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Items: 1 to 50 of 161

1.

Mesoscale model of the assembly and cross-linking of HPV virus-like particles.

Zavalov O, Irizarry R, Flamm M, Marek R.

Virology. 2019 Aug 20;537:53-64. doi: 10.1016/j.virol.2019.08.018. [Epub ahead of print]

PMID:
31450047
2.

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.

3.

Osteoradionecrosis of the sternoclavicular joint after laryngopharyngeal radiation.

Irizarry R, Shatzkes DR, Teng S, Kohli N, Har-El G.

Laryngoscope. 2019 Apr;129(4):865-870. doi: 10.1002/lary.27324. Epub 2018 Nov 19.

PMID:
30450587
4.

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.

5.

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
6.

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.

7.

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
8.

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.

9.

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.

10.

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.

11.

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.

12.

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.

13.

Minocycline plus N-acteylcysteine induces remyelination, synergistically protects oligodendrocytes and modifies neuroinflammation in a rat model of mild traumatic brain injury.

Haber M, James J, Kim J, Sangobowale M, Irizarry R, Ho J, Nikulina E, Grin'kina NM, Ramadani A, Hartman I, Bergold PJ.

J Cereb Blood Flow Metab. 2018 Aug;38(8):1312-1326. doi: 10.1177/0271678X17718106. Epub 2017 Jul 7.

14.

Challenges and emerging directions in single-cell analysis.

Yuan GC, Cai L, Elowitz M, Enver T, Fan G, Guo G, Irizarry R, Kharchenko P, Kim J, Orkin S, Quackenbush J, Saadatpour A, Schroeder T, Shivdasani R, Tirosh I.

Genome Biol. 2017 May 8;18(1):84. doi: 10.1186/s13059-017-1218-y. Review.

15.

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.

16.

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.

17.

Bisulfite-independent analysis of CpG island methylation enables genome-scale stratification of single cells.

Han L, Wu HJ, Zhu H, Kim KY, Marjani SL, Riester M, Euskirchen G, Zi X, Yang J, Han J, Snyder M, Park IH, Irizarry R, Weissman SM, Michor F, Fan R, Pan X.

Nucleic Acids Res. 2017 Jun 2;45(10):e77. doi: 10.1093/nar/gkx026.

18.

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.

19.

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.

20.

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.

21.

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.

22.

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.

23.

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.

24.

A multi-omic analysis of human naïve CD4+ T cells.

Mitchell CJ, Getnet D, Kim MS, Manda SS, Kumar P, Huang TC, Pinto SM, Nirujogi RS, Iwasaki M, Shaw PG, Wu X, Zhong J, Chaerkady R, Marimuthu A, Muthusamy B, Sahasrabuddhe NA, Raju R, Bowman C, Danilova L, Cutler J, Kelkar DS, Drake CG, Prasad TS, Marchionni L, Murakami PN, Scott AF, Shi L, Thierry-Mieg J, Thierry-Mieg D, Irizarry R, Cope L, Ishihama Y, Wang C, Gowda H, Pandey A.

BMC Syst Biol. 2015 Nov 6;9:75. doi: 10.1186/s12918-015-0225-4.

25.

A Systematic Review of Eligibility and Outcomes in Tinnitus Trials: Reassessment of Tinnitus Guideline.

Plein CT, Harounian J, Floyd E, Irizarry R, Ferzli G, Kidwai S, Rosenfeld RM.

Otolaryngol Head Neck Surg. 2016 Jan;154(1):24-32. doi: 10.1177/0194599815608160. Epub 2015 Oct 12. Review.

PMID:
26459245
26.

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.

27.

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.

28.

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.

29.

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.

30.

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.

31.

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.

32.

IVT-seq reveals extreme bias in RNA sequencing.

Lahens NF, Kavakli IH, Zhang R, Hayer K, Black MB, Dueck H, Pizarro A, Kim J, Irizarry R, Thomas RS, Grant GR, Hogenesch JB.

Genome Biol. 2014 Jun 30;15(6):R86. doi: 10.1186/gb-2014-15-6-r86.

33.

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.

34.

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.

35.

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.

36.

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.

37.

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.

38.

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.

39.

Genome-wide methylation profiling reveals Zinc finger protein 516 (ZNF516) and FK-506-binding protein 6 (FKBP6) promoters frequently methylated in cervical neoplasia, associated with HPV status and ethnicity in a Chilean population.

Brebi P, Maldonado L, Noordhuis MG, Ili C, Leal P, Garcia P, Brait M, Ribas J, Michailidi C, Perez J, Soudry E, Tapia O, Guzman P, Muñoz S, Van Neste L, Van Criekinge W, Irizarry R, Sidransky D, Roa JC, Guerrero-Preston R.

Epigenetics. 2014 Feb;9(2):308-17. doi: 10.4161/epi.27120. Epub 2013 Nov 15.

40.

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
41.

Minocycline plus N-acetylcysteine synergize to modulate inflammation and prevent cognitive and memory deficits in a rat model of mild traumatic brain injury.

Haber M, Abdel Baki SG, Grin'kina NM, Irizarry R, Ershova A, Orsi S, Grill RJ, Dash P, Bergold PJ.

Exp Neurol. 2013 Nov;249:169-77. doi: 10.1016/j.expneurol.2013.09.002. Epub 2013 Sep 10.

PMID:
24036416
42.

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.

43.

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.

44.

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.

45.

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.

46.

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.

47.

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.

48.

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.

49.

Reversible switching between epigenetic states in honeybee behavioral subcastes.

Herb BR, Wolschin F, Hansen KD, Aryee MJ, Langmead B, Irizarry R, Amdam GV, Feinberg AP.

Nat Neurosci. 2012 Oct;15(10):1371-3. doi: 10.1038/nn.3218. Epub 2012 Sep 16.

50.

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.

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