-
1
-
-
84884994218
-
The Cancer Genome Atlas Pan-Cancer analysis project
-
Weinstein, J. N. et al. The Cancer Genome Atlas Pan-Cancer analysis project. Nature genetics 45, 1113-1120, doi: 10.1038/ng.2764 (2013).
-
(2013)
Nature Genetics
, vol.45
, pp. 1113-1120
-
-
Weinstein, J.N.1
-
2
-
-
77951115122
-
International network of cancer genome projects
-
Hudson, T. J. et al. International network of cancer genome projects. Nature 464, 993-998, doi: 10.1038/nature08987 (2010).
-
(2010)
Nature
, vol.464
, pp. 993-998
-
-
Hudson, T.J.1
-
3
-
-
84863495094
-
The hallmarks of cancer: A long non-coding RNA point of view
-
Gutschner, T. & Diederichs, S. The hallmarks of cancer: a long non-coding RNA point of view. RNA biology 9, 703-719, doi: 10.4161/ rna.20481 (2012).
-
(2012)
RNA Biology
, vol.9
, pp. 703-719
-
-
Gutschner, T.1
Diederichs, S.2
-
4
-
-
84865727393
-
The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression
-
Derrien, T. et al. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome research 22, 1775-1789, doi: 10.1101/gr.132159.111 (2012).
-
(2012)
Genome Research
, vol.22
, pp. 1775-1789
-
-
Derrien, T.1
-
5
-
-
84879987789
-
LincRNAs: Genomics, evolution, and mechanisms
-
Ulitsky, I. & Bartel, D. P. lincRNAs: genomics, evolution, and mechanisms. Cell 154, 26-46, doi: 10.1016/j.cell.2013.06.020 (2013).
-
(2013)
Cell
, vol.154
, pp. 26-46
-
-
Ulitsky, I.1
Bartel, D.P.2
-
6
-
-
84963544829
-
Single-cell analysis of long non-coding RNAs in the developing human neocortex
-
Liu, S. J. et al. Single-cell analysis of long non-coding RNAs in the developing human neocortex. Genome biology 17, 67, doi: 10.1186/s13059-016-0932-1 (2016).
-
(2016)
Genome Biology
, vol.17
, pp. 67
-
-
Liu, S.J.1
-
7
-
-
84879671055
-
Pervasive transcription of the human genome produces thousands of previously unidentified long intergenic noncoding RNAS
-
Hangauer, M. J., Vaughn, I. W. & McManus, M. T. Pervasive Transcription of the Human Genome Produces Thousands of Previously Unidentified Long Intergenic Noncoding RNAs. PLoS genetics 9, e1003569, doi: 10.1371/journal.pgen.1003569 (2013).
-
(2013)
PLoS Genetics
, vol.9
-
-
Hangauer, M.J.1
Vaughn, I.W.2
McManus, M.T.3
-
8
-
-
84924063355
-
The landscape of long noncoding RNAs in the human transcriptome
-
Iyer, M. K. et al. The landscape of long noncoding RNAs in the human transcriptome. Nature genetics, doi: 10.1038/ng.3192 (2015).
-
(2015)
Nature Genetics
-
-
Iyer, M.K.1
-
9
-
-
84876125829
-
LncRNADisease: A database for long-non-coding RNA-associated diseases
-
Chen, G. et al. LncRNADisease: a database for long-non-coding RNA-associated diseases. Nucleic acids research 41, D983-986, doi: 10.1093/nar/gks1099 (2013).
-
(2013)
Nucleic Acids Research
, vol.41
, pp. D983-986
-
-
Chen, G.1
-
10
-
-
77955323879
-
A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response
-
Huarte, M. et al. A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell 142, 409-419, doi: 10.1016/j.cell.2010.06.040 (2010).
-
(2010)
Cell
, vol.142
, pp. 409-419
-
-
Huarte, M.1
-
11
-
-
77951118936
-
Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis
-
Gupta, R. A. et al. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 464, 1071-1076, doi: 10.1038/nature08975 (2010).
-
(2010)
Nature
, vol.464
, pp. 1071-1076
-
-
Gupta, R.A.1
-
12
-
-
84880154515
-
Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer
-
Du, Z. et al. Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer. Nature structural & molecular biology 20, 908-913, doi: 10.1038/nsmb.2591 (2013).
