-
1
-
-
84884994218
-
The Cancer Genome Atlas Pan-Cancer analysis project
-
Weinstein JN, Collisson EA, Mills GB, Shaw KRM, Ozenberger BA, Ellrott K, et al. The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet. 2013;45:1113-20.
-
(2013)
Nat Genet.
, vol.45
, pp. 1113-1120
-
-
Weinstein, J.N.1
Collisson, E.A.2
Mills, G.B.3
Shaw, K.R.M.4
Ozenberger, B.A.5
Ellrott, K.6
-
2
-
-
77951115122
-
International network of cancer genome projects
-
ICGC. International network of cancer genome projects. Nature. 2010;464:993-8.
-
(2010)
Nature
, vol.464
, pp. 993-998
-
-
-
3
-
-
84881396090
-
Computational approaches to identify functional genetic variants in cancer genomes
-
Gonzalez-Perez A, Mustonen V, Reva B, Ritchie GRS, Creixell P, Karchin R, et al. Computational approaches to identify functional genetic variants in cancer genomes. Nat Methods. 2013;10:723-9.
-
(2013)
Nat Methods.
, vol.10
, pp. 723-729
-
-
Gonzalez-Perez, A.1
Mustonen, V.2
Reva, B.3
Ritchie, G.R.S.4
Creixell, P.5
Karchin, R.6
-
4
-
-
84880507665
-
Mutational heterogeneity in cancer and the search for new cancer-associated genes
-
Lawrence MS, Stojanov P, Polak P, Kryukov GV, Cibulskis K, Sivachenko A, et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature. 2013;499:214-8.
-
(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
-
6
-
-
84883467378
-
OncodriveCLUST: Exploiting the positional clustering of somatic mutations to identify cancer genes
-
Tamborero D, Gonzalez-Perez A, Lopez-Bigas N. OncodriveCLUST: Exploiting the positional clustering of somatic mutations to identify cancer genes. Bioinformatics. 2013;29:2238-44.
-
(2013)
Bioinformatics.
, vol.29
, pp. 2238-2244
-
-
Tamborero, D.1
Gonzalez-Perez, A.2
Lopez-Bigas, N.3
-
7
-
-
84873802661
-
Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers
-
Reimand J, Bader GD. Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers. Mol Syst Biol. 2013;9:637.
-
(2013)
Mol Syst Biol.
, vol.9
, pp. 637
-
-
Reimand, J.1
Bader, G.D.2
-
8
-
-
84864598664
-
MuSiC: Identifying mutational significance in cancer genomes
-
Dees ND, Zhang Q, Kandoth C, Wendl MC, Schierding W, Koboldt DC, et al. MuSiC: Identifying mutational significance in cancer genomes. Genome Res. 2012;22:1589-98.
-
(2012)
Genome Res.
, vol.22
, pp. 1589-1598
-
-
Dees, N.D.1
Zhang, Q.2
Kandoth, C.3
Wendl, M.C.4
Schierding, W.5
Koboldt, D.C.6
-
10
-
-
84923358817
-
Cell-of-origin chromatin organization shapes the mutational landscape of cancer
-
Polak P, Karlic R, Koren A, Thurman R, Sandstrom R, Michael S, et al. Cell-of-origin chromatin organization shapes the mutational landscape of cancer. Nature. 2015;518:360-4.
-
(2015)
Nature.
, vol.518
, pp. 360-364
-
-
Polak, P.1
Karlic, R.2
Koren, A.3
Thurman, R.4
Sandstrom, R.5
Michael, S.6
-
11
-
-
84908894973
-
Genome-wide analysis of noncoding regulatory mutations in cancer
-
Weinhold N, Jacobsen A, Schultz N, Sander C, Lee W. Genome-wide analysis of noncoding regulatory mutations in cancer. Nat Genet. 2014;46:1160-5.
-
(2014)
Nat Genet.
, vol.46
, pp. 1160-1165
-
-
Weinhold, N.1
Jacobsen, A.2
Schultz, N.3
Sander, C.4
Lee, W.5
-
12
-
-
84922527340
-
Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types
-
Fredriksson NJ, Ny L, Nilsson JA, Larsson E. Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types. Nat Genet. 2014;46:1-7.
