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Deep oncopanel sequencing reveals within block position-dependent quality degradation in FFPE processed samples.
Zhang Y, Blomquist TM, Kusko R, Stetson D, Zhang Z, Yin L, Sebra R, Gong B, Lococo JS, Mittal VK, Novoradovskaya N, Yeo JY, Dominiak N, Hipp J, Raymond A, Qiu F, Arib H, Smith ML, Brock JE, Farkas DH, Craig DJ, Crawford EL, Li D, Morrison T, Tom N, Xiao W, Yang M, Mason CE, Richmond TA, Jones W, Johann DJ Jr, Shi L, Tong W, Willey JC, Xu J. Zhang Y, et al. Among authors: xu j. Genome Biol. 2022 Jun 29;23(1):141. doi: 10.1186/s13059-022-02709-8. Genome Biol. 2022. PMID: 35768876 Free PMC article.
The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models.
Shi L, Campbell G, Jones WD, Campagne F, Wen Z, Walker SJ, Su Z, Chu TM, Goodsaid FM, Pusztai L, Shaughnessy JD Jr, Oberthuer A, Thomas RS, Paules RS, Fielden M, Barlogie B, Chen W, Du P, Fischer M, Furlanello C, Gallas BD, Ge X, Megherbi DB, Symmans WF, Wang MD, Zhang J, Bitter H, Brors B, Bushel PR, Bylesjo M, Chen M, Cheng J, Cheng J, Chou J, Davison TS, Delorenzi M, Deng Y, Devanarayan V, Dix DJ, Dopazo J, Dorff KC, Elloumi F, Fan J, Fan S, Fan X, Fang H, Gonzaludo N, Hess KR, Hong H, Huan J, Irizarry RA, Judson R, Juraeva D, Lababidi S, Lambert CG, Li L, Li Y, Li Z, Lin SM, Liu G, Lobenhofer EK, Luo J, Luo W, McCall MN, Nikolsky Y, Pennello GA, Perkins RG, Philip R, Popovici V, Price ND, Qian F, Scherer A, Shi T, Shi W, Sung J, Thierry-Mieg D, Thierry-Mieg J, Thodima V, Trygg J, Vishnuvajjala L, Wang SJ, Wu J, Wu Y, Xie Q, Yousef WA, Zhang L, Zhang X, Zhong S, Zhou Y, Zhu S, Arasappan D, Bao W, Lucas AB, Berthold F, Brennan RJ, Buness A, Catalano JG, Chang C, Chen R, Cheng Y, Cui J, Czika W, Demichelis F, Deng X, Dosymbekov D, Eils R, Feng Y, Fostel J, Fulmer-Smentek S, Fuscoe JC, Gatto L, Ge W, Goldstein DR, Guo L, Halbert DN, Han J, Harris SC, Hatzis C, Herman D, Huang J, J… See abstract for full author list ➔ Shi L, et al. Among authors: xu l, xu j. Nat Biotechnol. 2010 Aug;28(8):827-38. doi: 10.1038/nbt.1665. Epub 2010 Jul 30. Nat Biotechnol. 2010. PMID: 20676074 Free PMC article.
Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures.
Munro SA, Lund SP, Pine PS, Binder H, Clevert DA, Conesa A, Dopazo J, Fasold M, Hochreiter S, Hong H, Jafari N, Kreil DP, Łabaj PP, Li S, Liao Y, Lin SM, Meehan J, Mason CE, Santoyo-Lopez J, Setterquist RA, Shi L, Shi W, Smyth GK, Stralis-Pavese N, Su Z, Tong W, Wang C, Wang J, Xu J, Ye Z, Yang Y, Yu Y, Salit M. Munro SA, et al. Among authors: xu j. Nat Commun. 2014 Sep 25;5:5125. doi: 10.1038/ncomms6125. Nat Commun. 2014. PMID: 25254650 Free article.
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