-
1
-
-
80052177544
-
Exome sequencing of head and neck squamous cell carcinoma reveals inactivating mutations in NOTCH1
-
Agrawal N., Frederick M.J., Pickering C.R., Bettegowda C., Chang K., Li R.J., Fakhry C., Xie T.-X., Zhang J., Wang J., et al. Exome sequencing of head and neck squamous cell carcinoma reveals inactivating mutations in NOTCH1. Science 2011, 333:1154-1157.
-
(2011)
Science
, vol.333
, pp. 1154-1157
-
-
Agrawal, N.1
Frederick, M.J.2
Pickering, C.R.3
Bettegowda, C.4
Chang, K.5
Li, R.J.6
Fakhry, C.7
Xie, T.-X.8
Zhang, J.9
Wang, J.10
-
2
-
-
84882837534
-
Signatures of mutational processes in human cancer
-
Australian Pancreatic Cancer Genome Initiative, ICGC Breast Cancer ConsortiumICGC Breast Cancer Consortium, ICGC MMML-Seq ConsortiumICGC MMML-Seq Consortium, ICGC PedBrainICGC PedBrain
-
Alexandrov L.B., Nik-Zainal S., Wedge D.C., Aparicio S.A.J.R., Behjati S., Biankin A.V., Bignell G.R., Bolli N., Borg A., Børresen-Dale A.-L., et al. Signatures of mutational processes in human cancer. Nature 2013, 500:415-421. Australian Pancreatic Cancer Genome Initiative, ICGC Breast Cancer ConsortiumICGC Breast Cancer Consortium, ICGC MMML-Seq ConsortiumICGC MMML-Seq Consortium, ICGC PedBrainICGC PedBrain.
-
(2013)
Nature
, vol.500
, pp. 415-421
-
-
Alexandrov, L.B.1
Nik-Zainal, S.2
Wedge, D.C.3
Aparicio, S.A.J.R.4
Behjati, S.5
Biankin, A.V.6
Bignell, G.R.7
Bolli, N.8
Borg, A.9
Børresen-Dale, A.-L.10
-
3
-
-
34249026300
-
High-resolution profiling of histone methylations in the human genome
-
Barski A., Cuddapah S., Cui K., Roh T.-Y., Schones D.E., Wang Z., Wei G., Chepelev I., Zhao K. High-resolution profiling of histone methylations in the human genome. Cell 2007, 129:823-837.
-
(2007)
Cell
, vol.129
, pp. 823-837
-
-
Barski, A.1
Cuddapah, S.2
Cui, K.3
Roh, T.-Y.4
Schones, D.E.5
Wang, Z.6
Wei, G.7
Chepelev, I.8
Zhao, K.9
-
4
-
-
84866002291
-
The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data
-
Cerami E., Gao J., Dogrusoz U., Gross B.E., Sumer S.O., Aksoy B.A., Jacobsen A., Byrne C.J., Heuer M.L., Larsson E., et al. The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov. 2012, 2:401-404.
-
(2012)
Cancer Discov.
, vol.2
, pp. 401-404
-
-
Cerami, E.1
Gao, J.2
Dogrusoz, U.3
Gross, B.E.4
Sumer, S.O.5
Aksoy, B.A.6
Jacobsen, A.7
Byrne, C.J.8
Heuer, M.L.9
Larsson, E.10
-
5
-
-
21744452376
-
Cancer in xeroderma pigmentosum and related disorders of DNA repair
-
Cleaver J.E. Cancer in xeroderma pigmentosum and related disorders of DNA repair. Nat. Rev. Cancer 2005, 5:564-573.
-
(2005)
Nat. Rev. Cancer
, vol.5
, pp. 564-573
-
-
Cleaver, J.E.1
-
6
-
-
33846235924
-
Xeroderma pigmentosum group C in an isolated region of Guatemala
-
Cleaver J.E., Feeney L., Tang J.Y., Tuttle P. Xeroderma pigmentosum group C in an isolated region of Guatemala. J.Invest. Dermatol. 2007, 127:493-496.
-
(2007)
J.Invest. Dermatol.
