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Items: 25

1.

Blind prediction of noncanonical RNA structure at atomic accuracy.

Watkins AM, Geniesse C, Kladwang W, Zakrevsky P, Jaeger L, Das R.

Sci Adv. 2018 May 25;4(5):eaar5316. doi: 10.1126/sciadv.aar5316. eCollection 2018 May.

2.

Allosteric mechanism of the V. vulnificus adenine riboswitch resolved by four-dimensional chemical mapping.

Tian S, Kladwang W, Das R.

Elife. 2018 Feb 15;7. pii: e29602. doi: 10.7554/eLife.29602.

3.

RNA structure inference through chemical mapping after accidental or intentional mutations.

Cheng CY, Kladwang W, Yesselman JD, Das R.

Proc Natl Acad Sci U S A. 2017 Sep 12;114(37):9876-9881. doi: 10.1073/pnas.1619897114. Epub 2017 Aug 29.

4.

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.

5.

Blind tests of RNA nearest-neighbor energy prediction.

Chou FC, Kladwang W, Kappel K, Das R.

Proc Natl Acad Sci U S A. 2016 Jul 26;113(30):8430-5. doi: 10.1073/pnas.1523335113. Epub 2016 Jul 8.

6.

Correction: Consistent global structures of complex RNA states through multidimensional chemical mapping.

Yu Cheng C, Chou FC, Kladwang W, Tian S, Cordero P, Das R.

Elife. 2015 Jul 21;4:e10095. doi: 10.7554/eLife.10095. No abstract available.

7.

Consistent global structures of complex RNA states through multidimensional chemical mapping.

Cheng CY, Chou FC, Kladwang W, Tian S, Cordero P, Das R.

Elife. 2015 Jun 2;4:e07600. doi: 10.7554/eLife.07600. Erratum in: Elife. 2015;4:e10095.

8.

RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures.

Miao Z, Adamiak RW, Blanchet MF, Boniecki M, Bujnicki JM, Chen SJ, Cheng C, Chojnowski G, Chou FC, Cordero P, Cruz JA, Ferré-D'Amaré AR, Das R, Ding F, Dokholyan NV, Dunin-Horkawicz S, Kladwang W, Krokhotin A, Lach G, Magnus M, Major F, Mann TH, Masquida B, Matelska D, Meyer M, Peselis A, Popenda M, Purzycka KJ, Serganov A, Stasiewicz J, Szachniuk M, Tandon A, Tian S, Wang J, Xiao Y, Xu X, Zhang J, Zhao P, Zok T, Westhof E.

RNA. 2015 Jun;21(6):1066-84. doi: 10.1261/rna.049502.114. Epub 2015 Apr 16.

9.

RNA regulons in Hox 5' UTRs confer ribosome specificity to gene regulation.

Xue S, Tian S, Fujii K, Kladwang W, Das R, Barna M.

Nature. 2015 Jan 1;517(7532):33-8. doi: 10.1038/nature14010. Epub 2014 Nov 19.

10.

High-throughput mutate-map-rescue evaluates SHAPE-directed RNA structure and uncovers excited states.

Tian S, Cordero P, Kladwang W, Das R.

RNA. 2014 Nov;20(11):1815-26. doi: 10.1261/rna.044321.114. Epub 2014 Sep 2.

11.

Standardization of RNA chemical mapping experiments.

Kladwang W, Mann TH, Becka A, Tian S, Kim H, Yoon S, Das R.

Biochemistry. 2014 May 20;53(19):3063-5. doi: 10.1021/bi5003426. Epub 2014 May 7.

12.

RNA design rules from a massive open laboratory.

Lee J, Kladwang W, Lee M, Cantu D, Azizyan M, Kim H, Limpaecher A, Yoon S, Treuille A, Das R; EteRNA Participants.

Proc Natl Acad Sci U S A. 2014 Feb 11;111(6):2122-7. doi: 10.1073/pnas.1313039111. Epub 2014 Jan 27. Erratum in: Proc Natl Acad Sci U S A. 2016 Jan 26;113(4):E490. Proc Natl Acad Sci U S A. 2015 Oct 27;112(43):E5900.