-
(2013)
Nature Structural & Molecular Biology
, vol.20
, pp. 908-913
-
-
Du, Z.1
-
13
-
-
84969753263
-
Pancreatic cancer risk variant in LINC00673 creates a miR-1231 binding site and interferes with PTPN11 degradation
-
Zheng, J. et al. Pancreatic cancer risk variant in LINC00673 creates a miR-1231 binding site and interferes with PTPN11 degradation. Nature genetics 48, 747-757, doi: 10.1038/ng.3568 (2016).
-
(2016)
Nature Genetics
, vol.48
, pp. 747-757
-
-
Zheng, J.1
-
14
-
-
84893092097
-
Comprehensive analysis of long non-coding RNAs in ovarian cancer reveals global patterns and targeted DNA amplification
-
Akrami, R. et al. Comprehensive analysis of long non-coding RNAs in ovarian cancer reveals global patterns and targeted DNA amplification. PloS one 8, e80306, doi: 10.1371/journal.pone.0080306 (2013).
-
(2013)
PloS One
, vol.8
-
-
Akrami, R.1
-
15
-
-
84961615874
-
Melanoma addiction to the long non-coding RNA SAMMSON
-
Leucci, E. et al. Melanoma addiction to the long non-coding RNA SAMMSON. Nature 531, 518-522, doi: 10.1038/nature17161 (2016).
-
(2016)
Nature
, vol.531
, pp. 518-522
-
-
Leucci, E.1
-
16
-
-
84870599966
-
Functional impact bias reveals cancer drivers
-
Gonzalez-Perez, A. & Lopez-Bigas, N. Functional impact bias reveals cancer drivers. Nucleic acids research 40, e169, doi: 10.1093/ nar/gks743 (2012).
-
(2012)
Nucleic Acids Research
, vol.40
, pp. e169
-
-
Gonzalez-Perez, A.1
Lopez-Bigas, N.2
-
17
-
-
84880507665
-
Mutational heterogeneity in cancer and the search for new cancer-associated genes
-
Lawrence, M. S. et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature 499, 214-218, doi: 10.1038/nature12213 (2013).
-
(2013)
Nature
, vol.499
, pp. 214-218
-
-
Lawrence, M.S.1
-
18
-
-
84885100832
-
The mutational landscape of phosphorylation signaling in cancer
-
Reimand, J., Wagih, O. & Bader, G. D. The mutational landscape of phosphorylation signaling in cancer. Scientific reports 3, 2651, doi: 10.1038/srep02651 (2013).
-
(2013)
Scientific Reports
, vol.3
, pp. 2651
-
-
Reimand, J.1
Wagih, O.2
Bader, G.D.3
-
19
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74, doi: 10.1038/nature11247 (2012).
-
(2012)
Nature
, vol.489
, pp. 57-74
-
-
-
20
-
-
84857066786
-
Modular regulatory principles of large non-coding RNAs
-
Guttman, M. & Rinn, J. L. Modular regulatory principles of large non-coding RNAs. Nature 482, 339-346, doi: 10.1038/nature10887 (2012).
-
(2012)
Nature
, vol.482
, pp. 339-346
-
-
Guttman, M.1
Rinn, J.L.2
-
21
-
-
84882837534
-
Signatures of mutational processes in human cancer
-
Alexandrov, L. B. et al. Signatures of mutational processes in human cancer. Nature 500, 415-421, doi: 10.1038/nature12477 (2013).
-
(2013)
Nature
, vol.500
, pp. 415-421
-
-
Alexandrov, L.B.1
-
22
-
-
84922984420
-
Unexpected selection to retain high GC content and splicing enhancers within exons of multiexonic lncRNA loci
-
Haerty, W. & Ponting, C. P. Unexpected selection to retain high GC content and splicing enhancers within exons of multiexonic lncRNA loci. RNA 21, 333-346, doi: 10.1261/rna.047324.114 (2015).
-
(2015)
RNA
, vol.21
, pp. 333-346
-
-
Haerty, W.1
Ponting, C.P.2
-
23
-
-
84864258996
-
A landscape of driver mutations in melanoma
-
Hodis, E. et al. A landscape of driver mutations in melanoma. Cell 150, 251-263, doi: 10.1016/j.cell.2012.06.024 (2012).