, vol.127
, pp. 493-496
-
-
Cleaver, J.E.1
Feeney, L.2
Tang, J.Y.3
Tuttle, P.4
-
8
-
-
84871809302
-
STAR: ultrafast universal RNA-seq aligner
-
Dobin A., Davis C.A., Schlesinger F., Drenkow J., Zaleski C., Jha S., Batut P., Chaisson M., Gingeras T.R. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 2013, 29:15-21.
-
(2013)
Bioinformatics
, vol.29
, pp. 15-21
-
-
Dobin, A.1
Davis, C.A.2
Schlesinger, F.3
Drenkow, J.4
Zaleski, C.5
Jha, S.6
Batut, P.7
Chaisson, M.8
Gingeras, T.R.9
-
9
-
-
80055101101
-
Temporal dissection of tumorigenesis in primary cancers
-
Durinck S., Ho C., Wang N.J., Liao W., Jakkula L.R., Collisson E.A., Pons J., Chan S.W., Lam E.T., Chu C., et al. Temporal dissection of tumorigenesis in primary cancers. Cancer Discov. 2011, 1:137-143.
-
(2011)
Cancer Discov.
, vol.1
, pp. 137-143
-
-
Durinck, S.1
Ho, C.2
Wang, N.J.3
Liao, W.4
Jakkula, L.R.5
Collisson, E.A.6
Pons, J.7
Chan, S.W.8
Lam, E.T.9
Chu, C.10
-
10
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
ENCODE Project Consortium
-
An integrated encyclopedia of DNA elements in the human genome. Nature 2012, 489:57-74. ENCODE Project Consortium.
-
(2012)
Nature
, vol.489
, pp. 57-74
-
-
-
11
-
-
84872649417
-
Shaping chromatin for repair
-
Gospodinov A., Herceg Z. Shaping chromatin for repair. Mutat. Res. 2013, 752:45-60.
-
(2013)
Mutat. Res.
, vol.752
, pp. 45-60
-
-
Gospodinov, A.1
Herceg, Z.2
-
12
-
-
84878682420
-
The Genotype-Tissue Expression (GTEx) project
-
GTEx Consortium
-
The Genotype-Tissue Expression (GTEx) project. Nat. Genet. 2013, 45:580-585. GTEx Consortium.
-
(2013)
Nat. Genet.
, vol.45
, pp. 580-585
-
-
-
13
-
-
76349123622
-
Sequencing newly replicated DNA reveals widespread plasticity in human replication timing
-
Hansen R.S., Thomas S., Sandstrom R., Canfield T.K., Thurman R.E., Weaver M., Dorschner M.O., Gartler S.M., Stamatoyannopoulos J.A. Sequencing newly replicated DNA reveals widespread plasticity in human replication timing. Proc. Natl. Acad. Sci. USA 2010, 107:139-144.
-
(2010)
Proc. Natl. Acad. Sci. USA
, vol.107
, pp. 139-144
-
-
Hansen, R.S.1
Thomas, S.2
Sandstrom, R.3
Canfield, T.K.4
Thurman, R.E.5
Weaver, M.6
Dorschner, M.O.7
Gartler, S.M.8
Stamatoyannopoulos, J.A.9
-
14
-
-
80054754012
-
The large-scale distribution of somatic mutations in cancer genomes
-
Hodgkinson A., Chen Y., Eyre-Walker A. The large-scale distribution of somatic mutations in cancer genomes. Hum. Mutat. 2012, 33:136-143.
-
(2012)
Hum. Mutat.
, vol.33
, pp. 136-143
-
-
Hodgkinson, A.1
Chen, Y.2
Eyre-Walker, A.3
-
15
-
-
84886784734
-
Hypermutation of the inactive X chromosome is a frequent event in cancer
-
Jäger N., Schlesner M., Jones D.T.W., Raffel S., Mallm J.-P., Junge K.M., Weichenhan D., Bauer T., Ishaque N., Kool M., et al. Hypermutation of the inactive X chromosome is a frequent event in cancer. Cell 2013, 155:567-581.
