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Items: 1 to 50 of 127

1.

Functional classification of long non-coding RNAs by k-mer content.

Kirk JM, Kim SO, Inoue K, Smola MJ, Lee DM, Schertzer MD, Wooten JS, Baker AR, Sprague D, Collins DW, Horning CR, Wang S, Chen Q, Weeks KM, Mucha PJ, Calabrese JM.

Nat Genet. 2018 Oct;50(10):1474-1482. doi: 10.1038/s41588-018-0207-8. Epub 2018 Sep 17.

PMID:
30224646
2.

Principles for targeting RNA with drug-like small molecules.

Warner KD, Hajdin CE, Weeks KM.

Nat Rev Drug Discov. 2018 Aug;17(8):547-558. doi: 10.1038/nrd.2018.93. Epub 2018 Jul 6. Review.

PMID:
29977051
3.

Messenger RNA Structure Regulates Translation Initiation: A Mechanism Exploited from Bacteria to Humans.

Mustoe AM, Corley M, Laederach A, Weeks KM.

Biochemistry. 2018 Jul 3;57(26):3537-3539. doi: 10.1021/acs.biochem.8b00395. Epub 2018 Jun 12. No abstract available.

PMID:
29894169
4.

In-cell RNA structure probing with SHAPE-MaP.

Smola MJ, Weeks KM.

Nat Protoc. 2018 Jun;13(6):1181-1195. doi: 10.1038/nprot.2018.010. Epub 2018 May 3.

PMID:
29725122
5.

mRNA structure determines specificity of a polyQ-driven phase separation.

Langdon EM, Qiu Y, Ghanbari Niaki A, McLaughlin GA, Weidmann CA, Gerbich TM, Smith JA, Crutchley JM, Termini CM, Weeks KM, Myong S, Gladfelter AS.

Science. 2018 May 25;360(6391):922-927. doi: 10.1126/science.aar7432. Epub 2018 Apr 12.

PMID:
29650703
6.

Pervasive Regulatory Functions of mRNA Structure Revealed by High-Resolution SHAPE Probing.

Mustoe AM, Busan S, Rice GM, Hajdin CE, Peterson BK, Ruda VM, Kubica N, Nutiu R, Baryza JL, Weeks KM.

Cell. 2018 Mar 22;173(1):181-195.e18. doi: 10.1016/j.cell.2018.02.034. Epub 2018 Mar 15.

PMID:
29551268
7.

Structure modeling of RNA using sparse NMR constraints.

Williams B 2nd, Zhao B, Tandon A, Ding F, Weeks KM, Zhang Q, Dokholyan NV.

Nucleic Acids Res. 2017 Dec 15;45(22):12638-12647. doi: 10.1093/nar/gkx1058.

8.

The roles of five conserved lentiviral RNA structures in HIV-1 replication.

Liu Y, Chen J, Nikolaitchik OA, Desimmie BA, Busan S, Pathak VK, Weeks KM, Hu WS.

Virology. 2018 Jan 15;514:1-8. doi: 10.1016/j.virol.2017.10.020. Epub 2017 Nov 9.

PMID:
29128752
9.

Accurate detection of chemical modifications in RNA by mutational profiling (MaP) with ShapeMapper 2.

Busan S, Weeks KM.

RNA. 2018 Feb;24(2):143-148. doi: 10.1261/rna.061945.117. Epub 2017 Nov 7.

PMID:
29114018
10.

An RNA structure-mediated, posttranscriptional model of human α-1-antitrypsin expression.

Corley M, Solem A, Phillips G, Lackey L, Ziehr B, Vincent HA, Mustoe AM, Ramos SBV, Weeks KM, Moorman NJ, Laederach A.

Proc Natl Acad Sci U S A. 2017 Nov 21;114(47):E10244-E10253. doi: 10.1073/pnas.1706539114. Epub 2017 Nov 6.

11.

Visualization of RNA structure models within the Integrative Genomics Viewer.

Busan S, Weeks KM.

RNA. 2017 Jul;23(7):1012-1018. doi: 10.1261/rna.060194.116. Epub 2017 Apr 20.

12.

Packaged and Free Satellite Tobacco Mosaic Virus (STMV) RNA Genomes Adopt Distinct Conformational States.

Larman BC, Dethoff EA, Weeks KM.

