-
1
-
-
84884365015
-
The causes and consequences of genetic heterogeneity in cancer evolution
-
Burrell RA, McGranahan N, Bartek J, Swanton C. The causes and consequences of genetic heterogeneity in cancer evolution. Nature 2013; 501:338–45.
-
(2013)
Nature
, vol.501
, pp. 338-345
-
-
Burrell, R.A.1
McGranahan, N.2
Bartek, J.3
Swanton, C.4
-
2
-
-
84875490185
-
Cancer genome landscapes
-
Vogelstein B, Papadopoulos N, Velculescu VE, Zhou S, Diaz LA Jr, Kinzler KW. Cancer genome landscapes. Science 2013;339:1546–58.
-
(2013)
Science
, vol.339
, pp. 1546-1558
-
-
Vogelstein, B.1
Papadopoulos, N.2
Velculescu, V.E.3
Zhou, S.4
Diaz, L.A.5
Kinzler, K.W.6
-
3
-
-
84892833777
-
Discovery and saturation analysis of cancer genes across 21 tumour types
-
Lawrence MS, Stojanov P, Mermel CH, Robinson JT, Garraway LA, Golub TR, et al. Discovery and saturation analysis of cancer genes across 21 tumour types. Nature 2014;505:495–501.
-
(2014)
Nature
, vol.505
, pp. 495-501
-
-
Lawrence, M.S.1
Stojanov, P.2
Mermel, C.H.3
Robinson, J.T.4
Garraway, L.A.5
Golub, T.R.6
-
5
-
-
84922683604
-
Science Direct "Latent drivers" expand the cancer mutational landscape
-
Nussinov R, Tsai C. Science Direct "Latent drivers" expand the cancer mutational landscape. Curr Opin Struct Biol 2015;32:25–32.
-
(2015)
Curr Opin Struct Biol
, vol.32
, pp. 25-32
-
-
Nussinov, R.1
Tsai, C.2
-
7
-
-
84959564974
-
Quantifying clonal and subclonal passenger mutations in cancer evolution
-
Bozic I, Gerold JM, Nowak MA. Quantifying clonal and subclonal passenger mutations in cancer evolution. PLoS Comput Biol 2016;12: e1004731.
-
(2016)
Plos Comput Biol
, vol.12
-
-
Bozic, I.1
Gerold, J.M.2
Nowak, M.A.3
-
8
-
-
84874231197
-
Impact of deleterious passenger mutations on cancer progression
-
McFarland CD, Korolev KS, Kryukov GV, Sunyaev SR, Mirny LA. Impact of deleterious passenger mutations on cancer progression. Proc Natl Acad Sci U S A 2013;110:2910–5.
-
(2013)
Proc Natl Acad Sci U S A
, vol.110
, pp. 2910-2915
-
-
McFarland, C.D.1
Korolev, K.S.2
Kryukov, G.V.3
Sunyaev, S.R.4
Mirny, L.A.5
-
9
-
-
84908032938
-
Tug-of-war between driver and passenger mutations in cancer and other adaptive processes
-
McFarland CD, Mirny LA, Korolev KS. Tug-of-war between driver and passenger mutations in cancer and other adaptive processes. Proc Natl Acad Sci U S A 2014;111:15138–43.
-
(2014)
Proc Natl Acad Sci U S A
, vol.111
, pp. 15138-15143
-
-
McFarland, C.D.1
Mirny, L.A.2
Korolev, K.S.3
-
10
-
-
84896531092
-
-
Kelly LM, Barila G, Liu P, Evdokimova VN, Trivedi S. Identification of the transforming STRN-ALK fusion as a potential therapeutic target in the aggressive forms of thyroid cancer. 2014;111:4233–8.
-
(2014)
Identification of The Transforming STRN-ALK Fusion as A Potential Therapeutic Target in The Aggressive Forms of Thyroid Cancer
, vol.111
, pp. 4233-4238
-
-
Kelly, L.M.1
Barila, G.2
Liu, P.3
Evdokimova, V.N.4
Trivedi, S.5
-
12
-
-
33144483078
-
Transitions to asexuality result in excess amino acid substitutions
-
Paland S, Lynch M. Transitions to asexuality result in excess amino acid substitutions. Science 2006;311:990–2.
-
(2006)
Science
, vol.311
, pp. 990-992
-
-
Paland, S.1
Lynch, M.2
-
13
-
-
0027134973
-
Muller's ratchet and mutational meltdowns
-
Gabriel W, Lynch M, Burger R. Muller's ratchet and mutational meltdowns. Evolution 1993;47:1744.