-
(2014)
Nat Genet.
, vol.46
, pp. 1-7
-
-
Fredriksson, N.J.1
Ny, L.2
Nilsson, J.A.3
Larsson, E.4
-
13
-
-
84936806687
-
Signatures of accelerated somatic evolution in gene promoters in multiple cancer types
-
Smith KS, Yadav VK, Pedersen BS, Shaknovich R, Geraci MW, Pollard KS, et al. Signatures of accelerated somatic evolution in gene promoters in multiple cancer types. Nucleic Acids Res. 2015;43:5307-17.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. 5307-5317
-
-
Smith, K.S.1
Yadav, V.K.2
Pedersen, B.S.3
Shaknovich, R.4
Geraci, M.W.5
Pollard, K.S.6
-
14
-
-
84949034526
-
LARVA: An integrative framework for large-scale analysis of recurrent variants in noncoding annotations
-
Lochovsky L, Zhang J, Fu Y, Khurana E, Gerstein M. LARVA: An integrative framework for large-scale analysis of recurrent variants in noncoding annotations. Nucleic Acids Res. 2015;43:8123-34.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. 8123-8134
-
-
Lochovsky, L.1
Zhang, J.2
Fu, Y.3
Khurana, E.4
Gerstein, M.5
-
15
-
-
84928105158
-
MSK-IMPACT: a hybridization capture-based next-generation sequencing clinical assay for solid tumor molecular oncology
-
Cheng DT, Mitchell T, Zehir A, Shah RH, Benayed R, Syed A, et al. MSK-IMPACT: a hybridization capture-based next-generation sequencing clinical assay for solid tumor molecular oncology. J Mol Diagn. 2015;17:251-64.
-
(2015)
J Mol Diagn.
, vol.17
, pp. 251-264
-
-
Cheng, D.T.1
Mitchell, T.2
Zehir, A.3
Shah, R.H.4
Benayed, R.5
Syed, A.6
-
16
-
-
84895858942
-
A general framework for estimating the relative pathogenicity of human genetic variants
-
Kircher M, Witten DM, Jain P, O'Roak BJ, Cooper GM, Shendure J, et al. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet. 2014;46:310-5.
-
(2014)
Nat Genet.
, vol.46
, pp. 310-315
-
-
Kircher, M.1
Witten, D.M.2
Jain, P.3
O'Roak, B.J.4
Cooper, G.M.5
Shendure, J.6
-
17
-
-
1542515338
-
A census of human cancer genes
-
Futreal PA, Coin L, Marshall M, Down T, Hubbard T, Wooster R, et al. A census of human cancer genes. Nat Rev Cancer. 2004;4:177-83.
-
(2004)
Nat Rev Cancer.
, vol.4
, pp. 177-183
-
-
Futreal, P.A.1
Coin, L.2
Marshall, M.3
Down, T.4
Hubbard, T.5
Wooster, R.6
-
18
-
-
84911379962
-
E-Driver: A novel method to identify protein regions driving cancer
-
Porta-Pardo E, Godzik A. E-Driver: A novel method to identify protein regions driving cancer. Bioinformatics. 2014;30:3109-14.
-
(2014)
Bioinformatics.
, vol.30
, pp. 3109-3114
-
-
Porta-Pardo, E.1
Godzik, A.2
-
19
-
-
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
-
20
-
-
84882837534
-
Signatures of mutational processes in human cancer
-
Alexandrov LB, Nik-Zainal S, Wedge DC, Aparicio Jr SA, Behjati S, Biankin AV, et al. Signatures of mutational processes in human cancer. Nature. 2013;500:415-21.
-
(2013)
Nature.
, vol.500
, pp. 415-421
-
-
Alexandrov, L.B.1
Nik-Zainal, S.2
Wedge, D.C.3
Aparicio, S.A.4
Behjati, S.5
Biankin, A.V.6
-
21
-
-
84874189784
-
Highly recurrent TERT promoter mutations in human melanoma
-
Huang FW, Hodis E, Xu MJ, Kryukov GV, Chin L, Garraway LA. Highly recurrent TERT promoter mutations in human melanoma. Science. 2013;339:957-9.
