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Items: 1 to 50 of 115

1.

Tissue- and strain-specific effects of a genotoxic carcinogen 1,3-butadiene on chromatin and transcription.

Israel JW, Chappell GA, Simon JM, Pott S, Safi A, Lewis L, Cotney P, Boulos HS, Bodnar W, Lieb JD, Crawford GE, Furey TS, Rusyn I.

Mamm Genome. 2018 Feb;29(1-2):153-167. doi: 10.1007/s00335-018-9739-6. Epub 2018 Feb 10.

PMID:
29429127
2.

Variation in DNA-Damage Responses to an Inhalational Carcinogen (1,3-Butadiene) in Relation to Strain-Specific Differences in Chromatin Accessibility and Gene Transcription Profiles in C57BL/6J and CAST/EiJ Mice.

Chappell GA, Israel JW, Simon JM, Pott S, Safi A, Eklund K, Sexton KG, Bodnar W, Lieb JD, Crawford GE, Rusyn I, Furey TS.

Environ Health Perspect. 2017 Oct 16;125(10):107006. doi: 10.1289/EHP1937.

3.

Nucleosome fragility is associated with future transcriptional response to developmental cues and stress in C. elegans.

Jeffers TE, Lieb JD.

Genome Res. 2017 Jan;27(1):75-86. doi: 10.1101/gr.208173.116. Epub 2016 Nov 14.

4.

Chromatin profiling of Drosophila CNS subpopulations identifies active transcriptional enhancers.

Pearson JC, McKay DJ, Lieb JD, Crews ST.

Development. 2016 Oct 15;143(20):3723-3732.

5.

Cisplatin DNA damage and repair maps of the human genome at single-nucleotide resolution.

Hu J, Lieb JD, Sancar A, Adar S.

Proc Natl Acad Sci U S A. 2016 Oct 11;113(41):11507-11512. Epub 2016 Sep 29.

6.

A Transcriptional Lineage of the Early C. elegans Embryo.

Tintori SC, Osborne Nishimura E, Golden P, Lieb JD, Goldstein B.

Dev Cell. 2016 Aug 22;38(4):430-44. doi: 10.1016/j.devcel.2016.07.025.

7.

Alterations to chromatin in intestinal macrophages link IL-10 deficiency to inappropriate inflammatory responses.

Simon JM, Davis JP, Lee SE, Schaner MR, Gipson GR, Weiser M, Sartor RB, Herfarth HH, Rahbar R, Sadiq TS, Koruda MJ, McGovern DP, Lieb JD, Mohlke KL, Furey TS, Sheikh SZ.

Eur J Immunol. 2016 Aug;46(8):1912-25. doi: 10.1002/eji.201546237. Epub 2016 Jun 1.

8.

Genome-wide kinetics of DNA excision repair in relation to chromatin state and mutagenesis.

Adar S, Hu J, Lieb JD, Sancar A.

Proc Natl Acad Sci U S A. 2016 Apr 12;113(15):E2124-33. doi: 10.1073/pnas.1603388113. Epub 2016 Mar 28.

9.

The function and regulation of the GATA factor ELT-2 in the C. elegans endoderm.

Wiesenfahrt T, Berg JY, Osborne Nishimura E, Robinson AG, Goszczynski B, Lieb JD, McGhee JD.

Development. 2016 Feb 1;143(3):483-91. doi: 10.1242/dev.130914. Epub 2015 Dec 23.

10.

Zelda is differentially required for chromatin accessibility, transcription factor binding, and gene expression in the early Drosophila embryo.

Schulz KN, Bondra ER, Moshe A, Villalta JE, Lieb JD, Kaplan T, McKay DJ, Harrison MM.

Genome Res. 2015 Nov;25(11):1715-26. doi: 10.1101/gr.192682.115. Epub 2015 Sep 2.

11.

Single-cell ATAC-seq: strength in numbers.

Pott S, Lieb JD.

Genome Biol. 2015 Aug 21;16:172. doi: 10.1186/s13059-015-0737-7.

12.

Histone modifications predispose genome regions to breakage and translocation.

Burman B, Zhang ZZ, Pegoraro G, Lieb JD, Misteli T.

Genes Dev. 2015 Jul 1;29(13):1393-402. doi: 10.1101/gad.262170.115. Epub 2015 Jun 23.

13.

Genome-wide analysis of human global and transcription-coupled excision repair of UV damage at single-nucleotide resolution.

Hu J, Adar S, Selby CP, Lieb JD, Sancar A.

Genes Dev. 2015 May 1;29(9):948-60. doi: 10.1101/gad.261271.115.

14.

Correction: Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association.