-
(1993)
Evolution
, vol.47
, pp. 1744
-
-
Gabriel, W.1
Lynch, M.2
Burger, R.3
-
14
-
-
84920962202
-
Article molecular and genetic properties of tumors associated with local immune cytolytic activity
-
Rooney MS, Shukla SA, Wu CJ, Getz G, Hacohen N. Article molecular and genetic properties of tumors associated with local immune cytolytic activity. Cell 2014;160:48–61.
-
(2014)
Cell
, vol.160
, pp. 48-61
-
-
Rooney, M.S.1
Shukla, S.A.2
Wu, C.J.3
Getz, G.4
Hacohen, N.5
-
15
-
-
84920956731
-
Predicting immunogenic tumour mutations by combining mass spectrometry and exome sequencing
-
Yadav M, Jhunjhunwala S, Phung QT, Lupardus P, Tanguay J, Bumbaca S, et al. Predicting immunogenic tumour mutations by combining mass spectrometry and exome sequencing. Nature 2014;515:572–6.
-
(2014)
Nature
, vol.515
, pp. 572-576
-
-
Yadav, M.1
Jhunjhunwala, S.2
Phung, Q.T.3
Lupardus, P.4
Tanguay, J.5
Bumbaca, S.6
-
16
-
-
84920921528
-
Checkpoint blockade cancer immunotherapy targets tumour-specific mutant antigens
-
Gubin MM, Zhang X, Schuster H, Caron E, Ward JP, Noguchi T, et al. Checkpoint blockade cancer immunotherapy targets tumour-specific mutant antigens. Nature 2014;515:577–81.
-
(2014)
Nature
, vol.515
, pp. 577-581
-
-
Gubin, M.M.1
Zhang, X.2
Schuster, H.3
Caron, E.4
Ward, J.P.5
Noguchi, T.6
-
17
-
-
84918828514
-
Genetic basis for clinical response to CTLA-4 blockade in melanoma
-
Snyder A, Makarov V, Merghoub T, Yuan J, Zaretsky JM, Desrichard A, et al. Genetic basis for clinical response to CTLA-4 blockade in melanoma. N Engl J Med 2014;371:2189–99.
-
(2014)
N Engl J Med
, vol.371
, pp. 2189-2199
-
-
Snyder, A.1
Makarov, V.2
Merghoub, T.3
Yuan, J.4
Zaretsky, J.M.5
Desrichard, A.6
-
18
-
-
79956160582
-
Paradoxical relationship between chromosomal instability and survival outcome in cancer
-
Birkbak NJ, Eklund AC, Li Q, McClelland SE, Endesfelder D, Tan P, et al. Paradoxical relationship between chromosomal instability and survival outcome in cancer. Cancer Res 2011;71:3447–52.
-
(2011)
Cancer Res
, vol.71
, pp. 3447-3452
-
-
Birkbak, N.J.1
Eklund, A.C.2
Li, Q.3
McClelland, S.E.4
Endesfelder, D.5
Tan, P.6
-
19
-
-
80054054260
-
The aneuploidy paradox: Costs and benefits of an incorrect karyotype
-
Sheltzer JM, Amon A. The aneuploidy paradox: costs and benefits of an incorrect karyotype. Trends Genet 2011;27:446–53.
-
(2011)
Trends Genet
, vol.27
, pp. 446-453
-
-
Sheltzer, J.M.1
Amon, A.2
-
20
-
-
84954242823
-
Pan-cancer analysis of the extent and consequences of intratumor heterogeneity
-
Andor N, Graham TA, Jansen M, Xia LC, Aktipis CA, Petritsch C, et al. Pan-cancer analysis of the extent and consequences of intratumor heterogeneity. Nat Med 2015;22:105–13.
-
(2015)
Nat Med
, vol.22
, pp. 105-113
-
-
Andor, N.1
Graham, T.A.2
Jansen, M.3
Xia, L.C.4
Aktipis, C.A.5
Petritsch, C.6
-
21
-
-
55349112533
-
Aneuploidy affects proliferation and spontaneous immortalization in mammalian cells
-
Williams BR, Prabhu VR, Hunter KE, Glazier CM, Whittaker CA, Housman DE, et al. Aneuploidy affects proliferation and spontaneous immortalization in mammalian cells. Science 2008;322:703–9.
