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Items: 1 to 50 of 73

1.

Genomic Subtypes of Non-invasive Bladder Cancer with Distinct Metabolic Profile and Female Gender Bias in KDM6A Mutation Frequency.

Hurst CD, Alder O, Platt FM, Droop A, Stead LF, Burns JE, Burghel GJ, Jain S, Klimczak LJ, Lindsay H, Roulson JA, Taylor CF, Thygesen H, Cameron AJ, Ridley AJ, Mott HR, Gordenin DA, Knowles MA.

Cancer Cell. 2017 Nov 13;32(5):701-715.e7. doi: 10.1016/j.ccell.2017.08.005.

PMID:
29136510
2.

Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer.

Robertson AG, Kim J, Al-Ahmadie H, Bellmunt J, Guo G, Cherniack AD, Hinoue T, Laird PW, Hoadley KA, Akbani R, Castro MAA, Gibb EA, Kanchi RS, Gordenin DA, Shukla SA, Sanchez-Vega F, Hansel DE, Czerniak BA, Reuter VE, Su X, de Sa Carvalho B, Chagas VS, Mungall KL, Sadeghi S, Pedamallu CS, Lu Y, Klimczak LJ, Zhang J, Choo C, Ojesina AI, Bullman S, Leraas KM, Lichtenberg TM, Wu CJ, Schultz N, Getz G, Meyerson M, Mills GB, McConkey DJ; TCGA Research Network, Weinstein JN, Kwiatkowski DJ, Lerner SP.

Cell. 2017 Oct 19;171(3):540-556.e25. doi: 10.1016/j.cell.2017.09.007. Epub 2017 Oct 5.

PMID:
28988769
3.

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.

PMID:
28351647
4.

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.

5.

Who Is Leading the Replication Fork, Pol ε or Pol δ?

Burgers PMJ, Gordenin D, Kunkel TA.

Mol Cell. 2016 Feb 18;61(4):492-493. doi: 10.1016/j.molcel.2016.01.017. No abstract available.

6.

Clusters of Multiple Mutations: Incidence and Molecular Mechanisms.

Chan K, Gordenin DA.

Annu Rev Genet. 2015;49:243-67. doi: 10.1146/annurev-genet-112414-054714. Review.

7.

APOBEC-Induced Cancer Mutations Are Uniquely Enriched in Early-Replicating, Gene-Dense, and Active Chromatin Regions.

Kazanov MD, Roberts SA, Polak P, Stamatoyannopoulos J, Klimczak LJ, Gordenin DA, Sunyaev SR.

Cell Rep. 2015 Nov 10;13(6):1103-1109. doi: 10.1016/j.celrep.2015.09.077. Epub 2015 Oct 29.

8.

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.

9.

Hypermutation in human cancer genomes: footprints and mechanisms.

Roberts SA, Gordenin DA.

Nat Rev Cancer. 2014 Dec;14(12):786-800. doi: 10.1038/nrc3816. Review. Erratum in: Nat Rev Cancer. 2015 Nov;15(11):694.

10.

Suppression of allelic recombination and aneuploidy by cohesin is independent of Chk1 in Saccharomyces cerevisiae.

Covo S, Chiou E, Gordenin DA, Resnick MA.

PLoS One. 2014 Dec 31;9(12):e113435. doi: 10.1371/journal.pone.0113435. eCollection 2014.

11.

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.

12.

The somatic genomic landscape of chromophobe renal cell carcinoma.

Davis CF, Ricketts CJ, Wang M, Yang L, Cherniack AD, Shen H, Buhay C, Kang H, Kim SC, Fahey CC, Hacker KE, Bhanot G, Gordenin DA, Chu A, Gunaratne PH, Biehl M, Seth S, Kaipparettu BA, Bristow CA, Donehower LA, Wallen EM, Smith AB, Tickoo SK, Tamboli P, Reuter V, Schmidt LS, Hsieh JJ, Choueiri TK, Hakimi AA; The Cancer Genome Atlas Research Network, Chin L, Meyerson M, Kucherlapati R, Park WY, Robertson AG, Laird PW, Henske EP, Kwiatkowski DJ, Park PJ, Morgan M, Shuch B, Muzny D, Wheeler DA, Linehan WM, Gibbs RA, Rathmell WK, Creighton CJ.