Biochemistry. 2017 Apr 25;56(16):2175-2183. doi: 10.1021/acs.biochem.6b01166. Epub 2017 Apr 16.

13.

RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme.

Miao Z, Adamiak RW, Antczak M, Batey RT, Becka AJ, Biesiada M, Boniecki MJ, Bujnicki JM, Chen SJ, Cheng CY, Chou FC, Ferré-D'Amaré AR, Das R, Dawson WK, Ding F, Dokholyan NV, Dunin-Horkawicz S, Geniesse C, Kappel K, Kladwang W, Krokhotin A, Łach GE, Major F, Mann TH, Magnus M, Pachulska-Wieczorek K, Patel DJ, Piccirilli JA, Popenda M, Purzycka KJ, Ren A, Rice GM, Santalucia J Jr, Sarzynska J, Szachniuk M, Tandon A, Trausch JJ, Tian S, Wang J, Weeks KM, Williams B 2nd, Xiao Y, Xu X, Zhang D, Zok T, Westhof E.

RNA. 2017 May;23(5):655-672. doi: 10.1261/rna.060368.116. Epub 2017 Jan 30.

14.

Direct identification of base-paired RNA nucleotides by correlated chemical probing.

Krokhotin A, Mustoe AM, Weeks KM, Dokholyan NV.

RNA. 2017 Jan;23(1):6-13. Epub 2016 Nov 1.

15.

SHAPE reveals transcript-wide interactions, complex structural domains, and protein interactions across the Xist lncRNA in living cells.

Smola MJ, Christy TW, Inoue K, Nicholson CO, Friedersdorf M, Keene JD, Lee DM, Calabrese JM, Weeks KM.

Proc Natl Acad Sci U S A. 2016 Sep 13;113(37):10322-7. doi: 10.1073/pnas.1600008113. Epub 2016 Aug 30.

16.

Direct Duplex Detection: An Emerging Tool in the RNA Structure Analysis Toolbox.

Weidmann CA, Mustoe AM, Weeks KM.

Trends Biochem Sci. 2016 Sep;41(9):734-736. doi: 10.1016/j.tibs.2016.07.001. Epub 2016 Jul 14.

17.

Detection of RNA-Protein Interactions in Living Cells with SHAPE.

Smola MJ, Calabrese JM, Weeks KM.

Biochemistry. 2015 Nov 24;54(46):6867-75. doi: 10.1021/acs.biochem.5b00977. Epub 2015 Nov 11.

18.

IFNL3 mRNA structure is remodeled by a functional non-coding polymorphism associated with hepatitis C virus clearance.

Lu YF, Mauger DM, Goldstein DB, Urban TJ, Weeks KM, Bradrick SS.

Sci Rep. 2015 Nov 4;5:16037. doi: 10.1038/srep16037.

19.

Challenge of mimicking the influences of the cellular environment on RNA structure by PEG-induced macromolecular crowding.

Tyrrell J, Weeks KM, Pielak GJ.

Biochemistry. 2015 Oct 27;54(42):6447-53. doi: 10.1021/acs.biochem.5b00767. Epub 2015 Oct 15.

20.

Selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) for direct, versatile and accurate RNA structure analysis.

Smola MJ, Rice GM, Busan S, Siegfried NA, Weeks KM.

Nat Protoc. 2015 Nov;10(11):1643-69. doi: 10.1038/nprot.2015.103. Epub 2015 Oct 1.

21.

Multiple conformations are a conserved and regulatory feature of the RB1 5' UTR.

Kutchko KM, Sanders W, Ziehr B, Phillips G, Solem A, Halvorsen M, Weeks KM, Moorman N, Laederach A.

RNA. 2015 Jul;21(7):1274-85. doi: 10.1261/rna.049221.114. Epub 2015 May 21.

22.

Structure-Based Alignment and Consensus Secondary Structures for Three HIV-Related RNA Genomes.

Lavender CA, Gorelick RJ, Weeks KM.

PLoS Comput Biol. 2015 May 20;11(5):e1004230. doi: 10.1371/journal.pcbi.1004230. eCollection 2015 May.

23.

Model-Free RNA Sequence and Structure Alignment Informed by SHAPE Probing Reveals a Conserved Alternate Secondary Structure for 16S rRNA.

