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Items: 37

1.

Genome-wide analysis of DNA replication timing in single cells: Yes! We're all individuals.

Donaldson AD, Nieduszynski CA.

Genome Biol. 2019 May 30;20(1):111. doi: 10.1186/s13059-019-1719-y.

2.

Interspecies conservation of organisation and function between nonhomologous regional centromeres.

Tong P, Pidoux AL, Toda NRT, Ard R, Berger H, Shukla M, Torres-Garcia J, Müller CA, Nieduszynski CA, Allshire RC.

Nat Commun. 2019 May 28;10(1):2343. doi: 10.1038/s41467-019-09824-4.

3.

Capturing the dynamics of genome replication on individual ultra-long nanopore sequence reads.

Müller CA, Boemo MA, Spingardi P, Kessler BM, Kriaucionis S, Simpson JT, Nieduszynski CA.

Nat Methods. 2019 May;16(5):429-436. doi: 10.1038/s41592-019-0394-y. Epub 2019 Apr 22.

PMID:
31011185
4.

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.

5.

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.

6.

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.

7.

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.

8.

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.

9.

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.

10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

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.

20.

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.

21.

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.

22.

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.

23.

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.

24.

A putative homologue of CDC20/CDH1 in the malaria parasite is essential for male gamete development.

Guttery DS, Ferguson DJ, Poulin B, Xu Z, Straschil U, Klop O, Solyakov L, Sandrini SM, Brady D, Nieduszynski CA, Janse CJ, Holder AA, Tobin AB, Tewari R.

PLoS Pathog. 2012 Feb;8(2):e1002554. doi: 10.1371/journal.ppat.1002554. Epub 2012 Feb 23. Erratum in: PLoS Pathog. 2012 Mar;8(3). doi: 10.1371/annotation/ef70d427-0816-4a63-aeaf-874b734793b0.

25.

OriDB, the DNA replication origin database updated and extended.

Siow CC, Nieduszynska SR, Müller CA, Nieduszynski CA.

Nucleic Acids Res. 2012 Jan;40(Database issue):D682-6. doi: 10.1093/nar/gkr1091. Epub 2011 Nov 24.

26.

Dynamics of DNA replication in yeast.

Retkute R, Nieduszynski CA, de Moura A.

Phys Rev Lett. 2011 Aug 5;107(6):068103. Epub 2011 Aug 4.

27.

Comparative functional genomics of the fission yeasts.

Rhind N, Chen Z, Yassour M, Thompson DA, Haas BJ, Habib N, Wapinski I, Roy S, Lin MF, Heiman DI, Young SK, Furuya K, Guo Y, Pidoux A, Chen HM, Robbertse B, Goldberg JM, Aoki K, Bayne EH, Berlin AM, Desjardins CA, Dobbs E, Dukaj L, Fan L, FitzGerald MG, French C, Gujja S, Hansen K, Keifenheim D, Levin JZ, Mosher RA, Müller CA, Pfiffner J, Priest M, Russ C, Smialowska A, Swoboda P, Sykes SM, Vaughn M, Vengrova S, Yoder R, Zeng Q, Allshire R, Baulcombe D, Birren BW, Brown W, Ekwall K, Kellis M, Leatherwood J, Levin H, Margalit H, Martienssen R, Nieduszynski CA, Spatafora JW, Friedman N, Dalgaard JZ, Baumann P, Niki H, Regev A, Nusbaum C.

Science. 2011 May 20;332(6032):930-6. doi: 10.1126/science.1203357. Epub 2011 Apr 21.

28.

From sequence to function: Insights from natural variation in budding yeasts.

Nieduszynski CA, Liti G.

Biochim Biophys Acta. 2011 Oct;1810(10):959-66. doi: 10.1016/j.bbagen.2011.02.004. Epub 2011 Feb 12. Review.

29.

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.

30.

The origin recognition complex interacts with a subset of metabolic genes tightly linked to origins of replication.

Shor E, Warren CL, Tietjen J, Hou Z, Müller U, Alborelli I, Gohard FH, Yemm AI, Borisov L, Broach JR, Weinreich M, Nieduszynski CA, Ansari AZ, Fox CA.

PLoS Genet. 2009 Dec;5(12):e1000755. doi: 10.1371/journal.pgen.1000755. Epub 2009 Dec 4.

31.

Detection of replication origins using comparative genomics and recombinational ARS assay.

Nieduszynski CA, Donaldson AD.

Methods Mol Biol. 2009;521:295-313. doi: 10.1007/978-1-60327-815-7_16.

PMID:
19563113
32.

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.

33.

OriDB: a DNA replication origin database.

Nieduszynski CA, Hiraga S, Ak P, Benham CJ, Donaldson AD.

Nucleic Acids Res. 2007 Jan;35(Database issue):D40-6. Epub 2006 Oct 25.

34.

Genome-wide identification of replication origins in yeast by comparative genomics.

Nieduszynski CA, Knox Y, Donaldson AD.

Genes Dev. 2006 Jul 15;20(14):1874-9.

35.

The requirement of yeast replication origins for pre-replication complex proteins is modulated by transcription.

Nieduszynski CA, Blow JJ, Donaldson AD.

Nucleic Acids Res. 2005 Apr 28;33(8):2410-20. Print 2005.

36.

Whole-genome analysis of animal A- and B-type cyclins.

Nieduszynski CA, Murray J, Carrington M.

Genome Biol. 2002;3(12):RESEARCH0070. Epub 2002 Nov 15.

37.

Ku complex controls the replication time of DNA in telomere regions.

Cosgrove AJ, Nieduszynski CA, Donaldson AD.

Genes Dev. 2002 Oct 1;16(19):2485-90.

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