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Items: 1 to 50 of 125

1.

Mortality in Puerto Rico after Hurricane Maria.

Kishore N, Marqués D, Mahmud A, Kiang MV, Rodriguez I, Fuller A, Ebner P, Sorensen C, Racy F, Lemery J, Maas L, Leaning J, Irizarry RA, Balsari S, Buckee CO.

N Engl J Med. 2018 Jul 12;379(2):162-170. doi: 10.1056/NEJMsa1803972. Epub 2018 May 29.

2.

Detection and accurate false discovery rate control of differentially methylated regions from whole genome bisulfite sequencing.

Korthauer K, Chakraborty S, Benjamini Y, Irizarry RA.

Biostatistics. 2018 Feb 22. doi: 10.1093/biostatistics/kxy007. [Epub ahead of print]

PMID:
29481604
3.

High-throughput identification of RNA nuclear enrichment sequences.

Shukla CJ, McCorkindale AL, Gerhardinger C, Korthauer KD, Cabili MN, Shechner DM, Irizarry RA, Maass PG, Rinn JL.

EMBO J. 2018 Mar 15;37(6). pii: e98452. doi: 10.15252/embj.201798452. Epub 2018 Jan 15.

4.

Meta-analysis of gut microbiome studies identifies disease-specific and shared responses.

Duvallet C, Gibbons SM, Gurry T, Irizarry RA, Alm EJ.

Nat Commun. 2017 Dec 5;8(1):1784. doi: 10.1038/s41467-017-01973-8.

5.

Missing data and technical variability in single-cell RNA-sequencing experiments.

Hicks SC, Townes FW, Teng M, Irizarry RA.

Biostatistics. 2017 Nov 6. doi: 10.1093/biostatistics/kxx053. [Epub ahead of print]

PMID:
29121214
6.

Smooth quantile normalization.

Hicks SC, Okrah K, Paulson JN, Quackenbush J, Irizarry RA, Bravo HC.

Biostatistics. 2018 Apr 1;19(2):185-198. doi: 10.1093/biostatistics/kxx028.

PMID:
29036413
7.

Accounting for GC-content bias reduces systematic errors and batch effects in ChIP-seq data.

Teng M, Irizarry RA.

Genome Res. 2017 Nov;27(11):1930-1938. doi: 10.1101/gr.220673.117. Epub 2017 Oct 12.

8.

SMARCB1 is required for widespread BAF complex-mediated activation of enhancers and bivalent promoters.

Nakayama RT, Pulice JL, Valencia AM, McBride MJ, McKenzie ZM, Gillespie MA, Ku WL, Teng M, Cui K, Williams RT, Cassel SH, Qing H, Widmer CJ, Demetri GD, Irizarry RA, Zhao K, Ranish JA, Kadoch C.

Nat Genet. 2017 Nov;49(11):1613-1623. doi: 10.1038/ng.3958. Epub 2017 Sep 25.

9.

Salmon provides fast and bias-aware quantification of transcript expression.

Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C.

Nat Methods. 2017 Apr;14(4):417-419. doi: 10.1038/nmeth.4197. Epub 2017 Mar 6.

10.

Correcting for cell-type heterogeneity in epigenome-wide association studies: revisiting previous analyses.

Zheng SC, Beck S, Jaffe AE, Koestler DC, Hansen KD, Houseman AE, Irizarry RA, Teschendorff AE.

Nat Methods. 2017 Feb 28;14(3):216-217. doi: 10.1038/nmeth.4187. No abstract available.

PMID:
28245219
11.

Proceedings of the third international molecular pathological epidemiology (MPE) meeting.

Campbell PT, Rebbeck TR, Nishihara R, Beck AH, Begg CB, Bogdanov AA, Cao Y, Coleman HG, Freeman GJ, Heng YJ, Huttenhower C, Irizarry RA, Kip NS, Michor F, Nevo D, Peters U, Phipps AI, Poole EM, Qian ZR, Quackenbush J, Robins H, Rogan PK, Slattery ML, Smith-Warner SA, Song M, VanderWeele TJ, Xia D, Zabor EC, Zhang X, Wang M, Ogino S.