Ding Z, Ni Y, Timmer SW, Lee BK, Battenhouse A, Louzada S, Yang F, Dunham I, Crawford GE, Lieb JD, Durbin R, Iyer VR, Birney E.

PLoS Genet. 2015 Apr 28;11(4):e1005177. doi: 10.1371/journal.pgen.1005177. eCollection 2015 Apr.

15.

Asymmetric transcript discovery by RNA-seq in C. elegans blastomeres identifies neg-1, a gene important for anterior morphogenesis.

Osborne Nishimura E, Zhang JC, Werts AD, Goldstein B, Lieb JD.

PLoS Genet. 2015 Apr 13;11(4):e1005117. doi: 10.1371/journal.pgen.1005117. eCollection 2015 Apr.

16.

STAT3 acts through pre-existing nucleosome-depleted regions bound by FOS during an epigenetic switch linking inflammation to cancer.

Fleming JD, Giresi PG, Lindahl-Allen M, Krall EB, Lieb JD, Struhl K.

Epigenetics Chromatin. 2015 Feb 14;8:7. doi: 10.1186/1756-8935-8-7. eCollection 2015.

17.

Interrogating the function of metazoan histones using engineered gene clusters.

McKay DJ, Klusza S, Penke TJ, Meers MP, Curry KP, McDaniel SL, Malek PY, Cooper SW, Tatomer DC, Lieb JD, Strahl BD, Duronio RJ, Matera AG.

Dev Cell. 2015 Feb 9;32(3):373-86. doi: 10.1016/j.devcel.2014.12.025.

18.

Ancient transposable elements transformed the uterine regulatory landscape and transcriptome during the evolution of mammalian pregnancy.

Lynch VJ, Nnamani MC, Kapusta A, Brayer K, Plaza SL, Mazur EC, Emera D, Sheikh SZ, Grützner F, Bauersachs S, Graf A, Young SL, Lieb JD, DeMayo FJ, Feschotte C, Wagner GP.

Cell Rep. 2015 Feb 3;10(4):551-61. doi: 10.1016/j.celrep.2014.12.052. Epub 2015 Jan 29.

19.

What are super-enhancers?

Pott S, Lieb JD.

Nat Genet. 2015 Jan;47(1):8-12. doi: 10.1038/ng.3167.

PMID:
25547603
20.

A split personality for nucleosomes.

McKay DJ, Lieb JD.

Cell. 2014 Dec 4;159(6):1249-51. doi: 10.1016/j.cell.2014.11.030.

21.

Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association.

Ding Z, Ni Y, Timmer SW, Lee BK, Battenhouse A, Louzada S, Yang F, Dunham I, Crawford GE, Lieb JD, Durbin R, Iyer VR, Birney E.

PLoS Genet. 2014 Nov 20;10(11):e1004798. doi: 10.1371/journal.pgen.1004798. eCollection 2014 Nov. Erratum in: PLoS Genet. 2015 Apr;11(4):e1005177.

22.

Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease.

Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, Giddings MC, Gilbert DM, Gingeras TR, Green ED, Guigo R, Hubbard T, Kent J, Lieb JD, Myers RM, Pazin MJ, Ren B, Stamatoyannopoulos J, Weng Z, White KP, Hardison RC.

Proc Natl Acad Sci U S A. 2014 Aug 19;111(33):E3366. No abstract available.

23.

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.

24.

Defining functional DNA elements in the human genome.

Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, Giddings MC, Gilbert DM, Gingeras TR, Green ED, Guigo R, Hubbard T, Kent J, Lieb JD, Myers RM, Pazin MJ, Ren B, Stamatoyannopoulos JA, Weng Z, White KP, Hardison RC.

Proc Natl Acad Sci U S A. 2014 Apr 29;111(17):6131-8. doi: 10.1073/pnas.1318948111. Epub 2014 Apr 21. Review.

25.

Regulation of the X chromosomes in Caenorhabditis elegans.

Strome S, Kelly WG, Ercan S, Lieb JD.

Cold Spring Harb Perspect Biol. 2014 Mar 1;6(3). pii: a018366. doi: 10.1101/cshperspect.a018366. Review.

26.

Genome-wide analysis links emerin to neuromuscular junction activity in Caenorhabditis elegans.

González-Aguilera C, Ikegami K, Ayuso C, de Luis A, Íñiguez M, Cabello J, Lieb JD, Askjaer P.

Genome Biol. 2014 Feb 3;15(2):R21. doi: 10.1186/gb-2014-15-2-r21.

27.

Gene model 129 (Gm129) encodes a novel transcriptional repressor that modulates circadian gene expression.

