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Items: 1 to 20 of 127

1.

A gene expression atlas of embryonic neurogenesis in Drosophila reveals complex spatiotemporal regulation of lncRNAs.

McCorkindale AL, Wahle P, Werner S, Jungreis I, Menzel P, Shukla CJ, Abreu RLP, Irizarry RA, Meyer IM, Kellis M, Zinzen RP.

Development. 2019 Mar 28;146(6). pii: dev175265. doi: 10.1242/dev.175265.

2.

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.

3.

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. 2019 Jul 1;20(3):367-383. doi: 10.1093/biostatistics/kxy007.

PMID:
29481604
4.

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.

5.

A Guide to Teaching Data Science.

Hicks SC, Irizarry RA.

Am Stat. 2018;72(4):382-391. doi: 10.1080/00031305.2017.1356747. Epub 2018 Nov 14.

PMID:
31105314
6.

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.

7.

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

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

Biostatistics. 2018 Oct 1;19(4):562-578. doi: 10.1093/biostatistics/kxx053.

PMID:
29121214
8.

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.

9.

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.

10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

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

16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

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