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Items: 42

1.

Evaluating the Information Content of Shallow Shotgun Metagenomics.

Hillmann B, Al-Ghalith GA, Shields-Cutler RR, Zhu Q, Gohl DM, Beckman KB, Knight R, Knights D.

mSystems. 2018 Nov 13;3(6). pii: e00069-18. doi: 10.1128/mSystems.00069-18. eCollection 2018 Nov-Dec.

2.

Comprehensive Functional Analysis of the Enterococcus faecalis Core Genome Using an Ordered, Sequence-Defined Collection of Insertional Mutations in Strain OG1RF.

Dale JL, Beckman KB, Willett JLE, Nilson JL, Palani NP, Baller JA, Hauge A, Gohl DM, Erickson R, Manias DA, Sadowsky MJ, Dunny GM.

mSystems. 2018 Sep 11;3(5). pii: e00062-18. doi: 10.1128/mSystems.00062-18. eCollection 2018 Sep-Oct.

3.

Leukocyte telomere length in relation to risk of lung adenocarcinoma incidence: Findings from the Singapore Chinese Health Study.

Yuan JM, Beckman KB, Wang R, Bull C, Adams-Haduch J, Huang JY, Jin A, Opresko P, Newman AB, Zheng YL, Fenech M, Koh WP.

Int J Cancer. 2018 Jun 1;142(11):2234-2243. doi: 10.1002/ijc.31251. Epub 2018 Jan 25.

PMID:
29318605
4.

Single-Strand Consensus Sequencing Reveals that HIV Type but not Subtype Significantly Impacts Viral Mutation Frequencies and Spectra.

Rawson JMO, Gohl DM, Landman SR, Roth ME, Meissner ME, Peterson TS, Hodges JS, Beckman KB, Mansky LM.

J Mol Biol. 2017 Jul 21;429(15):2290-2307. doi: 10.1016/j.jmb.2017.05.010. Epub 2017 May 11.

5.

Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies.

Gohl DM, Vangay P, Garbe J, MacLean A, Hauge A, Becker A, Gould TJ, Clayton JB, Johnson TJ, Hunter R, Knights D, Beckman KB.

Nat Biotechnol. 2016 Sep;34(9):942-9. doi: 10.1038/nbt.3601. Epub 2016 Jul 25.

PMID:
27454739
6.

Genome-wide imputation study identifies novel HLA locus for pulmonary fibrosis and potential role for auto-immunity in fibrotic idiopathic interstitial pneumonia.

Fingerlin TE, Zhang W, Yang IV, Ainsworth HC, Russell PH, Blumhagen RZ, Schwarz MI, Brown KK, Steele MP, Loyd JE, Cosgrove GP, Lynch DA, Groshong S, Collard HR, Wolters PJ, Bradford WZ, Kossen K, Seiwert SD, du Bois RM, Garcia CK, Devine MS, Gudmundsson G, Isaksson HJ, Kaminski N, Zhang Y, Gibson KF, Lancaster LH, Maher TM, Molyneaux PL, Wells AU, Moffatt MF, Selman M, Pardo A, Kim DS, Crapo JD, Make BJ, Regan EA, Walek DS, Daniel JJ, Kamatani Y, Zelenika D, Murphy E, Smith K, McKean D, Pedersen BS, Talbert J, Powers J, Markin CR, Beckman KB, Lathrop M, Freed B, Langefeld CD, Schwartz DA.

BMC Genet. 2016 Jun 7;17(1):74. doi: 10.1186/s12863-016-0377-2.

7.

No Association between the Mitochondrial Genome and Prostate Cancer Risk: The Multiethnic Cohort.

Giorgi EE, Li Y, Caberto CP, Beckman KB, Lum-Jones A, Haiman CA, Le Marchand L, Stram DO, Saxena R, Cheng I.

Cancer Epidemiol Biomarkers Prev. 2016 Jun;25(6):1001-3. doi: 10.1158/1055-9965.EPI-16-0111. Epub 2016 Mar 28.

8.

Toward clinical genomics in everyday medicine: perspectives and recommendations.

Delaney SK, Hultner ML, Jacob HJ, Ledbetter DH, McCarthy JJ, Ball M, Beckman KB, Belmont JW, Bloss CS, Christman MF, Cosgrove A, Damiani SA, Danis T, Delledonne M, Dougherty MJ, Dudley JT, Faucett WA, Friedman JR, Haase DH, Hays TS, Heilsberg S, Huber J, Kaminsky L, Ledbetter N, Lee WH, Levin E, Libiger O, Linderman M, Love RL, Magnus DC, Martland A, McClure SL, Megill SE, Messier H, Nussbaum RL, Palaniappan L, Patay BA, Popovich BW, Quackenbush J, Savant MJ, Su MM, Terry SF, Tucker S, Wong WT, Green RC.

