-
1
-
-
83255189766
-
DNA replication timing and long-range DNA interactions predict mutational landscapes of cancer genomes
-
De, S. & Michor, F. DNA replication timing and long-range DNA interactions predict mutational landscapes of cancer genomes. Nat. Biotechnol. 29, 1103-1108 (2011).
-
(2011)
Nat. Biotechnol
, vol.29
, pp. 1103-1108
-
-
De, S.1
Michor, F.2
-
2
-
-
84873390533
-
Somatic rearrangements across cancer reveal classes of samples with distinct patterns of DNA breakage and rearrangement-induced hypermutability
-
Drier, Y. et al. Somatic rearrangements across cancer reveal classes of samples with distinct patterns of DNA breakage and rearrangement-induced hypermutability. Genome Res. 23, 228-235 (2013).
-
(2013)
Genome Res.
, vol.23
, pp. 228-235
-
-
Drier, Y.1
-
3
-
-
84870955253
-
Differential relationship of DNA replication timing to different forms of human mutation and variation
-
Koren, A. et al. Differential relationship of DNA replication timing to different forms of human mutation and variation. Am. J. Hum. Genet. 91, 1033-1040 (2012).
-
(2012)
Am. J. Hum. Genet.
, vol.91
, pp. 1033-1040
-
-
Koren, A.1
-
4
-
-
84865777820
-
Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements
-
Kundaje, A. et al. Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements. Genome Res. 22, 1735-1747 (2012).
-
(2012)
Genome Res.
, vol.22
, pp. 1735-1747
-
-
Kundaje, A.1
-
5
-
-
84874585488
-
DNA replication timing and higher-order nuclear organization determine single-nucleotide substitution patterns in cancer genomes
-
Liu, L., De, S. & Michor, F. DNA replication timing and higher-order nuclear organization determine single-nucleotide substitution patterns in cancer genomes. Nat. Commun. 4, 1502 (2013).
-
(2013)
Nat. Commun.
, vol.4
, pp. 1502
-
-
Liu, L.1
De, S.2
Michor, F.3
-
6
-
-
84925615834
-
Differential DNA mismatch repair underlies mutation rate variation across the human genome
-
Supek, F. & Lehner, B. Differential DNA mismatch repair underlies mutation rate variation across the human genome. Nature 521, 81-84 (2015).
-
(2015)
Nature
, vol.521
, pp. 81-84
-
-
Supek, F.1
Lehner, B.2
-
7
-
-
84866067741
-
DNA replication timing and selection shape the landscape of nucleotide variation in cancer genomes
-
Woo, Y. H. & Li, W. H. DNA replication timing and selection shape the landscape of nucleotide variation in cancer genomes. Nat. Commun. 3, 1004 (2012).
-
(2012)
Nat. Commun.
, vol.3
, pp. 1004
-
-
Woo, Y.H.1
Li, W.H.2
-
8
-
-
63449141981
-
Human mutation rate associated with DNA replication timing
-
Stamatoyannopoulos, J. A. et al. Human mutation rate associated with DNA replication timing. Nat. Genet. 41, 393-395 (2009).
-
(2009)
Nat. Genet.
, vol.41
, pp. 393-395
-
-
Stamatoyannopoulos, J.A.1
-
9
-
-
84865248380
-
Chromatin organization is a major influence on regional mutation rates in human cancer cells
-
Schuster-Bockler, B. & Lehner, B. Chromatin organization is a major influence on regional mutation rates in human cancer cells. Nature 488, 504-507 (2012).
-
(2012)
Nature
, vol.488
, pp. 504-507
-
-
Schuster-Bockler, B.1
Lehner, B.2
-
10
-
-
84923358817
-
Cell-of-origin chromatin organization shapes the mutational landscape of cancer
-
Polak, P. et al. Cell-of-origin chromatin organization shapes the mutational landscape of cancer. Nature 518, 360-364 (2015).
-
(2015)
Nature
, vol.518
, pp. 360-364
-
-
Polak, P.1
-
11
-
-
84861541343
-
Mutational processes molding the genomes of 21 breast cancers
-
Nik-Zainal, S. et al. Mutational processes molding the genomes of 21 breast cancers. Cell 149, 979-993 (2012).
