subsets and quantification of the tetanus response using a density-based method for the automated identification of cell populations in multidimensional flow cytometry data. Cytometry B Clin Cytom. 2010;78(Suppl 1):S69-82. doi:10.1002/cyto.b.20554.
2. Li L, Khatri P, Sigdel TK, Tran T, Ying L, Vitalone MJ, et al. A peripheral blood diagnostic test for acute rejection in renal transplantation. Am J Transplant. 2012;12(10):2710-8. doi:10.1111/j.1600-6143.2012.04253.x.
3. Benfield MR, Bartosh S, Ikle D, Warshaw B, Bridges N, Morrison Y, et al. A randomized double-blind, placebo controlled trial of steroid withdrawal after pediatric renal transplantation. Am J Transplant. 2010;10(1):81-8. doi:10.1111/j.1600-6143.2009.02767.x.
4. De Serres SA, Mfarrej BG, Magee CN, Benitez F, Ashoor I, Sayegh MH, et al. Immune profile of pediatric renal transplant recipients following alemtuzumab induction. J Am Soc Nephrol. 2012;23(1):174-82. doi:10.1681/ASN. 2011040360.
5. Harmon W, Meyers K, Ingelfinger J, McDonald R, McIntosh M, Ho M, et al. Safety and efficacy of a calcineurin inhibitor avoidance regimen in pediatric renal transplantation. J Am Soc Nephrol. 2006;17(6):1735-45. doi:10.1681/ASN.2006010049. (Pubitemid 43794677)
6. Hoerning A, Koss K, Datta D, Boneschansker L, Jones CN, Wong IY, et al. Subsets of human CD4(+) regulatory T cells express the peripheral homing receptor CXCR3. Eur J Immunol. 2011;41(8):2291-302. doi:10.1002/eji.201041095.
7. McDonald RA, Smith JM, Ho M, Lindblad R, Ikle D, Grimm P, et al. Incidence of PTLD in pediatric renal transplant recipients receiving basiliximab, calcineurin inhibitor, sirolimus and steroids. Am J Transplant. 2008;8(5):984-9. doi:10.1111/j.1600-6143.2008.02167.x. (Pubitemid 351537758)
8. Casale TB, Busse WW, Kline JN, Ballas ZK, Moss MH, Townley RG, et al. Omalizumab pretreatment decreases acute reactions after rush immunotherapy for ragweed-induced seasonal allergic rhinitis. J Allergy Clin Immunol. 2006;117(1):134-40. doi:10.1016/j.jaci.2005.09.036. (Pubitemid 43017150)
9. Klunker S, Saggar LR, Seyfert-Margolis V, Asare AL, Casale TB, Durham SR, et al. Combination treatment with omalizumab and rush immunotherapy for ragweed-induced allergic rhinitis: inhibition of IgE-facilitated allergen binding. J Allergy Clin Immunol. 2007;120(3):688-95. doi:10.1016/j.jaci.2007.05. 034. (Pubitemid 47320761)
10. Newell EW, Sigel N, Bendall SC, Nolan GP, Davis MM. Cytometry by time-of-flight shows combinatorial cytokine expression and virus-specific cell niches within a continuum of CD8(+) T cell phenotypes (vol 36, pg 142, 2012). Immunity. 2013;38(1):198-9. doi:10.1016/j.immuni.2012.12.002.
11. Horowitz A, Strauss-Albee DM, Leipold M, Kubo J, Nemat-Gorgani N, Dogan OC, et al. Genetic and environmental determinants of human NK cell diversity revealed by mass cytometry. Sci Transl Med. 2013;5(208):208ra145. doi:10.1126/scitranslmed.3006702.
12. Stone JH, Merkel PA, Spiera R, Seo P, Langford CA, Hoffman GS, et al. Rituximab versus cyclophosphamide for ANCA-associated vasculitis. N Engl J Med. 2010;363(3):221-32. doi:10.1056/NEJMoa0909905.
13. Holdren JP. Increasing access to the results of federally funded scientific research. Executive Office of the President, Washington, DC. 2013. http://www.whitehouse.gov/sites/default/files/microsites/ostp/ ostp-public-access-memo-2013.pdf. Accessed Feb 22, 2013.
14. Shen-Orr SS, Goldberger O, Garten Y, Rosenberg-Hasson Y, Lovelace PA, Hirschberg DL et al. Towards a cytokine-cell interaction knowledgebase of the adaptive immune system. Pac Symp Biocomput. 2009. http://www.ncbi.nlm.nih.gov/ pubmed/?term=19209721.
15. Piwowar HA, Vision TJ. Data reuse and the open data citation advantage. Peer J. 2013;1:e175. doi:10.7717/peerj.175.
16. Begley CG, Ellis LM. Drug development: raise standards for preclinical cancer research. Nature. 2012;483(7391):531-3. doi:10.1038/483531a.
17. Ioannidis JP, Allison DB, Ball CA, Coulibaly I, Cui X, Culhane AC, et al. Repeatability of published microarray gene expression analyses. Nat Genet. 2009;41(2):149-55. doi:10.1038/ng.295.
18. Micheel C, Nass SJ, Omenn GS, Institute of Medicine (U.S.). Committee on the review of omics-based tests for predicting patient outcomes in clinical trials. Evolution of translational omics: lessons learned and the path forward. Washington, D.C.: National Academies Press; 2012.
19. Chen R, Sigdel TK, Li L, Kambham N, Dudley JT, Hsieh SC et al. Differentially expressed RNA from public microarray data identifies serum protein biomarkers for cross-organ transplant rejection and other conditions. PLoS Comput Biol. 2010;6(9). doi:10.1371/journal.pcbi.1000940.
20. Kodama K, Horikoshi M, Toda K, Yamada S, Hara K, Irie J, et al. Expression-based genome-wide association study links the receptor CD44 in adipose tissue with type 2 diabetes. Proc Natl Acad Sci U S A. 2012;109(18):7049-54. doi:10.1073/pnas.1114513109.
21. Roberts SA, Lawrence MS, Klimczak LJ, Grimm SA, Fargo D, Stojanov P, et al. An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers. Nat Genet. 2013;45(9):970-6. doi:10.1038/ng.2702.
22. Sirota M, Dudley JT, Kim J, Chiang AP, Morgan AA, Sweet-CorderoA, et al.Discovery and preclinical validation of drug indications using compendia of public gene expression data. Sci Transl Med. 2011;3(96):96ra77. doi:10.1126/scitranslmed.3001318.
23. Dudley JT, Sirota M, Shenoy M, Pai RK, Roedder S, Chiang AP, et al. Computational repositioning of the anticonvulsant topiramate for inflammatory bowel disease. Sci Transl Med. 2011;3(96):96-976. doi:10.1126/scitranslmed. 3002648.