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Items: 26

1.

Good laboratory practice for clinical next-generation sequencing informatics pipelines.

Gargis AS, Kalman L, Bick DP, da Silva C, Dimmock DP, Funke BH, Gowrisankar S, Hegde MR, Kulkarni S, Mason CE, Nagarajan R, Voelkerding KV, Worthey EA, Aziz N, Barnes J, Bennett SF, Bisht H, Church DM, Dimitrova Z, Gargis SR, Hafez N, Hambuch T, Hyland FC, Luna RA, MacCannell D, Mann T, McCluskey MR, McDaniel TK, Ganova-Raeva LM, Rehm HL, Reid J, Campo DS, Resnick RB, Ridge PG, Salit ML, Skums P, Wong LJ, Zehnbauer BA, Zook JM, Lubin IM.

Nat Biotechnol. 2015 Jul;33(7):689-93. doi: 10.1038/nbt.3237. No abstract available.

2.

Personalized treatment of Sézary syndrome by targeting a novel CTLA4:CD28 fusion.

Sekulic A, Liang WS, Tembe W, Izatt T, Kruglyak S, Kiefer JA, Cuyugan L, Zismann V, Legendre C, Pittelkow MR, Gohmann JJ, De Castro FR, Trent J, Carpten J, Craig DW, McDaniel TK.

Mol Genet Genomic Med. 2015 Mar;3(2):130-6. doi: 10.1002/mgg3.121. Epub 2014 Nov 27.

3.

Open-access synthetic spike-in mRNA-seq data for cancer gene fusions.

Tembe WD, Pond SJ, Legendre C, Chuang HY, Liang WS, Kim NE, Montel V, Wong S, McDaniel TK, Craig DW, Carpten JD.

BMC Genomics. 2014 Sep 30;15:824. doi: 10.1186/1471-2164-15-824.

4.

Survey of culture, goldengate assay, universal biosensor assay, and 16S rRNA Gene sequencing as alternative methods of bacterial pathogen detection.

Lindsay B, Pop M, Antonio M, Walker AW, Mai V, Ahmed D, Oundo J, Tamboura B, Panchalingam S, Levine MM, Kotloff K, Li S, Magder LS, Paulson JN, Liu B, Ikumapayi U, Ebruke C, Dione M, Adeyemi M, Rance R, Stares MD, Ukhanova M, Barnes B, Lewis I, Ahmed F, Alam MT, Amin R, Siddiqui S, Ochieng JB, Ouma E, Juma J, Mailu E, Omore R, O'Reilly CE, Hannis J, Manalili S, Deleon J, Yasuda I, Blyn L, Ranken R, Li F, Housley R, Ecker DJ, Hossain MA, Breiman RF, Morris JG, McDaniel TK, Parkhill J, Saha D, Sampath R, Stine OC, Nataro JP.

J Clin Microbiol. 2013 Oct;51(10):3263-9. doi: 10.1128/JCM.01342-13. Epub 2013 Jul 24.

5.

Medium- to high-throughput SNP genotyping using VeraCode microbeads.

Lin CH, Yeakley JM, McDaniel TK, Shen R.

Methods Mol Biol. 2009;496:129-42. doi: 10.1007/978-1-59745-553-4_10. Review.

PMID:
18839109
6.

Expanding the Helicobacter pylori genetic toolbox: modification of an endogenous plasmid for use as a transcriptional reporter and complementation vector.

Carpenter BM, McDaniel TK, Whitmire JM, Gancz H, Guidotti S, Censini S, Merrell DS.

Appl Environ Microbiol. 2007 Dec;73(23):7506-14. Epub 2007 Oct 5.

7.

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.

BMC Genomics. 2007 Aug 29;8:296.

8.

A model of technical variation of microarray signals.

Chudin E, Kruglyak S, Baker SC, Oeser S, Barker D, McDaniel TK.

J Comput Biol. 2006 May;13(4):996-1003.

PMID:
16761924
9.

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.

BMC Dev Biol. 2006 May 3;6:20.

10.

NTera2: a model system to study dopaminergic differentiation of human embryonic stem cells.

Schwartz CM, Spivak CE, Baker SC, McDaniel TK, Loring JF, Nguyen C, Chrest FJ, Wersto R, Arenas E, Zeng X, Freed WJ, Rao MS.