-
(2013)
Science.
, vol.339
, pp. 957-959
-
-
Huang, F.W.1
Hodis, E.2
Xu, M.J.3
Kryukov, G.V.4
Chin, L.5
Garraway, L.A.6
-
22
-
-
84874191269
-
TERT promoter mutations in familial and sporadic melanoma
-
Horn S, Figl A, Rachakonda PS, Fischer C, Sucker A, Gast A, et al. TERT promoter mutations in familial and sporadic melanoma. Science. 2013;339:959-61.
-
(2013)
Science.
, vol.339
, pp. 959-961
-
-
Horn, S.1
Figl, A.2
Rachakonda, P.S.3
Fischer, C.4
Sucker, A.5
Gast, A.6
-
23
-
-
84940163320
-
Involvement of p29/SYF2/fSAP29/NTC31 in the progression of NSCLC via modulating cell proliferation
-
Liu Y, Ni T, Xue Q, Lv L, Chen B, Cui X, et al. Involvement of p29/SYF2/fSAP29/NTC31 in the progression of NSCLC via modulating cell proliferation. Pathol Res Pract. 2015;211:36-42.
-
(2015)
Pathol Res Pract.
, vol.211
, pp. 36-42
-
-
Liu, Y.1
Ni, T.2
Xue, Q.3
Lv, L.4
Chen, B.5
Cui, X.6
-
24
-
-
84878726903
-
Expression of p114RhoGEF predicts lymph node metastasis and poor survival of squamous-cell lung carcinoma patients
-
Song C, Gao Y, Tian Y, Han X, Chen Y, Tian DL. Expression of p114RhoGEF predicts lymph node metastasis and poor survival of squamous-cell lung carcinoma patients. Tumor Biol. 2013;34:1925-33.
-
(2013)
Tumor Biol.
, vol.34
, pp. 1925-1933
-
-
Song, C.1
Gao, Y.2
Tian, Y.3
Han, X.4
Chen, Y.5
Tian, D.L.6
-
25
-
-
34547628200
-
Proteasome function is required for DNA damage response and fanconi anemia pathway activation
-
Jacquemont C, Taniguchi T. Proteasome function is required for DNA damage response and fanconi anemia pathway activation. Cancer Res. 2007;67:7395-405.
-
(2007)
Cancer Res.
, vol.67
, pp. 7395-7405
-
-
Jacquemont, C.1
Taniguchi, T.2
-
26
-
-
84903301074
-
Chromosomal aneuploidy affects the global proteome equilibrium of colorectal cancer cells
-
Gemoll T, Habermann JK, Becker S, Szymczak S, Upender MB, Bruch HP, et al. Chromosomal aneuploidy affects the global proteome equilibrium of colorectal cancer cells. Anal Cell Pathol. 2013;36:149-61.
-
(2013)
Anal Cell Pathol.
, vol.36
, pp. 149-161
-
-
Gemoll, T.1
Habermann, J.K.2
Becker, S.3
Szymczak, S.4
Upender, M.B.5
Bruch, H.P.6
-
27
-
-
84896267878
-
Cancer-associated CD43 glycoforms as target of immunotherapy
-
Tuccillo FM, Palmieri C, Fiume G, de Laurentiis A, Schiavone M, Falcone C, et al. Cancer-associated CD43 glycoforms as target of immunotherapy. Mol Cancer Ther. 2014;13:752-62.
-
(2014)
Mol Cancer Ther.
, vol.13
, pp. 752-762
-
-
Tuccillo, F.M.1
Palmieri, C.2
Fiume, G.3
Laurentiis, A.4
Schiavone, M.5
Falcone, C.6
-
28
-
-
84956615603
-
Identification of significantly mutated regions across cancer types highlights a rich landscape of functional molecular alterations
-
Araya CL, Cenik C, Reuter JA, Kiss G, Pande VS, Snyder MP, et al. Identification of significantly mutated regions across cancer types highlights a rich landscape of functional molecular alterations. Nat Genet. 2016;48:117-25.