-
(2012)
Cell
, vol.150
, pp. 251-263
-
-
Hodis, E.1
-
24
-
-
1542515338
-
A census of human cancer genes
-
Futreal, P. A. et al. A census of human cancer genes. Nature reviews. Cancer 4, 177-183, doi: 10.1038/nrc1299 (2004).
-
(2004)
Nature Reviews. Cancer
, vol.4
, pp. 177-183
-
-
Futreal, P.A.1
-
25
-
-
84893669233
-
Exploring the potential benefits of stratified false discovery rates for region-based testing of association with rare genetic variation
-
Xu, C., Ciampi, A. & Greenwood, C. M. Exploring the potential benefits of stratified false discovery rates for region-based testing of association with rare genetic variation. Frontiers in genetics 5, 11, doi: 10.3389/fgene.2014.00011 (2014).
-
(2014)
Frontiers in Genetics
, vol.5
, pp. 11
-
-
Xu, C.1
Ciampi, A.2
Greenwood, C.M.3
-
26
-
-
33747595466
-
Stratified false discovery control for large-scale hypothesis testing with application to genome-wide association studies
-
Sun, L., Craiu, R. V., Paterson, A. D. & Bull, S. B. Stratified false discovery control for large-scale hypothesis testing with application to genome-wide association studies. Genetic epidemiology 30, 519-530, doi: 10.1002/gepi.20164 (2006).
-
(2006)
Genetic Epidemiology
, vol.30
, pp. 519-530
-
-
Sun, L.1
Craiu, R.V.2
Paterson, A.D.3
Bull, S.B.4
-
27
-
-
84963588792
-
Whole-genome mutational landscape and characterization of noncoding and structural mutations in liver cancer
-
Fujimoto, A. et al. Whole-genome mutational landscape and characterization of noncoding and structural mutations in liver cancer. Nature genetics 48, 500-509, doi: 10.1038/ng.3547 (2016).
-
(2016)
Nature Genetics
, vol.48
, pp. 500-509
-
-
Fujimoto, A.1
-
28
-
-
84964313637
-
Genome-wide analysis of the human p53 transcriptional network unveils a lncRNA tumour suppressor signature
-
Sanchez, Y. et al. Genome-wide analysis of the human p53 transcriptional network unveils a lncRNA tumour suppressor signature. Nature communications 5, 5812, doi: 10.1038/ncomms6812 (2014).
-
(2014)
Nature Communications
, vol.5
, pp. 5812
-
-
Sanchez, Y.1
-
29
-
-
84944077358
-
Comprehensive Genomic Characterization of Long Non-coding RNAs across Human Cancers
-
Yan, X. et al. Comprehensive Genomic Characterization of Long Non-coding RNAs across Human Cancers. Cancer cell 28, 529-540, doi: 10.1016/j.ccell.2015.09.006 (2015).
-
(2015)
Cancer Cell
, vol.28
, pp. 529-540
-
-
Yan, X.1
-
30
-
-
84885129618
-
Comprehensive identification of mutational cancer driver genes across 12 tumor types
-
Tamborero, D. et al. Comprehensive identification of mutational cancer driver genes across 12 tumor types. Scientific reports 3, 2650, doi: 10.1038/srep02650 (2013).
-
(2013)
Scientific Reports
, vol.3
, pp. 2650
-
-
Tamborero, D.1
-
31
-
-
84870654685
-
ANKRD18A as a novel epigenetic regulation gene in lung cancer
-
Liu, W. B. et al. ANKRD18A as a novel epigenetic regulation gene in lung cancer. Biochemical and biophysical research communications 429, 180-185, doi: 10.1016/j.bbrc.2012.10.116 (2012).
-
(2012)
Biochemical and Biophysical Research Communications
, vol.429
, pp. 180-185
-
-
Liu, W.B.1
-
32
-
-
84887032986
-
IntOGen-mutations identifies cancer drivers across tumor types
-
Gonzalez-Perez, A. et al. IntOGen-mutations identifies cancer drivers across tumor types. Nature methods 10, 1081-1082, doi: 10.1038/nmeth.2642 (2013).
-
(2013)
Nature Methods
, vol.10
, pp. 1081-1082
-
-
Gonzalez-Perez, A.1
-
33
-
-
84949501820
-
The profile of heparanase expression distinguishes differentiated thyroid carcinoma from benign neoplasms
-
Matos, L. L. et al. The Profile of Heparanase Expression Distinguishes Differentiated Thyroid Carcinoma from Benign Neoplasms. PloS one 10, e0141139, doi: 10.1371/journal.pone.0141139 (2015).
