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Items: 21

1.

Metformin pharmacogenomics: a genome-wide association study to identify genetic and epigenetic biomarkers involved in metformin anticancer response using human lymphoblastoid cell lines.

Niu N, Liu T, Cairns J, Ly RC, Tan X, Deng M, Fridley BL, Kalari KR, Abo RP, Jenkins G, Batzler A, Carlson EE, Barman P, Moran S, Heyn H, Esteller M, Wang L.

Hum Mol Genet. 2016 Nov 1;25(21):4819-4834. doi: 10.1093/hmg/ddw301.

2.

Institutional implementation of clinical tumor profiling on an unselected cancer population.

Sholl LM, Do K, Shivdasani P, Cerami E, Dubuc AM, Kuo FC, Garcia EP, Jia Y, Davineni P, Abo RP, Pugh TJ, van Hummelen P, Thorner AR, Ducar M, Berger AH, Nishino M, Janeway KA, Church A, Harris M, Ritterhouse LL, Campbell JD, Rojas-Rudilla V, Ligon AH, Ramkissoon S, Cleary JM, Matulonis U, Oxnard GR, Chao R, Tassell V, Christensen J, Hahn WC, Kantoff PW, Kwiatkowski DJ, Johnson BE, Meyerson M, Garraway LA, Shapiro GI, Rollins BJ, Lindeman NI, MacConaill LE.

JCI Insight. 2016 Nov 17;1(19):e87062. doi: 10.1172/jci.insight.87062.

3.

Myeloid neoplasm demonstrating a STAT5B-RARA rearrangement and genetic alterations associated with all-trans retinoic acid resistance identified by a custom next-generation sequencing assay.

Kluk MJ, Abo RP, Brown RD, Kuo FC, Dal Cin P, Pozdnyakova O, Morgan EA, Lindeman NI, DeAngelo DJ, Aster JC.

Cold Spring Harb Mol Case Stud. 2015 Oct;1(1):a000307. doi: 10.1101/mcs.a000307.

4.

Diffuse large B-cell lymphoma patient-derived xenograft models capture the molecular and biological heterogeneity of the disease.

Chapuy B, Cheng H, Watahiki A, Ducar MD, Tan Y, Chen L, Roemer MG, Ouyang J, Christie AL, Zhang L, Gusenleitner D, Abo RP, Farinha P, von Bonin F, Thorner AR, Sun HH, Gascoyne RD, Pinkus GS, van Hummelen P, Wulf GG, Aster JC, Weinstock DM, Monti S, Rodig SJ, Wang Y, Shipp MA.

Blood. 2016 May 5;127(18):2203-13. doi: 10.1182/blood-2015-09-672352. Epub 2016 Jan 15.

5.

Targetable genetic features of primary testicular and primary central nervous system lymphomas.

Chapuy B, Roemer MG, Stewart C, Tan Y, Abo RP, Zhang L, Dunford AJ, Meredith DM, Thorner AR, Jordanova ES, Liu G, Feuerhake F, Ducar MD, Illerhaus G, Gusenleitner D, Linden EA, Sun HH, Homer H, Aono M, Pinkus GS, Ligon AH, Ligon KL, Ferry JA, Freeman GJ, van Hummelen P, Golub TR, Getz G, Rodig SJ, de Jong D, Monti S, Shipp MA.

Blood. 2016 Feb 18;127(7):869-81. doi: 10.1182/blood-2015-10-673236. Epub 2015 Dec 23.

6.

BreaKmer: detection of structural variation in targeted massively parallel sequencing data using kmers.

Abo RP, Ducar M, Garcia EP, Thorner AR, Rojas-Rudilla V, Lin L, Sholl LM, Hahn WC, Meyerson M, Lindeman NI, Van Hummelen P, MacConaill LE.

Nucleic Acids Res. 2015 Feb 18;43(3):e19. doi: 10.1093/nar/gku1211. Epub 2014 Nov 26.

7.

Multiplexed DNA repair assays for multiple lesions and multiple doses via transcription inhibition and transcriptional mutagenesis.

Nagel ZD, Margulies CM, Chaim IA, McRee SK, Mazzucato P, Ahmad A, Abo RP, Butty VL, Forget AL, Samson LD.

Proc Natl Acad Sci U S A. 2014 May 6;111(18):E1823-32. doi: 10.1073/pnas.1401182111. Epub 2014 Apr 22.

8.

Global analysis of cell cycle gene expression of the legume symbiont Sinorhizobium meliloti.

De Nisco NJ, Abo RP, Wu CM, Penterman J, Walker GC.

Proc Natl Acad Sci U S A. 2014 Mar 4;111(9):3217-24. doi: 10.1073/pnas.1400421111. Epub 2014 Feb 5.

9.

Host plant peptides elicit a transcriptional response to control the Sinorhizobium meliloti cell cycle during symbiosis.

Penterman J, Abo RP, De Nisco NJ, Arnold MF, Longhi R, Zanda M, Walker GC.

Proc Natl Acad Sci U S A. 2014 Mar 4;111(9):3561-6. doi: 10.1073/pnas.1400450111. Epub 2014 Feb 5.