-
(2016)
Nat Genet.
, vol.48
, pp. 117-125
-
-
Araya, C.L.1
Cenik, C.2
Reuter, J.A.3
Kiss, G.4
Pande, V.S.5
Snyder, M.P.6
-
29
-
-
84905029258
-
Comprehensive molecular profiling of lung adenocarcinoma
-
Collisson EA, Campbell JD, Brooks AN, Berger AH, Lee W, Chmielecki J, et al. Comprehensive molecular profiling of lung adenocarcinoma. Nature. 2014;511:543-50.
-
(2014)
Nature.
, vol.511
, pp. 543-550
-
-
Collisson, E.A.1
Campbell, J.D.2
Brooks, A.N.3
Berger, A.H.4
Lee, W.5
Chmielecki, J.6
-
30
-
-
0036645286
-
Inactivation of LKB1/STK11 is a common event in adenocarcinomas of the lung
-
Sanchez-Cespedes M, Parrella P, Esteller M, Nomoto S, Trink B, Engles JM, et al. Inactivation of LKB1/STK11 is a common event in adenocarcinomas of the lung. Cancer Res. 2002;62:3659-62.
-
(2002)
Cancer Res.
, vol.62
, pp. 3659-3662
-
-
Sanchez-Cespedes, M.1
Parrella, P.2
Esteller, M.3
Nomoto, S.4
Trink, B.5
Engles, J.M.6
-
31
-
-
84875535693
-
RNAsnp: efficient detection of local RNA secondary structure changes induced by SNPs
-
Sabarinathan R, Tafer H, Seemann SE, Hofacker IL, Stadler PF, Gorodkin J. RNAsnp: efficient detection of local RNA secondary structure changes induced by SNPs. Hum Mutat. 2013;34:546-56.
-
(2013)
Hum Mutat.
, vol.34
, pp. 546-556
-
-
Sabarinathan, R.1
Tafer, H.2
Seemann, S.E.3
Hofacker, I.L.4
Stadler, P.F.5
Gorodkin, J.6
-
32
-
-
0029011919
-
The p150 and p60 subunits of chromatin assembly factor I: a molecular link between newly synthesized histones and DNA replication
-
Kaufman PD, Kobayashi R, Kessler N, Stillman B. The p150 and p60 subunits of chromatin assembly factor I: a molecular link between newly synthesized histones and DNA replication. Cell. 1995;81:1105-14.
-
(1995)
Cell.
, vol.81
, pp. 1105-1114
-
-
Kaufman, P.D.1
Kobayashi, R.2
Kessler, N.3
Stillman, B.4
-
33
-
-
33746544622
-
Mitotic activation of the kinase aurora-a requires its binding partner bora
-
Hutterer A, Berdnik D, Wirtz-Peitz F, Zigman M, Schleiffer A, Knoblich JA. Mitotic activation of the kinase aurora-a requires its binding partner bora. Dev Cell. 2006;11:147-57.
-
(2006)
Dev Cell.
, vol.11
, pp. 147-157
-
-
Hutterer, A.1
Berdnik, D.2
Wirtz-Peitz, F.3
Zigman, M.4
Schleiffer, A.5
Knoblich, J.A.6
-
35
-
-
79961202865
-
Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression
-
Prensner JR, Iyer MK, Balbin OA, Dhanasekaran SM, Cao Q, Brenner JC, et al. Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression. Nat Biotech. 2011;29:742-9.
-
(2011)
Nat Biotech.
, vol.29
, pp. 742-749
-
-
Prensner, J.R.1
Iyer, M.K.2
Balbin, O.A.3
Dhanasekaran, S.M.4
Cao, Q.5
Brenner, J.C.6
-
36
-
-
67650921949
-
Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression
-
Khalil AM, Guttman M, Huarte M, Garber M, Raj A, Rivea Morales D, et al. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci U S A. 2009;106:11667-72.
-
(2009)
Proc Natl Acad Sci U S A.
