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M K. Raghuraman - Publications

Affiliations: 
Molecular and Cellular Biology University of Washington, Seattle, Seattle, WA 
Area:
Molecular Biology, Genetics, Cell Biology, Biochemistry
Website:
http://fangman-brewer.genetics.washington.edu/
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44 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Brewer BJ, Dunham MJ, Raghuraman MK. A unifying model that explains the origins of human inverted copy number variants. Plos Genetics. 20: e1011091. PMID 38175827 DOI: 10.1371/journal.pgen.1011091  0.682
2024 Martin R, Espinoza CY, Large CRL, Rosswork J, Van Bruinisse C, Miller AW, Sanchez JC, Miller M, Paskvan S, Alvino GM, Dunham MJ, Raghuraman MK, Brewer BJ. Template switching between the leading and lagging strands at replication forks generates inverted copy number variants through hairpin-capped extrachromosomal DNA. Plos Genetics. 20: e1010850. PMID 38175823 DOI: 10.1371/journal.pgen.1010850  0.701
2023 Kwan EX, Alvino GM, Lynch KL, Levan PF, Amemiya HM, Wang XS, Johnson SA, Sanchez JC, Miller MA, Croy M, Lee SB, Naushab M, Bedalov A, Cuperus JT, Brewer BJ, ... ... Raghuraman MK, et al. Ribosomal DNA replication time coordinates completion of genome replication and anaphase in yeast. Cell Reports. 42: 112161. PMID 36842087 DOI: 10.1016/j.celrep.2023.112161  0.721
2023 Hoerr RE, Eng A, Payen C, Di Rienzi SC, Raghuraman MK, Dunham MJ, Brewer BJ, Friedman KL. Hotspot of de novo telomere addition stabilizes linear amplicons in yeast grown in sulfate-limiting conditions. Genetics. PMID 36702776 DOI: 10.1093/genetics/iyad010  0.786
2020 Kwan EX, Alvino GM, Queitsch C, Brewer BJ, Raghuraman MK. Small but greedy: a minimal rDNA array outcompetes the genome for replication initiation The Faseb Journal. 34: 1-1. DOI: 10.1096/Fasebj.2020.34.S1.04683  0.67
2019 Lynch KL, Alvino GM, Kwan EX, Brewer BJ, Raghuraman MK. The effects of manipulating levels of replication initiation factors on origin firing efficiency in yeast. Plos Genetics. 15: e1008430. PMID 31584938 DOI: 10.1371/Journal.Pgen.1008430  0.706
2019 Sanchez JC, Ollodart A, Large CRL, Clough C, Alvino GM, Tsuchiya M, Crane M, Kwan EX, Kaeberlein M, Dunham MJ, Raghuraman MK, Brewer BJ. Phenotypic and Genotypic Consequences of CRISPR/Cas9 Editing of the Replication Origins in the rDNA of . Genetics. PMID 31292210 DOI: 10.1534/Genetics.119.302351  0.706
2017 Sanchez JC, Kwan EX, Pohl TJ, Amemiya HM, Raghuraman MK, Brewer BJ. Defective replication initiation results in locus specific chromosome breakage and a ribosomal RNA deficiency in yeast. Plos Genetics. 13: e1007041. PMID 29036220 DOI: 10.1371/Journal.Pgen.1007041  0.804
2016 Kwan EX, Wang XS, Amemiya HM, Brewer BJ, Raghuraman MK. rDNA Copy Number Variants Are Frequent Passenger Mutations in S. cerevisiae Deletion Collections and De Novo Transformants. G3 (Bethesda, Md.). PMID 27449518 DOI: 10.1534/G3.116.030296  0.664
2015 Brewer BJ, Payen C, Di Rienzi SC, Higgins MM, Ong G, Dunham MJ, Raghuraman MK. Origin-Dependent Inverted-Repeat Amplification: Tests of a Model for Inverted DNA Amplification. Plos Genetics. 11: e1005699. PMID 26700858 DOI: 10.1371/Journal.Pgen.1005699  0.746
2014 Peng J, Raghuraman MK, Feng W. Analysis of ssDNA gaps and DSBs in genetically unstable yeast cultures. Methods in Molecular Biology (Clifton, N.J.). 1170: 501-15. PMID 24906332 DOI: 10.1007/978-1-4939-0888-2_27  0.536
2014 Peng J, Raghuraman MK, Feng W. Analysis of replication timing using synchronized budding yeast cultures. Methods in Molecular Biology (Clifton, N.J.). 1170: 477-99. PMID 24906331 DOI: 10.1007/978-1-4939-0888-2_26  0.539
2014 Liachko I, Youngblood RA, Tsui K, Bubb KL, Queitsch C, Raghuraman MK, Nislow C, Brewer BJ, Dunham MJ. GC-rich DNA elements enable replication origin activity in the methylotrophic yeast Pichia pastoris. Plos Genetics. 10: e1004169. PMID 24603708 DOI: 10.1371/Journal.Pgen.1004169  0.678
