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Genome-wide landscape of position effects on heterogeneous gene expression in Saccharomyces cerevisiae.

Wu XL, Li BZ, Zhang WZ, Song K, Qi H, Dai JB, Yuan YJ.

Biotechnol Biofuels. 2017 Jul 18;10:189. doi: 10.1186/s13068-017-0872-3. eCollection 2017.


Context based computational analysis and characterization of ARS consensus sequences (ACS) of Saccharomyces cerevisiae genome.

Singh VK, Krishnamachari A.

Genom Data. 2016 Jul 19;9:130-6. doi: 10.1016/j.gdata.2016.07.005. eCollection 2016 Sep.


Initiation of DNA replication from non-canonical sites on an origin-depleted chromosome.

Bogenschutz NL, Rodriguez J, Tsukiyama T.

PLoS One. 2014 Dec 8;9(12):e114545. doi: 10.1371/journal.pone.0114545. eCollection 2014.


GC-rich DNA elements enable replication origin activity in the methylotrophic yeast Pichia pastoris.

Liachko I, Youngblood RA, Tsui K, Bubb KL, Queitsch C, Raghuraman MK, Nislow C, Brewer BJ, Dunham MJ.

PLoS Genet. 2014 Mar 6;10(3):e1004169. doi: 10.1371/journal.pgen.1004169. eCollection 2014 Mar.


The reference genome sequence of Saccharomyces cerevisiae: then and now.

Engel SR, Dietrich FS, Fisk DG, Binkley G, Balakrishnan R, Costanzo MC, Dwight SS, Hitz BC, Karra K, Nash RS, Weng S, Wong ED, Lloyd P, Skrzypek MS, Miyasato SR, Simison M, Cherry JM.

G3 (Bethesda). 2014 Mar 20;4(3):389-98. doi: 10.1534/g3.113.008995.


The dynamics of genome replication using deep sequencing.

Müller CA, Hawkins M, Retkute R, Malla S, Wilson R, Blythe MJ, Nakato R, Komata M, Shirahige K, de Moura AP, Nieduszynski CA.

Nucleic Acids Res. 2014 Jan;42(1):e3. doi: 10.1093/nar/gkt878. Epub 2013 Oct 1.


A Link between ORC-origin binding mechanisms and origin activation time revealed in budding yeast.

Hoggard T, Shor E, Müller CA, Nieduszynski CA, Fox CA.

PLoS Genet. 2013;9(9):e1003798. doi: 10.1371/journal.pgen.1003798. Epub 2013 Sep 12.


A natural polymorphism in rDNA replication origins links origin activation with calorie restriction and lifespan.

Kwan EX, Foss EJ, Tsuchiyama S, Alvino GM, Kruglyak L, Kaeberlein M, Raghuraman MK, Brewer BJ, Kennedy BK, Bedalov A.

PLoS Genet. 2013;9(3):e1003329. doi: 10.1371/journal.pgen.1003329. Epub 2013 Mar 7.


Senataxin associates with replication forks to protect fork integrity across RNA-polymerase-II-transcribed genes.

Alzu A, Bermejo R, Begnis M, Lucca C, Piccini D, Carotenuto W, Saponaro M, Brambati A, Cocito A, Foiani M, Liberi G.

Cell. 2012 Nov 9;151(4):835-46. doi: 10.1016/j.cell.2012.09.041.


Conservation of replication timing reveals global and local regulation of replication origin activity.

Müller CA, Nieduszynski CA.

Genome Res. 2012 Oct;22(10):1953-62. doi: 10.1101/gr.139477.112. Epub 2012 Jul 5.


Optimal placement of origins for DNA replication.

Karschau J, Blow JJ, de Moura AP.

Phys Rev Lett. 2012 Feb 3;108(5):058101. Epub 2012 Jan 30.


Novel features of ARS selection in budding yeast Lachancea kluyveri.

Liachko I, Tanaka E, Cox K, Chung SC, Yang L, Seher A, Hallas L, Cha E, Kang G, Pace H, Barrow J, Inada M, Tye BK, Keich U.

BMC Genomics. 2011 Dec 28;12:633. doi: 10.1186/1471-2164-12-633.


High-resolution analysis of four efficient yeast replication origins reveals new insights into the ORC and putative MCM binding elements.

Chang F, May CD, Hoggard T, Miller J, Fox CA, Weinreich M.

Nucleic Acids Res. 2011 Aug;39(15):6523-35. doi: 10.1093/nar/gkr301. Epub 2011 May 9.


A comprehensive genome-wide map of autonomously replicating sequences in a naive genome.

Liachko I, Bhaskar A, Lee C, Chung SC, Tye BK, Keich U.

PLoS Genet. 2010 May 13;6(5):e1000946. doi: 10.1371/journal.pgen.1000946.


Genome-wide estimation of firing efficiencies of origins of DNA replication from time-course copy number variation data.

Luo H, Li J, Eshaghi M, Liu J, Karuturi RK.

BMC Bioinformatics. 2010 May 13;11:247. doi: 10.1186/1471-2105-11-247.


Mathematical modelling of whole chromosome replication.

de Moura AP, Retkute R, Hawkins M, Nieduszynski CA.

Nucleic Acids Res. 2010 Sep;38(17):5623-33. doi: 10.1093/nar/gkq343. Epub 2010 May 10.


Early initiation of a replication origin tethered at the nuclear periphery.

Ebrahimi H, Robertson ED, Taddei A, Gasser SM, Donaldson AD, Hiraga S.

J Cell Sci. 2010 Apr 1;123(Pt 7):1015-9. doi: 10.1242/jcs.060392. Epub 2010 Mar 2.


A model for the spatiotemporal organization of DNA replication in Saccharomyces cerevisiae.

Spiesser TW, Klipp E, Barberis M.

Mol Genet Genomics. 2009 Jul;282(1):25-35. doi: 10.1007/s00438-009-0443-9. Epub 2009 Mar 22.


Beyond heterochromatin: SIR2 inhibits the initiation of DNA replication.

Fox CA, Weinreich M.

Cell Cycle. 2008 Nov 1;7(21):3330-4. Epub 2008 Nov 10.


Analysis of chromosome III replicators reveals an unusual structure for the ARS318 silencer origin and a conserved WTW sequence within the origin recognition complex binding site.

Chang F, Theis JF, Miller J, Nieduszynski CA, Newlon CS, Weinreich M.

Mol Cell Biol. 2008 Aug;28(16):5071-81. doi: 10.1128/MCB.00206-08. Epub 2008 Jun 23.

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