Cancer Causes Control. 2017 Feb;28(2):167-176. doi: 10.1007/s10552-016-0845-z. Epub 2017 Jan 17. Review.

12.

Modeling of RNA-seq fragment sequence bias reduces systematic errors in transcript abundance estimation.

Love MI, Hogenesch JB, Irizarry RA.

Nat Biotechnol. 2016 Dec;34(12):1287-1291. doi: 10.1038/nbt.3682. Epub 2016 Sep 26.

13.

Erratum to: A benchmark for RNA-seq quantification pipelines.

Teng M, Love MI, Davis CA, Djebali S, Dobin A, Graveley BR, Li S, Mason CE, Olson S, Pervouchine D, Sloan CA, Wei X, Zhan L, Irizarry RA.

Genome Biol. 2016 Sep 30;17(1):203. No abstract available.

14.

Flexible expressed region analysis for RNA-seq with derfinder.

Collado-Torres L, Nellore A, Frazee AC, Wilks C, Love MI, Langmead B, Irizarry RA, Leek JT, Jaffe AE.

Nucleic Acids Res. 2017 Jan 25;45(2):e9. doi: 10.1093/nar/gkw852. Epub 2016 Sep 29.

15.

Erratum to: A benchmark for RNA-seq quantification pipelines.

Teng M, Love MI, Davis CA, Djebali S, Dobin A, Graveley BR, Li S, Mason CE, Olson S, Pervouchine D, Sloan CA, Wei X, Zhan L, Irizarry RA.

Genome Biol. 2016 May 23;17(1):107. No abstract available.

16.

A benchmark for RNA-seq quantification pipelines.

Teng M, Love MI, Davis CA, Djebali S, Dobin A, Graveley BR, Li S, Mason CE, Olson S, Pervouchine D, Sloan CA, Wei X, Zhan L, Irizarry RA.

Genome Biol. 2016 Apr 23;17:74. doi: 10.1186/s13059-016-0940-1. Erratum in: Genome Biol. 2016;17(1):107. Genome Biol. 2016 Sep 30;17 (1):203.

17.

quantro: a data-driven approach to guide the choice of an appropriate normalization method.

Hicks SC, Irizarry RA.

Genome Biol. 2015 Jun 4;16:117. doi: 10.1186/s13059-015-0679-0.

18.

Proceedings of the second international molecular pathological epidemiology (MPE) meeting.

Ogino S, Campbell PT, Nishihara R, Phipps AI, Beck AH, Sherman ME, Chan AT, Troester MA, Bass AJ, Fitzgerald KC, Irizarry RA, Kelsey KT, Nan H, Peters U, Poole EM, Qian ZR, Tamimi RM, Tchetgen Tchetgen EJ, Tworoger SS, Zhang X, Giovannucci EL, van den Brandt PA, Rosner BA, Wang M, Chatterjee N, Begg CB.

Cancer Causes Control. 2015 Jul;26(7):959-72. doi: 10.1007/s10552-015-0596-2. Epub 2015 May 9.

19.

Age and sun exposure-related widespread genomic blocks of hypomethylation in nonmalignant skin.

Vandiver AR, Irizarry RA, Hansen KD, Garza LA, Runarsson A, Li X, Chien AL, Wang TS, Leung SG, Kang S, Feinberg AP.

Genome Biol. 2015 Apr 16;16:80. doi: 10.1186/s13059-015-0644-y.

20.

Orchestrating high-throughput genomic analysis with Bioconductor.

Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M.

Nat Methods. 2015 Feb;12(2):115-21. doi: 10.1038/nmeth.3252. Review.

21.

MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens.