-
(2015)
PloS One
, vol.10
-
-
Matos, L.L.1
-
34
-
-
84863617167
-
Inactivation of MYO5B promotes invasion and motility in gastric cancer cells
-
Dong, W. et al. Inactivation of MYO5B promotes invasion and motility in gastric cancer cells. Digestive diseases and sciences 57, 1247-1252, doi: 10.1007/s10620-011-1989-z (2012).
-
(2012)
Digestive Diseases and Sciences
, vol.57
, pp. 1247-1252
-
-
Dong, W.1
-
35
-
-
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 29, 2238-2244, doi: 10.1093/bioinformatics/btt395 (2013).
-
(2013)
Bioinformatics
, vol.29
, pp. 2238-2244
-
-
Tamborero, D.1
Gonzalez-Perez, A.2
Lopez-Bigas, N.3
-
36
-
-
84888232130
-
Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs
-
Marques, A. C. et al. Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs. Genome biology 14, R131, doi: 10.1186/gb-2013-14-11-r131 (2013).
-
(2013)
Genome Biology
, vol.14
, pp. R131
-
-
Marques, A.C.1
-
37
-
-
84929705123
-
Principles of long noncoding RNA evolution derived from direct comparison of transcriptomes in 17 species
-
Hezroni, H. et al. Principles of long noncoding RNA evolution derived from direct comparison of transcriptomes in 17 species. Cell reports 11, 1110-1122, doi: 10.1016/j.celrep.2015.04.023 (2015).
-
(2015)
Cell Reports
, vol.11
, pp. 1110-1122
-
-
Hezroni, H.1
-
38
-
-
33144462258
-
Structural and functional properties of genes involved in human cancer
-
Furney, S. J., Higgins, D. G., Ouzounis, C. A. & Lopez-Bigas, N. Structural and functional properties of genes involved in human cancer. BMC genomics 7, 3, doi: 10.1186/1471-2164-7-3 (2006).
-
(2006)
BMC Genomics
, vol.7
, pp. 3
-
-
Furney, S.J.1
Higgins, D.G.2
Ouzounis, C.A.3
Lopez-Bigas, N.4
-
39
-
-
84904086862
-
Transcriptional landscape of repetitive elements in normal and cancer human cells
-
Criscione, S. W., Zhang, Y., Thompson, W., Sedivy, J. M. & Neretti, N. Transcriptional landscape of repetitive elements in normal and cancer human cells. BMC genomics 15, 583, doi: 10.1186/1471-2164-15-583 (2014).
-
(2014)
BMC Genomics
, vol.15
, pp. 583
-
-
Criscione, S.W.1
Zhang, Y.2
Thompson, W.3
Sedivy, J.M.4
Neretti, N.5
-
40
-
-
84893699492
-
Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia
-
Ferreira, P. G. et al. Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia. Genome research 24, 212-226, doi: 10.1101/gr.152132.112 (2014).
-
(2014)
Genome Research
, vol.24
, pp. 212-226
-
-
Ferreira, P.G.1
-
41
-
-
84902682913
-
The RIDL hypothesis: Transposable elements as functional domains of long noncoding RNAs
-
Johnson, R. & Guigo, R. The RIDL hypothesis: transposable elements as functional domains of long noncoding RNAs. RNA 20, 959-976, doi: 10.1261/rna.044560.114 (2014).
-
(2014)
RNA
, vol.20
, pp. 959-976
-
-
Johnson, R.1
Guigo, R.2
-
42
-
-
33745577150
-
A mutation creating a potential illegitimate microRNA target site in the myostatin gene affects muscularity in sheep
-
Clop, A. et al. A mutation creating a potential illegitimate microRNA target site in the myostatin gene affects muscularity in sheep. Nature genetics 38, 813-818, doi: 10.1038/ng1810 (2006).
-
(2006)
Nature Genetics
, vol.38
, pp. 813-818
-
-
Clop, A.1
-
43
-
-
84925855241
-
Identification of common genetic variants controlling transcript isoform variation in human whole blood
-
Zhang, X. et al. Identification of common genetic variants controlling transcript isoform variation in human whole blood. Nature genetics 47, 345-352, doi: 10.1038/ng.3220 (2015).
