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Results: 1 to 20 of 104

1.

Large hypomethylated blocks as a universal defining epigenetic alteration in human solid tumors.

Timp W, Bravo HC, McDonald OG, Goggins M, Umbricht C, Zeiger M, Feinberg AP, Irizarry RA.

Genome Med. 2014 Aug 26;6(8):61. doi: 10.1186/s13073-014-0061-y. eCollection 2014.

PMID:
25191524
[PubMed]
Free PMC Article
2.

KRLMM: an adaptive genotype calling method for common and low frequency variants.

Liu R, Dai Z, Yeager M, Irizarry RA, Ritchie ME.

BMC Bioinformatics. 2014 May 23;15:158. doi: 10.1186/1471-2105-15-158.

PMID:
24886250
[PubMed - in process]
Free PMC Article
3.

Visualization and probability-based scoring of structural variants within repetitive sequences.

Halper-Stromberg E, Steranka J, Burns KH, Sabunciyan S, Irizarry RA.

Bioinformatics. 2014 Jun 1;30(11):1514-21. doi: 10.1093/bioinformatics/btu054. Epub 2014 Feb 4.

PMID:
24501098
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Accounting for cellular heterogeneity is critical in epigenome-wide association studies.

Jaffe AE, Irizarry RA.

Genome Biol. 2014 Feb 4;15(2):R31. doi: 10.1186/gb-2014-15-2-r31.

PMID:
24495553
[PubMed - in process]
Free PMC Article
5.

Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays.

Aryee MJ, Jaffe AE, Corrada-Bravo H, Ladd-Acosta C, Feinberg AP, Hansen KD, Irizarry RA.

Bioinformatics. 2014 May 15;30(10):1363-9. doi: 10.1093/bioinformatics/btu049. Epub 2014 Jan 28.

PMID:
24478339
[PubMed - indexed for MEDLINE]
6.

Differential expression analysis of RNA-seq data at single-base resolution.

Frazee AC, Sabunciyan S, Hansen KD, Irizarry RA, Leek JT.

Biostatistics. 2014 Jul;15(3):413-26. doi: 10.1093/biostatistics/kxt053. Epub 2014 Jan 6.

PMID:
24398039
[PubMed - in process]
Free PMC Article
7.

The Gene Expression Barcode 3.0: improved data processing and mining tools.

McCall MN, Jaffee HA, Zelisko SJ, Sinha N, Hooiveld G, Irizarry RA, Zilliox MJ.

Nucleic Acids Res. 2014 Jan;42(Database issue):D938-43. doi: 10.1093/nar/gkt1204. Epub 2013 Nov 22.

PMID:
24271388
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Recommendations for the design and analysis of epigenome-wide association studies.

Michels KB, Binder AM, Dedeurwaerder S, Epstein CB, Greally JM, Gut I, Houseman EA, Izzi B, Kelsey KT, Meissner A, Milosavljevic A, Siegmund KD, Bock C, Irizarry RA.

Nat Methods. 2013 Oct;10(10):949-55. doi: 10.1038/nmeth.2632. Review.

PMID:
24076989
[PubMed - indexed for MEDLINE]
9.

Measuring cell-type specific differential methylation in human brain tissue.

MontaƱo CM, Irizarry RA, Kaufmann WE, Talbot K, Gur RE, Feinberg AP, Taub MA.

Genome Biol. 2013 Aug 30;14(8):R94. doi: 10.1186/gb-2013-14-8-r94.

PMID:
24000956
[PubMed - in process]
Free PMC Article
10.

ChIP-PED enhances the analysis of ChIP-seq and ChIP-chip data.

Wu G, Yustein JT, McCall MN, Zilliox M, Irizarry RA, Zeller K, Dang CV, Ji H.

Bioinformatics. 2013 May 1;29(9):1182-9. doi: 10.1093/bioinformatics/btt108. Epub 2013 Mar 1.

PMID:
23457041
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

DNA methylation alterations exhibit intraindividual stability and interindividual heterogeneity in prostate cancer metastases.

Aryee MJ, Liu W, Engelmann JC, Nuhn P, Gurel M, Haffner MC, Esopi D, Irizarry RA, Getzenberg RH, Nelson WG, Luo J, Xu J, Isaacs WB, Bova GS, Yegnasubramanian S.

Sci Transl Med. 2013 Jan 23;5(169):169ra10. doi: 10.1126/scitranslmed.3005211.

PMID:
23345608
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Improved base-calling and quality scores for 454 sequencing based on a Hurdle Poisson model.

Beuf KD, Schrijver JD, Thas O, Criekinge WV, Irizarry RA, Clement L.

BMC Bioinformatics. 2012 Nov 15;13:303. doi: 10.1186/1471-2105-13-303.

PMID:
23151247
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Gene expression anti-profiles as a basis for accurate universal cancer signatures.

Bravo HC, Pihur V, McCall M, Irizarry RA, Leek JT.

BMC Bioinformatics. 2012 Oct 22;13:272. doi: 10.1186/1471-2105-13-272.

PMID:
23088656
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

fRMA ST: frozen robust multiarray analysis for Affymetrix Exon and Gene ST arrays.

McCall MN, Jaffee HA, Irizarry RA.

Bioinformatics. 2012 Dec 1;28(23):3153-4. doi: 10.1093/bioinformatics/bts588. Epub 2012 Oct 7.

PMID:
23044545
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions.

Hansen KD, Langmead B, Irizarry RA.

Genome Biol. 2012 Oct 3;13(10):R83. doi: 10.1186/gb-2012-13-10-r83.

PMID:
23034175
[PubMed - in process]
Free PMC Article
16.

The partitioned LASSO-patternsearch algorithm with application to gene expression data.

Shi W, Wahba G, Irizarry RA, Bravo HC, Wright SJ.

BMC Bioinformatics. 2012 May 15;13:98. doi: 10.1186/1471-2105-13-98.

PMID:
22587526
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

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
18.

Genome-wide DNA methylation scan in major depressive disorder.

Sabunciyan S, Aryee MJ, Irizarry RA, Rongione M, Webster MJ, Kaufman WE, Murakami P, Lessard A, Yolken RH, Feinberg AP, Potash JB; GenRED Consortium.

PLoS One. 2012;7(4):e34451. doi: 10.1371/journal.pone.0034451. Epub 2012 Apr 12.

PMID:
22511943
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Fast wavelet based functional models for transcriptome analysis with tiling arrays.

Clement L, De Beuf K, Thas O, Vuylsteke M, Irizarry RA, Crainiceanu CM.

Stat Appl Genet Mol Biol. 2012 Jan 6;11(1):Article 4. doi: 10.2202/1544-6115.1726.

PMID:
22499683
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies.

Jaffe AE, Murakami P, Lee H, Leek JT, Fallin MD, Feinberg AP, Irizarry RA.

Int J Epidemiol. 2012 Feb;41(1):200-9. doi: 10.1093/ije/dyr238.

PMID:
22422453
[PubMed - indexed for MEDLINE]
Free PMC Article

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