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Items: 19

1.

Minimum information for reporting next generation sequence genotyping (MIRING): Guidelines for reporting HLA and KIR genotyping via next generation sequencing.

Mack SJ, Milius RP, Gifford BD, Sauter J, Hofmann J, Osoegawa K, Robinson J, Groeneweg M, Turenchalk GS, Adai A, Holcomb C, Rozemuller EH, Penning MT, Heuer ML, Wang C, Salit ML, Schmidt AH, Parham PR, Müller C, Hague T, Fischer G, Fernandez-Viňa M, Hollenbach JA, Norman PJ, Maiers M.

Hum Immunol. 2015 Dec;76(12):954-62. doi: 10.1016/j.humimm.2015.09.011. Epub 2015 Sep 25.

2.

Evaluation of an integrated clinical workflow for targeted next-generation sequencing of low-quality tumor DNA using a 51-gene enrichment panel.

Choudhary A, Mambo E, Sanford T, Boedigheimer M, Twomey B, Califano J, Hadd A, Oliner KS, Beaudenon S, Latham GJ, Adai AT.

BMC Med Genomics. 2014 Nov 14;7:62. doi: 10.1186/s12920-014-0062-0.

3.

Novel insight into mutational landscape of head and neck squamous cell carcinoma.

Gaykalova DA, Mambo E, Choudhary A, Houghton J, Buddavarapu K, Sanford T, Darden W, Adai A, Hadd A, Latham G, Danilova LV, Bishop J, Li RJ, Westra WH, Hennessey P, Koch WM, Ochs MF, Califano JA, Sun W.

PLoS One. 2014 Mar 25;9(3):e93102. doi: 10.1371/journal.pone.0093102. eCollection 2014.

4.

A microRNA-based test improves endoscopic ultrasound-guided cytologic diagnosis of pancreatic cancer.

Brand RE, Adai AT, Centeno BA, Lee LS, Rateb G, Vignesh S, Menard C, Wiechowska-Kozłowska A, Bołdys H, Hartleb M, Sanders MK, Munding JB, Tannapfel A, Hahn SA, Stefańczyk L, Tsongalis GJ, Whitcomb DC, Conwell DL, Morisset JA, Gardner TB, Gordon SR, Suriawinata AA, Lloyd MB, Wylie D, Labourier E, Andruss BF, Szafranska-Schwarzbach AE.

Clin Gastroenterol Hepatol. 2014 Oct;12(10):1717-23. doi: 10.1016/j.cgh.2014.02.038. Epub 2014 Mar 21.

PMID:
24662333
5.

Activation of the NOTCH pathway in head and neck cancer.

Sun W, Gaykalova DA, Ochs MF, Mambo E, Arnaoutakis D, Liu Y, Loyo M, Agrawal N, Howard J, Li R, Ahn S, Fertig E, Sidransky D, Houghton J, Buddavarapu K, Sanford T, Choudhary A, Darden W, Adai A, Latham G, Bishop J, Sharma R, Westra WH, Hennessey P, Chung CH, Califano JA.

Cancer Res. 2014 Feb 15;74(4):1091-104. doi: 10.1158/0008-5472.CAN-13-1259. Epub 2013 Dec 18.

6.

Targeted, high-depth, next-generation sequencing of cancer genes in formalin-fixed, paraffin-embedded and fine-needle aspiration tumor specimens.

Hadd AG, Houghton J, Choudhary A, Sah S, Chen L, Marko AC, Sanford T, Buddavarapu K, Krosting J, Garmire L, Wylie D, Shinde R, Beaudenon S, Alexander EK, Mambo E, Adai AT, Latham GJ.

J Mol Diagn. 2013 Mar;15(2):234-47. doi: 10.1016/j.jmoldx.2012.11.006. Epub 2013 Jan 13.

PMID:
23321017
7.

miRNA biomarkers in cyst fluid augment the diagnosis and management of pancreatic cysts.

Matthaei H, Wylie D, Lloyd MB, Dal Molin M, Kemppainen J, Mayo SC, Wolfgang CL, Schulick RD, Langfield L, Andruss BF, Adai AT, Hruban RH, Szafranska-Schwarzbach AE, Maitra A.

Clin Cancer Res. 2012 Sep 1;18(17):4713-24. doi: 10.1158/1078-0432.CCR-12-0035. Epub 2012 Jun 21.

8.

Serum microRNA biomarkers for detection of non-small cell lung cancer.