-
(2008)
Science
, vol.322
, pp. 703-709
-
-
Williams, B.R.1
Prabhu, V.R.2
Hunter, K.E.3
Glazier, C.M.4
Whittaker, C.A.5
Housman, D.E.6
-
22
-
-
33846065784
-
Aneuploidy acts both oncogenically and as a tumor suppressor
-
Weaver BAA, Silk AD, Montagna C, Verdier-Pinard P, Cleveland DW. Aneuploidy acts both oncogenically and as a tumor suppressor. Cancer Cell 2007;11:25–36.
-
(2007)
Cancer Cell
, vol.11
, pp. 25-36
-
-
Weaver, B.A.A.1
Silk, A.D.2
Montagna, C.3
Verdier-Pinard, P.4
Cleveland, D.W.5
-
23
-
-
75149140916
-
Mitotic chromosomal instability and cancer: Mouse modelling of the human disease
-
Schvartzman J-M, Sotillo R, Benezra R. Mitotic chromosomal instability and cancer: mouse modelling of the human disease. Nat Rev Cancer 2010;10:102–15.
-
(2010)
Nat Rev Cancer
, vol.10
, pp. 102-115
-
-
Schvartzman, J.-M.1
Sotillo, R.2
Benezra, R.3
-
24
-
-
84907969859
-
Oncogene-triggered suppression of DNA repair leads to DNA instability in cancer
-
Yaglom JA, McFarland C, Mirny L, Sherman MY. Oncogene-triggered suppression of DNA repair leads to DNA instability in cancer. Oncotarget 2014;5:8367–78.
-
(2014)
Oncotarget
, vol.5
, pp. 8367-8378
-
-
Yaglom, J.A.1
McFarland, C.2
Mirny, L.3
Sherman, M.Y.4
-
25
-
-
84861400043
-
Cn.MOPS: Mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate
-
Klambauer G, Schwarzbauer K, Mayr A, Clevert DA, Mitterecker A, Bodenhofer U, et al. Cn.MOPS: Mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate. Nucleic Acids Res 2012;40:1–14.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 1-14
-
-
Klambauer, G.1
Schwarzbauer, K.2
Mayr, A.3
Clevert, D.A.4
Mitterecker, A.5
Bodenhofer, U.6
-
26
-
-
84855386495
-
BioMart Central Portal: An open database network for the biological community
-
Guberman JM, Ai J, Arnaiz O, Baran J, Blake A, Baldock R, et al. BioMart Central Portal: an open database network for the biological community. Database 2011;2011:bar041.
-
(2011)
Database
, vol.2011
, pp. bar041
-
-
Guberman, J.M.1
Ai, J.2
Arnaiz, O.3
Baran, J.4
Blake, A.5
Baldock, R.6
-
27
-
-
84884416048
-
Human housekeeping genes, revisited
-
Eisenberg E, Levanon EY. Human housekeeping genes, revisited. Trends Genet 2013;29:569–74.
-
(2013)
Trends Genet
, vol.29
, pp. 569-574
-
-
Eisenberg, E.1
Levanon, E.Y.2
-
28
-
-
0036079158
-
The human genome browser at UCSC
-
Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, et al. The human genome browser at UCSC. Genome Res 2002;12: 996–1006.
-
(2002)
Genome Res
, vol.12
, pp. 996-1006
-
-
Kent, W.J.1
Sugnet, C.W.2
Furey, T.S.3
Roskin, K.M.4
Pringle, T.H.5
Zahler, A.M.6
-
29
-
-
84867297810
-
Co-expression of HER2 and HER3 receptor tyrosine kinases enhances invasion of breast cells via stimulation of interleukin-8 autocrine secretion
-
Aceto N, Duss S, MacDonald G, Meyer DS, Roloff TC, Hynes NE, et al. Co-expression of HER2 and HER3 receptor tyrosine kinases enhances invasion of breast cells via stimulation of interleukin-8 autocrine secretion. Breast Cancer Res 2012;14:R131.
-
(2012)
Breast Cancer Res
, vol.14
, pp. R131
-
-
Aceto, N.1
Duss, S.2
MacDonald, G.3
Meyer, D.S.4
Roloff, T.C.5
Hynes, N.E.6
-
30
-
-
84861576201
-
The landscape of cancer genes and mutational processes in breast cancer
-
Stephens PJ, Tarpey PS, Davies H, Van Loo P, Greenman C, Wedge DC, et al. The landscape of cancer genes and mutational processes in breast cancer. Nature 2012;486:400–4.
-
(2012)
Nature
, vol.486
, pp. 400-404
-
-
Stephens, P.J.1
Tarpey, P.S.2
Davies, H.3
Van Loo, P.4
Greenman, C.5
Wedge, D.C.6
-
31
-
-
80555140075
-
Scikit-learn: Machine learning in Python
-
Pedregosa F, Varoquaux G, Gramfort A, Michel V, Thirion B, Grisel O, et al. Scikit-learn: machine learning in Python. J Mach Learn Res 2011; 12:2825–30.
