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Items: 1 to 20 of 29

1.

Environmental influences on RNA processing: Biochemical, molecular and genetic regulators of cellular response.

Pai AA, Luca F.

Wiley Interdiscip Rev RNA. 2019 Jan;10(1):e1503. doi: 10.1002/wrna.1503. Epub 2018 Sep 14. Review.

PMID:
30216698
2.

Nuclear Localization of Huntingtin mRNA Is Specific to Cells of Neuronal Origin.

Didiot MC, Ferguson CM, Ly S, Coles AH, Smith AO, Bicknell AA, Hall LM, Sapp E, Echeverria D, Pai AA, DiFiglia M, Moore MJ, Hayward LJ, Aronin N, Khvorova A.

Cell Rep. 2018 Sep 4;24(10):2553-2560.e5. doi: 10.1016/j.celrep.2018.07.106.

3.

Numerous recursive sites contribute to accuracy of splicing in long introns in flies.

Pai AA, Paggi JM, Yan P, Adelman K, Burge CB.

PLoS Genet. 2018 Aug 27;14(8):e1007588. doi: 10.1371/journal.pgen.1007588. eCollection 2018 Aug.

4.

Bayesian nonparametric discovery of isoforms and individual specific quantification.

Aguiar D, Cheng LF, Dumitrascu B, Mordelet F, Pai AA, Engelhardt BE.

Nat Commun. 2018 Apr 27;9(1):1681. doi: 10.1038/s41467-018-03402-w.

5.

The kinetics of pre-mRNA splicing in the Drosophila genome and the influence of gene architecture.

Pai AA, Henriques T, McCue K, Burkholder A, Adelman K, Burge CB.

Elife. 2017 Dec 27;6. pii: e32537. doi: 10.7554/eLife.32537.

6.

Environmental perturbations lead to extensive directional shifts in RNA processing.

Richards AL, Watza D, Findley A, Alazizi A, Wen X, Pai AA, Pique-Regi R, Luca F.

PLoS Genet. 2017 Oct 12;13(10):e1006995. doi: 10.1371/journal.pgen.1006995. eCollection 2017 Oct.

7.

Widespread Shortening of 3' Untranslated Regions and Increased Exon Inclusion Are Evolutionarily Conserved Features of Innate Immune Responses to Infection.

Pai AA, Baharian G, Pagé Sabourin A, Brinkworth JF, Nédélec Y, Foley JW, Grenier JC, Siddle KJ, Dumaine A, Yotova V, Johnson ZP, Lanford RE, Burge CB, Barreiro LB.

PLoS Genet. 2016 Sep 30;12(9):e1006338. doi: 10.1371/journal.pgen.1006338. eCollection 2016 Sep.

8.

Principles for RNA metabolism and alternative transcription initiation within closely spaced promoters.

Chen Y, Pai AA, Herudek J, Lubas M, Meola N, Järvelin AI, Andersson R, Pelechano V, Steinmetz LM, Jensen TH, Sandelin A.

Nat Genet. 2016 Sep;48(9):984-94. doi: 10.1038/ng.3616. Epub 2016 Jul 25.

9.

Bacterial infection remodels the DNA methylation landscape of human dendritic cells.

Pacis A, Tailleux L, Morin AM, Lambourne J, MacIsaac JL, Yotova V, Dumaine A, Danckaert A, Luca F, Grenier JC, Hansen KD, Gicquel B, Yu M, Pai A, He C, Tung J, Pastinen T, Kobor MS, Pique-Regi R, Gilad Y, Barreiro LB.

Genome Res. 2015 Dec;25(12):1801-11. doi: 10.1101/gr.192005.115. Epub 2015 Sep 21.

10.

The genetic and mechanistic basis for variation in gene regulation.

Pai AA, Pritchard JK, Gilad Y.

PLoS Genet. 2015 Jan 8;11(1):e1004857. doi: 10.1371/journal.pgen.1004857. eCollection 2015 Jan.

11.

Comparative studies of gene regulatory mechanisms.

Pai AA, Gilad Y.

Curr Opin Genet Dev. 2014 Dec;29:68-74. doi: 10.1016/j.gde.2014.08.010. Epub 2014 Sep 16. Review.

12.

RNA-seq: impact of RNA degradation on transcript quantification.

Gallego Romero I, Pai AA, Tung J, Gilad Y.

BMC Biol. 2014 May 30;12:42. doi: 10.1186/1741-7007-12-42.

13.

Controls of nucleosome positioning in the human genome.

Gaffney DJ, McVicker G, Pai AA, Fondufe-Mittendorf YN, Lewellen N, Michelini K, Widom J, Gilad Y, Pritchard JK.

PLoS Genet. 2012;8(11):e1003036. doi: 10.1371/journal.pgen.1003036. Epub 2012 Nov 15.

14.

The contribution of RNA decay quantitative trait loci to inter-individual variation in steady-state gene expression levels.

Pai AA, Cain CE, Mizrahi-Man O, De Leon S, Lewellen N, Veyrieras JB, Degner JF, Gaffney DJ, Pickrell JK, Stephens M, Pritchard JK, Gilad Y.

PLoS Genet. 2012;8(10):e1003000. doi: 10.1371/journal.pgen.1003000. Epub 2012 Oct 11.

15.

Regulatory element copy number differences shape primate expression profiles.

Iskow RC, Gokcumen O, Abyzov A, Malukiewicz J, Zhu Q, Sukumar AT, Pai AA, Mills RE, Habegger L, Cusanovich DA, Rubel MA, Perry GH, Gerstein M, Stone AC, Gilad Y, Lee C.

Proc Natl Acad Sci U S A. 2012 Jul 31;109(31):12656-61. doi: 10.1073/pnas.1205199109. Epub 2012 Jul 13.

16.

DNase I sensitivity QTLs are a major determinant of human expression variation.

Degner JF, Pai AA, Pique-Regi R, Veyrieras JB, Gaffney DJ, Pickrell JK, De Leon S, Michelini K, Lewellen N, Crawford GE, Stephens M, Gilad Y, Pritchard JK.

Nature. 2012 Feb 5;482(7385):390-4. doi: 10.1038/nature10808.

17.

Dissecting the regulatory architecture of gene expression QTLs.

Gaffney DJ, Veyrieras JB, Degner JF, Pique-Regi R, Pai AA, Crawford GE, Stephens M, Gilad Y, Pritchard JK.

Genome Biol. 2012 Jan 31;13(1):R7. doi: 10.1186/gb-2012-13-1-r7.

18.

The combination of a genome-wide association study of lymphocyte count and analysis of gene expression data reveals novel asthma candidate genes.

Cusanovich DA, Billstrand C, Zhou X, Chavarria C, De Leon S, Michelini K, Pai AA, Ober C, Gilad Y.

Hum Mol Genet. 2012 May 1;21(9):2111-23. doi: 10.1093/hmg/dds021. Epub 2012 Jan 27.

19.

Deciphering the genetic architecture of variation in the immune response to Mycobacterium tuberculosis infection.

Barreiro LB, Tailleux L, Pai AA, Gicquel B, Marioni JC, Gilad Y.

Proc Natl Acad Sci U S A. 2012 Jan 24;109(4):1204-9. doi: 10.1073/pnas.1115761109. Epub 2012 Jan 10.

20.

A genome-wide study of DNA methylation patterns and gene expression levels in multiple human and chimpanzee tissues.

Pai AA, Bell JT, Marioni JC, Pritchard JK, Gilad Y.

PLoS Genet. 2011 Feb;7(2):e1001316. doi: 10.1371/journal.pgen.1001316. Epub 2011 Feb 24.

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