Hennessey PT, Sanford T, Choudhary A, Mydlarz WW, Brown D, Adai AT, Ochs MF, Ahrendt SA, Mambo E, Califano JA.

PLoS One. 2012;7(2):e32307. doi: 10.1371/journal.pone.0032307. Epub 2012 Feb 28.

9.

A novel mean-centering method for normalizing microRNA expression from high-throughput RT-qPCR data.

Wylie D, Shelton J, Choudhary A, Adai AT.

BMC Res Notes. 2011 Dec 21;4:555. doi: 10.1186/1756-0500-4-555.

10.

Global microRNA expression profiling of microdissected tissues identifies miR-135b as a novel biomarker for pancreatic ductal adenocarcinoma.

Munding JB, Adai AT, Maghnouj A, Urbanik A, Zöllner H, Liffers ST, Chromik AM, Uhl W, Szafranska-Schwarzbach AE, Tannapfel A, Hahn SA.

Int J Cancer. 2012 Jul 15;131(2):E86-95. doi: 10.1002/ijc.26466. Epub 2011 Nov 19.

11.

miR-221/222 targeting of trichorhinophalangeal 1 (TRPS1) promotes epithelial-to-mesenchymal transition in breast cancer.

Stinson S, Lackner MR, Adai AT, Yu N, Kim HJ, O'Brien C, Spoerke J, Jhunjhunwala S, Boyd Z, Januario T, Newman RJ, Yue P, Bourgon R, Modrusan Z, Stern HM, Warming S, de Sauvage FJ, Amler L, Yeh RF, Dornan D.

Sci Signal. 2011 Aug 9;4(186):pt5. doi: 10.1126/scisignal.2002258.

PMID:
21868360
12.

Development and evaluation of a genomic signature for the prediction and mechanistic assessment of nongenotoxic hepatocarcinogens in the rat.

Fielden MR, Adai A, Dunn RT 2nd, Olaharski A, Searfoss G, Sina J, Aubrecht J, Boitier E, Nioi P, Auerbach S, Jacobson-Kram D, Raghavan N, Yang Y, Kincaid A, Sherlock J, Chen SJ, Car B; Predictive Safety Testing Consortium, Carcinogenicity Working Group.

Toxicol Sci. 2011 Nov;124(1):54-74. doi: 10.1093/toxsci/kfr202. Epub 2011 Aug 2.

PMID:
21813463
13.

TRPS1 targeting by miR-221/222 promotes the epithelial-to-mesenchymal transition in breast cancer.

Stinson S, Lackner MR, Adai AT, Yu N, Kim HJ, O'Brien C, Spoerke J, Jhunjhunwala S, Boyd Z, Januario T, Newman RJ, Yue P, Bourgon R, Modrusan Z, Stern HM, Warming S, de Sauvage FJ, Amler L, Yeh RF, Dornan D.

Sci Signal. 2011 Jun 14;4(177):ra41. doi: 10.1126/scisignal.2001538.

14.

Development of a miRNA-based diagnostic assay for pancreatic ductal adenocarcinoma.

Szafranska-Schwarzbach AE, Adai AT, Lee LS, Conwell DL, Andruss BF.

Expert Rev Mol Diagn. 2011 Apr;11(3):249-57. doi: 10.1586/erm.11.10.

PMID:
21463235
15.

CSRDB: a small RNA integrated database and browser resource for cereals.

Johnson C, Bowman L, Adai AT, Vance V, Sundaresan V.

Nucleic Acids Res. 2007 Jan;35(Database issue):D829-33. Epub 2006 Dec 14.

16.

Comparative whole genome transcriptome analysis of three Plasmodium falciparum strains.

Llinás M, Bozdech Z, Wong ED, Adai AT, DeRisi JL.

Nucleic Acids Res. 2006 Feb 21;34(4):1166-73. Print 2006.

17.

Computational prediction of miRNAs in Arabidopsis thaliana.

Adai A, Johnson C, Mlotshwa S, Archer-Evans S, Manocha V, Vance V, Sundaresan V.

Genome Res. 2005 Jan;15(1):78-91.

18.

A probabilistic functional network of yeast genes.

Lee I, Date SV, Adai AT, Marcotte EM.

Science. 2004 Nov 26;306(5701):1555-8.

19.

LGL: creating a map of protein function with an algorithm for visualizing very large biological networks.

Adai AT, Date SV, Wieland S, Marcotte EM.

J Mol Biol. 2004 Jun 25;340(1):179-90.

PMID:
15184029

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