-
(2015)
Nature Genetics
, vol.47
, pp. 345-352
-
-
Zhang, X.1
-
44
-
-
84875535693
-
RNAsnp: Efficient detection of local RNA secondary structure changes induced by SNPs
-
Sabarinathan, R. et al. RNAsnp: efficient detection of local RNA secondary structure changes induced by SNPs. Human mutation 34, 546-556, doi: 10.1002/humu.22273 (2013).
-
(2013)
Human Mutation
, vol.34
, pp. 546-556
-
-
Sabarinathan, R.1
-
45
-
-
77956873295
-
Disease-associated mutations that alter the RNA structural ensemble
-
Halvorsen, M., Martin, J. S., Broadaway, S. & Laederach, A. Disease-associated mutations that alter the RNA structural ensemble. PLoS genetics 6, e1001074, doi: 10.1371/journal.pgen.1001074 (2010).
-
(2010)
PLoS Genetics
, vol.6
-
-
Halvorsen, M.1
Martin, J.S.2
Broadaway, S.3
Laederach, A.4
-
46
-
-
84949564442
-
A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing
-
Alioto, T. S. et al. A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing. Nature communications 6, 10001, doi: 10.1038/ncomms10001 (2015).
-
(2015)
Nature Communications
, vol.6
, pp. 10001
-
-
Alioto, T.S.1
-
47
-
-
84865760395
-
GENCODE: The reference human genome annotation for the ENCODE Project
-
Harrow, J. et al. GENCODE: the reference human genome annotation for The ENCODE Project. Genome research 22, 1760-1774, doi: 10.1101/gr.135350.111 (2012).
-
(2012)
Genome Research
, vol.22
, pp. 1760-1774
-
-
Harrow, J.1
-
48
-
-
84901680089
-
Whole-genome sequencing and comprehensive molecular profiling identify new driver mutations in gastric cancer
-
Wang, K. et al. Whole-genome sequencing and comprehensive molecular profiling identify new driver mutations in gastric cancer. Nature genetics 46, 573-582, doi: 10.1038/ng.2983 (2014).
-
(2014)
Nature Genetics
, vol.46
, pp. 573-582
-
-
Wang, K.1
-
49
-
-
84876020023
-
CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model
-
Wang, L. et al. CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model. Nucleic acids research 41, e74, doi: 10.1093/nar/gkt006 (2013).
-
(2013)
Nucleic Acids Research
, vol.41
, pp. e74
-
-
Wang, L.1
-
50
-
-
78651271733
-
Integrative genomics viewer
-
Robinson, J. T. et al. Integrative genomics viewer. Nature biotechnology 29, 24-26, doi: 10.1038/nbt.1754 (2011).
-
(2011)
Nature Biotechnology
, vol.29
, pp. 24-26
-
-
Robinson, J.T.1
-
51
-
-
78651325932
-
LncRNAdb: A reference database for long noncoding RNAs
-
Amaral, P. P., Clark, M. B., Gascoigne, D. K., Dinger, M. E. & Mattick, J. S. lncRNAdb: a reference database for long noncoding RNAs. Nucleic acids research 39, D146-151, doi: 10.1093/nar/gkq1138 (2011).
-
(2011)
Nucleic Acids Research
, vol.39
, pp. D146-151
-
-
Amaral, P.P.1
Clark, M.B.2
Gascoigne, D.K.3
Dinger, M.E.4
Mattick, J.S.5
-
52
-
-
84874754080
-
Grape RNA-Seq analysis pipeline environment
-
Knowles, D. G., Roder, M., Merkel, A. & Guigo, R. Grape RNA-Seq analysis pipeline environment. Bioinformatics 29, 614-621, doi: 10.1093/bioinformatics/btt016 (2013).
-
(2013)
Bioinformatics
, vol.29
, pp. 614-621
-
-
Knowles, D.G.1
Roder, M.2
Merkel, A.3
Guigo, R.4
-
53
-
-
77950661675
-
Impact of replication timing on non-CpG and CpG substitution rates in mammalian genomes
-
Chen, C. L. et al. Impact of replication timing on non-CpG and CpG substitution rates in mammalian genomes. Genome research 20, 447-457, doi: 10.1101/gr.098947.109 (2010).
-
(2010)
Genome Research
, vol.20
, pp. 447-457
-
-
Chen, C.L.1
|