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tRNA gene identity affects nuclear positioning.

Rodley CD, Pai DA, Mills TA, Engelke DR, O'Sullivan JM.

PLoS One. 2011;6(12):e29267. doi: 10.1371/journal.pone.0029267. Epub 2011 Dec 19.


Comparative analysis of T4 DNA ligases and DNA polymerases used in chromosome conformation capture assays.

Schwartz M, Sarusi A, Deitch RT, Tal M, Raz D, Sung MH, Kaplan T, Hakim O.

Biotechniques. 2015 Apr 1;58(4):195-9. doi: 10.2144/000114276. eCollection 2015 Apr.


Interpreting 4C-Seq data: how far can we go?

Raviram R, Rocha PP, Bonneau R, Skok JA.

Epigenomics. 2014;6(5):455-7. doi: 10.2217/epi.14.47. No abstract available.


A sequence-specific interaction between the Saccharomyces cerevisiae rRNA gene repeats and a locus encoding an RNA polymerase I subunit affects ribosomal DNA stability.

Cahyani I, Cridge AG, Engelke DR, Ganley AR, O'Sullivan JM.

Mol Cell Biol. 2015 Feb;35(3):544-54. doi: 10.1128/MCB.01249-14. Epub 2014 Nov 24.


A comprehensive tRNA deletion library unravels the genetic architecture of the tRNA pool.

Bloom-Ackermann Z, Navon S, Gingold H, Towers R, Pilpel Y, Dahan O.

PLoS Genet. 2014 Jan;10(1):e1004084. doi: 10.1371/journal.pgen.1004084. Epub 2014 Jan 16.


Dynamic trans interactions in yeast chromosomes.

Mirkin EV, Chang FS, Kleckner N.

PLoS One. 2013 Sep 30;8(9):e75895. doi: 10.1371/journal.pone.0075895. eCollection 2013.


The statistical-mechanics of chromosome conformation capture.

O'Sullivan JM, Hendy MD, Pichugina T, Wake GC, Langowski J.

Nucleus. 2013 Sep-Oct;4(5):390-8. doi: 10.4161/nucl.26513. Epub 2013 Sep 18. Review.


How to build a yeast nucleus.

Wong H, Arbona JM, Zimmer C.

Nucleus. 2013 Sep-Oct;4(5):361-6. doi: 10.4161/nucl.26226. Epub 2013 Aug 22.


Systematic characterization of the conformation and dynamics of budding yeast chromosome XII.

Albert B, Mathon J, Shukla A, Saad H, Normand C, L├ęger-Silvestre I, Villa D, Kamgoue A, Mozziconacci J, Wong H, Zimmer C, Bhargava P, Bancaud A, Gadal O.

J Cell Biol. 2013 Jul 22;202(2):201-10. doi: 10.1083/jcb.201208186.


Analysis of interactions between genomic loci through Chromosome Conformation Capture (3C).

El Kaderi B, Medler S, Ansari A.

Curr Protoc Cell Biol. 2012 Sep;Chapter 22:Unit22.15. doi: 10.1002/0471143030.cb2215s56.


A predictive computational model of the dynamic 3D interphase yeast nucleus.

Wong H, Marie-Nelly H, Herbert S, Carrivain P, Blanc H, Koszul R, Fabre E, Zimmer C.

Curr Biol. 2012 Oct 23;22(20):1881-90. doi: 10.1016/j.cub.2012.07.069. Epub 2012 Aug 30.


Normalization of a chromosomal contact map.

Cournac A, Marie-Nelly H, Marbouty M, Koszul R, Mozziconacci J.

BMC Genomics. 2012 Aug 30;13:436. doi: 10.1186/1471-2164-13-436.


Chromosome positioning and the clustering of functionally related loci in yeast is driven by chromosomal interactions.

Gehlen LR, Gruenert G, Jones MB, Rodley CD, Langowski J, O'Sullivan JM.

Nucleus. 2012 Jul 1;3(4):370-83. Epub 2012 Jun 12.


Physical tethering and volume exclusion determine higher-order genome organization in budding yeast.

Tjong H, Gong K, Chen L, Alber F.

Genome Res. 2012 Jul;22(7):1295-305. doi: 10.1101/gr.129437.111. Epub 2012 May 22.


Mitochondrial-nuclear DNA interactions contribute to the regulation of nuclear transcript levels as part of the inter-organelle communication system.

Rodley CD, Grand RS, Gehlen LR, Greyling G, Jones MB, O'Sullivan JM.

PLoS One. 2012;7(1):e30943. doi: 10.1371/journal.pone.0030943. Epub 2012 Jan 23.


A decade of 3C technologies: insights into nuclear organization.

de Wit E, de Laat W.

Genes Dev. 2012 Jan 1;26(1):11-24. doi: 10.1101/gad.179804.111. Review.


Unravelling global genome organization by 3C-seq.

Tanizawa H, Noma K.

Semin Cell Dev Biol. 2012 Apr;23(2):213-21. doi: 10.1016/j.semcdb.2011.11.003. Epub 2011 Nov 18. Review.


Tracking chromosome dynamics in live yeast cells: coordinated movement of rDNA homologs and anaphase disassembly of the nucleolus during meiosis.

Li P, Jin H, Hoang ML, Yu HG.

Chromosome Res. 2011 Nov;19(8):1013-26. doi: 10.1007/s10577-011-9253-0.


A quantitative systems approach reveals dynamic control of tRNA modifications during cellular stress.

Chan CT, Dyavaiah M, DeMott MS, Taghizadeh K, Dedon PC, Begley TJ.

PLoS Genet. 2010 Dec 16;6(12):e1001247. doi: 10.1371/journal.pgen.1001247. Erratum in: PLoS Genet. 2011 Feb;7(2). doi: 10.1371/annotation/6549d0b1-efde-4aa4-9cda-1cef43f66b30.


Quantitative localization of chromosomal loci by immunofluorescence.

Brickner DG, Light W, Brickner JH.

Methods Enzymol. 2010;470:569-80. doi: 10.1016/S0076-6879(10)70022-7. Epub 2010 Mar 1.

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