Lavender CA, Lorenz R, Zhang G, Tamayo R, Hofacker IL, Weeks KM.

PLoS Comput Biol. 2015 May 20;11(5):e1004126. doi: 10.1371/journal.pcbi.1004126. eCollection 2015 May.

24.

RNA clubs.

Weeks KM.

RNA. 2015 Apr;21(4):760-1. doi: 10.1261/rna.050476.115. No abstract available.

25.

Functionally conserved architecture of hepatitis C virus RNA genomes.

Mauger DM, Golden M, Yamane D, Williford S, Lemon SM, Martin DP, Weeks KM.

Proc Natl Acad Sci U S A. 2015 Mar 24;112(12):3692-7. doi: 10.1073/pnas.1416266112. Epub 2015 Mar 9.

26.

In-cell SHAPE reveals that free 30S ribosome subunits are in the inactive state.

McGinnis JL, Liu Q, Lavender CA, Devaraj A, McClory SP, Fredrick K, Weeks KM.

Proc Natl Acad Sci U S A. 2015 Feb 24;112(8):2425-30. doi: 10.1073/pnas.1411514112. Epub 2015 Feb 9.

27.

Review toward all RNA structures, concisely.

Weeks KM.

Biopolymers. 2015 Aug;103(8):438-48. doi: 10.1002/bip.22601. Review.

28.

Catalysts from synthetic genetic polymers.

Taylor AI, Pinheiro VB, Smola MJ, Morgunov AS, Peak-Chew S, Cozens C, Weeks KM, Herdewijn P, Holliger P.

Nature. 2015 Feb 19;518(7539):427-30. doi: 10.1038/nature13982. Epub 2014 Dec 1.

29.

SHAPE analysis of small RNAs and riboswitches.

Rice GM, Busan S, Karabiber F, Favorov OV, Weeks KM.

Methods Enzymol. 2014;549:165-87. doi: 10.1016/B978-0-12-801122-5.00008-8.

30.

RNA tertiary structure analysis by 2'-hydroxyl molecular interference.

Homan PJ, Tandon A, Rice GM, Ding F, Dokholyan NV, Weeks KM.

Biochemistry. 2014 Nov 4;53(43):6825-33. doi: 10.1021/bi501218g. Epub 2014 Oct 23.

31.

Single-molecule correlated chemical probing of RNA.

Homan PJ, Favorov OV, Lavender CA, Kursun O, Ge X, Busan S, Dokholyan NV, Weeks KM.

Proc Natl Acad Sci U S A. 2014 Sep 23;111(38):13858-63. doi: 10.1073/pnas.1407306111. Epub 2014 Sep 9.

32.

RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP).

Siegfried NA, Busan S, Rice GM, Nelson JA, Weeks KM.

Nat Methods. 2014 Sep;11(9):959-65. doi: 10.1038/nmeth.3029. Epub 2014 Jul 13.

33.

Structure and dynamics of the HIV-1 frameshift element RNA.

Low JT, Garcia-Miranda P, Mouzakis KD, Gorelick RJ, Butcher SE, Weeks KM.

Biochemistry. 2014 Jul 8;53(26):4282-91. doi: 10.1021/bi5004926. Epub 2014 Jun 27.

34.

Ribosome RNA assembly intermediates visualized in living cells.

McGinnis JL, Weeks KM.

Biochemistry. 2014 May 20;53(19):3237-47. doi: 10.1021/bi500198b. Epub 2014 May 12.

35.

Validating fragment-based drug discovery for biological RNAs: lead fragments bind and remodel the TPP riboswitch specifically.

Warner KD, Homan P, Weeks KM, Smith AG, Abell C, Ferré-D'Amaré AR.

Chem Biol. 2014 May 22;21(5):591-5. doi: 10.1016/j.chembiol.2014.03.007. Epub 2014 Apr 24.

36.

RNA secondary structure modeling at consistent high accuracy using differential SHAPE.

Rice GM, Leonard CW, Weeks KM.

RNA. 2014 Jun;20(6):846-54. doi: 10.1261/rna.043323.113. Epub 2014 Apr 17.

37.

An immature retroviral RNA genome resembles a kinetically trapped intermediate state.

Grohman JK, Gorelick RJ, Kottegoda S, Allbritton NL, Rein A, Weeks KM.

