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Results: 1 to 20 of 26

1.

Detecting disease variants in case-parent trio studies using the bioconductor software package trio.

Schwender H, Li Q, Neumann C, Taub MA, Younkin SG, Berger P, Scharpf RB, Beaty TH, Ruczinski I.

Genet Epidemiol. 2014 Sep;38(6):516-22. doi: 10.1002/gepi.21836. Epub 2014 Jul 21.

PMID:
25048299
[PubMed - indexed for MEDLINE]
2.

Copy number polymorphisms near SLC2A9 are associated with serum uric acid concentrations.

Scharpf RB, Mireles L, Yang Q, Köttgen A, Ruczinski I, Susztak K, Halper-Stromberg E, Tin A, Cristiano S, Chakravarti A, Boerwinkle E, Fox CS, Coresh J, Linda Kao WH.

BMC Genet. 2014 Jul 9;15:81. doi: 10.1186/1471-2156-15-81.

PMID:
25007794
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Characterization of the genomic architecture and mutational spectrum of a small cell prostate carcinoma.

Scott AF, Mohr DW, Ling H, Scharpf RB, Zhang P, Liptak GS.

Genes (Basel). 2014 May 12;5(2):366-84. doi: 10.3390/genes5020366.

PMID:
24823478
[PubMed]
Free PMC Article
4.

A genome-wide study of de novo deletions identifies a candidate locus for non-syndromic isolated cleft lip/palate risk.

Younkin SG, Scharpf RB, Schwender H, Parker MM, Scott AF, Marazita ML, Beaty TH, Ruczinski I.

BMC Genet. 2014 Feb 14;15:24. doi: 10.1186/1471-2156-15-24.

PMID:
24528994
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Fast detection of de novo copy number variants from SNP arrays for case-parent trios.

Scharpf RB, Beaty TH, Schwender H, Younkin SG, Scott AF, Ruczinski I.

BMC Bioinformatics. 2012 Dec 12;13:330. doi: 10.1186/1471-2105-13-330.

PMID:
23234608
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Detectable clonal mosaicism from birth to old age and its relationship to cancer.

Laurie CC, Laurie CA, Rice K, Doheny KF, Zelnick LR, McHugh CP, Ling H, Hetrick KN, Pugh EW, Amos C, Wei Q, Wang LE, Lee JE, Barnes KC, Hansel NN, Mathias R, Daley D, Beaty TH, Scott AF, Ruczinski I, Scharpf RB, Bierut LJ, Hartz SM, Landi MT, Freedman ND, Goldin LR, Ginsburg D, Li J, Desch KC, Strom SS, Blot WJ, Signorello LB, Ingles SA, Chanock SJ, Berndt SI, Le Marchand L, Henderson BE, Monroe KR, Heit JA, de Andrade M, Armasu SM, Regnier C, Lowe WL, Hayes MG, Marazita ML, Feingold E, Murray JC, Melbye M, Feenstra B, Kang JH, Wiggs JL, Jarvik GP, McDavid AN, Seshan VE, Mirel DB, Crenshaw A, Sharopova N, Wise A, Shen J, Crosslin DR, Levine DM, Zheng X, Udren JI, Bennett S, Nelson SC, Gogarten SM, Conomos MP, Heagerty P, Manolio T, Pasquale LR, Haiman CA, Caporaso N, Weir BS.

Nat Genet. 2012 May 6;44(6):642-50. doi: 10.1038/ng.2271.

PMID:
22561516
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Using the R Package crlmm for Genotyping and Copy Number Estimation.

Scharpf RB, Irizarry RA, Ritchie ME, Carvalho B, Ruczinski I.

J Stat Softw. 2011 May 1;40(12):1-32.

PMID:
22523482
[PubMed]
Free PMC Article
8.

Cross-platform Comparison of Two Pancreatic Cancer Phenotypes.

Scharpf RB, Iacobuzio-Donahue CA, Cope L, Ruczinski I, Garrett-Mayer E, Lakkur S, Campagna D, Parmigiani G.

Cancer Inform. 2010 Nov 1;9:257-64. doi: 10.4137/CIN.S5755.

PMID:
21082040
[PubMed]
Free PMC Article
9.

Tackling the widespread and critical impact of batch effects in high-throughput data.

Leek JT, Scharpf RB, Bravo HC, Simcha D, Langmead B, Johnson WE, Geman D, Baggerly K, Irizarry RA.

Nat Rev Genet. 2010 Oct;11(10):733-9. doi: 10.1038/nrg2825. Epub 2010 Sep 14.