2014 Hiraga S, Alvino GM, Chang F, Lian HY, Sridhar A, Kubota T, Brewer BJ, Weinreich M, Raghuraman MK, Donaldson AD. Rif1 controls DNA replication by directing Protein Phosphatase 1 to reverse Cdc7-mediated phosphorylation of the MCM complex. Genes & Development. 28: 372-83. PMID 24532715 DOI: 10.1101/Gad.231258.113  0.668
2014 Payen C, Di Rienzi SC, Ong GT, Pogachar JL, Sanchez JC, Sunshine AB, Raghuraman MK, Brewer BJ, Dunham MJ. The dynamics of diverse segmental amplifications in populations of Saccharomyces cerevisiae adapting to strong selection. G3 (Bethesda, Md.). 4: 399-409. PMID 24368781 DOI: 10.1534/G3.113.009365  0.596
2013 Pohl TJ, Kolor K, Fangman WL, Brewer BJ, Raghuraman MK. A DNA sequence element that advances replication origin activation time in Saccharomyces cerevisiae. G3 (Bethesda, Md.). 3: 1955-63. PMID 24022751 DOI: 10.1534/G3.113.008250  0.788
2013 Kwan EX, Foss EJ, Tsuchiyama S, Alvino GM, Kruglyak L, Kaeberlein M, Raghuraman MK, Brewer BJ, Kennedy BK, Bedalov A. A natural polymorphism in rDNA replication origins links origin activation with calorie restriction and lifespan. Plos Genetics. 9: e1003329. PMID 23505383 DOI: 10.1371/Journal.Pgen.1003329  0.704
2012 Di Rienzi SC, Lindstrom KC, Mann T, Noble WS, Raghuraman MK, Brewer BJ. Maintaining replication origins in the face of genomic change. Genome Research. 22: 1940-52. PMID 22665441 DOI: 10.1101/Gr.138248.112  0.732
2012 Pohl TJ, Brewer BJ, Raghuraman MK. Functional centromeres determine the activation time of pericentric origins of DNA replication in Saccharomyces cerevisiae. Plos Genetics. 8: e1002677. PMID 22589733 DOI: 10.1371/Journal.Pgen.1002677  0.807
2011 Feng W, Di Rienzi SC, Raghuraman MK, Brewer BJ. Replication stress-induced chromosome breakage is correlated with replication fork progression and is preceded by single-stranded DNA formation. G3 (Bethesda, Md.). 1: 327-35. PMID 22384343 DOI: 10.1534/G3.111.000554  0.751
2011 Lian HY, Robertson ED, Hiraga S, Alvino GM, Collingwood D, McCune HJ, Sridhar A, Brewer BJ, Raghuraman MK, Donaldson AD. The effect of Ku on telomere replication time is mediated by telomere length but is independent of histone tail acetylation. Molecular Biology of the Cell. 22: 1753-65. PMID 21441303 DOI: 10.1091/Mbc.E10-06-0549  0.741
2011 Brewer BJ, Payen C, Raghuraman MK, Dunham MJ. Origin-dependent inverted-repeat amplification: a replication-based model for generating palindromic amplicons. Plos Genetics. 7: e1002016. PMID 21437266 DOI: 10.1371/Journal.Pgen.1002016  0.74
2011 Di Rienzi SC, Lindstrom KC, Lancaster R, Rolczynski L, Raghuraman MK, Brewer BJ. Genetic, genomic, and molecular tools for studying the protoploid yeast, L. waltii. Yeast (Chichester, England). 28: 137-51. PMID 21246627 DOI: 10.1002/Yea.1826  0.649
2010 Raghuraman MK, Brewer BJ. Molecular analysis of the replication program in unicellular model organisms. Chromosome Research : An International Journal On the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology. 18: 19-34. PMID 20012185 DOI: 10.1007/S10577-009-9099-X  0.655
2009 Di Rienzi SC, Collingwood D, Raghuraman MK, Brewer BJ. Fragile genomic sites are associated with origins of replication. Genome Biology and Evolution. 1: 350-63. PMID 20333204 DOI: 10.1093/Gbe/Evp034  0.701
2009 Feng W, Bachant J, Collingwood D, Raghuraman MK, Brewer BJ. Centromere replication timing determines different forms of genomic instability in Saccharomyces cerevisiae checkpoint mutants during replication stress. Genetics. 183: 1249-60. PMID 19805819 DOI: 10.1534/Genetics.109.107508  0.729
2008 McCune HJ, Danielson LS, Alvino GM, Collingwood D, Delrow JJ, Fangman WL, Brewer BJ, Raghuraman MK. The temporal program of chromosome replication: genomewide replication in clb5{Delta} Saccharomyces cerevisiae. Genetics. 180: 1833-47. PMID 18832352 DOI: 10.1534/Genetics.108.094359  0.741
