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Items: 21

1.

Repair of multiple simultaneous double-strand breaks causes bursts of genome-wide clustered hypermutation.

Sakofsky CJ, Saini N, Klimczak LJ, Chan K, Malc EP, Mieczkowski PA, Burkholder AB, Fargo D, Gordenin DA.

PLoS Biol. 2019 Sep 30;17(9):e3000464. doi: 10.1371/journal.pbio.3000464. eCollection 2019 Sep.

2.

Repair of base damage within break-induced replication intermediates promotes kataegis associated with chromosome rearrangements.

Elango R, Osia B, Harcy V, Malc E, Mieczkowski PA, Roberts SA, Malkova A.

Nucleic Acids Res. 2019 Oct 10;47(18):9666-9684. doi: 10.1093/nar/gkz651.

3.

Corrigendum to "APOBEC3B cytidine deaminase targets the non-transcribed strand of tRNA genes in yeast" [DNA Repair 53 (2017) 4-14].

Saini N, Roberts SA, Sterling JF, Malc EP, Mieczkowski PA, Gordenin DA.

DNA Repair (Amst). 2019 Aug;80:94-95. doi: 10.1016/j.dnarep.2019.05.006. Epub 2019 Jun 7. No abstract available.

PMID:
31182349
4.

A Case Study of Genomic Instability in an Industrial Strain of Saccharomyces cerevisiae.

Rodrigues-Prause A, Sampaio NMV, Gurol TM, Aguirre GM, Sedam HNC, Chapman MJ, Malc EP, Ajith VP, Chakraborty P, Tizei PA, Pereira GAG, Mieczkowski PA, Nishant KT, Argueso JL.

G3 (Bethesda). 2018 Nov 6;8(11):3703-3713. doi: 10.1534/g3.118.200446.

5.

Genome-wide maps of alkylation damage, repair, and mutagenesis in yeast reveal mechanisms of mutational heterogeneity.

Mao P, Brown AJ, Malc EP, Mieczkowski PA, Smerdon MJ, Roberts SA, Wyrick JJ.

Genome Res. 2017 Oct;27(10):1674-1684. doi: 10.1101/gr.225771.117. Epub 2017 Sep 14.

6.

APOBEC3B cytidine deaminase targets the non-transcribed strand of tRNA genes in yeast.

Saini N, Roberts SA, Sterling JF, Malc EP, Mieczkowski PA, Gordenin DA.

DNA Repair (Amst). 2017 May;53:4-14. doi: 10.1016/j.dnarep.2017.03.003. Epub 2017 Mar 21. Erratum in: DNA Repair (Amst). 2019 Aug;80:94-95.

7.

The Impact of Environmental and Endogenous Damage on Somatic Mutation Load in Human Skin Fibroblasts.

Saini N, Roberts SA, Klimczak LJ, Chan K, Grimm SA, Dai S, Fargo DC, Boyer JC, Kaufmann WK, Taylor JA, Lee E, Cortes-Ciriano I, Park PJ, Schurman SH, Malc EP, Mieczkowski PA, Gordenin DA.

PLoS Genet. 2016 Oct 27;12(10):e1006385. doi: 10.1371/journal.pgen.1006385. eCollection 2016 Oct.

8.

APOBEC3A and APOBEC3B Preferentially Deaminate the Lagging Strand Template during DNA Replication.

Hoopes JI, Cortez LM, Mertz TM, Malc EP, Mieczkowski PA, Roberts SA.

Cell Rep. 2016 Feb 16;14(6):1273-1282. doi: 10.1016/j.celrep.2016.01.021. Epub 2016 Jan 28.

9.

An APOBEC3A hypermutation signature is distinguishable from the signature of background mutagenesis by APOBEC3B in human cancers.

Chan K, Roberts SA, Klimczak LJ, Sterling JF, Saini N, Malc EP, Kim J, Kwiatkowski DJ, Fargo DC, Mieczkowski PA, Getz G, Gordenin DA.

Nat Genet. 2015 Sep;47(9):1067-72. doi: 10.1038/ng.3378. Epub 2015 Aug 10.

10.

Cavitation Enhancing Nanodroplets Mediate Efficient DNA Fragmentation in a Bench Top Ultrasonic Water Bath.

Kasoji SK, Pattenden SG, Malc EP, Jayakody CN, Tsuruta JK, Mieczkowski PA, Janzen WP, Dayton PA.

PLoS One. 2015 Jul 17;10(7):e0133014. doi: 10.1371/journal.pone.0133014. eCollection 2015.

11.

Tracking replication enzymology in vivo by genome-wide mapping of ribonucleotide incorporation.

