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Challenges and Approaches to Genotyping Repetitive DNA.

Morton EA, Hall AN, Kwan E, Mok C, Queitsch K, Nandakumar V, Stamatoyannopoulos J, Brewer BJ, Waterston R, Queitsch C.

G3 (Bethesda). 2019 Nov 22. pii: g3.400771.2019. doi: 10.1534/g3.119.400771. [Epub ahead of print]


The effects of manipulating levels of replication initiation factors on origin firing efficiency in yeast.

Lynch KL, Alvino GM, Kwan EX, Brewer BJ, Raghuraman MK.

PLoS Genet. 2019 Oct 4;15(10):e1008430. doi: 10.1371/journal.pgen.1008430. eCollection 2019 Oct.


Two major accretion epochs in M31 from two distinct populations of globular clusters.

Mackey D, Lewis GF, Brewer BJ, Ferguson AMN, Veljanoski J, Huxor AP, Collins MLM, Côté P, Ibata RA, Irwin MJ, Martin N, McConnachie AW, Peñarrubia J, Tanvir N, Wan Z.

Nature. 2019 Oct;574(7776):69-71. doi: 10.1038/s41586-019-1597-1. Epub 2019 Oct 2.


Phenotypic and Genotypic Consequences of CRISPR/Cas9 Editing of the Replication Origins in the rDNA of Saccharomyces cerevisiae.

Sanchez JC, Ollodart A, Large CRL, Clough C, Alvino GM, Tsuchiya M, Crane M, Kwan EX, Kaeberlein M, Dunham MJ, Raghuraman MK, Brewer BJ.

Genetics. 2019 Sep;213(1):229-249. doi: 10.1534/genetics.119.302351. Epub 2019 Jul 10.


Model Selection and Parameter Inference in Phylogenetics Using Nested Sampling.

Russel PM, Brewer BJ, Klaere S, Bouckaert RR.

Syst Biol. 2019 Mar 1;68(2):219-233. doi: 10.1093/sysbio/syy050.


Defective replication initiation results in locus specific chromosome breakage and a ribosomal RNA deficiency in yeast.

Sanchez JC, Kwan EX, Pohl TJ, Amemiya HM, Raghuraman MK, Brewer BJ.

PLoS Genet. 2017 Oct 16;13(10):e1007041. doi: 10.1371/journal.pgen.1007041. eCollection 2017 Oct.


rDNA Copy Number Variants Are Frequent Passenger Mutations in Saccharomyces cerevisiae Deletion Collections and de Novo Transformants.

Kwan EX, Wang XS, Amemiya HM, Brewer BJ, Raghuraman MK.

G3 (Bethesda). 2016 Sep 8;6(9):2829-38. doi: 10.1534/g3.116.030296.


Origin-Dependent Inverted-Repeat Amplification: Tests of a Model for Inverted DNA Amplification.

Brewer BJ, Payen C, Di Rienzi SC, Higgins MM, Ong G, Dunham MJ, Raghuraman MK.

PLoS Genet. 2015 Dec 23;11(12):e1005699. doi: 10.1371/journal.pgen.1005699. eCollection 2015 Dec.


The B. subtilis Accessory Helicase PcrA Facilitates DNA Replication through Transcription Units.

Merrikh CN, Brewer BJ, Merrikh H.

PLoS Genet. 2015 Jun 12;11(6):e1005289. doi: 10.1371/journal.pgen.1005289. eCollection 2015 Jun.


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.


Rif1 controls DNA replication by directing Protein Phosphatase 1 to reverse Cdc7-mediated phosphorylation of the MCM complex.

Hiraga S, Alvino GM, Chang F, Lian HY, Sridhar A, Kubota T, Brewer BJ, Weinreich M, Raghuraman MK, Donaldson AD.

Genes Dev. 2014 Feb 15;28(4):372-83. doi: 10.1101/gad.231258.113.


The dynamics of diverse segmental amplifications in populations of Saccharomyces cerevisiae adapting to strong selection.

Payen C, Di Rienzi SC, Ong GT, Pogachar JL, Sanchez JC, Sunshine AB, Raghuraman MK, Brewer BJ, Dunham MJ.

G3 (Bethesda). 2014 Mar 20;4(3):399-409. doi: 10.1534/g3.113.009365.


A DNA sequence element that advances replication origin activation time in Saccharomyces cerevisiae.

Pohl TJ, Kolor K, Fangman WL, Brewer BJ, Raghuraman MK.

G3 (Bethesda). 2013 Nov 6;3(11):1955-63. doi: 10.1534/g3.113.008250.


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.