Expert Rev Mol Diagn. 2016;16(5):521-32. doi: 10.1586/14737159.2016.1146593. Epub 2016 Feb 24.

9.

Persistent microbial dysbiosis in preterm premature rupture of membranes from onset until delivery.

Baldwin EA, Walther-Antonio M, MacLean AM, Gohl DM, Beckman KB, Chen J, White B, Creedon DJ, Chia N.

PeerJ. 2015 Nov 26;3:e1398. doi: 10.7717/peerj.1398. eCollection 2015.

10.

Association of Genes, Pathways, and Haplogroups of the Mitochondrial Genome with the Risk of Colorectal Cancer: The Multiethnic Cohort.

Li Y, Beckman KB, Caberto C, Kazma R, Lum-Jones A, Haiman CA, Le Marchand L, Stram DO, Saxena R, Cheng I.

PLoS One. 2015 Sep 4;10(9):e0136796. doi: 10.1371/journal.pone.0136796. eCollection 2015.

11.

Next generation sequencing in endocrine practice.

Forlenza GP, Calhoun A, Beckman KB, Halvorsen T, Hamdoun E, Zierhut H, Sarafoglou K, Polgreen LE, Miller BS, Nathan B, Petryk A.

Mol Genet Metab. 2015 Jun-Jul;115(2-3):61-71. doi: 10.1016/j.ymgme.2015.05.002. Epub 2015 May 3. Review.

12.

Genome-wide association study of breast cancer in Latinas identifies novel protective variants on 6q25.

Fejerman L, Ahmadiyeh N, Hu D, Huntsman S, Beckman KB, Caswell JL, Tsung K, John EM, Torres-Mejia G, Carvajal-Carmona L, Echeverry MM, Tuazon AM, Ramirez C; COLUMBUS Consortium, Gignoux CR, Eng C, Gonzalez-Burchard E, Henderson B, Le Marchand L, Kooperberg C, Hou L, Agalliu I, Kraft P, Lindström S, Perez-Stable EJ, Haiman CA, Ziv E.

Nat Commun. 2014 Oct 20;5:5260. doi: 10.1038/ncomms6260.

13.

Implementation of Cloud based next generation sequencing data analysis in a clinical laboratory.

Onsongo G, Erdmann J, Spears MD, Chilton J, Beckman KB, Hauge A, Yohe S, Schomaker M, Bower M, Silverstein KA, Thyagarajan B.

BMC Res Notes. 2014 May 23;7:314. doi: 10.1186/1756-0500-7-314.

14.

Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals.

Battle A, Mostafavi S, Zhu X, Potash JB, Weissman MM, McCormick C, Haudenschild CD, Beckman KB, Shi J, Mei R, Urban AE, Montgomery SB, Levinson DF, Koller D.

Genome Res. 2014 Jan;24(1):14-24. doi: 10.1101/gr.155192.113. Epub 2013 Oct 3.

15.

Genome-wide association study identifies multiple susceptibility loci for pulmonary fibrosis.

Fingerlin TE, Murphy E, Zhang W, Peljto AL, Brown KK, Steele MP, Loyd JE, Cosgrove GP, Lynch D, Groshong S, Collard HR, Wolters PJ, Bradford WZ, Kossen K, Seiwert SD, du Bois RM, Garcia CK, Devine MS, Gudmundsson G, Isaksson HJ, Kaminski N, Zhang Y, Gibson KF, Lancaster LH, Cogan JD, Mason WR, Maher TM, Molyneaux PL, Wells AU, Moffatt MF, Selman M, Pardo A, Kim DS, Crapo JD, Make BJ, Regan EA, Walek DS, Daniel JJ, Kamatani Y, Zelenika D, Smith K, McKean D, Pedersen BS, Talbert J, Kidd RN, Markin CR, Beckman KB, Lathrop M, Schwarz MI, Schwartz DA.

Nat Genet. 2013 Jun;45(6):613-20. doi: 10.1038/ng.2609. Epub 2013 Apr 14. Erratum in: Nat Genet. 2013 Nov;45(11):1409.

16.

Association between celiac disease and iron deficiency in Caucasians, but not non-Caucasians.

Murray JA, McLachlan S, Adams PC, Eckfeldt JH, Garner CP, Vulpe CD, Gordeuk VR, Brantner T, Leiendecker-Foster C, Killeen AA, Acton RT, Barcellos LF, Nickerson DA, Beckman KB, McLaren GD, McLaren CE.

Clin Gastroenterol Hepatol. 2013 Jul;11(7):808-14. doi: 10.1016/j.cgh.2013.02.009. Epub 2013 Feb 13.

