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Analysis of Individual Signaling Complexes by mMAPS, a Flow-Proteometric System.

Chou CK, Tsou PH, Hsu JL, Lee HH, Wang YN, Kameoka J, Hung MC.

Curr Protoc Mol Biol. 2016 Apr 1;114:20.11.1-20.11.22. doi: 10.1002/0471142727.mb2011s114.


Nucleosome architecture throughout the cell cycle.

Deniz Ö, Flores O, Aldea M, Soler-López M, Orozco M.

Sci Rep. 2016 Jan 28;6:19729. doi: 10.1038/srep19729.


Theoretical estimates of exposure timescales of protein binding sites on DNA regulated by nucleosome kinetics.

Parmar JJ, Das D, Padinhateeri R.

Nucleic Acids Res. 2016 Feb 29;44(4):1630-41. doi: 10.1093/nar/gkv1153. Epub 2015 Nov 8.


Improved DNase-seq protocol facilitates high resolution mapping of DNase I hypersensitive sites in roots in Arabidopsis thaliana.

Cumbie JS, Filichkin SA, Megraw M.

Plant Methods. 2015 Sep 4;11:42. doi: 10.1186/s13007-015-0087-1. eCollection 2015.


Chromatin accessibility: a window into the genome.

Tsompana M, Buck MJ.

Epigenetics Chromatin. 2014 Nov 20;7(1):33. doi: 10.1186/1756-8935-7-33. eCollection 2014. Review.


Promoter-proximal transcription factor binding is transcriptionally active when coupled with nucleosome repositioning in immediate vicinity.

Yadav VK, Thakur RK, Eckloff B, Baral A, Singh A, Halder R, Kumar A, Alam MP, Kundu TK, Pandita R, Pandita TK, Wieben ED, Chowdhury S.

Nucleic Acids Res. 2014 Sep;42(15):9602-11. doi: 10.1093/nar/gku596. Epub 2014 Jul 31.


Evolution and genetic architecture of chromatin accessibility and function in yeast.

Connelly CF, Wakefield J, Akey JM.

PLoS Genet. 2014 Jul 3;10(7):e1004427. doi: 10.1371/journal.pgen.1004427. eCollection 2014 Jul.


Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer.

Taberlay PC, Statham AL, Kelly TK, Clark SJ, Jones PA.

Genome Res. 2014 Sep;24(9):1421-32. doi: 10.1101/gr.163485.113. Epub 2014 Jun 10.


Nucleosome positioning and histone modifications define relationships between regulatory elements and nearby gene expression in breast epithelial cells.

Rhie SK, Hazelett DJ, Coetzee SG, Yan C, Noushmehr H, Coetzee GA.

BMC Genomics. 2014 May 2;15:331. doi: 10.1186/1471-2164-15-331.


Transcription of nuclear organellar DNA in a model plant system.

Wang D, Qu Z, Adelson DL, Zhu JK, Timmis JN.

Genome Biol Evol. 2014 May 27;6(6):1327-34. doi: 10.1093/gbe/evu111.


A dynamic interplay of nucleosome and Msn2 binding regulates kinetics of gene activation and repression following stress.

Elfving N, Chereji RV, Bharatula V, Björklund S, Morozov AV, Broach JR.

Nucleic Acids Res. 2014 May;42(9):5468-82. doi: 10.1093/nar/gku176. Epub 2014 Mar 5.


Peroxisome proliferator-activated receptor γ and C/EBPα synergistically activate key metabolic adipocyte genes by assisted loading.

Madsen MS, Siersbæk R, Boergesen M, Nielsen R, Mandrup S.

Mol Cell Biol. 2014 Mar;34(6):939-54. doi: 10.1128/MCB.01344-13. Epub 2013 Dec 30.


Genome-wide identification of regulatory elements and reconstruction of gene regulatory networks of the green alga Chlamydomonas reinhardtii under carbon deprivation.

Winck FV, Arvidsson S, Riaño-Pachón DM, Hempel S, Koseska A, Nikoloski Z, Urbina Gomez DA, Rupprecht J, Mueller-Roeber B.

PLoS One. 2013 Nov 1;8(11):e79909. doi: 10.1371/journal.pone.0079909. eCollection 2013. Erratum in: PLoS One. 2014;9(1). doi:10.1371/annotation/63d1c5f9-82c8-406b-b60e-b7d9ecba9408. Vischi Winck, Flavia [corrected to Winck, Flavia Vischi].


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.


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.


Cytoplasmic organelle DNA preferentially inserts into open chromatin.

Wang D, Timmis JN.

Genome Biol Evol. 2013;5(6):1060-4. doi: 10.1093/gbe/evt070.


Genomes of replicatively senescent cells undergo global epigenetic changes leading to gene silencing and activation of transposable elements.

De Cecco M, Criscione SW, Peckham EJ, Hillenmeyer S, Hamm EA, Manivannan J, Peterson AL, Kreiling JA, Neretti N, Sedivy JM.

Aging Cell. 2013 Apr;12(2):247-56. doi: 10.1111/acel.12047. Epub 2013 Jan 30.


Characterization of Chromatin Structure-associated Histone Modifications in Breast Cancer Cells.

Hong CP, Choe MK, Roh TY.

Genomics Inform. 2012 Sep;10(3):145-52. doi: 10.5808/GI.2012.10.3.145. Epub 2012 Sep 28.


Defining flexible vs. inherent promoter architectures: the importance of dynamics and environmental considerations.

Huebert DJ, Gasch AP.

Nucleus. 2012 Sep-Oct;3(5):399-403. doi: 10.4161/nucl.21172. Epub 2012 Jul 3.


A generalized hidden Markov model for determining sequence-based predictors of nucleosome positioning.

Moser C, Gupta M.

Stat Appl Genet Mol Biol. 2012 Jan 6;11(2). pii: /j/sagmb.2012.11.issue-2/1544-6115.1707/1544-6115.1707.xml. doi: 10.2202/1544-6115.1707.

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