Maintaining replication origins in the face of genomic change.

Di Rienzi SC, Lindstrom KC, Mann T, Noble WS, Raghuraman MK, Brewer BJ.

Genome Res. 2012 Oct;22(10):1940-52. doi: 10.1101/gr.138248.112. Epub 2012 Jun 4.


Functional centromeres determine the activation time of pericentric origins of DNA replication in Saccharomyces cerevisiae.

Pohl TJ, Brewer BJ, Raghuraman MK.

PLoS Genet. 2012;8(5):e1002677. doi: 10.1371/journal.pgen.1002677. Epub 2012 May 10.


Replication stress-induced chromosome breakage is correlated with replication fork progression and is preceded by single-stranded DNA formation.

Feng W, Di Rienzi SC, Raghuraman MK, Brewer BJ.

G3 (Bethesda). 2011 Oct;1(5):327-35. doi: 10.1534/g3.111.000554. Epub 2011 Oct 1.


The effect of Ku on telomere replication time is mediated by telomere length but is independent of histone tail acetylation.

Lian HY, Robertson ED, Hiraga S, Alvino GM, Collingwood D, McCune HJ, Sridhar A, Brewer BJ, Raghuraman MK, Donaldson AD.

Mol Biol Cell. 2011 May 15;22(10):1753-65. doi: 10.1091/mbc.E10-06-0549. Epub 2011 Mar 25.


Origin-dependent inverted-repeat amplification: a replication-based model for generating palindromic amplicons.

Brewer BJ, Payen C, Raghuraman MK, Dunham MJ.

PLoS Genet. 2011 Mar;7(3):e1002016. doi: 10.1371/journal.pgen.1002016. Epub 2011 Mar 17. No abstract available.


Genetic, genomic, and molecular tools for studying the protoploid yeast, L. waltii.

Di Rienzi SC, Lindstrom KC, Lancaster R, Rolczynski L, Raghuraman MK, Brewer BJ.

Yeast. 2011 Feb;28(2):137-51. doi: 10.1002/yea.1826. Epub 2010 Nov 2.


Molecular analysis of the replication program in unicellular model organisms.

Raghuraman MK, Brewer BJ.

Chromosome Res. 2010 Jan;18(1):19-34. doi: 10.1007/s10577-009-9099-x.


Centromere replication timing determines different forms of genomic instability in Saccharomyces cerevisiae checkpoint mutants during replication stress.

Feng W, Bachant J, Collingwood D, Raghuraman MK, Brewer BJ.

Genetics. 2009 Dec;183(4):1249-60. doi: 10.1534/genetics.109.107508. Epub 2009 Oct 5.


Fragile genomic sites are associated with origins of replication.

Di Rienzi SC, Collingwood D, Raghuraman MK, Brewer BJ.

Genome Biol Evol. 2009 Sep 9;1:350-63. doi: 10.1093/gbe/evp034.


The temporal program of chromosome replication: genomewide replication in clb5{Delta} Saccharomyces cerevisiae.

McCune HJ, Danielson LS, Alvino GM, Collingwood D, Delrow JJ, Fangman WL, Brewer BJ, Raghuraman MK.

Genetics. 2008 Dec;180(4):1833-47. doi: 10.1534/genetics.108.094359. Epub 2008 Oct 1.


Structural changes in Mcm5 protein bypass Cdc7-Dbf4 function and reduce replication origin efficiency in Saccharomyces cerevisiae.

Hoang ML, Leon RP, Pessoa-Brandao L, Hunt S, Raghuraman MK, Fangman WL, Brewer BJ, Sclafani RA.

Mol Cell Biol. 2007 Nov;27(21):7594-602. Epub 2007 Aug 27.


Replication in hydroxyurea: it's a matter of time.

Alvino GM, Collingwood D, Murphy JM, Delrow J, Brewer BJ, Raghuraman MK.

Mol Cell Biol. 2007 Sep;27(18):6396-406. Epub 2007 Jul 16.


Mapping yeast origins of replication via single-stranded DNA detection.

Feng W, Raghuraman MK, Brewer BJ.

Methods. 2007 Feb;41(2):151-7.


Genomic mapping of single-stranded DNA in hydroxyurea-challenged yeasts identifies origins of replication.

Feng W, Collingwood D, Boeck ME, Fox LA, Alvino GM, Fangman WL, Raghuraman MK, Brewer BJ.

Nat Cell Biol. 2006 Feb;8(2):148-55. Epub 2006 Jan 22.


Histone acetylation regulates the time of replication origin firing.

Vogelauer M, Rubbi L, Lucas I, Brewer BJ, Grunstein M.

