-
1
-
-
33847076849
-
Chromatin modifications and their function
-
Kouzarides, T. Chromatin modifications and their function. Cell 128, 693-705 (2007).
-
(2007)
Cell
, vol.128
, pp. 693-705
-
-
Kouzarides, T.1
-
2
-
-
84865527768
-
Detecting differential usage of exons from RNAseq data
-
Anders, S., Reyes, A. & Huber, W. Detecting differential usage of exons from RNAseq data. Genome Res. 22, 2008-2017 (2012).
-
(2012)
Genome Res.
, vol.22
, pp. 2008-2017
-
-
Anders, S.1
Reyes, A.2
Huber, W.3
-
3
-
-
84878682420
-
The Genotype-Tissue Expression (GTEx) project
-
GTEx Consortium. The Genotype-Tissue Expression (GTEx) project. Nature Genet. 45, 580-585 (2013).
-
(2013)
Nature Genet.
, vol.45
, pp. 580-585
-
-
GTEx Consortium.1
-
4
-
-
79955674240
-
mRNA transcript quantification in archival samples using multiplexed, color-coded probes
-
Reis, P. P. et al. mRNA transcript quantification in archival samples using multiplexed, color-coded probes. BMC Biotechnol. 11, 46 (2011).
-
(2011)
BMC Biotechnol.
, vol.11
, pp. 46
-
-
Reis, P.P.1
-
5
-
-
84904816744
-
Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma
-
Northcott, P. A. et al. Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma. Nature 511, 428-434 (2014).
-
(2014)
Nature
, vol.511
, pp. 428-434
-
-
Northcott, P.A.1
-
6
-
-
84879611157
-
DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape
-
Xie, M. et al. DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape. Nature Genet. 45, 836-841 (2013).
-
(2013)
Nature Genet.
, vol.45
, pp. 836-841
-
-
Xie, M.1
-
7
-
-
84876836223
-
Modification of enhancer chromatin: What, how, and why?
-
Calo, E. & Wysocka, J. Modification of enhancer chromatin: what, how, and why? Mol. Cell 49, 825-837 (2013).
-
(2013)
Mol. Cell
, vol.49
, pp. 825-837
-
-
Calo, E.1
Wysocka, J.2
-
8
-
-
79953300078
-
FIMO: Scanning for occurrences of a given motif
-
Grant, C. E., Bailey, T. L. & Noble, W. S. FIMO: scanning for occurrences of a given motif. Bioinformatics 27, 1017-1018 (2011).
-
(2011)
Bioinformatics
, vol.27
, pp. 1017-1018
-
-
Grant, C.E.1
Bailey, T.L.2
Noble, W.S.3
-
9
-
-
34547638047
-
Identification of the transforming EML4-ALK fusion gene in nonsmall-cell lung cancer
-
Soda, M. et al. Identification of the transforming EML4-ALK fusion gene in nonsmall-cell lung cancer. Nature 448, 561-566 (2007).
-
(2007)
Nature
, vol.448
, pp. 561-566
-
-
Soda, M.1
-
10
-
-
77953896432
-
Cell signaling by receptor tyrosine kinases
-
Lemmon, M. A. & Schlessinger, J. Cell signaling by receptor tyrosine kinases. Cell 141, 1117-1134 (2010).
-
(2010)
Cell
, vol.141
, pp. 1117-1134
-
-
Lemmon, M.A.1
Schlessinger, J.2
-
11
-
-
81055126433
-
Differential inhibitor sensitivity of anaplastic lymphoma kinase variants found in neuroblastoma
-
Bresler, S. C. et al. Differential inhibitor sensitivity of anaplastic lymphoma kinase variants found in neuroblastoma. Sci. Transl. Med. 3, 108ra114 (2011).
-
(2011)
Sci. Transl. Med.
, vol.3
, pp. 108ra114
-
-
Bresler, S.C.1
-
12
-
-
54049094708
-
Identification of ALK as a major familial neuroblastoma predisposition gene
-
Mossé, Y. P. et al. Identification of ALK as a major familial neuroblastoma predisposition gene. Nature 455, 930-935 (2008).