Li W, Xu H, Xiao T, Cong L, Love MI, Zhang F, Irizarry RA, Liu JS, Brown M, Liu XS.

Genome Biol. 2014;15(12):554.

22.

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.

23.

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.

24.

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.

25.

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.

26.

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.

27.

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. Erratum in: Biostatistics. 2014 Jul;15(3):584-5.

28.

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.

29.

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
30.

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

Montaño 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.

31.

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.

32.

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.

33.

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.

34.

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.

35.

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.

36.

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.

37.

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.

38.

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.

39.

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.

40.

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.

41.

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.

42.

DNA methylation shows genome-wide association of NFIX, RAPGEF2 and MSRB3 with gestational age at birth.

Lee H, Jaffe AE, Feinberg JI, Tryggvadottir R, Brown S, Montano C, Aryee MJ, Irizarry RA, Herbstman J, Witter FR, Goldman LR, Feinberg AP, Fallin MD.

Int J Epidemiol. 2012 Feb;41(1):188-99. doi: 10.1093/ije/dyr237.

43.

Removing technical variability in RNA-seq data using conditional quantile normalization.

Hansen KD, Irizarry RA, Wu Z.

Biostatistics. 2012 Apr;13(2):204-16. doi: 10.1093/biostatistics/kxr054. Epub 2012 Jan 27.

44.

Thawing Frozen Robust Multi-array Analysis (fRMA).

McCall MN, Irizarry RA.

BMC Bioinformatics. 2011 Sep 16;12:369. doi: 10.1186/1471-2105-12-369.

45.

Sequencing technology does not eliminate biological variability.

Hansen KD, Wu Z, Irizarry RA, Leek JT.

Nat Biotechnol. 2011 Jul 11;29(7):572-3. doi: 10.1038/nbt.1910. No abstract available.

46.

Increased methylation variation in epigenetic domains across cancer types.

Hansen KD, Timp W, Bravo HC, Sabunciyan S, Langmead B, McDonald OG, Wen B, Wu H, Liu Y, Diep D, Briem E, Zhang K, Irizarry RA, Feinberg AP.

Nat Genet. 2011 Jun 26;43(8):768-75. doi: 10.1038/ng.865.

47.

Significance analysis and statistical dissection of variably methylated regions.

Jaffe AE, Feinberg AP, Irizarry RA, Leek JT.

Biostatistics. 2012 Jan;13(1):166-78. doi: 10.1093/biostatistics/kxr013. Epub 2011 Jun 17.

48.

Chromosome-wide mapping of DNA methylation patterns in normal and malignant prostate cells reveals pervasive methylation of gene-associated and conserved intergenic sequences.

Yegnasubramanian S, Wu Z, Haffner MC, Esopi D, Aryee MJ, Badrinath R, He TL, Morgan JD, Carvalho B, Zheng Q, De Marzo AM, Irizarry RA, Nelson WG.

BMC Genomics. 2011 Jun 13;12:313. doi: 10.1186/1471-2164-12-313.

49.

NID2 and HOXA9 promoter hypermethylation as biomarkers for prevention and early detection in oral cavity squamous cell carcinoma tissues and saliva.

Guerrero-Preston R, Soudry E, Acero J, Orera M, Moreno-López L, Macía-Colón G, Jaffe A, Berdasco M, Ili-Gangas C, Brebi-Mieville P, Fu Y, Engstrom C, Irizarry RA, Esteller M, Westra W, Koch W, Califano J, Sidransky D.

Cancer Prev Res (Phila). 2011 Jul;4(7):1061-72. doi: 10.1158/1940-6207.CAPR-11-0006. Epub 2011 May 10.

50.

Assessing affymetrix GeneChip microarray quality.

McCall MN, Murakami PN, Lukk M, Huber W, Irizarry RA.

BMC Bioinformatics. 2011 May 7;12:137. doi: 10.1186/1471-2105-12-137.

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