17.

Genetic and environmental predictors of serum 25-hydroxyvitamin D concentrations among middle-aged and elderly Chinese in Singapore.

Robien K, Butler LM, Wang R, Beckman KB, Walek D, Koh WP, Yuan JM.

Br J Nutr. 2013 Feb 14;109(3):493-502. doi: 10.1017/S0007114512001675. Epub 2012 May 15.

18.

AR intragenic deletions linked to androgen receptor splice variant expression and activity in models of prostate cancer progression.

Li Y, Hwang TH, Oseth LA, Hauge A, Vessella RL, Schmechel SC, Hirsch B, Beckman KB, Silverstein KA, Dehm SM.

Oncogene. 2012 Nov 8;31(45):4759-67. doi: 10.1038/onc.2011.637. Epub 2012 Jan 23.

19.

Development and initial characterization of a HAPPY panel for mapping the X. tropicalis genome.

Jiang Z, Michal JJ, Beckman KB, Lyons JB, Zhang M, Pan Z, Rokhsar DS, Harland RM.

Int J Biol Sci. 2011;7(7):1037-44. Epub 2011 Aug 24.

20.

The rs4774 CIITA missense variant is associated with risk of systemic lupus erythematosus.

Bronson PG, Goldstein BA, Ramsay PP, Beckman KB, Noble JA, Lane JA, Seldin MF, Kelly JA, Harley JB, Moser KL, Gaffney PM, Behrens TW, Criswell LA, Barcellos LF.

Genes Immun. 2011 Dec;12(8):667-71. doi: 10.1038/gene.2011.36. Epub 2011 May 26.

21.

Genome-wide association study identifies genetic loci associated with iron deficiency.

McLaren CE, Garner CP, Constantine CC, McLachlan S, Vulpe CD, Snively BM, Gordeuk VR, Nickerson DA, Cook JD, Leiendecker-Foster C, Beckman KB, Eckfeldt JH, Barcellos LF, Murray JA, Adams PC, Acton RT, Killeen AA, McLaren GD.

PLoS One. 2011 Mar 31;6(3):e17390. doi: 10.1371/journal.pone.0017390.

22.

Cadmium, copper, iron, and zinc concentrations in kidneys of grey wolves, Canis lupus, from Alaska, Idaho, Montana (USA) and the Northwest Territories (Canada).

Hoffmann SR, Blunck SA, Petersen KN, Jones EM, Koval JC, Misek R, Frick JA, Cluff HD, Sime CA, McNay M, Beckman KB, Atkinson MW, Drew M, Collinge MD, Bangs EE, Harper RG.

Bull Environ Contam Toxicol. 2010 Nov;85(5):481-5. doi: 10.1007/s00128-010-0126-6. Epub 2010 Oct 24.

PMID:
20972865
23.

European ancestry is positively associated with breast cancer risk in Mexican women.

Fejerman L, Romieu I, John EM, Lazcano-Ponce E, Huntsman S, Beckman KB, Pérez-Stable EJ, González Burchard E, Ziv E, Torres-Mejía G.

Cancer Epidemiol Biomarkers Prev. 2010 Apr;19(4):1074-82. doi: 10.1158/1055-9965.EPI-09-1193. Epub 2010 Mar 23.

24.

CpG methylation of a silent controlling element in the murine Avy allele is incomplete and unresponsive to methyl donor supplementation.

Cropley JE, Suter CM, Beckman KB, Martin DI.

PLoS One. 2010 Feb 4;5(2):e9055. doi: 10.1371/journal.pone.0009055.

25.

A novel association between a SNP in CYBRD1 and serum ferritin levels in a cohort study of HFE hereditary haemochromatosis.

Constantine CC, Anderson GJ, Vulpe CD, McLaren CE, Bahlo M, Yeap HL, Gertig DM, Osborne NJ, Bertalli NA, Beckman KB, Chen V, Matak P, McKie AT, Delatycki MB, Olynyk JK, English DR, Southey MC, Giles GG, Hopper JL, Allen KJ, Gurrin LC.

Br J Haematol. 2009 Oct;147(1):140-9. doi: 10.1111/j.1365-2141.2009.07843.x. Epub 2009 Aug 10.

26.

Comparing genetic ancestry and self-described race in african americans born in the United States and in Africa.

Yaeger R, Avila-Bront A, Abdul K, Nolan PC, Grann VR, Birchette MG, Choudhry S, Burchard EG, Beckman KB, Gorroochurn P, Ziv E, Consedine NS, Joe AK.

Cancer Epidemiol Biomarkers Prev. 2008 Jun;17(6):1329-38. doi: 10.1158/1055-9965.EPI-07-2505.