Mol Cell. 2002 Nov;10(5):1223-33.


Replication dynamics of the yeast genome.

Raghuraman MK, Winzeler EA, Collingwood D, Hunt S, Wodicka L, Conway A, Lockhart DJ, Davis RW, Brewer BJ, Fangman WL.

Science. 2001 Oct 5;294(5540):115-21.


An origin-deficient yeast artificial chromosome triggers a cell cycle checkpoint.

van Brabant AJ, Buchanan CD, Charboneau E, Fangman WL, Brewer BJ.

Mol Cell. 2001 Apr;7(4):705-13.


Ribosomal DNA replication fork barrier and HOT1 recombination hot spot: shared sequences but independent activities.

Ward TR, Hoang ML, Prusty R, Lau CK, Keil RL, Fangman WL, Brewer BJ.

Mol Cell Biol. 2000 Jul;20(13):4948-57.


Active role of a human genomic insert in replication of a yeast artificial chromosome.

van Brabant AJ, Fangman WL, Brewer BJ.

Mol Cell Biol. 1999 Jun;19(6):4231-40.


CLB5-dependent activation of late replication origins in S. cerevisiae.

Donaldson AD, Raghuraman MK, Friedman KL, Cross FR, Brewer BJ, Fangman WL.

Mol Cell. 1998 Aug;2(2):173-82.


Identifying sites of replication initiation in yeast chromosomes: looking for origins in all the right places.

van Brabant AJ, Hunt SY, Fangman WL, Brewer BJ.

Electrophoresis. 1998 Jun;19(8-9):1239-46.


Cdc7 is required throughout the yeast S phase to activate replication origins.

Donaldson AD, Fangman WL, Brewer BJ.

Genes Dev. 1998 Feb 15;12(4):491-501.


Replication profile of Saccharomyces cerevisiae chromosome VI.

Friedman KL, Brewer BJ, Fangman WL.

Genes Cells. 1997 Nov;2(11):667-78.


Cell cycle-dependent establishment of a late replication program.

Raghuraman MK, Brewer BJ, Fangman WL.

Science. 1997 May 2;276(5313):806-9.


Multiple determinants controlling activation of yeast replication origins late in S phase.

Friedman KL, Diller JD, Ferguson BM, Nyland SV, Brewer BJ, Fangman WL.

Genes Dev. 1996 Jul 1;10(13):1595-607.


A test of the transcription model for biased inheritance of yeast mitochondrial DNA.

Lorimer HE, Brewer BJ, Fangman WL.

Mol Cell Biol. 1995 Sep;15(9):4803-9.


A role for recombination junctions in the segregation of mitochondrial DNA in yeast.

Lockshon D, Zweifel SG, Freeman-Cook LL, Lorimer HE, Brewer BJ, Fangman WL.

Cell. 1995 Jun 16;81(6):947-55.


Analysis of the temporal program of replication initiation in yeast chromosomes.

Friedman KL, Raghuraman MK, Fangman WL, Brewer BJ.

J Cell Sci Suppl. 1995;19:51-8.


Analysis of replication intermediates by two-dimensional agarose gel electrophoresis.

Friedman KL, Brewer BJ.

Methods Enzymol. 1995;262:613-27. No abstract available.


Initiation preference at a yeast origin of replication.

Brewer BJ, Fangman WL.

Proc Natl Acad Sci U S A. 1994 Apr 12;91(8):3418-22.


Intergenic DNA and the sequence requirements for replication initiation in eukaryotes.

Brewer BJ.

Curr Opin Genet Dev. 1994 Apr;4(2):196-202. Review.


Activation of a yeast replication origin near a double-stranded DNA break.

Raghuraman MK, Brewer BJ, Fangman WL.

Genes Dev. 1994 Mar 1;8(5):554-62.


Initiation at closely spaced replication origins in a yeast chromosome.

Brewer BJ, Fangman WL.

Science. 1993 Dec 10;262(5140):1728-31.


The topography of chromosome replication in yeast.

Brewer BJ, Diller JD, Friedman KL, Kolor KM, Raghuraman MK, Fangman WL.

Cold Spring Harb Symp Quant Biol. 1993;58:425-34. No abstract available.


A question of time: replication origins of eukaryotic chromosomes.

Fangman WL, Brewer BJ.

Cell. 1992 Oct 30;71(3):363-6. Review. No abstract available.


The arrest of replication forks in the rDNA of yeast occurs independently of transcription.

Brewer BJ, Lockshon D, Fangman WL.

Cell. 1992 Oct 16;71(2):267-76.


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