-
(2011)
J Mach Learn Res
, vol.12
, pp. 2825-2830
-
-
Pedregosa, F.1
Varoquaux, G.2
Gramfort, A.3
Michel, V.4
Thirion, B.5
Grisel, O.6
-
32
-
-
81155148160
-
Oncogenes induce senescence with incomplete growth arrest and suppress the DNA damage response in immortalized cells
-
Sherman MY, Meng L, Stampfer M, Gabai VL, Yaglom JA. Oncogenes induce senescence with incomplete growth arrest and suppress the DNA damage response in immortalized cells. Aging Cell 2011;10: 949–61.
-
(2011)
Aging Cell
, vol.10
, pp. 949-961
-
-
Sherman, M.Y.1
Meng, L.2
Stampfer, M.3
Gabai, V.L.4
Yaglom, J.A.5
-
33
-
-
0037201964
-
Antioxidant nutrients and adriamycin toxicity
-
Quiles JL, Huertas JR, Battino M, Mataix J, Ramírez-Tortosa MC. Antioxidant nutrients and adriamycin toxicity. Toxicology 2002;180: 79–95.
-
(2002)
Toxicology
, vol.180
, pp. 79-95
-
-
Quiles, J.L.1
Huertas, J.R.2
Battino, M.3
Mataix, J.4
Ramírez-Tortosa, M.C.5
-
34
-
-
33746835007
-
Carcinogens induce genome-wide loss of heterozygosity in normal stem cells without persistent chromosomal instability
-
Donahue SL, Lin Q, Cao S, Ruley HE. Carcinogens induce genome-wide loss of heterozygosity in normal stem cells without persistent chromosomal instability. Proc Natl Acad Sci U S A 2006;103:11642–6.
-
(2006)
Proc Natl Acad Sci U S A
, vol.103
, pp. 11642-11646
-
-
Donahue, S.L.1
Lin, Q.2
Cao, S.3
Ruley, H.E.4
-
35
-
-
83255165727
-
High order chromatin architecture shapes the landscape of chromosomal alterations in cancer
-
Fudenberg G, Getz G, Meyerson M, Mirny LA. High order chromatin architecture shapes the landscape of chromosomal alterations in cancer. Nat Biotechnol 2011;29:1109–13.
-
(2011)
Nat Biotechnol
, vol.29
, pp. 1109-1113
-
-
Fudenberg, G.1
Getz, G.2
Meyerson, M.3
Mirny, L.A.4
-
36
-
-
84885008220
-
Pan-cancer patterns of somatic copy number alteration
-
Zack TI, Schumacher SE, Carter SL, Cherniack AD, Saksena G, Tabak B, et al. Pan-cancer patterns of somatic copy number alteration. Nat Genet 2013;45:1134–40.
-
(2013)
Nat Genet
, vol.45
, pp. 1134-1140
-
-
Zack, T.I.1
Schumacher, S.E.2
Carter, S.L.3
Cherniack, A.D.4
Saksena, G.5
Tabak, B.6
-
37
-
-
33748286796
-
A signature of chromosomal instability inferred from gene expression profiles predicts clinical outcome in multiple human cancers
-
Carter SL, Eklund AC, Kohane IS, Harris LN, Szallasi Z. A signature of chromosomal instability inferred from gene expression profiles predicts clinical outcome in multiple human cancers. Nat Genet 2006;38:1043–8.
-
(2006)
Nat Genet
, vol.38
, pp. 1043-1048
-
-
Carter, S.L.1
Eklund, A.C.2
Kohane, I.S.3
Harris, L.N.4
Szallasi, Z.5
-
38
-
-
84888019491
-
Defining stem cell dynamics in models of intestinal tumor initiation
-
Vermeulen L, Morrissey E, van der Heijden M, Nicholson AM, Sottoriva A, Buczacki S, et al. Defining stem cell dynamics in models of intestinal tumor initiation. Science 2013;342:995–8.
-
(2013)
Science
, vol.342
, pp. 995-998
-
-
Vermeulen, L.1
Morrissey, E.2
Van Der Heijden, M.3
Nicholson, A.M.4
Sottoriva, A.5
Buczacki, S.6
-
39
-
-
0034687650
-
Explaining the high mutation rates of cancer cells to drug and multidrug resistance by chromosome reassort-ments that are catalyzed by aneuploidy
-
Duesberg P, Stindl R, Hehlmann R. Explaining the high mutation rates of cancer cells to drug and multidrug resistance by chromosome reassort-ments that are catalyzed by aneuploidy. Proc Natl Acad Sci U S A 2000;97:14295–300.