Annayev Y, Adar S, Chiou YY, Lieb JD, Sancar A, Ye R.

J Biol Chem. 2014 Feb 21;289(8):5013-24. doi: 10.1074/jbc.M113.534651. Epub 2014 Jan 2.

28.

A common set of DNA regulatory elements shapes Drosophila appendages.

McKay DJ, Lieb JD.

Dev Cell. 2013 Nov 11;27(3):306-18. doi: 10.1016/j.devcel.2013.10.009.

29.

Variation in chromatin accessibility in human kidney cancer links H3K36 methyltransferase loss with widespread RNA processing defects.

Simon JM, Hacker KE, Singh D, Brannon AR, Parker JS, Weiser M, Ho TH, Kuan PF, Jonasch E, Furey TS, Prins JF, Lieb JD, Rathmell WK, Davis IJ.

Genome Res. 2014 Feb;24(2):241-50. doi: 10.1101/gr.158253.113. Epub 2013 Oct 24.

30.

TRA-1 ChIP-seq reveals regulators of sexual differentiation and multilevel feedback in nematode sex determination.

Berkseth M, Ikegami K, Arur S, Lieb JD, Zarkower D.

Proc Natl Acad Sci U S A. 2013 Oct 1;110(40):16033-8. doi: 10.1073/pnas.1312087110. Epub 2013 Sep 17.

31.

Integral nuclear pore proteins bind to Pol III-transcribed genes and are required for Pol III transcript processing in C. elegans.

Ikegami K, Lieb JD.

Mol Cell. 2013 Sep 26;51(6):840-9. doi: 10.1016/j.molcel.2013.08.001. Epub 2013 Sep 5.

32.

The open chromatin landscape of Kaposi's sarcoma-associated herpesvirus.

Hilton IB, Simon JM, Lieb JD, Davis IJ, Damania B, Dittmer DP.

J Virol. 2013 Nov;87(21):11831-42. doi: 10.1128/JVI.01685-13. Epub 2013 Aug 28.

33.

Genome-wide measurement of protein-DNA binding dynamics using competition ChIP.

Lickwar CR, Mueller F, Lieb JD.

Nat Protoc. 2013;8(7):1337-53. doi: 10.1038/nprot.2013.077. Epub 2013 Jun 13.

PMID:
23764940
34.

A detailed protocol for formaldehyde-assisted isolation of regulatory elements (FAIRE).

Simon JM, Giresi PG, Davis IJ, Lieb JD.

Curr Protoc Mol Biol. 2013;Chapter 21:Unit21.26. doi: 10.1002/0471142727.mb2126s102.

PMID:
23547014
35.

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.

36.

Promoter- and RNA polymerase II-dependent hsp-16 gene association with nuclear pores in Caenorhabditis elegans.

Rohner S, Kalck V, Wang X, Ikegami K, Lieb JD, Gasser SM, Meister P.

J Cell Biol. 2013 Mar 4;200(5):589-604. doi: 10.1083/jcb.201207024.

37.

H4K20me1 contributes to downregulation of X-linked genes for C. elegans dosage compensation.

Vielle A, Lang J, Dong Y, Ercan S, Kotwaliwale C, Rechtsteiner A, Appert A, Chen QB, Dose A, Egelhofer T, Kimura H, Stempor P, Dernburg A, Lieb JD, Strome S, Ahringer J.

PLoS Genet. 2012 Sep;8(9):e1002933. doi: 10.1371/journal.pgen.1002933. Epub 2012 Sep 13.

38.

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.

Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, Gerstein M, Gertz J, Hartemink AJ, Hoffman MM, Iyer VR, Jung YL, Karmakar S, Kellis M, Kharchenko PV, Li Q, Liu T, Liu XS, Ma L, Milosavljevic A, Myers RM, Park PJ, Pazin MJ, Perry MD, Raha D, Reddy TE, Rozowsky J, Shoresh N, Sidow A, Slattery M, Stamatoyannopoulos JA, Tolstorukov MY, White KP, Xi S, Farnham PJ, Lieb JD, Wold BJ, Snyder M.

Genome Res. 2012 Sep;22(9):1813-31. doi: 10.1101/gr.136184.111.

39.

The accessible chromatin landscape of the human genome.

Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B, Garg K, John S, Sandstrom R, Bates D, Boatman L, Canfield TK, Diegel M, Dunn D, Ebersol AK, Frum T, Giste E, Johnson AK, Johnson EM, Kutyavin T, Lajoie B, Lee BK, Lee K, London D, Lotakis D, Neph S, Neri F, Nguyen ED, Qu H, Reynolds AP, Roach V, Safi A, Sanchez ME, Sanyal A, Shafer A, Simon JM, Song L, Vong S, Weaver M, Yan Y, Zhang Z, Zhang Z, Lenhard B, Tewari M, Dorschner MO, Hansen RS, Navas PA, Stamatoyannopoulos G, Iyer VR, Lieb JD, Sunyaev SR, Akey JM, Sabo PJ, Kaul R, Furey TS, Dekker J, Crawford GE, Stamatoyannopoulos JA.