Cancer Cell. 2014 Sep 8;26(3):319-330. doi: 10.1016/j.ccr.2014.07.014. Epub 2014 Aug 21.

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.

Clustered and genome-wide transient mutagenesis in human cancers: Hypermutation without permanent mutators or loss of fitness.

Roberts SA, Gordenin DA.

Bioessays. 2014 Feb 26. doi: 10.1002/bies.201300140. [Epub ahead of print]

15.

The sister chromatid cohesion pathway suppresses multiple chromosome gain and chromosome amplification.

Covo S, Puccia CM, Argueso JL, Gordenin DA, Resnick MA.

Genetics. 2014 Feb;196(2):373-84. doi: 10.1534/genetics.113.159202. Epub 2013 Dec 2.

16.

The choice of nucleotide inserted opposite abasic sites formed within chromosomal DNA reveals the polymerase activities participating in translesion DNA synthesis.

Chan K, Resnick MA, Gordenin DA.

DNA Repair (Amst). 2013 Nov;12(11):878-89. doi: 10.1016/j.dnarep.2013.07.008. Epub 2013 Aug 26.

17.

Oxidative stress-induced mutagenesis in single-strand DNA occurs primarily at cytosines and is DNA polymerase zeta-dependent only for adenines and guanines.

Degtyareva NP, Heyburn L, Sterling J, Resnick MA, Gordenin DA, Doetsch PW.

Nucleic Acids Res. 2013 Oct;41(19):8995-9005. doi: 10.1093/nar/gkt671. Epub 2013 Aug 7.

18.

An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers.

Roberts SA, Lawrence MS, Klimczak LJ, Grimm SA, Fargo D, Stojanov P, Kiezun A, Kryukov GV, Carter SL, Saksena G, Harris S, Shah RR, Resnick MA, Getz G, Gordenin DA.

Nat Genet. 2013 Sep;45(9):970-6. doi: 10.1038/ng.2702. Epub 2013 Jul 14.

19.

Mutational heterogeneity in cancer and the search for new cancer-associated genes.

Lawrence MS, Stojanov P, Polak P, Kryukov GV, Cibulskis K, Sivachenko A, Carter SL, Stewart C, Mermel CH, Roberts SA, Kiezun A, Hammerman PS, McKenna A, Drier Y, Zou L, Ramos AH, Pugh TJ, Stransky N, Helman E, Kim J, Sougnez C, Ambrogio L, Nickerson E, Shefler E, Cortés ML, Auclair D, Saksena G, Voet D, Noble M, DiCara D, Lin P, Lichtenstein L, Heiman DI, Fennell T, Imielinski M, Hernandez B, Hodis E, Baca S, Dulak AM, Lohr J, Landau DA, Wu CJ, Melendez-Zajgla J, Hidalgo-Miranda A, Koren A, McCarroll SA, Mora J, Crompton B, Onofrio R, Parkin M, Winckler W, Ardlie K, Gabriel SB, Roberts CWM, Biegel JA, Stegmaier K, Bass AJ, Garraway LA, Meyerson M, Golub TR, Gordenin DA, Sunyaev S, Lander ES, Getz G.

Nature. 2013 Jul 11;499(7457):214-218. doi: 10.1038/nature12213. Epub 2013 Jun 16.

20.

Base damage within single-strand DNA underlies in vivo hypermutability induced by a ubiquitous environmental agent.

Chan K, Sterling JF, Roberts SA, Bhagwat AS, Resnick MA, Gordenin DA.

PLoS Genet. 2012;8(12):e1003149. doi: 10.1371/journal.pgen.1003149. Epub 2012 Dec 13.

21.

Understanding the origins of UV-induced recombination through manipulation of sister chromatid cohesion.

Covo S, Ma W, Westmoreland JW, Gordenin DA, Resnick MA.

Cell Cycle. 2012 Nov 1;11(21):3937-44. doi: 10.4161/cc.21945. Epub 2012 Sep 17.

22.

