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Genome wide profiling of human embryonic stem cells (hESCs), their derivatives and embryonal carcinoma cells to develop base profiles of U.S. Federal government approved hESC lines.
Liu Y, Shin S, Zeng X, Zhan M, Gonzalez R, Mueller FJ, Schwartz CM, Xue H, Li H, Baker SC, Chudin E, Barker DL, McDaniel TK, Oeser S, Loring JF, Mattson MP, Rao MS. Liu Y, et al. Among authors: mcdaniel tk. BMC Dev Biol. 2006 May 3;6:20. doi: 10.1186/1471-213X-6-20. BMC Dev Biol. 2006. PMID: 16672070 Free PMC article.
A model of technical variation of microarray signals.
Chudin E, Kruglyak S, Baker SC, Oeser S, Barker D, McDaniel TK. Chudin E, et al. Among authors: mcdaniel tk. J Comput Biol. 2006 May;13(4):996-1003. doi: 10.1089/cmb.2006.13.996. J Comput Biol. 2006. PMID: 16761924
The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements.
MAQC Consortium; Shi L, Reid LH, Jones WD, Shippy R, Warrington JA, Baker SC, Collins PJ, de Longueville F, Kawasaki ES, Lee KY, Luo Y, Sun YA, Willey JC, Setterquist RA, Fischer GM, Tong W, Dragan YP, Dix DJ, Frueh FW, Goodsaid FM, Herman D, Jensen RV, Johnson CD, Lobenhofer EK, Puri RK, Schrf U, Thierry-Mieg J, Wang C, Wilson M, Wolber PK, Zhang L, Amur S, Bao W, Barbacioru CC, Lucas AB, Bertholet V, Boysen C, Bromley B, Brown D, Brunner A, Canales R, Cao XM, Cebula TA, Chen JJ, Cheng J, Chu TM, Chudin E, Corson J, Corton JC, Croner LJ, Davies C, Davison TS, Delenstarr G, Deng X, Dorris D, Eklund AC, Fan XH, Fang H, Fulmer-Smentek S, Fuscoe JC, Gallagher K, Ge W, Guo L, Guo X, Hager J, Haje PK, Han J, Han T, Harbottle HC, Harris SC, Hatchwell E, Hauser CA, Hester S, Hong H, Hurban P, Jackson SA, Ji H, Knight CR, Kuo WP, LeClerc JE, Levy S, Li QZ, Liu C, Liu Y, Lombardi MJ, Ma Y, Magnuson SR, Maqsodi B, McDaniel T, Mei N, Myklebost O, Ning B, Novoradovskaya N, Orr MS, Osborn TW, Papallo A, Patterson TA, Perkins RG, Peters EH, Peterson R, Philips KL, Pine PS, Pusztai L, Qian F, Ren H, Rosen M, Rosenzweig BA, Samaha RR, Schena M, Schroth GP, Shchegrova S, Smith DD, Staedtler F, Su … See abstract for full author list ➔ MAQC Consortium, et al. Nat Biotechnol. 2006 Sep;24(9):1151-61. doi: 10.1038/nbt1239. Nat Biotechnol. 2006. PMID: 16964229 Free PMC article.
Cis sequence effects on gene expression.
Bergen AW, Baccarelli A, McDaniel TK, Kuhn K, Pfeiffer R, Kakol J, Bender P, Jacobs K, Packer B, Chanock SJ, Yeager M. Bergen AW, et al. Among authors: mcdaniel tk. BMC Genomics. 2007 Aug 29;8:296. doi: 10.1186/1471-2164-8-296. BMC Genomics. 2007. PMID: 17727713 Free PMC article.
The locus of enterocyte effacement (LEE)-encoded regulator controls expression of both LEE- and non-LEE-encoded virulence factors in enteropathogenic and enterohemorrhagic Escherichia coli.
Elliott SJ, Sperandio V, Girón JA, Shin S, Mellies JL, Wainwright L, Hutcheson SW, McDaniel TK, Kaper JB. Elliott SJ, et al. Among authors: mcdaniel tk. Infect Immun. 2000 Nov;68(11):6115-26. doi: 10.1128/IAI.68.11.6115-6126.2000. Infect Immun. 2000. PMID: 11035714 Free PMC article.
Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing.
Fang LT, Zhu B, Zhao Y, Chen W, Yang Z, Kerrigan L, Langenbach K, de Mars M, Lu C, Idler K, Jacob H, Zheng Y, Ren L, Yu Y, Jaeger E, Schroth GP, Abaan OD, Talsania K, Lack J, Shen TW, Chen Z, Stanbouly S, Tran B, Shetty J, Kriga Y, Meerzaman D, Nguyen C, Petitjean V, Sultan M, Cam M, Mehta M, Hung T, Peters E, Kalamegham R, Sahraeian SME, Mohiyuddin M, Guo Y, Yao L, Song L, Lam HYK, Drabek J, Vojta P, Maestro R, Gasparotto D, Kõks S, Reimann E, Scherer A, Nordlund J, Liljedahl U, Jensen RV, Pirooznia M, Li Z, Xiao C, Sherry ST, Kusko R, Moos M, Donaldson E, Tezak Z, Ning B, Tong W, Li J, Duerken-Hughes P, Catalanotti C, Maheshwari S, Shuga J, Liang WS, Keats J, Adkins J, Tassone E, Zismann V, McDaniel T, Trent J, Foox J, Butler D, Mason CE, Hong H, Shi L, Wang C, Xiao W; Somatic Mutation Working Group of Sequencing Quality Control Phase II Consortium. Fang LT, et al. Nat Biotechnol. 2021 Sep;39(9):1151-1160. doi: 10.1038/s41587-021-00993-6. Epub 2021 Sep 9. Nat Biotechnol. 2021. PMID: 34504347 Free PMC article.
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