10.

Discovery of genetic biomarkers contributing to variation in drug response of cytidine analogues using human lymphoblastoid cell lines.

Li L, Fridley BL, Kalari K, Niu N, Jenkins G, Batzler A, Abo RP, Schaid D, Wang L.

BMC Genomics. 2014 Feb 1;15:93. doi: 10.1186/1471-2164-15-93.

11.

Arsenic exposure perturbs the gut microbiome and its metabolic profile in mice: an integrated metagenomics and metabolomics analysis.

Lu K, Abo RP, Schlieper KA, Graffam ME, Levine S, Wishnok JS, Swenberg JA, Tannenbaum SR, Fox JG.

Environ Health Perspect. 2014 Mar;122(3):284-91. doi: 10.1289/ehp.1307429. Epub 2014 Jan 10.

12.

Gut microbiome perturbations induced by bacterial infection affect arsenic biotransformation.

Lu K, Cable PH, Abo RP, Ru H, Graffam ME, Schlieper KA, Parry NM, Levine S, Bodnar WM, Wishnok JS, Styblo M, Swenberg JA, Fox JG, Tannenbaum SR.

Chem Res Toxicol. 2013 Dec 16;26(12):1893-903. doi: 10.1021/tx4002868. Epub 2013 Nov 18.

13.

Genome-wide association study for biomarker identification of Rapamycin and Everolimus using a lymphoblastoid cell line system.

Jiang J, Fridley BL, Feng Q, Abo RP, Brisbin A, Batzler A, Jenkins G, Long PA, Wang L.

Front Genet. 2013 Aug 30;4:166. doi: 10.3389/fgene.2013.00166. eCollection 2013.

14.

Genetic association with overall survival of taxane-treated lung cancer patients - a genome-wide association study in human lymphoblastoid cell lines followed by a clinical association study.

Niu N, Schaid DJ, Abo RP, Kalari K, Fridley BL, Feng Q, Jenkins G, Batzler A, Brisbin AG, Cunningham JM, Li L, Sun Z, Yang P, Wang L.

BMC Cancer. 2012 Sep 24;12:422. doi: 10.1186/1471-2407-12-422.

15.

Shared genomic segment analysis: the power to find rare disease variants.

Knight S, Abo RP, Abel HJ, Neklason DW, Tuohy TM, Burt RW, Thomas A, Camp NJ.

Ann Hum Genet. 2012 Nov;76(6):500-9. doi: 10.1111/j.1469-1809.2012.00728.x. Epub 2012 Sep 19.

16.

Human liver methionine cycle: MAT1A and GNMT gene resequencing, functional genomics, and hepatic genotype-phenotype correlation.

Ji Y, Nordgren KK, Chai Y, Hebbring SJ, Jenkins GD, Abo RP, Peng Y, Pelleymounter LL, Moon I, Eckloff BW, Chai X, Zhang J, Fridley BL, Yee VC, Wieben ED, Weinshilboum RM.

Drug Metab Dispos. 2012 Oct;40(10):1984-92. doi: 10.1124/dmd.112.046953. Epub 2012 Jul 17.

17.

Serine hydroxymethyltransferase 1 and 2: gene sequence variation and functional genomic characterization.

Hebbring SJ, Chai Y, Ji Y, Abo RP, Jenkins GD, Fridley B, Zhang J, Eckloff BW, Wieben ED, Weinshilboum RM.

J Neurochem. 2012 Mar;120(6):881-90. doi: 10.1111/j.1471-4159.2012.07646.x. Epub 2012 Feb 6.

18.

Gemcitabine metabolic pathway genetic polymorphisms and response in patients with non-small cell lung cancer.

Li L, Schaid DJ, Fridley BL, Kalari KR, Jenkins GD, Abo RP, Batzler A, Moon I, Pelleymounter L, Eckloff BW, Wieben ED, Sun Z, Yang P, Wang L.

Pharmacogenet Genomics. 2012 Feb;22(2):105-16. doi: 10.1097/FPC.0b013e32834dd7e2.

19.

Genetic variation predicting cisplatin cytotoxicity associated with overall survival in lung cancer patients receiving platinum-based chemotherapy.

Tan XL, Moyer AM, Fridley BL, Schaid DJ, Niu N, Batzler AJ, Jenkins GD, Abo RP, Li L, Cunningham JM, Sun Z, Yang P, Wang L.

Clin Cancer Res. 2011 Sep 1;17(17):5801-11. doi: 10.1158/1078-0432.CCR-11-1133. Epub 2011 Jul 20.

20.

Evaluation of genetic risk scores for lipid levels using genome-wide markers in the Framingham Heart Study.

Piccolo SR, Abo RP, Allen-Brady K, Camp NJ, Knight S, Anderson JL, Horne BD.

BMC Proc. 2009 Dec 15;3 Suppl 7:S46.

21.

Pedigree association: assigning individual weights to pedigree members for genetic association analysis.

Knight S, Abo RP, Wong J, Thomas A, Camp NJ.

BMC Proc. 2009 Dec 15;3 Suppl 7:S121.

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