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.

23.

RAD53 is limiting in double-strand break repair and in protection against toxicity associated with ribonucleotide reductase inhibition.

Covo S, Westmoreland JW, Reddy AK, Gordenin DA, Resnick MA.

DNA Repair (Amst). 2012 Mar 1;11(3):317-23. doi: 10.1016/j.dnarep.2011.12.008. Epub 2012 Jan 23.

24.

Alkylation base damage is converted into repairable double-strand breaks and complex intermediates in G2 cells lacking AP endonuclease.

Ma W, Westmoreland JW, Gordenin DA, Resnick MA.

PLoS Genet. 2011 Apr;7(4):e1002059. doi: 10.1371/journal.pgen.1002059. Epub 2011 Apr 28.

25.

Damage-induced localized hypermutability.

Burch LH, Yang Y, Sterling JF, Roberts SA, Chao FG, Xu H, Zhang L, Walsh J, Resnick MA, Mieczkowski PA, Gordenin DA.

Cell Cycle. 2011 Apr 1;10(7):1073-85. Epub 2011 Apr 1.

26.

Genome-wide model for the normal eukaryotic DNA replication fork.

Larrea AA, Lujan SA, Nick McElhinny SA, Mieczkowski PA, Resnick MA, Gordenin DA, Kunkel TA.

Proc Natl Acad Sci U S A. 2010 Oct 12;107(41):17674-9. doi: 10.1073/pnas.1010178107. Epub 2010 Sep 27.

27.

A single-strand specific lesion drives MMS-induced hyper-mutability at a double-strand break in yeast.

Yang Y, Gordenin DA, Resnick MA.

DNA Repair (Amst). 2010 Aug 5;9(8):914-21. doi: 10.1016/j.dnarep.2010.06.005. Epub 2010 Jul 21.

28.

Cohesin Is limiting for the suppression of DNA damage-induced recombination between homologous chromosomes.

Covo S, Westmoreland JW, Gordenin DA, Resnick MA.

PLoS Genet. 2010 Jul 1;6(7):e1001006. doi: 10.1371/journal.pgen.1001006.

29.

The transition of closely opposed lesions to double-strand breaks during long-patch base excision repair is prevented by the coordinated action of DNA polymerase delta and Rad27/Fen1.

Ma W, Panduri V, Sterling JF, Van Houten B, Gordenin DA, Resnick MA.

Mol Cell Biol. 2009 Mar;29(5):1212-21. doi: 10.1128/MCB.01499-08. Epub 2008 Dec 15.

30.

Hypermutability of damaged single-strand DNA formed at double-strand breaks and uncapped telomeres in yeast Saccharomyces cerevisiae.

Yang Y, Sterling J, Storici F, Resnick MA, Gordenin DA.

PLoS Genet. 2008 Nov;4(11):e1000264. doi: 10.1371/journal.pgen.1000264. Epub 2008 Nov 21.

31.

Flexibility of eukaryotic Okazaki fragment maturation through regulated strand displacement synthesis.

Stith CM, Sterling J, Resnick MA, Gordenin DA, Burgers PM.

J Biol Chem. 2008 Dec 5;283(49):34129-40. doi: 10.1074/jbc.M806668200. Epub 2008 Oct 16.

32.

Division of labor at the eukaryotic replication fork.

Nick McElhinny SA, Gordenin DA, Stith CM, Burgers PM, Kunkel TA.

Mol Cell. 2008 Apr 25;30(2):137-44. doi: 10.1016/j.molcel.2008.02.022.

33.

Apn1 and Apn2 endonucleases prevent accumulation of repair-associated DNA breaks in budding yeast as revealed by direct chromosomal analysis.

Ma W, Resnick MA, Gordenin DA.

Nucleic Acids Res. 2008 Apr;36(6):1836-46. doi: 10.1093/nar/gkm1148. Epub 2008 Feb 11.

34.

RNA-templated DNA repair.

Storici F, Bebenek K, Kunkel TA, Gordenin DA, Resnick MA.

Nature. 2007 May 17;447(7142):338-41. Epub 2007 Apr 11. Erratum in: Nature. 2007 Aug 30;448(7157):1076.