-
(2012)
Cell
, vol.149
, pp. 979-993
-
-
Nik-Zainal, S.1
-
12
-
-
84861550476
-
The life history of 21 breast cancers
-
Nik-Zainal, S. et al. The life history of 21 breast cancers. Cell 149, 994-1007 (2012).
-
(2012)
Cell
, vol.149
, pp. 994-1007
-
-
Nik-Zainal, S.1
-
13
-
-
84906303775
-
Mechanisms underlying mutational signatures in human cancers
-
Helleday, T., Eshtad, S. & Nik-Zainal, S. Mechanisms underlying mutational signatures in human cancers. Nat. Rev. Genet. 15, 585-598 (2014).
-
(2014)
Nat. Rev. Genet.
, vol.15
, pp. 585-598
-
-
Helleday, T.1
Eshtad, S.2
Nik-Zainal, S.3
-
14
-
-
84882837534
-
Signatures of mutational processes in human cancer
-
Alexandrov, L. B. et al. Signatures of mutational processes in human cancer. Nature 500, 415-421 (2013).
-
(2013)
Nature
, vol.500
, pp. 415-421
-
-
Alexandrov, L.B.1
-
15
-
-
84973594792
-
Landscape of somatic mutations in 560 breast cancer whole-genome sequences
-
Nik-Zainal, S. et al. Landscape of somatic mutations in 560 breast cancer whole-genome sequences. Nature http://dx.doi.org/10.1038/nature17676 (2016).
-
(2016)
Nature
-
-
Nik-Zainal, S.1
-
16
-
-
84860510016
-
Mammalian mismatch repair: Error-free or error-prone?
-
Pena-Diaz, J. & Jiricny, J. Mammalian mismatch repair: error-free or error-prone? Trends Biochem. Sci. 37, 206-214 (2012).
-
(2012)
Trends Biochem. Sci.
, vol.37
, pp. 206-214
-
-
Pena-Diaz, J.1
Jiricny, J.2
-
17
-
-
84879750259
-
Principles and concepts of DNA replication in bacteria, archaea, and eukarya
-
O'Donnell, M., Langston, L. & Stillman, B. Principles and concepts of DNA replication in bacteria, archaea, and eukarya. Cold Spring Harb. Perspect. Biol. 5, a010108 (2013).
-
(2013)
Cold Spring Harb. Perspect. Biol.
, vol.5
-
-
O'Donnell, M.1
Langston, L.2
Stillman, B.3
-
19
-
-
84930012955
-
DNA replication origin activation in space and time
-
Fragkos, M., Ganier, O., Coulombe, P. & Mechali, M. DNA replication origin activation in space and time. Nat. Rev. Mol. Cell Biol. 16, 360-374 (2015).
-
(2015)
Nat. Rev. Mol. Cell Biol.
, vol.16
, pp. 360-374
-
-
Fragkos, M.1
Ganier, O.2
Coulombe, P.3
Mechali, M.4
-
20
-
-
84965109911
-
-
ENCODE. https://http://www.encodeproject.org (2012).
-
(2012)
-
-
-
21
-
-
74049163810
-
Decreased replication origin activity in temporal transition regions
-
Guan, Z. et al. Decreased replication origin activity in temporal transition regions. J. Cell Biol. 187, 623-635 (2009).
-
(2009)
J. Cell Biol.
, vol.187
, pp. 623-635
-
-
Guan, Z.1
-
22
-
-
84855272663
-
Evidence for sequential and increasing activation of replication origins along replication timing gradients in the human genome
-
Guilbaud, G. et al. Evidence for sequential and increasing activation of replication origins along replication timing gradients in the human genome. PLoS Comput. Biol. 7, e1002322 (2011).
-
(2011)
PLoS Comput. Biol.
, vol.7
-
-
Guilbaud, G.1
-
23
-
-
84965111648
-
-
Signatures, C. M. http://cancer.sanger.ac.uk/cosmic/signatures (2015).
-
(2015)
Signatures C.M.
-
-
-
24
-
-
50349093233
-
The AID/APOBEC family of nucleic acid mutators
-
Conticello, S. G. The AID/APOBEC family of nucleic acid mutators. Genome Biol. 9, 229 (2008).
-
(2008)
Genome Biol.
, vol.9
, pp. 229
-
-
Conticello, S.G.1
-
25
-
-
0036863733
-
RNA editing enzyme APOBEC1 and some of its homologs can act as DNA mutators
-
Harris, R. S., Petersen-Mahrt, S. K. & Neuberger, M. S. RNA editing enzyme APOBEC1 and some of its homologs can act as DNA mutators. Mol. Cell 10, 1247-1253 (2002).
