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A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB.
Rayner TF, Rocca-Serra P, Spellman PT, Causton HC, Farne A, Holloway E, Irizarry RA, Liu J, Maier DS, Miller M, Petersen K, Quackenbush J, Sherlock G, Stoeckert CJ Jr, White J, Whetzel PL, Wymore F, Parkinson H, Sarkans U, Ball CA, Brazma A. Rayner TF, et al. Among authors: miller m. BMC Bioinformatics. 2006 Nov 6;7:489. doi: 10.1186/1471-2105-7-489. BMC Bioinformatics. 2006. PMID: 17087822 Free PMC article.
Design and implementation of microarray gene expression markup language (MAGE-ML).
Spellman PT, Miller M, Stewart J, Troup C, Sarkans U, Chervitz S, Bernhart D, Sherlock G, Ball C, Lepage M, Swiatek M, Marks WL, Goncalves J, Markel S, Iordan D, Shojatalab M, Pizarro A, White J, Hubley R, Deutsch E, Senger M, Aronow BJ, Robinson A, Bassett D, Stoeckert CJ Jr, Brazma A. Spellman PT, et al. Among authors: miller m. Genome Biol. 2002 Aug 23;3(9):RESEARCH0046. doi: 10.1186/gb-2002-3-9-research0046. Epub 2002 Aug 23. Genome Biol. 2002. PMID: 12225585 Free PMC article.
The first RSBI (ISA-TAB) workshop: "can a simple format work for complex studies?".
Sansone SA, Rocca-Serra P, Brandizi M, Brazma A, Field D, Fostel J, Garrow AG, Gilbert J, Goodsaid F, Hardy N, Jones P, Lister A, Miller M, Morrison N, Rayner T, Sklyar N, Taylor C, Tong W, Warner G, Wiemann S; Members of the RSBI Working Group. Sansone SA, et al. Among authors: miller m. OMICS. 2008 Jun;12(2):143-9. doi: 10.1089/omi.2008.0019. OMICS. 2008. PMID: 18447634
The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics.
Jones AR, Miller M, Aebersold R, Apweiler R, Ball CA, Brazma A, Degreef J, Hardy N, Hermjakob H, Hubbard SJ, Hussey P, Igra M, Jenkins H, Julian RK Jr, Laursen K, Oliver SG, Paton NW, Sansone SA, Sarkans U, Stoeckert CJ Jr, Taylor CF, Whetzel PL, White JA, Spellman P, Pizarro A. Jones AR, et al. Among authors: miller m. Nat Biotechnol. 2007 Oct;25(10):1127-33. doi: 10.1038/nbt1347. Nat Biotechnol. 2007. PMID: 17921998
FuGE: Functional Genomics Experiment Object Model.
Jones AR, Pizarro A, Spellman P, Miller M; FuGE Working Group. Jones AR, et al. Among authors: miller m. OMICS. 2006 Summer;10(2):179-84. doi: 10.1089/omi.2006.10.179. OMICS. 2006. PMID: 16901224 Review.
Translating standards into practice - one Semantic Web API for Gene Expression.
Deus HF, Prud'hommeaux E, Miller M, Zhao J, Malone J, Adamusiak T, McCusker J, Das S, Rocca Serra P, Fox R, Marshall MS. Deus HF, et al. Among authors: miller m. J Biomed Inform. 2012 Aug;45(4):782-94. doi: 10.1016/j.jbi.2012.03.002. Epub 2012 Mar 24. J Biomed Inform. 2012. PMID: 22449719 Free article.
COVID-19 Admission Rates and Changes in Care Quality in US Hospitals.
Meille G, Owens PL, Decker SL, Selden TM, Miller MA, Perdue-Puli JK, Grace EN, Umscheid CA, Cohen JW, Valdez RB. Meille G, et al. Among authors: miller ma. JAMA Netw Open. 2024 May 1;7(5):e2413127. doi: 10.1001/jamanetworkopen.2024.13127. JAMA Netw Open. 2024. PMID: 38787558
Systems biology dissection of PTSD and MDD across brain regions, cell types, and blood.
Daskalakis NP, Iatrou A, Chatzinakos C, Jajoo A, Snijders C, Wylie D, DiPietro CP, Tsatsani I, Chen CY, Pernia CD, Soliva-Estruch M, Arasappan D, Bharadwaj RA, Collado-Torres L, Wuchty S, Alvarez VE, Dammer EB, Deep-Soboslay A, Duong DM, Eagles N, Huber BR, Huuki L, Holstein VL, Logue MW, Lugenbühl JF, Maihofer AX, Miller MW, Nievergelt CM, Pertea G, Ross D, Sendi MSE, Sun BB, Tao R, Tooke J, Wolf EJ, Zeier Z; PTSD Working Group of Psychiatric Genomics Consortium**; Berretta S, Champagne FA, Hyde T, Seyfried NT, Shin JH, Weinberger DR, Nemeroff CB, Kleinman JE, Ressler KJ; PTSD Working Group of Psychiatric Genomics Consortium. Daskalakis NP, et al. Among authors: miller mw. Science. 2024 May 24;384(6698):eadh3707. doi: 10.1126/science.adh3707. Epub 2024 May 24. Science. 2024. PMID: 38781393
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