-
(2013)
Cell
, vol.155
, pp. 567-581
-
-
Jäger, N.1
Schlesner, M.2
Jones, D.T.W.3
Raffel, S.4
Mallm, J.-P.5
Junge, K.M.6
Weichenhan, D.7
Bauer, T.8
Ishaque, N.9
Kool, M.10
-
16
-
-
84885645853
-
Transcriptome and genome sequencing uncovers functional variation in humans
-
Geuvadis Consortium
-
Lappalainen T., Sammeth M., Friedländer M.R., 't Hoen P.A.C., Monlong J., Rivas M.A., Gonzàlez-Porta M., Kurbatova N., Griebel T., Ferreira P.G., et al. Transcriptome and genome sequencing uncovers functional variation in humans. Nature 2013, 501:506-511. Geuvadis Consortium.
-
(2013)
Nature
, vol.501
, pp. 506-511
-
-
Lappalainen, T.1
Sammeth, M.2
Friedländer, M.R.3
't Hoen, P.A.C.4
Monlong, J.5
Rivas, M.A.6
Gonzàlez-Porta, M.7
Kurbatova, N.8
Griebel, T.9
Ferreira, P.G.10
-
17
-
-
84880507665
-
Mutational heterogeneity in cancer and the search for new cancer-associated genes
-
Lawrence M.S., Stojanov P., Polak P., Kryukov G.V., Cibulskis K., Sivachenko A., Carter S.L., Stewart C., Mermel C.H., Roberts S.A., et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature 2013, 499:214-218.
-
(2013)
Nature
, vol.499
, pp. 214-218
-
-
Lawrence, M.S.1
Stojanov, P.2
Polak, P.3
Kryukov, G.V.4
Cibulskis, K.5
Sivachenko, A.6
Carter, S.L.7
Stewart, C.8
Mermel, C.H.9
Roberts, S.A.10
-
19
-
-
55549097836
-
Mapping short DNA sequencing reads and calling variants using mapping quality scores
-
Li H., Ruan J., Durbin R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 2008, 18:1851-1858.
-
(2008)
Genome Res.
, vol.18
, pp. 1851-1858
-
-
Li, H.1
Ruan, J.2
Durbin, R.3
-
20
-
-
68549104404
-
The Sequence Alignment/Map format and SAMtools
-
1000 Genome Project Data Processing Subgroup
-
Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009, 25:2078-2079. 1000 Genome Project Data Processing Subgroup.
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
Fennell, T.4
Ruan, J.5
Homer, N.6
Marth, G.7
Abecasis, G.8
Durbin, R.9
-
21
-
-
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. 2013, 4:1502.
-
(2013)
Nat. Commun.
, vol.4
, pp. 1502
-
-
Liu, L.1
De, S.2
Michor, F.3
-
22
-
-
34547624303
-
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
-
Mikkelsen T.S., Ku M., Jaffe D.B., Issac B., Lieberman E., Giannoukos G., Alvarez P., Brockman W., Kim T.-K., Koche R.P., et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 2007, 448:553-560.
-
(2007)
Nature
, vol.448
, pp. 553-560
-
-
Mikkelsen, T.S.1
Ku, M.2
Jaffe, D.B.3
Issac, B.4
Lieberman, E.5
Giannoukos, G.6
Alvarez, P.7
Brockman, W.8
Kim, T.-K.9
Koche, R.P.10
-
23
-
-
0033961277
-
Terminally differentiated human neurons repair transcribed genes but display attenuated global DNA repair and modulation of repair gene expression
-
Nouspikel T., Hanawalt P.C. Terminally differentiated human neurons repair transcribed genes but display attenuated global DNA repair and modulation of repair gene expression. Mol. Cell. Biol. 2000, 20:1562-1570.
-
(2000)
Mol. Cell. Biol.
, vol.20
, pp. 1562-1570
-
-
Nouspikel, T.1
Hanawalt, P.C.2
-
25
-
-
74449093973
-
A comprehensive catalogue of somatic mutations from a human cancer genome
-
Pleasance E.D., Cheetham R.K., Stephens P.J., McBride D.J., Humphray S.J., Greenman C.D., Varela I., Lin M.-L., Ordóñez G.R., Bignell G.R., et al. A comprehensive catalogue of somatic mutations from a human cancer genome. Nature 2010, 463:191-196.