35.

Conservative repair of a chromosomal double-strand break by single-strand DNA through two steps of annealing.

Storici F, Snipe JR, Chan GK, Gordenin DA, Resnick MA.

Mol Cell Biol. 2006 Oct;26(20):7645-57. Epub 2006 Aug 14.

36.

The multiple biological roles of the 3'-->5' exonuclease of Saccharomyces cerevisiae DNA polymerase delta require switching between the polymerase and exonuclease domains.

Jin YH, Garg P, Stith CM, Al-Refai H, Sterling JF, Murray LJ, Kunkel TA, Resnick MA, Burgers PM, Gordenin DA.

Mol Cell Biol. 2005 Jan;25(1):461-71.

37.

Chromosomal site-specific double-strand breaks are efficiently targeted for repair by oligonucleotides in yeast.

Storici F, Durham CL, Gordenin DA, Resnick MA.

Proc Natl Acad Sci U S A. 2003 Dec 9;100(25):14994-9. Epub 2003 Nov 20.

38.

Cadmium is a mutagen that acts by inhibiting mismatch repair.

Jin YH, Clark AB, Slebos RJ, Al-Refai H, Taylor JA, Kunkel TA, Resnick MA, Gordenin DA.

Nat Genet. 2003 Jul;34(3):326-9.

39.

Okazaki fragment maturation in yeast. I. Distribution of functions between FEN1 AND DNA2.

Ayyagari R, Gomes XV, Gordenin DA, Burgers PM.

J Biol Chem. 2003 Jan 17;278(3):1618-25. Epub 2002 Nov 6.

40.

Okazaki fragment maturation in yeast. II. Cooperation between the polymerase and 3'-5'-exonuclease activities of Pol delta in the creation of a ligatable nick.

Jin YH, Ayyagari R, Resnick MA, Gordenin DA, Burgers PM.

J Biol Chem. 2003 Jan 17;278(3):1626-33. Epub 2002 Nov 6.

41.

The flexible loop of human FEN1 endonuclease is required for flap cleavage during DNA replication and repair.

Storici F, Henneke G, Ferrari E, Gordenin DA, Hübscher U, Resnick MA.

EMBO J. 2002 Nov 1;21(21):5930-42.

42.
43.

The 3'-->5' exonuclease of DNA polymerase delta can substitute for the 5' flap endonuclease Rad27/Fen1 in processing Okazaki fragments and preventing genome instability.

Jin YH, Obert R, Burgers PM, Kunkel TA, Resnick MA, Gordenin DA.

Proc Natl Acad Sci U S A. 2001 Apr 24;98(9):5122-7. Epub 2001 Apr 17.

44.

Biased distribution of inverted and direct Alus in the human genome: implications for insertion, exclusion, and genome stability.

Stenger JE, Lobachev KS, Gordenin D, Darden TA, Jurka J, Resnick MA.

Genome Res. 2001 Jan;11(1):12-27.

45.

Inverted Alu repeats unstable in yeast are excluded from the human genome.

Lobachev KS, Stenger JE, Kozyreva OG, Jurka J, Gordenin DA, Resnick MA.

EMBO J. 2000 Jul 17;19(14):3822-30.

46.

Functional analysis of human FEN1 in Saccharomyces cerevisiae and its role in genome stability.

Greene AL, Snipe JR, Gordenin DA, Resnick MA.

Hum Mol Genet. 1999 Nov;8(12):2263-73.

PMID:
10545607
47.

A novel role in DNA metabolism for the binding of Fen1/Rad27 to PCNA and implications for genetic risk.

Gary R, Park MS, Nolan JP, Cornelius HL, Kozyreva OG, Tran HT, Lobachev KS, Resnick MA, Gordenin DA.

Mol Cell Biol. 1999 Aug;19(8):5373-82.

48.
49.

Mutator phenotypes of yeast strains heterozygous for mutations in the MSH2 gene.

Drotschmann K, Clark AB, Tran HT, Resnick MA, Gordenin DA, Kunkel TA.

Proc Natl Acad Sci U S A. 1999 Mar 16;96(6):2970-5.

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