J Virol. 2014 Jun;88(11):6061-8. doi: 10.1128/JVI.03277-13. Epub 2014 Mar 12.

38.

The cellular environment stabilizes adenine riboswitch RNA structure.

Tyrrell J, McGinnis JL, Weeks KM, Pielak GJ.

Biochemistry. 2013 Dec 3;52(48):8777-85. doi: 10.1021/bi401207q. Epub 2013 Nov 20.

39.

Role of context in RNA structure: flanking sequences reconfigure CAG motif folding in huntingtin exon 1 transcripts.

Busan S, Weeks KM.

Biochemistry. 2013 Nov 19;52(46):8219-25. doi: 10.1021/bi401129r. Epub 2013 Nov 7.

40.

Long-range architecture in a viral RNA genome.

Archer EJ, Simpson MA, Watts NJ, O'Kane R, Wang B, Erie DA, McPherson A, Weeks KM.

Biochemistry. 2013 May 7;52(18):3182-90. doi: 10.1021/bi4001535. Epub 2013 Apr 25.

41.

Comparison of SIV and HIV-1 genomic RNA structures reveals impact of sequence evolution on conserved and non-conserved structural motifs.

Pollom E, Dang KK, Potter EL, Gorelick RJ, Burch CL, Weeks KM, Swanstrom R.

PLoS Pathog. 2013;9(4):e1003294. doi: 10.1371/journal.ppat.1003294. Epub 2013 Apr 4.

42.

Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots.

Hajdin CE, Bellaousov S, Huggins W, Leonard CW, Mathews DH, Weeks KM.

Proc Natl Acad Sci U S A. 2013 Apr 2;110(14):5498-503. doi: 10.1073/pnas.1219988110. Epub 2013 Mar 15.

43.

The genetic code as expressed through relationships between mRNA structure and protein function.

Mauger DM, Siegfried NA, Weeks KM.

FEBS Lett. 2013 Apr 17;587(8):1180-1188. doi: 10.1016/j.febslet.2013.03.002. Epub 2013 Mar 13. Review.

44.

A guanosine-centric mechanism for RNA chaperone function.

Grohman JK, Gorelick RJ, Lickwar CR, Lieb JD, Bower BD, Znosko BM, Weeks KM.

Science. 2013 Apr 12;340(6129):190-5. doi: 10.1126/science.1230715. Epub 2013 Mar 7.

45.

Principles for understanding the accuracy of SHAPE-directed RNA structure modeling.

Leonard CW, Hajdin CE, Karabiber F, Mathews DH, Favorov OV, Dokholyan NV, Weeks KM.

Biochemistry. 2013 Jan 29;52(4):588-95. doi: 10.1021/bi300755u. Epub 2013 Jan 14.

46.

Statistical analysis of SHAPE-directed RNA secondary structure modeling.

Ramachandran S, Ding F, Weeks KM, Dokholyan NV.

Biochemistry. 2013 Jan 29;52(4):596-9. doi: 10.1021/bi300756s. Epub 2013 Jan 14.

47.

QuShape: rapid, accurate, and best-practices quantification of nucleic acid probing information, resolved by capillary electrophoresis.

Karabiber F, McGinnis JL, Favorov OV, Weeks KM.

RNA. 2013 Jan;19(1):63-73. doi: 10.1261/rna.036327.112. Epub 2012 Nov 27.

48.

Fingerprinting noncanonical and tertiary RNA structures by differential SHAPE reactivity.

Steen KA, Rice GM, Weeks KM.

J Am Chem Soc. 2012 Aug 15;134(32):13160-3. doi: 10.1021/ja304027m. Epub 2012 Aug 1.

49.

Three-dimensional RNA structure refinement by hydroxyl radical probing.

Ding F, Lavender CA, Weeks KM, Dokholyan NV.

Nat Methods. 2012 Apr 15;9(6):603-8. doi: 10.1038/nmeth.1976.

50.

The mechanisms of RNA SHAPE chemistry.

McGinnis JL, Dunkle JA, Cate JH, Weeks KM.

J Am Chem Soc. 2012 Apr 18;134(15):6617-24. doi: 10.1021/ja2104075. Epub 2012 Apr 5. Erratum in: J Am Chem Soc. 2012 Jul 25;134(29):12319.

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