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Items: 33

1.

Multiplexed primer extension sequencing: A targeted RNA-seq method that enables high-precision quantitation of mRNA splicing isoforms and rare pre-mRNA splicing intermediates.

Gildea MA, Dwyer ZW, Pleiss JA.

Methods. 2019 May 21. pii: S1046-2023(18)30383-9. doi: 10.1016/j.ymeth.2019.05.013. [Epub ahead of print]

PMID:
31121301
2.

Detection of splice isoforms and rare intermediates using multiplexed primer extension sequencing.

Xu H, Fair BJ, Dwyer ZW, Gildea M, Pleiss JA.

Nat Methods. 2019 Jan;16(1):55-58. doi: 10.1038/s41592-018-0258-x. Epub 2018 Dec 20.

3.

Sde2 is an intron-specific pre-mRNA splicing regulator activated by ubiquitin-like processing.

Thakran P, Pandit PA, Datta S, Kolathur KK, Pleiss JA, Mishra SK.

EMBO J. 2018 Jan 4;37(1):89-101. doi: 10.15252/embj.201796751. Epub 2017 Sep 25.

4.

The conserved AU dinucleotide at the 5' end of nascent U1 snRNA is optimized for the interaction with nuclear cap-binding-complex.

Yeh CS, Chang SL, Chen JH, Wang HK, Chou YC, Wang CH, Huang SH, Larson A, Pleiss JA, Chang WH, Chang TH.

Nucleic Acids Res. 2017 Sep 19;45(16):9679-9693. doi: 10.1093/nar/gkx608.

5.

Structural toggle in the RNaseH domain of Prp8 helps balance splicing fidelity and catalytic efficiency.

Mayerle M, Raghavan M, Ledoux S, Price A, Stepankiw N, Hadjivassiliou H, Moehle EA, Mendoza SD, Pleiss JA, Guthrie C, Abelson J.

Proc Natl Acad Sci U S A. 2017 May 2;114(18):4739-4744. doi: 10.1073/pnas.1701462114. Epub 2017 Apr 17.

6.

Phospho-site mutants of the RNA Polymerase II C-terminal domain alter subtelomeric gene expression and chromatin modification state in fission yeast.

Inada M, Nichols RJ, Parsa JY, Homer CM, Benn RA, Hoxie RS, Madhani HD, Shuman S, Schwer B, Pleiss JA.

Nucleic Acids Res. 2016 Nov 2;44(19):9180-9189. Epub 2016 Jul 8.

7.

The power of fission: yeast as a tool for understanding complex splicing.

Fair BJ, Pleiss JA.

Curr Genet. 2017 Jun;63(3):375-380. doi: 10.1007/s00294-016-0647-6. Epub 2016 Sep 14. Review.

8.
9.

Mating-Induced Transcriptome Changes in the Reproductive Tract of Female Aedes aegypti.

Alfonso-Parra C, Ahmed-Braimah YH, Degner EC, Avila FW, Villarreal SM, Pleiss JA, Wolfner MF, Harrington LC.

PLoS Negl Trop Dis. 2016 Feb 22;10(2):e0004451. doi: 10.1371/journal.pntd.0004451. eCollection 2016 Feb.

10.

A Proteome-wide Fission Yeast Interactome Reveals Network Evolution Principles from Yeasts to Human.

Vo TV, Das J, Meyer MJ, Cordero NA, Akturk N, Wei X, Fair BJ, Degatano AG, Fragoza R, Liu LG, Matsuyama A, Trickey M, Horibata S, Grimson A, Yamano H, Yoshida M, Roth FP, Pleiss JA, Xia Y, Yu H.

Cell. 2016 Jan 14;164(1-2):310-323. doi: 10.1016/j.cell.2015.11.037.

11.

Mdm1/Snx13 is a novel ER-endolysosomal interorganelle tethering protein.

Henne WM, Zhu L, Balogi Z, Stefan C, Pleiss JA, Emr SD.

J Cell Biol. 2015 Aug 17;210(4):541-51. doi: 10.1083/jcb.201503088.

12.

Widespread alternative and aberrant splicing revealed by lariat sequencing.

Stepankiw N, Raghavan M, Fogarty EA, Grimson A, Pleiss JA.

Nucleic Acids Res. 2015 Sep 30;43(17):8488-501. doi: 10.1093/nar/gkv763. Epub 2015 Aug 10.

13.

Cytoplasmic polyadenylation is a major mRNA regulator during oogenesis and egg activation in Drosophila.

Cui J, Sartain CV, Pleiss JA, Wolfner MF.

Dev Biol. 2013 Nov 1;383(1):121-31. doi: 10.1016/j.ydbio.2013.08.013. Epub 2013 Aug 23.

14.

Lariat sequencing in a unicellular yeast identifies regulated alternative splicing of exons that are evolutionarily conserved with humans.

Awan AR, Manfredo A, Pleiss JA.

Proc Natl Acad Sci U S A. 2013 Jul 30;110(31):12762-7. doi: 10.1073/pnas.1218353110. Epub 2013 Jul 16.

15.

Cross-species protein interactome mapping reveals species-specific wiring of stress response pathways.

Das J, Vo TV, Wei X, Mellor JC, Tong V, Degatano AG, Wang X, Wang L, Cordero NA, Kruer-Zerhusen N, Matsuyama A, Pleiss JA, Lipkin SM, Yoshida M, Roth FP, Yu H.