Nature. 2012 Sep 6;489(7414):75-82. doi: 10.1038/nature11232.

40.

In vivo effects of histone H3 depletion on nucleosome occupancy and position in Saccharomyces cerevisiae.

Gossett AJ, Lieb JD.

PLoS Genet. 2012;8(6):e1002771. doi: 10.1371/journal.pgen.1002771. Epub 2012 Jun 21.

41.

Systematic evaluation of factors influencing ChIP-seq fidelity.

Chen Y, Negre N, Li Q, Mieczkowska JO, Slattery M, Liu T, Zhang Y, Kim TK, He HH, Zieba J, Ruan Y, Bickel PJ, Myers RM, Wold BJ, White KP, Lieb JD, Liu XS.

Nat Methods. 2012 Jun;9(6):609-14. doi: 10.1038/nmeth.1985. Epub 2012 Apr 22.

42.

Genome-wide protein-DNA binding dynamics suggest a molecular clutch for transcription factor function.

Lickwar CR, Mueller F, Hanlon SE, McNally JG, Lieb JD.

Nature. 2012 Apr 11;484(7393):251-5. doi: 10.1038/nature10985.

43.

An inverse relationship to germline transcription defines centromeric chromatin in C. elegans.

Gassmann R, Rechtsteiner A, Yuen KW, Muroyama A, Egelhofer T, Gaydos L, Barron F, Maddox P, Essex A, Monen J, Ercan S, Lieb JD, Oegema K, Strome S, Desai A.

Nature. 2012 Apr 8;484(7395):534-7. doi: 10.1038/nature10973.

44.

Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA.

Simon JM, Giresi PG, Davis IJ, Lieb JD.

Nat Protoc. 2012 Jan 19;7(2):256-67. doi: 10.1038/nprot.2011.444. Erratum in: Nat Protoc. 2014 Feb;9(2):501-3.

45.

Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells.

Lee BK, Bhinge AA, Battenhouse A, McDaniell RM, Liu Z, Song L, Ni Y, Birney E, Lieb JD, Furey TS, Crawford GE, Iyer VR.

Genome Res. 2012 Jan;22(1):9-24. doi: 10.1101/gr.127597.111. Epub 2011 Nov 16.

46.

Tumor-specific retargeting of an oncogenic transcription factor chimera results in dysregulation of chromatin and transcription.

Patel M, Simon JM, Iglesia MD, Wu SB, McFadden AW, Lieb JD, Davis IJ.

Genome Res. 2012 Feb;22(2):259-70. doi: 10.1101/gr.125666.111. Epub 2011 Nov 15.

47.

Evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster.

Deng X, Hiatt JB, Nguyen DK, Ercan S, Sturgill D, Hillier LW, Schlesinger F, Davis CA, Reinke VJ, Gingeras TR, Shendure J, Waterston RH, Oliver B, Lieb JD, Disteche CM.

Nat Genet. 2011 Oct 23;43(12):1179-85. doi: 10.1038/ng.948.

48.

A conserved PHD finger protein and endogenous RNAi modulate insulin signaling in Caenorhabditis elegans.

Mansisidor AR, Cecere G, Hoersch S, Jensen MB, Kawli T, Kennedy LM, Chavez V, Tan MW, Lieb JD, Grishok A.

PLoS Genet. 2011 Sep;7(9):e1002299. doi: 10.1371/journal.pgen.1002299. Epub 2011 Sep 29.

49.

ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions.

Rashid NU, Giresi PG, Ibrahim JG, Sun W, Lieb JD.

Genome Biol. 2011 Jul 25;12(7):R67. doi: 10.1186/gb-2011-12-7-r67.

50.

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity.

Song L, Zhang Z, Grasfeder LL, Boyle AP, Giresi PG, Lee BK, Sheffield NC, Gräf S, Huss M, Keefe D, Liu Z, London D, McDaniell RM, Shibata Y, Showers KA, Simon JM, Vales T, Wang T, Winter D, Zhang Z, Clarke ND, Birney E, Iyer VR, Crawford GE, Lieb JD, Furey TS.

Genome Res. 2011 Oct;21(10):1757-67. doi: 10.1101/gr.121541.111. Epub 2011 Jul 12.

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