Clausen AR, Lujan SA, Burkholder AB, Orebaugh CD, Williams JS, Clausen MF, Malc EP, Mieczkowski PA, Fargo DC, Smith DJ, Kunkel TA.

Nat Struct Mol Biol. 2015 Mar;22(3):185-91. doi: 10.1038/nsmb.2957. Epub 2015 Jan 26.

12.

Heterogeneous polymerase fidelity and mismatch repair bias genome variation and composition.

Lujan SA, Clausen AR, Clark AB, MacAlpine HK, MacAlpine DM, Malc EP, Mieczkowski PA, Burkholder AB, Fargo DC, Gordenin DA, Kunkel TA.

Genome Res. 2014 Nov;24(11):1751-64. doi: 10.1101/gr.178335.114. Epub 2014 Sep 12.

13.

Break-induced replication is a source of mutation clusters underlying kataegis.

Sakofsky CJ, Roberts SA, Malc E, Mieczkowski PA, Resnick MA, Gordenin DA, Malkova A.

Cell Rep. 2014 Jun 12;7(5):1640-1648. doi: 10.1016/j.celrep.2014.04.053. Epub 2014 May 29.

14.

Variant calling in low-coverage whole genome sequencing of a Native American population sample.

Bizon C, Spiegel M, Chasse SA, Gizer IR, Li Y, Malc EP, Mieczkowski PA, Sailsbery JK, Wang X, Ehlers CL, Wilhelmsen KC.

BMC Genomics. 2014 Jan 30;15:85. doi: 10.1186/1471-2164-15-85.

15.

Gene copy-number variation in haploid and diploid strains of the yeast Saccharomyces cerevisiae.

Zhang H, Zeidler AF, Song W, Puccia CM, Malc E, Greenwell PW, Mieczkowski PA, Petes TD, Argueso JL.

Genetics. 2013 Mar;193(3):785-801. doi: 10.1534/genetics.112.146522. Epub 2013 Jan 10.

16.

The generation of oxidative stress-induced rearrangements in Saccharomyces cerevisiae mtDNA is dependent on the Nuc1 (EndoG/ExoG) nuclease and is enhanced by inactivation of the MRX complex.

Dzierzbicki P, Kaniak-Golik A, Malc E, Mieczkowski P, Ciesla Z.

Mutat Res. 2012 Dec;740(1-2):21-33. doi: 10.1016/j.mrfmmm.2012.12.004. Epub 2012 Dec 28.

PMID:
23276591
17.

Clustered mutations in yeast and in human cancers can arise from damaged long single-strand DNA regions.

Roberts SA, Sterling J, Thompson C, Harris S, Mav D, Shah R, Klimczak LJ, Kryukov GV, Malc E, Mieczkowski PA, Resnick MA, Gordenin DA.

Mol Cell. 2012 May 25;46(4):424-35. doi: 10.1016/j.molcel.2012.03.030. Epub 2012 May 17.

18.

High-resolution genome-wide analysis of irradiated (UV and γ-rays) diploid yeast cells reveals a high frequency of genomic loss of heterozygosity (LOH) events.

St Charles J, Hazkani-Covo E, Yin Y, Andersen SL, Dietrich FS, Greenwell PW, Malc E, Mieczkowski P, Petes TD.

Genetics. 2012 Apr;190(4):1267-84. doi: 10.1534/genetics.111.137927. Epub 2012 Jan 20.

19.

Inactivation of the 20S proteasome maturase, Ump1p, leads to the instability of mtDNA in Saccharomyces cerevisiae.

Malc E, Dzierzbicki P, Kaniak A, Skoneczna A, Ciesla Z.

Mutat Res. 2009 Oct 2;669(1-2):95-103. doi: 10.1016/j.mrfmmm.2009.05.008. Epub 2009 May 23.

PMID:
19467248
20.

Msh1p counteracts oxidative lesion-induced instability of mtDNA and stimulates mitochondrial recombination in Saccharomyces cerevisiae.

Kaniak A, Dzierzbicki P, Rogowska AT, Malc E, Fikus M, Ciesla Z.

DNA Repair (Amst). 2009 Mar 1;8(3):318-29. doi: 10.1016/j.dnarep.2008.11.004. Epub 2008 Dec 18.

PMID:
19056520
21.

Repair of oxidative damage in mitochondrial DNA of Saccharomyces cerevisiae: involvement of the MSH1-dependent pathway.

Dzierzbicki P, Koprowski P, Fikus MU, Malc E, Ciesla Z.

DNA Repair (Amst). 2004 Apr 1;3(4):403-11.

PMID:
15010316

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