-
(2002)
Mol. Cell
, vol.10
, pp. 1247-1253
-
-
Harris, R.S.1
Petersen-Mahrt, S.K.2
Neuberger, M.S.3
-
26
-
-
84878677763
-
NMR structure of human restriction factor APOBEC3A reveals substrate binding and enzyme specificity
-
Byeon, I. J. et al. NMR structure of human restriction factor APOBEC3A reveals substrate binding and enzyme specificity. Nat. Commun. 4, 1890 (2013).
-
(2013)
Nat. Commun.
, vol.4
, pp. 1890
-
-
Byeon, I.J.1
-
27
-
-
84880231858
-
APOBEC3G cytosine deamination hotspots are defined by both sequence context and single-stranded DNA secondary structure
-
Holtz, C. M., Sadler, H. A. & Mansky, L. M. APOBEC3G cytosine deamination hotspots are defined by both sequence context and single-stranded DNA secondary structure. Nucleic Acids Res. 41, 6139-6148 (2013).
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. 6139-6148
-
-
Holtz, C.M.1
Sadler, H.A.2
Mansky, L.M.3
-
28
-
-
84899645475
-
Association of a germline copy number polymorphism of APOBEC3A and APOBEC3B with burden of putative APOBEC-dependent mutations in breast cancer
-
Nik-Zainal, S. et al. Association of a germline copy number polymorphism of APOBEC3A and APOBEC3B with burden of putative APOBEC-dependent mutations in breast cancer. Nat. Genet. 46, 487-491 (2014).
-
(2014)
Nat. Genet.
, vol.46
, pp. 487-491
-
-
Nik-Zainal, S.1
-
29
-
-
62349131315
-
DNA repair in mammalian cells : Nucleotide excision repair: Variations on versatility
-
Nouspikel, T. DNA repair in mammalian cells : Nucleotide excision repair: variations on versatility. Cell. Mol. Life Sci. 66, 994-1009 (2009).
-
(2009)
Cell. Mol. Life Sci.
, vol.66
, pp. 994-1009
-
-
Nouspikel, T.1
-
30
-
-
74449093973
-
A comprehensive catalogue of somatic mutations from a human cancer genome
-
Pleasance, E. D. et al. A comprehensive catalogue of somatic mutations from a human cancer genome. Nature 463, 191-196 (2010).
-
(2010)
Nature
, vol.463
, pp. 191-196
-
-
Pleasance, E.D.1
-
31
-
-
56749157389
-
Transcription-coupled DNA repair: Two decades of progress and surprises
-
Hanawalt, P. C. & Spivak, G. Transcription-coupled DNA repair: two decades of progress and surprises. Nature Rev. Mol. Cell Biol. 9, 958-970 (2008).
-
(2008)
Nature Rev. Mol. Cell Biol.
, vol.9
, pp. 958-970
-
-
Hanawalt, P.C.1
Spivak, G.2
-
32
-
-
33644530369
-
Transcriptional inhibition by an oxidized abasic site in DNA
-
Wang, Y., Sheppard, T. L., Tornaletti, S., Maeda, L. S. & Hanawalt, P. C. Transcriptional inhibition by an oxidized abasic site in DNA. Chem. Res. Toxicol. 19, 234-241 (2006).
-
(2006)
Chem. Res. Toxicol.
, vol.19
, pp. 234-241
-
-
Wang, Y.1
Sheppard, T.L.2
Tornaletti, S.3
Maeda, L.S.4
Hanawalt, P.C.5
-
33
-
-
33748990904
-
Transcription arrest at an abasic site in the transcribed strand of template DNA
-
Tornaletti, S., Maeda, L. S. & Hanawalt, P. C. Transcription arrest at an abasic site in the transcribed strand of template DNA. Chem. Res. Toxicol. 19, 1215-1220 (2006).
-
(2006)
Chem. Res. Toxicol.
, vol.19
, pp. 1215-1220
-
-
Tornaletti, S.1
Maeda, L.S.2
Hanawalt, P.C.3
-
34
-
-
79953788666
-
Impact of chromatin structure on sequence variability in the human genome
-
Tolstorukov, M. Y., Volfovsky, N., Stephens, R. M. & Park, P. J. Impact of chromatin structure on sequence variability in the human genome. Nat. Struct. Mol. Biol. 18, 510-515 (2011).