, vol.106
, pp. 11667-11672
-
-
Khalil, A.M.1
Guttman, M.2
Huarte, M.3
Garber, M.4
Raj, A.5
Rivea Morales, D.6
-
37
-
-
84879837310
-
MALAT1 - A paradigm for long noncoding RNA function in cancer.
-
Gutschner T, Hämmerle M, Diederichs S. MALAT1 - A paradigm for long noncoding RNA function in cancer. J Mol Med. 2013;791-801.
-
(2013)
J Mol Med.
, pp. 791-801
-
-
Gutschner, T.1
Hämmerle, M.2
Diederichs, S.3
-
38
-
-
84929991442
-
High burden and pervasive positive selection of somatic mutations in normal human skin
-
Martincorena I, Roshan A, Gerstung M, Ellis P, Van Loo P, McLaren S, et al. High burden and pervasive positive selection of somatic mutations in normal human skin. Science (80-). 2015;348:880-6.
-
(2015)
Science (80-)
, vol.348
, pp. 880-886
-
-
Martincorena, I.1
Roshan, A.2
Gerstung, M.3
Ellis, P.4
Loo, P.5
McLaren, S.6
-
39
-
-
84964403759
-
Nucleotide excision repair is impaired by binding of transcription factors to DNA
-
Sabarinathan R, Mularoni L, Deu-Pons J, Gonzalez-Perez A, Lopez-Bigas N. Nucleotide excision repair is impaired by binding of transcription factors to DNA. Nature. 2016;532:264-7.
-
(2016)
Nature.
, vol.532
, pp. 264-267
-
-
Sabarinathan, R.1
Mularoni, L.2
Deu-Pons, J.3
Gonzalez-Perez, A.4
Lopez-Bigas, N.5
-
40
-
-
84878220465
-
Targeted next-generation sequencing of head and neck squamous cell carcinoma identifies novel genetic alterations in HPV+ and HPV- tumors
-
Lechner M, Frampton GM, Fenton T, Feber A, Palmer G, Jay A, et al. Targeted next-generation sequencing of head and neck squamous cell carcinoma identifies novel genetic alterations in HPV+ and HPV- tumors. Genome Med. 2013;5:49.
-
(2013)
Genome Med.
, vol.5
, pp. 49
-
-
Lechner, M.1
Frampton, G.M.2
Fenton, T.3
Feber, A.4
Palmer, G.5
Jay, A.6
-
41
-
-
84901680089
-
Whole-genome sequencing and comprehensive molecular profiling identify new driver mutations in gastric cancer
-
Wang K, Yuen ST, Xu J, Lee SP, Yan HHN, Shi ST, et al. Whole-genome sequencing and comprehensive molecular profiling identify new driver mutations in gastric cancer. Nat Genet. 2014;46:573-82.
-
(2014)
Nat Genet.
, vol.46
, pp. 573-582
-
-
Wang, K.1
Yuen, S.T.2
Xu, J.3
Lee, S.P.4
Yan, H.H.N.5
Shi, S.T.6
-
42
-
-
84928987900
-
HTSeq - A Python framework to work with high-throughput sequencing data.
-
Anders S, Pyl PT, Huber W. HTSeq - A Python framework to work with high-throughput sequencing data. Bioinformatics. 2015;31:166-9.
-
(2015)
Bioinformatics.
, vol.31
, pp. 166-169
-
-
Anders, S.1
Pyl, P.T.2
Huber, W.3
-
43
-
-
84893092097
-
Comprehensive analysis of long non-coding RNAS in ovarian cancer reveals global patterns and targeted DNA amplification.
-
Akrami R, Jacobsen A, Hoell J, Schultz N, Sander C, Larsson E. Comprehensive analysis of long non-coding RNAS in ovarian cancer reveals global patterns and targeted DNA amplification. PLoS One. 2013;8:e80306.
-
(2013)
PLoS One.
, vol.8
, pp. e80306
-
-
Akrami, R.1
Jacobsen, A.2
Hoell, J.3
Schultz, N.4
Sander, C.5
Larsson, E.6
|