2007 Hoang ML, Leon RP, Pessoa-Brandao L, Hunt S, Raghuraman MK, Fangman WL, Brewer BJ, Sclafani RA. Structural changes in Mcm5 protein bypass Cdc7-Dbf4 function and reduce replication origin efficiency in Saccharomyces cerevisiae. Molecular and Cellular Biology. 27: 7594-602. PMID 17724082 DOI: 10.1128/Mcb.00997-07  0.658
2007 Alvino GM, Collingwood D, Murphy JM, Delrow J, Brewer BJ, Raghuraman MK. Replication in hydroxyurea: it's a matter of time. Molecular and Cellular Biology. 27: 6396-406. PMID 17636020 DOI: 10.1128/Mcb.00719-07  0.703
2007 Feng W, Raghuraman MK, Brewer BJ. Mapping yeast origins of replication via single-stranded DNA detection. Methods (San Diego, Calif.). 41: 151-7. PMID 17189857 DOI: 10.1016/J.Ymeth.2006.07.023  0.69
2006 Feng W, Collingwood D, Boeck ME, Fox LA, Alvino GM, Fangman WL, Raghuraman MK, Brewer BJ. Genomic mapping of single-stranded DNA in hydroxyurea-challenged yeasts identifies origins of replication Nature Cell Biology. 8: 148-155. PMID 16429127 DOI: 10.1038/Ncb1358  0.734
2003 Lucas IA, Raghuraman MK. The dynamics of chromosome replication in yeast. Current Topics in Developmental Biology. 55: 1-73. PMID 12959193 DOI: 10.1016/S0070-2153(03)01001-9  0.367
2001 Raghuraman MK, Winzeler EA, Collingwood D, Hunt S, Wodicka L, Conway A, Lockhart DJ, Davis RW, Brewer BJ, Fangman WL. Replication dynamics of the yeast genome. Science (New York, N.Y.). 294: 115-21. PMID 11588253 DOI: 10.1126/Science.294.5540.115  0.754
2001 Heun P, Laroche T, Raghuraman MK, Gasser SM. The positioning and dynamics of origins of replication in the budding yeast nucleus. The Journal of Cell Biology. 152: 385-400. PMID 11266454 DOI: 10.1083/jcb.152.2.385  0.399
1998 Donaldson AD, Raghuraman MK, Friedman KL, Cross FR, Brewer BJ, Fangman WL. CLB5-dependent activation of late replication origins in S. cerevisiae. Molecular Cell. 2: 173-82. PMID 9734354 DOI: 10.1016/S1097-2765(00)80127-6  0.778
1997 Raghuraman MK, Brewer BJ, Fangman WL. Cell cycle-dependent establishment of a late replication program. Science (New York, N.Y.). 276: 806-9. PMID 9115207 DOI: 10.1126/Science.276.5313.806  0.69
1995 Friedman KL, Raghuraman MK, Fangman WL, Brewer BJ. Analysis of the temporal program of replication initiation in yeast chromosomes. Journal of Cell Science. Supplement. 19: 51-8. PMID 8655647 DOI: 10.1242/Jcs.1995.Supplement_19.7  0.831
1994 Diller JD, Raghuraman MK. Eukaryotic replication origins: control in space and time. Trends in Biochemical Sciences. 19: 320-5. PMID 7940676 DOI: 10.1016/0968-0004(94)90070-1  0.469
1994 Raghuraman MK, Brewer BJ, Fangman WL. Activation of a yeast replication origin near a double-stranded DNA break. Genes & Development. 8: 554-62. PMID 7926750 DOI: 10.1101/Gad.8.5.554  0.723
1993 Brewer BJ, Diller JD, Friedman KL, Kolor KM, Raghuraman MK, Fangman WL. The topography of chromosome replication in yeast. Cold Spring Harbor Symposia On Quantitative Biology. 58: 425-34. PMID 7956056 DOI: 10.1101/Sqb.1993.058.01.049  0.787
1990 Raghuraman MK, Cech TR. Effect of monovalent cation-induced telomeric DNA structure on the binding of Oxytricha telomeric protein. Nucleic Acids Research. 18: 4543-52. PMID 2388834 DOI: 10.1093/Nar/18.15.4543  0.503
1989 Williamson JR, Raghuraman MK, Cech TR. Monovalent cation-induced structure of telomeric DNA: the G-quartet model. Cell. 59: 871-80. PMID 2590943 DOI: 10.1016/0092-8674(89)90610-7  0.608
1989 Raghuraman MK, Cech TR. Assembly and self-association of oxytricha telomeric nucleoprotein complexes. Cell. 59: 719-28. PMID 2582492 DOI: 10.1016/0092-8674(89)90018-4  0.534
1989 Raghuraman MK, Dunn CJ, Hicke BJ, Cech TR. Oxytricha telomeric nucleoprotein complexes reconstituted with synthetic DNA. Nucleic Acids Research. 17: 4235-53. PMID 2500641 DOI: 10.1093/Nar/17.11.4235  0.511
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