-
(2011)
Nat. Struct. Mol. Biol.
, vol.18
, pp. 510-515
-
-
Tolstorukov, M.Y.1
Volfovsky, N.2
Stephens, R.M.3
Park, P.J.4
-
35
-
-
58449116917
-
Chromatin-associated periodicity in genetic variation downstream of transcriptional start sites
-
Sasaki, S. et al. Chromatin-associated periodicity in genetic variation downstream of transcriptional start sites. Science 323, 401-404 (2009).
-
(2009)
Science
, vol.323
, pp. 401-404
-
-
Sasaki, S.1
-
36
-
-
84857131972
-
Interplay between mismatch repair and chromatin assembly
-
Schopf, B. et al. Interplay between mismatch repair and chromatin assembly. Proc. Natl Acad. Sci. USA 109, 1895-1900 (2012).
-
(2012)
Proc. Natl Acad. Sci. USA
, vol.109
, pp. 1895-1900
-
-
Schopf, B.1
-
37
-
-
84923948943
-
Heterogeneous polymerase fidelity and mismatch repair bias genome variation and composition
-
Lujan, S. A. et al. Heterogeneous polymerase fidelity and mismatch repair bias genome variation and composition. Genome Res. 24, 1751-1764 (2014).
-
(2014)
Genome Res.
, vol.24
, pp. 1751-1764
-
-
Lujan, S.A.1
-
38
-
-
0036012782
-
The "A" rule revisited: Polymerases as determinants of mutational specificity
-
Strauss, B. S. The "A" rule revisited: polymerases as determinants of mutational specificity. DNA Repair 1, 125-135 (2002).
-
(2002)
DNA Repair
, vol.1
, pp. 125-135
-
-
Strauss, B.S.1
-
39
-
-
77955841149
-
Collaboration and competition between DNA double-strand break repair pathways
-
Kass, E. M. & Jasin, M. Collaboration and competition between DNA double-strand break repair pathways. FEBS Lett. 584, 3703-3708 (2010).
-
(2010)
FEBS Lett.
, vol.584
, pp. 3703-3708
-
-
Kass, E.M.1
Jasin, M.2
-
40
-
-
84923090502
-
Mammalian polymerase theta promotes alternative NHEJ and suppresses recombination
-
Mateos-Gomez, P. A. et al. Mammalian polymerase theta promotes alternative NHEJ and suppresses recombination. Nature 518, 254-257 (2015).
-
(2015)
Nature
, vol.518
, pp. 254-257
-
-
Mateos-Gomez, P.A.1
-
41
-
-
84923082911
-
Homologous-recombination-deficient tumours are dependent on Poltheta-mediated repair
-
Ceccaldi, R. et al. Homologous-recombination-deficient tumours are dependent on Poltheta-mediated repair. Nature 518, 258-262 (2015).
-
(2015)
Nature
, vol.518
, pp. 258-262
-
-
Ceccaldi, R.1
-
42
-
-
84892743776
-
Break-induced replication repair of damaged forks induces genomic duplications in human cells
-
Costantino, L. et al. Break-induced replication repair of damaged forks induces genomic duplications in human cells. Science 343, 88-91 (2014).
-
(2014)
Science
, vol.343
, pp. 88-91
-
-
Costantino, L.1
-
43
-
-
25444517122
-
Good timing in the cell cycle for precise DNA repair by BRCA1
-
Durant, S. T. & Nickoloff, J. A. Good timing in the cell cycle for precise DNA repair by BRCA1. Cell Cycle 4, 1216-1222 (2005).
-
(2005)
Cell Cycle
, vol.4
, pp. 1216-1222
-
-
Durant, S.T.1
Nickoloff, J.A.2
-
44
-
-
39449096135
-
Genome instability: A mechanistic view of its causes and consequences
-
Aguilera, A. & Gomez-Gonzalez, B. Genome instability: a mechanistic view of its causes and consequences. Nat. Rev. Genet. 9, 204-217 (2008).
-
(2008)
Nat. Rev. Genet.