Sci Signal. 2013 May 21;6(276):ra38. doi: 10.1126/scisignal.2003350.

16.

Systematic dissection of roles for chromatin regulators in a yeast stress response.

Weiner A, Chen HV, Liu CL, Rahat A, Klien A, Soares L, Gudipati M, Pfeffner J, Regev A, Buratowski S, Pleiss JA, Friedman N, Rando OJ.

PLoS Biol. 2012;10(7):e1001369. doi: 10.1371/journal.pbio.1001369. Epub 2012 Jul 31.

17.

A quantitative, high-throughput reverse genetic screen reveals novel connections between Pre-mRNA splicing and 5' and 3' end transcript determinants.

Albulescu LO, Sabet N, Gudipati M, Stepankiw N, Bergman ZJ, Huffaker TC, Pleiss JA.

PLoS Genet. 2012;8(3):e1002530. doi: 10.1371/journal.pgen.1002530. Epub 2012 Mar 29.

18.

Genome-wide approaches to monitor pre-mRNA splicing.

Inada M, Pleiss JA.

Methods Enzymol. 2010;470:51-75. doi: 10.1016/S0076-6879(10)70003-3. Epub 2010 Mar 1.

PMID:
20946806
19.

Conformational dynamics of single pre-mRNA molecules during in vitro splicing.

Abelson J, Blanco M, Ditzler MA, Fuller F, Aravamudhan P, Wood M, Villa T, Ryan DE, Pleiss JA, Maeder C, Guthrie C, Walter NG.

Nat Struct Mol Biol. 2010 Apr;17(4):504-12. doi: 10.1038/nsmb.1767. Epub 2010 Mar 21.

20.

Cwc23, an essential J protein critical for pre-mRNA splicing with a dispensable J domain.

Sahi C, Lee T, Inada M, Pleiss JA, Craig EA.

Mol Cell Biol. 2010 Jan;30(1):33-42. doi: 10.1128/MCB.00842-09.

21.

Structural evidence for consecutive Hel308-like modules in the spliceosomal ATPase Brr2.

Zhang L, Xu T, Maeder C, Bud LO, Shanks J, Nix J, Guthrie C, Pleiss JA, Zhao R.

Nat Struct Mol Biol. 2009 Jul;16(7):731-9. doi: 10.1038/nsmb.1625. Epub 2009 Jun 14.

22.

Genome-wide search for yeast RNase P substrates reveals role in maturation of intron-encoded box C/D small nucleolar RNAs.

Coughlin DJ, Pleiss JA, Walker SC, Whitworth GB, Engelke DR.

Proc Natl Acad Sci U S A. 2008 Aug 26;105(34):12218-23. doi: 10.1073/pnas.0801906105. Epub 2008 Aug 19.

23.

Rapid, transcript-specific changes in splicing in response to environmental stress.

Pleiss JA, Whitworth GB, Bergkessel M, Guthrie C.

Mol Cell. 2007 Sep 21;27(6):928-37.

24.

Transcript specificity in yeast pre-mRNA splicing revealed by mutations in core spliceosomal components.

Pleiss JA, Whitworth GB, Bergkessel M, Guthrie C.

PLoS Biol. 2007 Apr;5(4):e90.

25.

An RNA ligase-mediated method for the efficient creation of large, synthetic RNAs.

Stark MR, Pleiss JA, Deras M, Scaringe SA, Rader SD.

RNA. 2006 Nov;12(11):2014-9. Epub 2006 Sep 18.

26.

tRNA conformity.

Wolfson AD, LaRiviere FJ, Pleiss JA, Dale T, Asahara H, Uhlenbeck OC.

Cold Spring Harb Symp Quant Biol. 2001;66:185-93. Review. No abstract available.

PMID:
12762021
27.

Spliceosomal snRNAs: Mg(2+)-dependent chemistry at the catalytic core?

Villa T, Pleiss JA, Guthrie C.

Cell. 2002 Apr 19;109(2):149-52. Review.

28.

Identification of thermodynamically relevant interactions between EF-Tu and backbone elements of tRNA.

Pleiss JA, Uhlenbeck OC.

J Mol Biol. 2001 May 18;308(5):895-905.

PMID:
11352580
29.

Mapping contacts between Escherichia coli alanyl tRNA synthetase and 2' hydroxyls using a complete tRNA molecule.

Pleiss JA, Wolfson AD, Uhlenbeck OC.

Biochemistry. 2000 Jul 18;39(28):8250-8.

PMID:
10889033
30.

Intact aminoacyl-tRNA is required to trigger GTP hydrolysis by elongation factor Tu on the ribosome.

Piepenburg O, Pape T, Pleiss JA, Wintermeyer W, Uhlenbeck OC, Rodnina MV.

Biochemistry. 2000 Feb 22;39(7):1734-8.

PMID:
10677222
31.
32.

A new assay for tRNA aminoacylation kinetics.

Wolfson AD, Pleiss JA, Uhlenbeck OC.

RNA. 1998 Aug;4(8):1019-23.

33.

The treatment of bacterial endocarditis.

PLEISS JA.

Nebr State Med J. 1950 May;35(5):149-51. No abstract available.

PMID:
15412670

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