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Items: 1 to 20 of 70

1.

Experimental maps of DNA structure at nucleotide resolution distinguish intrinsic from protein-induced DNA deformations.

Azad RN, Zafiropoulos D, Ober D, Jiang Y, Chiu TP, Sagendorf JM, Rohs R, Tullius TD.

Nucleic Acids Res. 2018 Mar 16;46(5):2636-2647. doi: 10.1093/nar/gky033.

2.

GBshape: a genome browser database for DNA shape annotations.

Chiu TP, Yang L, Zhou T, Main BJ, Parker SC, Nuzhdin SV, Tullius TD, Rohs R.

Nucleic Acids Res. 2015 Jan;43(Database issue):D103-9. doi: 10.1093/nar/gku977. Epub 2014 Oct 17.

3.

Chemical probing of RNA with the hydroxyl radical at single-atom resolution.

Ingle S, Azad RN, Jain SS, Tullius TD.

Nucleic Acids Res. 2014 Nov 10;42(20):12758-67. doi: 10.1093/nar/gku934. Epub 2014 Oct 13.

4.

Comparative analysis of metazoan chromatin organization.

Ho JW, Jung YL, Liu T, Alver BH, Lee S, Ikegami K, Sohn KA, Minoda A, Tolstorukov MY, Appert A, Parker SC, Gu T, Kundaje A, Riddle NC, Bishop E, Egelhofer TA, Hu SS, Alekseyenko AA, Rechtsteiner A, Asker D, Belsky JA, Bowman SK, Chen QB, Chen RA, Day DS, Dong Y, Dose AC, Duan X, Epstein CB, Ercan S, Feingold EA, Ferrari F, Garrigues JM, Gehlenborg N, Good PJ, Haseley P, He D, Herrmann M, Hoffman MM, Jeffers TE, Kharchenko PV, Kolasinska-Zwierz P, Kotwaliwale CV, Kumar N, Langley SA, Larschan EN, Latorre I, Libbrecht MW, Lin X, Park R, Pazin MJ, Pham HN, Plachetka A, Qin B, Schwartz YB, Shoresh N, Stempor P, Vielle A, Wang C, Whittle CM, Xue H, Kingston RE, Kim JH, Bernstein BE, Dernburg AF, Pirrotta V, Kuroda MI, Noble WS, Tullius TD, Kellis M, MacAlpine DM, Strome S, Elgin SC, Liu XS, Lieb JD, Ahringer J, Karpen GH, Park PJ.

Nature. 2014 Aug 28;512(7515):449-52. doi: 10.1038/nature13415.

5.

A map of minor groove shape and electrostatic potential from hydroxyl radical cleavage patterns of DNA.

Bishop EP, Rohs R, Parker SC, West SM, Liu P, Mann RS, Honig B, Tullius TD.

ACS Chem Biol. 2011 Dec 16;6(12):1314-20. doi: 10.1021/cb200155t. Epub 2011 Oct 13.

6.

A computational method to search for DNA structural motifs in functional genomic elements.

Parker SC, Harlap A, Tullius TD.

Methods Mol Biol. 2011;759:367-79. doi: 10.1007/978-1-61779-173-4_21.

PMID:
21863498
7.

DNA shape, genetic codes, and evolution.

Parker SC, Tullius TD.

Curr Opin Struct Biol. 2011 Jun;21(3):342-7. doi: 10.1016/j.sbi.2011.03.002. Epub 2011 Mar 23. Review.

8.

Local DNA topography correlates with functional noncoding regions of the human genome.

Parker SC, Hansen L, Abaan HO, Tullius TD, Margulies EH.

Science. 2009 Apr 17;324(5925):389-92. doi: 10.1126/science.1169050. Epub 2009 Mar 12.

9.

Footprinting protein-DNA complexes using the hydroxyl radical.

Jain SS, Tullius TD.

Nat Protoc. 2008;3(6):1092-1100.

PMID:
18546600
10.

Probing DNA structure with hydroxyl radicals.

Tullius TD.

Curr Protoc Nucleic Acid Chem. 2002 Feb;Chapter 6:Unit 6.7. doi: 10.1002/0471142700.nc0607s07. Review.

PMID:
18428898
11.
12.

Effects of discontinuities in the DNA template on abortive initiation and promoter escape by Escherichia coli RNA polymerase.

Wang Q, Tullius TD, Levin JR.

J Biol Chem. 2007 Sep 14;282(37):26917-27. Epub 2007 Jul 24.

13.

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA; NISC Comparative Sequencing Program; Baylor College of Medicine Human Genome Sequencing Center; Washington University Genome Sequencing Center; Broad Institute; Children's Hospital Oakland Research Institute, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ.

Nature. 2007 Jun 14;447(7146):799-816.

14.

Construction of a genome-scale structural map at single-nucleotide resolution.

Greenbaum JA, Pang B, Tullius TD.

Genome Res. 2007 Jun;17(6):947-53.

15.

Detection of DNA structural motifs in functional genomic elements.

Greenbaum JA, Parker SC, Tullius TD.

Genome Res. 2007 Jun;17(6):940-6.

16.

Platinum anticancer drug damage enforces a particular rotational setting of DNA in nucleosomes.

Danford AJ, Wang D, Wang Q, Tullius TD, Lippard SJ.

Proc Natl Acad Sci U S A. 2005 Aug 30;102(35):12311-6. Epub 2005 Aug 22.

17.

Mapping nucleic acid structure by hydroxyl radical cleavage.

Tullius TD, Greenbaum JA.

Curr Opin Chem Biol. 2005 Apr;9(2):127-34. Review.

PMID:
15811796
18.

Research Corporation and John Schaefer.

Deardorff D, Dorhout P, Haegel N, Iverson BL, Morrison M, Pladziewicz J, Selen M, Tullius TD, Zwier TS.

Science. 2004 Nov 12;306(5699):1133. No abstract available.

PMID:
15539585
19.

Gapped DNA is anisotropically bent.

Guo H, Tullius TD.

Proc Natl Acad Sci U S A. 2003 Apr 1;100(7):3743-7. Epub 2003 Mar 18.

20.

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