27.

An african-specific functional polymorphism in KCNMB1 shows sex-specific association with asthma severity.

Seibold MA, Wang B, Eng C, Kumar G, Beckman KB, Sen S, Choudhry S, Meade K, Lenoir M, Watson HG, Thyne S, Williams LK, Kumar R, Weiss KB, Grammer LC, Avila PC, Schleimer RP, Burchard EG, Brenner R.

Hum Mol Genet. 2008 Sep 1;17(17):2681-90. doi: 10.1093/hmg/ddn168. Epub 2008 Jun 4.

28.

Ethnicity-specific gene-gene interaction between IL-13 and IL-4Ralpha among African Americans with asthma.

Battle NC, Choudhry S, Tsai HJ, Eng C, Kumar G, Beckman KB, Naqvi M, Meade K, Watson HG, Lenoir M, Burchard EG; SAGE Investigators.

Am J Respir Crit Care Med. 2007 May 1;175(9):881-7. Epub 2007 Feb 15.

29.

Dramatic age-related changes in nuclear and genome copy number in the nematode Caenorhabditis elegans.

Golden TR, Beckman KB, Lee AH, Dudek N, Hubbard A, Samper E, Melov S.

Aging Cell. 2007 Apr;6(2):179-88. Epub 2007 Feb 5.

30.

Germ-line epigenetic modification of the murine A vy allele by nutritional supplementation.

Cropley JE, Suter CM, Beckman KB, Martin DI.

Proc Natl Acad Sci U S A. 2006 Nov 14;103(46):17308-12. Epub 2006 Nov 13.

31.

Using DNA pools for genotyping trios.

Beckman KB, Abel KJ, Braun A, Halperin E.

Nucleic Acids Res. 2006;34(19):e129. Epub 2006 Oct 4.

32.

Gene expression profiling in mitochondrial disease: assessment of microarray accuracy by high-throughput Q-PCR.

Beckman KB, Lee KY, Golden T, Melov S.

Mitochondrion. 2004 Sep;4(5-6):453-70. Epub 2004 Sep 30.

PMID:
16120406
33.

A simpler, more robust method for the analysis of 8-oxoguanine in DNA.

Beckman KB, Saljoughi S, Mashiyama ST, Ames BN.

Free Radic Biol Med. 2000 Aug;29(3-4):357-67.

PMID:
11035265
34.

Fluorescence detection of 8-oxoguanine in nuclear and mitochondrial DNA of cultured cells using a recombinant Fab and confocal scanning laser microscopy.

Soultanakis RP, Melamede RJ, Bespalov IA, Wallace SS, Beckman KB, Ames BN, Taatjes DJ, Janssen-Heininger YM.

Free Radic Biol Med. 2000 Mar 15;28(6):987-98.

PMID:
10802231
35.

Subacute necrotising encephalopathy in an Alaskan husky.

Wakshlag JJ, de Lahunta A, Robinson T, Cooper BJ, Brenner O, O'Toole TD, Olson J, Beckman KB, Glass E, Reynolds AJ.

J Small Anim Pract. 1999 Dec;40(12):585-9.

PMID:
10664957
36.

Endogenous oxidative damage of mtDNA.

Beckman KB, Ames BN.

Mutat Res. 1999 Mar 8;424(1-2):51-8. Review.

PMID:
10064849
37.

Mitochondrial aging: open questions.

Beckman KB, Ames BN.

Ann N Y Acad Sci. 1998 Nov 20;854:118-27. Review.

PMID:
9928425
38.

8-Hydroxydeoxyguanosine and 8-hydroxyguanine as biomarkers of oxidative DNA damage.

Helbock HJ, Beckman KB, Ames BN.

Methods Enzymol. 1999;300:156-66. Review. No abstract available.

PMID:
9919519
39.

The free radical theory of aging matures.

Beckman KB, Ames BN.

Physiol Rev. 1998 Apr;78(2):547-81. Review.

40.

DNA oxidation matters: the HPLC-electrochemical detection assay of 8-oxo-deoxyguanosine and 8-oxo-guanine.

Helbock HJ, Beckman KB, Shigenaga MK, Walter PB, Woodall AA, Yeo HC, Ames BN.

Proc Natl Acad Sci U S A. 1998 Jan 6;95(1):288-93.

41.

Oxidative decay of DNA.

Beckman KB, Ames BN.

J Biol Chem. 1997 Aug 8;272(32):19633-6. Review. No abstract available.

42.

Detection and quantification of oxidative adducts of mitochondrial DNA.

Beckman KB, Ames BN.

Methods Enzymol. 1996;264:442-53. No abstract available.

PMID:
8965717

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