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Items: 1 to 20 of 37


Bayesian inference of origin firing time distributions, origin interference and licencing probabilities from Next Generation Sequencing data.

Bazarova A, Nieduszynski CA, Akerman I, Burroughs NJ.

Nucleic Acids Res. 2019 Mar 18;47(5):2229-2243. doi: 10.1093/nar/gkz094.


Cohesin-Mediated Genome Architecture Does Not Define DNA Replication Timing Domains.

Oldach P, Nieduszynski CA.

Genes (Basel). 2019 Mar 4;10(3). pii: E196. doi: 10.3390/genes10030196.


Rapid high-resolution measurement of DNA replication timing by droplet digital PCR.

Batrakou DG, Heron ED, Nieduszynski CA.

Nucleic Acids Res. 2018 Nov 2;46(19):e112. doi: 10.1093/nar/gky590.


Investigating the role of Rts1 in DNA replication initiation.

Wallis ABA, Nieduszynski CA.

Wellcome Open Res. 2018 Mar 6;3:23. doi: 10.12688/wellcomeopenres.13884.1. eCollection 2018.


Evolution of Genome Architecture in Archaea: Spontaneous Generation of a New Chromosome in Haloferax volcanii.

Ausiannikava D, Mitchell L, Marriott H, Smith V, Hawkins M, Makarova KS, Koonin EV, Nieduszynski CA, Allers T.

Mol Biol Evol. 2018 Aug 1;35(8):1855-1868. doi: 10.1093/molbev/msy075.


Rif1 acts through Protein Phosphatase 1 but independent of replication timing to suppress telomere extension in budding yeast.

Kedziora S, Gali VK, Wilson RHC, Clark KRM, Nieduszynski CA, Hiraga SI, Donaldson AD.

Nucleic Acids Res. 2018 May 4;46(8):3993-4003. doi: 10.1093/nar/gky132.


DNA replication timing influences gene expression level.

Müller CA, Nieduszynski CA.

J Cell Biol. 2017 Jul 3;216(7):1907-1914. doi: 10.1083/jcb.201701061. Epub 2017 May 24.


Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome.

Shen Y, Wang Y, Chen T, Gao F, Gong J, Abramczyk D, Walker R, Zhao H, Chen S, Liu W, Luo Y, Müller CA, Paul-Dubois-Taine A, Alver B, Stracquadanio G, Mitchell LA, Luo Z, Fan Y, Zhou B, Wen B, Tan F, Wang Y, Zi J, Xie Z, Li B, Yang K, Richardson SM, Jiang H, French CE, Nieduszynski CA, Koszul R, Marston AL, Yuan Y, Wang J, Bader JS, Dai J, Boeke JD, Xu X, Cai Y, Yang H.

Science. 2017 Mar 10;355(6329). pii: eaaf4791. doi: 10.1126/science.aaf4791.


Discovery of an unconventional centromere in budding yeast redefines evolution of point centromeres.

Kobayashi N, Suzuki Y, Schoenfeld LW, Müller CA, Nieduszynski C, Wolfe KH, Tanaka TU.

Curr Biol. 2015 Aug 3;25(15):2026-33. doi: 10.1016/j.cub.2015.06.023. Epub 2015 Jul 9.


A global profile of replicative polymerase usage.

Daigaku Y, Keszthelyi A, Müller CA, Miyabe I, Brooks T, Retkute R, Hubank M, Nieduszynski CA, Carr AM.

Nat Struct Mol Biol. 2015 Mar;22(3):192-198. doi: 10.1038/nsmb.2962. Epub 2015 Feb 9.


High-resolution replication profiles define the stochastic nature of genome replication initiation and termination.

Hawkins M, Retkute R, Müller CA, Saner N, Tanaka TU, de Moura AP, Nieduszynski CA.

Cell Rep. 2013 Nov 27;5(4):1132-41. doi: 10.1016/j.celrep.2013.10.014. Epub 2013 Nov 7.


Accelerated growth in the absence of DNA replication origins.

Hawkins M, Malla S, Blythe MJ, Nieduszynski CA, Allers T.

Nature. 2013 Nov 28;503(7477):544-547. doi: 10.1038/nature12650. Epub 2013 Nov 3.


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.


Stochastic association of neighboring replicons creates replication factories in budding yeast.

Saner N, Karschau J, Natsume T, Gierlinski M, Retkute R, Hawkins M, Nieduszynski CA, Blow JJ, de Moura AP, Tanaka TU.

J Cell Biol. 2013 Sep 30;202(7):1001-12. doi: 10.1083/jcb.201306143. Epub 2013 Sep 23.


Replisome stall events have shaped the distribution of replication origins in the genomes of yeasts.

Newman TJ, Mamun MA, Nieduszynski CA, Blow JJ.

Nucleic Acids Res. 2013 Nov;41(21):9705-18. doi: 10.1093/nar/gkt728. Epub 2013 Aug 19.


Avoiding chromosome pathology when replication forks collide.

Rudolph CJ, Upton AL, Stockum A, Nieduszynski CA, Lloyd RG.

Nature. 2013 Aug 29;500(7464):608-11. doi: 10.1038/nature12312. Epub 2013 Jul 28.


Kinetochores coordinate pericentromeric cohesion and early DNA replication by Cdc7-Dbf4 kinase recruitment.

Natsume T, Müller CA, Katou Y, Retkute R, Gierliński M, Araki H, Blow JJ, Shirahige K, Nieduszynski CA, Tanaka TU.

Mol Cell. 2013 Jun 6;50(5):661-74. doi: 10.1016/j.molcel.2013.05.011.


High quality de novo sequencing and assembly of the Saccharomyces arboricolus genome.

Liti G, Nguyen Ba AN, Blythe M, Müller CA, Bergström A, Cubillos FA, Dafhnis-Calas F, Khoshraftar S, Malla S, Mehta N, Siow CC, Warringer J, Moses AM, Louis EJ, Nieduszynski CA.

BMC Genomics. 2013 Jan 31;14:69. doi: 10.1186/1471-2164-14-69.


Mathematical modeling of genome replication.

Retkute R, Nieduszynski CA, de Moura A.

Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Sep;86(3 Pt 1):031916. Epub 2012 Sep 17.

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