, vol.9
, pp. 204-217
-
-
Aguilera, A.1
Gomez-Gonzalez, B.2
-
45
-
-
84887402750
-
Replication stress-induced genome instability: The dark side of replication maintenance by homologous recombination
-
Carr, A. M. & Lambert, S. Replication stress-induced genome instability: the dark side of replication maintenance by homologous recombination. J. Mol. Biol. 425, 4733-4744 (2013).
-
(2013)
J. Mol. Biol.
, vol.425
, pp. 4733-4744
-
-
Carr, A.M.1
Lambert, S.2
-
46
-
-
0037388452
-
Rev1 is essential for DNA damage tolerance and non-templated immunoglobulin gene mutation in a vertebrate cell line
-
Simpson, L. J. & Sale, J. E. Rev1 is essential for DNA damage tolerance and non-templated immunoglobulin gene mutation in a vertebrate cell line. EMBO J. 22, 1654-1664 (2003).
-
(2003)
EMBO J
, vol.22
, pp. 1654-1664
-
-
Simpson, L.J.1
Sale, J.E.2
-
47
-
-
84873186179
-
Deciphering signatures of mutational processes operative in human cancer
-
Alexandrov, L. B., Nik-Zainal, S., Wedge, D. C., Campbell, P. J. & Stratton, M. R. Deciphering signatures of mutational processes operative in human cancer. Cell Rep. 3, 246-259 (2013).
-
(2013)
Cell Rep.
, vol.3
, pp. 246-259
-
-
Alexandrov, L.B.1
Nik-Zainal, S.2
Wedge, D.C.3
Campbell, P.J.4
Stratton, M.R.5
-
48
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
Consortium, E. P. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74 (2012).
-
(2012)
Nature
, vol.489
, pp. 57-74
-
-
-
49
-
-
84923920881
-
The spatial and temporal organization of origin firing during the S-phase of fission yeast
-
Kaykov, A. & Nurse, P. The spatial and temporal organization of origin firing during the S-phase of fission yeast. Genome Res. 25, 391-401 (2015).
-
(2015)
Genome Res.
, vol.25
, pp. 391-401
-
-
Kaykov, A.1
Nurse, P.2
-
50
-
-
0035812742
-
Making sense of eukaryotic DNA replication origins
-
Gilbert, D. M. Making sense of eukaryotic DNA replication origins. Science 294, 96-100 (2001).
-
(2001)
Science
, vol.294
, pp. 96-100
-
-
Gilbert, D.M.1
-
51
-
-
33751520767
-
DNA replication timing: Random thoughts about origin firing
-
Rhind, N. DNA replication timing: random thoughts about origin firing. Nat. Cell Biol. 8, 1313-1316 (2006).
-
(2006)
Nat. Cell Biol.
, vol.8
, pp. 1313-1316
-
-
Rhind, N.1
-
52
-
-
1842733112
-
RNase-sensitive DNA modification(s) initiates S. pombe mating-type switching
-
Vengrova, S. & Dalgaard, J. Z. RNase-sensitive DNA modification(s) initiates S. pombe mating-type switching. Genes Dev. 18, 794-804 (2004).
-
(2004)
Genes Dev.
, vol.18
, pp. 794-804
-
-
Vengrova, S.1
Dalgaard, J.Z.2
-
53
-
-
0034654537
-
Fission yeast switches mating type by a replication-recombination coupled process
-
Arcangioli, B. & de Lahondes, R. Fission yeast switches mating type by a replication-recombination coupled process. EMBO J. 19, 1389-1396 (2000).
-
(2000)
EMBO J
, vol.19
, pp. 1389-1396
-
-
Arcangioli, B.1
De Lahondes, R.2
-
54
-
-
84955559498
-
Molecular combing of single DNA molecules on the 10 megabase scale
-
Kaykov, A., Taillefumier, T., Bensimon, A. & Nurse, P. Molecular combing of single DNA molecules on the 10 megabase scale. Sci. Rep. 6, 19636 (2016).
-
(2016)
Sci. Rep.
, vol.6
-
-
Kaykov, A.1
Taillefumier, T.2
Bensimon, A.3
Nurse, P.4
-
55
-
-
84870674869
-
Controls of nucleosome positioning in the human genome
-
Gaffney, D. J. et al. Controls of nucleosome positioning in the human genome. PLoS Genet. 8, e1003036 (2012).
-
(2012)
PLoS Genet.
, vol.8
-
-
Gaffney, D.J.1
|