13.

Massively parallel RNA chemical mapping with a reduced bias MAP-seq protocol.

Seetin MG, Kladwang W, Bida JP, Das R.

Methods Mol Biol. 2014;1086:95-117. doi: 10.1007/978-1-62703-667-2_6.

PMID:
24136600
14.

The mutate-and-map protocol for inferring base pairs in structured RNA.

Cordero P, Kladwang W, VanLang CC, Das R.

Methods Mol Biol. 2014;1086:53-77. doi: 10.1007/978-1-62703-667-2_4.

15.

Quantitative dimethyl sulfate mapping for automated RNA secondary structure inference.

Cordero P, Kladwang W, VanLang CC, Das R.

Biochemistry. 2012 Sep 11;51(36):7037-9. Epub 2012 Aug 29.

16.

Ultraviolet shadowing of RNA can cause significant chemical damage in seconds.

Kladwang W, Hum J, Das R.

Sci Rep. 2012;2:517. doi: 10.1038/srep00517. Epub 2012 Jul 18.

17.

Automated RNA structure prediction uncovers a kink-turn linker in double glycine riboswitches.

Kladwang W, Chou FC, Das R.

J Am Chem Soc. 2012 Jan 25;134(3):1404-7. doi: 10.1021/ja2093508. Epub 2012 Jan 12.

PMID:
22192063
18.

An enumerative stepwise ansatz enables atomic-accuracy RNA loop modeling.

Sripakdeevong P, Kladwang W, Das R.

Proc Natl Acad Sci U S A. 2011 Dec 20;108(51):20573-8. doi: 10.1073/pnas.1106516108. Epub 2011 Dec 5.

19.

A two-dimensional mutate-and-map strategy for non-coding RNA structure.

Kladwang W, VanLang CC, Cordero P, Das R.

Nat Chem. 2011 Oct 30;3(12):954-62. doi: 10.1038/nchem.1176.

20.

Understanding the errors of SHAPE-directed RNA structure modeling.

Kladwang W, VanLang CC, Cordero P, Das R.

Biochemistry. 2011 Sep 20;50(37):8049-56. doi: 10.1021/bi200524n. Epub 2011 Aug 25.

21.

HiTRACE: high-throughput robust analysis for capillary electrophoresis.

Yoon S, Kim J, Hum J, Kim H, Park S, Kladwang W, Das R.

Bioinformatics. 2011 Jul 1;27(13):1798-805. doi: 10.1093/bioinformatics/btr277. Epub 2011 May 10.

PMID:
21561922
22.

A mutate-and-map strategy accurately infers the base pairs of a 35-nucleotide model RNA.

Kladwang W, Cordero P, Das R.

RNA. 2011 Mar;17(3):522-34. doi: 10.1261/rna.2516311. Epub 2011 Jan 14.

23.

A mutate-and-map strategy for inferring base pairs in structured nucleic acids: proof of concept on a DNA/RNA helix.

Kladwang W, Das R.

Biochemistry. 2010 Sep 7;49(35):7414-6. doi: 10.1021/bi101123g.

PMID:
20677780
24.

Hypersaline stress induces the turnover of phosphatidylcholine and results in the synthesis of the renal osmoprotectant glycerophosphocholine in Saccharomyces cerevisiae.

Kiewietdejonge A, Pitts M, Cabuhat L, Sherman C, Kladwang W, Miramontes G, Floresvillar J, Chan J, Ramirez RM.

FEMS Yeast Res. 2006 Mar;6(2):205-17.

25.

Antiplasmodial compounds from the wood-decayed fungus Xylaria sp. BCC 1067.

Isaka M, Jaturapat A, Kladwang W, Punya J, Lertwerawat Y, Tanticharoen M, Thebtaranonth Y.

Planta Med. 2000 Jun;66(5):473-5.

PMID:
10909272

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