-
(2000)
Proc Natl Acad Sci U S A
, vol.97
, pp. 14295-14300
-
-
Duesberg, P.1
Stindl, R.2
Hehlmann, R.3
-
40
-
-
84867536072
-
Profiles of genomic instability in high-grade serous ovarian cancer predict treatment outcome
-
Wang ZC, Birkbak NJ, Culhane AC, Drapkin R, Fatima A, Tian R, et al. Profiles of genomic instability in high-grade serous ovarian cancer predict treatment outcome. Clin Cancer Res 2012;18:5806–15.
-
(2012)
Clin Cancer Res
, vol.18
, pp. 5806-5815
-
-
Wang, Z.C.1
Birkbak, N.J.2
Culhane, A.C.3
Drapkin, R.4
Fatima, A.5
Tian, R.6
-
42
-
-
0031953260
-
The mutation rate and cancer
-
Jackson AL, Loeb LA. The mutation rate and cancer. Genetics 1998;148: 1483–90.
-
(1998)
Genetics
, vol.148
, pp. 1483-1490
-
-
Jackson, A.L.1
Loeb, L.A.2
-
44
-
-
0027305597
-
The effect of deleterious mutations on neutral molecular variation
-
Charlesworth B, Morgan MT, Charlesworth D. The effect of deleterious mutations on neutral molecular variation. Genetics 1993;134:1289–303.
-
(1993)
Genetics
, vol.134
, pp. 1289-1303
-
-
Charlesworth, B.1
Morgan, M.T.2
Charlesworth, D.3
-
45
-
-
3543125439
-
Adaptive evolution of asexual populations under Muller's ratchet
-
Bachtrog D, Gordo I. Adaptive evolution of asexual populations under Muller's ratchet. Evolution 2004;58:1403–13.
-
(2004)
Evolution
, vol.58
, pp. 1403-1413
-
-
Bachtrog, D.1
Gordo, I.2
-
46
-
-
44949129000
-
Assessing the evolutionary impact of amino acid mutations in the human genome
-
Boyko AR, Williamson SH, Indap AR, Degenhardt JD, Hernandez RD, Lohmueller KE, et al. Assessing the evolutionary impact of amino acid mutations in the human genome. PLoS Genet 2008;4:e1000083.
-
(2008)
Plos Genet
, vol.4
-
-
Boyko, A.R.1
Williamson, S.H.2
Indap, A.R.3
Degenhardt, J.D.4
Hernandez, R.D.5
Lohmueller, K.E.6
-
47
-
-
77955590137
-
Human allelic variation: Perspective from protein function, structure, and evolution
-
Jordan DM, Ramensky VE, Sunyaev SR. Human allelic variation: perspective from protein function, structure, and evolution. Curr Opin Struct Biol 2010;20:342–50.
-
(2010)
Curr Opin Struct Biol
, vol.20
, pp. 342-350
-
-
Jordan, D.M.1
Ramensky, V.E.2
Sunyaev, S.R.3
-
48
-
-
84865134914
-
Passenger deletions generate therapeutic vulnerabilities in cancer
-
Muller FL, Colla S, Aquilanti E, Manzo VE, Genovese G, Lee J, et al. Passenger deletions generate therapeutic vulnerabilities in cancer. Nature 2012;488:337–42.
-
(2012)
Nature
, vol.488
, pp. 337-342
-
-
Muller, F.L.1
Colla, S.2
Aquilanti, E.3
Manzo, V.E.4
Genovese, G.5
Lee, J.6
-
49
-
-
84858005794
-
Tumour heterogeneity and drug resistance: Persona-lising cancer medicine through functional genomics
-
Lee AJX, Swanton C. Tumour heterogeneity and drug resistance: persona-lising cancer medicine through functional genomics. Biochem Pharmacol 2012;83:1013–20.
-
(2012)
Biochem Pharmacol
, vol.83
, pp. 1013-1020
-
-
Lee, A.J.X.1
Swanton, C.2
-
50
-
-
0002344794
-
Bootstrap methods: Another look at the jackknife
-
Efron B. Bootstrap methods: another look at the jackknife. Ann Stat 1979;7:1–26.
-
(1979)
Ann Stat
, vol.7
, pp. 1-26
-
-
Efron, B.1
|