-
(2010)
Nature
, vol.463
, pp. 191-196
-
-
Pleasance, E.D.1
Cheetham, R.K.2
Stephens, P.J.3
McBride, D.J.4
Humphray, S.J.5
Greenman, C.D.6
Varela, I.7
Lin, M.-L.8
Ordóñez, G.R.9
Bignell, G.R.10
-
26
-
-
84892161493
-
Reduced local mutation density in regulatory DNA of cancer genomes is linked to DNA repair
-
Polak P., Lawrence M.S., Haugen E., Stoletzki N., Stojanov P., Thurman R.E., Garraway L.A., Mirkin S., Getz G., Stamatoyannopoulos J.A., Sunyaev S.R. Reduced local mutation density in regulatory DNA of cancer genomes is linked to DNA repair. Nat. Biotechnol. 2014, 32:71-75.
-
(2014)
Nat. Biotechnol.
, vol.32
, pp. 71-75
-
-
Polak, P.1
Lawrence, M.S.2
Haugen, E.3
Stoletzki, N.4
Stojanov, P.5
Thurman, R.E.6
Garraway, L.A.7
Mirkin, S.8
Getz, G.9
Stamatoyannopoulos, J.A.10
Sunyaev, S.R.11
-
27
-
-
84455200582
-
Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells
-
Ram O., Goren A., Amit I., Shoresh N., Yosef N., Ernst J., Kellis M., Gymrek M., Issner R., Coyne M., et al. Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells. Cell 2011, 147:1628-1639.
-
(2011)
Cell
, vol.147
, pp. 1628-1639
-
-
Ram, O.1
Goren, A.2
Amit, I.3
Shoresh, N.4
Yosef, N.5
Ernst, J.6
Kellis, M.7
Gymrek, M.8
Issner, R.9
Coyne, M.10
-
28
-
-
84865248380
-
Chromatin organization is a major influence on regional mutation rates in human cancer cells
-
Schuster-Böckler B., Lehner B. Chromatin organization is a major influence on regional mutation rates in human cancer cells. Nature 2012, 488:504-507.
-
(2012)
Nature
, vol.488
, pp. 504-507
-
-
Schuster-Böckler, B.1
Lehner, B.2
-
29
-
-
63449141981
-
Human mutation rate associated with DNA replication timing
-
Stamatoyannopoulos J.A., Adzhubei I., Thurman R.E., Kryukov G.V., Mirkin S.M., Sunyaev S.R. Human mutation rate associated with DNA replication timing. Nat. Genet. 2009, 41:393-395.
-
(2009)
Nat. Genet.
, vol.41
, pp. 393-395
-
-
Stamatoyannopoulos, J.A.1
Adzhubei, I.2
Thurman, R.E.3
Kryukov, G.V.4
Mirkin, S.M.5
Sunyaev, S.R.6
-
30
-
-
0028985014
-
Transcription-coupled repair removes both cyclobutane pyrimidine dimers and 6-4 photoproducts with equal efficiency and in a sequential way from transcribed DNA in xeroderma pigmentosum group C fibroblasts
-
van Hoffen A., Venema J., Meschini R., van Zeeland A.A., Mullenders L.H. Transcription-coupled repair removes both cyclobutane pyrimidine dimers and 6-4 photoproducts with equal efficiency and in a sequential way from transcribed DNA in xeroderma pigmentosum group C fibroblasts. EMBO J. 1995, 14:360-367.
-
(1995)
EMBO J.
, vol.14
, pp. 360-367
-
-
van Hoffen, A.1
Venema, J.2
Meschini, R.3
van Zeeland, A.A.4
Mullenders, L.H.5
-
31
-
-
80055092549
-
Loss-of-function mutations in Notch receptors in cutaneous and lung squamous cell carcinoma
-
Wang N.J., Sanborn Z., Arnett K.L., Bayston L.J., Liao W., Proby C.M., Leigh I.M., Collisson E.A., Gordon P.B., Jakkula L., et al. Loss-of-function mutations in Notch receptors in cutaneous and lung squamous cell carcinoma. Proc. Natl. Acad. Sci. USA 2011, 108:17761-17766.
-
(2011)
Proc. Natl. Acad. Sci. USA
, vol.108
, pp. 17761-17766
-
-
Wang, N.J.1
Sanborn, Z.2
Arnett, K.L.3
Bayston, L.J.4
Liao, W.5
Proby, C.M.6
Leigh, I.M.7
Collisson, E.A.8
Gordon, P.B.9
Jakkula, L.10
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