PMID:
20838408
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

A multilevel model to address batch effects in copy number estimation using SNP arrays.

Scharpf RB, Ruczinski I, Carvalho B, Doan B, Chakravarti A, Irizarry RA.

Biostatistics. 2011 Jan;12(1):33-50. doi: 10.1093/biostatistics/kxq043. Epub 2010 Jul 12.

PMID:
20625178
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

R classes and methods for SNP array data.

Scharpf RB, Ruczinski I.

Methods Mol Biol. 2010;593:67-79. doi: 10.1007/978-1-60327-194-3_4.

PMID:
19957145
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Rejoinder.

Scharpf RB, Tjelmeland H, Parmigiani G, Nobel AB.

J Am Stat Assoc. 2009 Dec;104(488):1318-1323. No abstract available.

PMID:
21904418
[PubMed]
Free PMC Article
13.

Hidden Markov models for the assessment of chromosomal alterations using high-throughput SNP arrays.

Scharpf RB, Parmigiani G, Pevsner J, Ruczinski I.

Ann Appl Stat. 2008 Jun 1;2(2):687-713.

PMID:
19609370
[PubMed]
Free PMC Article
14.

Multiple loci associated with indices of renal function and chronic kidney disease.

Köttgen A, Glazer NL, Dehghan A, Hwang SJ, Katz R, Li M, Yang Q, Gudnason V, Launer LJ, Harris TB, Smith AV, Arking DE, Astor BC, Boerwinkle E, Ehret GB, Ruczinski I, Scharpf RB, Chen YD, de Boer IH, Haritunians T, Lumley T, Sarnak M, Siscovick D, Benjamin EJ, Levy D, Upadhyay A, Aulchenko YS, Hofman A, Rivadeneira F, Uitterlinden AG, van Duijn CM, Chasman DI, Paré G, Ridker PM, Kao WH, Witteman JC, Coresh J, Shlipak MG, Fox CS.

Nat Genet. 2009 Jun;41(6):712-7. doi: 10.1038/ng.377. Epub 2009 May 10.

PMID:
19430482
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Genome-wide association study of blood pressure and hypertension.

Levy D, Ehret GB, Rice K, Verwoert GC, Launer LJ, Dehghan A, Glazer NL, Morrison AC, Johnson AD, Aspelund T, Aulchenko Y, Lumley T, Köttgen A, Vasan RS, Rivadeneira F, Eiriksdottir G, Guo X, Arking DE, Mitchell GF, Mattace-Raso FU, Smith AV, Taylor K, Scharpf RB, Hwang SJ, Sijbrands EJ, Bis J, Harris TB, Ganesh SK, O'Donnell CJ, Hofman A, Rotter JI, Coresh J, Benjamin EJ, Uitterlinden AG, Heiss G, Fox CS, Witteman JC, Boerwinkle E, Wang TJ, Gudnason V, Larson MG, Chakravarti A, Psaty BM, van Duijn CM.

Nat Genet. 2009 Jun;41(6):677-87. doi: 10.1038/ng.384. Epub 2009 May 10.

PMID:
19430479
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

A Bayesian model for cross-study differential gene expression.

Scharpf RB, Tjelmeland H, Parmigiani G, Nobel AB.

J Am Stat Assoc. 2009;104(488):1295-1310.

PMID:
21127725
[PubMed]
Free PMC Article
17.

Likelihood estimation of conjugacy relationships in linear models with applications to high-throughput genomics.

Caffo BS, Liu D, Scharpf RB, Parmigiani G.

Int J Biostat. 2009 May 29;5(1):Article 18. doi: 10.2202/1557-4679.1129.

PMID:
20224629
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Pre-processing Agilent microarray data.

Zahurak M, Parmigiani G, Yu W, Scharpf RB, Berman D, Schaeffer E, Shabbeer S, Cope L.

BMC Bioinformatics. 2007 May 1;8:142.

PMID:
17472750
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

SNPchip: R classes and methods for SNP array data.

Scharpf RB, Ting JC, Pevsner J, Ruczinski I.

Bioinformatics. 2007 Mar 1;23(5):627-8. Epub 2007 Jan 4.

PMID:
17204461
[PubMed - indexed for MEDLINE]
Free Article
20.

When should one subtract background fluorescence in 2-color microarrays?

Scharpf RB, Iacobuzio-Donahue CA, Sneddon JB, Parmigiani G.

Biostatistics. 2007 Oct;8(4):695-707. Epub 2006 Dec 12.

PMID:
17164465
[PubMed - indexed for MEDLINE]
Free Article
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