Stem Cells Dev. 2005 Oct;14(5):517-34.

PMID:
16305337
11.

A novel, high-performance random array platform for quantitative gene expression profiling.

Kuhn K, Baker SC, Chudin E, Lieu MH, Oeser S, Bennett H, Rigault P, Barker D, McDaniel TK, Chee MS.

Genome Res. 2004 Nov;14(11):2347-56.

12.

New approaches for validation of lethal phenotypes and genetic reversion in Helicobacter pylori.

McDaniel TK, Dewalt KC, Salama NR, Falkow S.

Helicobacter. 2001 Mar;6(1):15-23.

PMID:
11328361
13.

A whole-genome microarray reveals genetic diversity among Helicobacter pylori strains.

Salama N, Guillemin K, McDaniel TK, Sherlock G, Tompkins L, Falkow S.

Proc Natl Acad Sci U S A. 2000 Dec 19;97(26):14668-73.

14.

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.

Infect Immun. 2000 Nov;68(11):6115-26.

15.

Sequence anomalies in the Cag7 gene of the Helicobacter pylori pathogenicity island.

Liu G, McDaniel TK, Falkow S, Karlin S.

Proc Natl Acad Sci U S A. 1999 Jun 8;96(12):7011-6.

16.

The complete sequence of the locus of enterocyte effacement (LEE) from enteropathogenic Escherichia coli E2348/69.

Elliott SJ, Wainwright LA, McDaniel TK, Jarvis KG, Deng YK, Lai LC, McNamara BP, Donnenberg MS, Kaper JB.

Mol Microbiol. 1998 Apr;28(1):1-4. No abstract available.

18.

Genetics of virulence of enteropathogenic E. coli.

Kaper JB, McDaniel TK, Jarvis KG, Gomez-Duarte O.

Adv Exp Med Biol. 1997;412:279-87. Review.

PMID:
9192031
19.

Cloning of the RDEC-1 locus of enterocyte effacement (LEE) and functional analysis of the phenotype on HEp-2 cells.

Karaolis DK, McDaniel TK, Kaper JB, Boedeker EC.

Adv Exp Med Biol. 1997;412:241-5.

PMID:
9192020
21.

Attaching and effacing of host cells by enteropathogenic Escherichia coli in the absence of detectable tyrosine kinase mediated signal transduction.

Rabinowitz RP, Lai LC, Jarvis K, McDaniel TK, Kaper JB, Stone KD, Donnenberg MS.

Microb Pathog. 1996 Sep;21(3):157-71.

PMID:
8878013
22.

Enteropathogenic Escherichia coli contains a putative type III secretion system necessary for the export of proteins involved in attaching and effacing lesion formation.

Jarvis KG, Girón JA, Jerse AE, McDaniel TK, Donnenberg MS, Kaper JB.

Proc Natl Acad Sci U S A. 1995 Aug 15;92(17):7996-8000.

23.

A genetic locus of enterocyte effacement conserved among diverse enterobacterial pathogens.

McDaniel TK, Jarvis KG, Donnenberg MS, Kaper JB.

Proc Natl Acad Sci U S A. 1995 Feb 28;92(5):1664-8.

24.

Loss of heterozygosity involves multiple tumor suppressor genes in human esophageal cancers.

Huang Y, Boynton RF, Blount PL, Silverstein RJ, Yin J, Tong Y, McDaniel TK, Newkirk C, Resau JH, Sridhara R, Reid BJ, Meltzer SJ.

Cancer Res. 1992 Dec 1;52(23):6525-30.

25.

Direct radioactive labeling of unpurified PCR products using Klenow fragment.

McDaniel TK, Huang Y, Yin J, Needleman SW, Meltzer SJ.

Biotechniques. 1991 Aug;11(2):164, 166.

PMID:
1931010
26.

Reduction to homozygosity involving p53 in esophageal cancers demonstrated by the polymerase chain reaction.

Meltzer SJ, Yin J, Huang Y, McDaniel TK, Newkirk C, Iseri O, Vogelstein B, Resau JH.

Proc Natl Acad Sci U S A. 1991 Jun 1;88(11):4976-80.

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