-
(2008)
Nature
, vol.455
, pp. 930-935
-
-
Mossé, Y.P.1
-
13
-
-
54049149961
-
Somatic and germline activating mutations of the ALK kinase receptor in neuroblastoma
-
Janoueix-Lerosey, I. et al. Somatic and germline activating mutations of the ALK kinase receptor in neuroblastoma. Nature 455, 967-970 (2008).
-
(2008)
Nature
, vol.455
, pp. 967-970
-
-
Janoueix-Lerosey, I.1
-
14
-
-
70349733112
-
Mutation-independent anaplastic lymphoma kinase overexpression in poor prognosis neuroblastoma patients
-
Passoni, L. et al. Mutation-independent anaplastic lymphoma kinase overexpression in poor prognosis neuroblastoma patients. Cancer Res. 69, 7338-7346 (2009).
-
(2009)
Cancer Res.
, vol.69
, pp. 7338-7346
-
-
Passoni, L.1
-
15
-
-
84905086382
-
Wild-type ALK and activating ALK-R1275Q and ALK-F1174L mutations upregulate Myc and initiate tumor formation in murine neural crest progenitor cells
-
Montavon, G. et al. Wild-type ALK and activating ALK-R1275Q and ALK-F1174L mutations upregulate Myc and initiate tumor formation in murine neural crest progenitor cells. Oncotarget 5, 4452-4466 (2014).
-
(2014)
Oncotarget
, vol.5
, pp. 4452-4466
-
-
Montavon, G.1
-
16
-
-
79961002472
-
High ALK receptor tyrosine kinase expression supersedes ALK mutation as a determining factor of an unfavorable phenotype in primary neuroblastoma
-
Schulte, J. H. et al. High ALK receptor tyrosine kinase expression supersedes ALK mutation as a determining factor of an unfavorable phenotype in primary neuroblastoma. Clin. Cancer Res. 17, 5082-5092 (2011).
-
(2011)
Clin. Cancer Res.
, vol.17
, pp. 5082-5092
-
-
Schulte, J.H.1
-
17
-
-
84928105158
-
Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT): A hybridization capture-based nextgeneration sequencing clinical assay for solid tumor molecular oncology
-
Cheng, D. T. et al. Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT): A hybridization capture-based nextgeneration sequencing clinical assay for solid tumor molecular oncology. J. Mol. Diagn. 17, 251-264 (2015).
-
(2015)
J. Mol. Diagn.
, vol.17
, pp. 251-264
-
-
Cheng, D.T.1
-
18
-
-
68549104404
-
The sequence alignment/map format and SAMtools
-
Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
-
19
-
-
65449136284
-
TopHat: Discovering splice junctions with RNA-Seq
-
Trapnell, C., Pachter, L. & Salzberg, S. L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105-1111 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 1105-1111
-
-
Trapnell, C.1
Pachter, L.2
Salzberg, S.L.3
-
20
-
-
77956295988
-
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
-
McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297-1303 (2010).
-
(2010)
Genome Res.
, vol.20
, pp. 1297-1303
-
-
McKenna, A.1
-
21
-
-
78651271733
-
Integrative genomics viewer
-
Robinson, J. T. et al. Integrative genomics viewer. Nature Biotechnol. 29, 24-26 (2011).
-
(2011)
Nature Biotechnol.
, vol.29
, pp. 24-26
-
-
Robinson, J.T.1
-
22
-
-
58349111875
-
AmiGO: Online access to ontology and annotation data
-
Carbon, S. et al. AmiGO: online access to ontology and annotation data. Bioinformatics 25, 288-289 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 288-289
-
-
Carbon, S.1
-
23
-
-
84891808382
-
JASPAR 2014: An extensively expanded and updated openaccess database of transcription factor binding profiles
-
Mathelier, A. et al. JASPAR 2014: an extensively expanded and updated openaccess database of transcription factor binding profiles. Nucleic Acids Res. 42, D142-D147 (2014).
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D142-D147
-
-
Mathelier, A.1
-
24
-
-
77957943127
-
ETV1 is a lineage survival factor that cooperates with KIT in gastrointestinal stromal tumours
-
Chi, P. et al. ETV1 is a lineage survival factor that cooperates with KIT in gastrointestinal stromal tumours. Nature 467, 849-853 (2010).
-
(2010)
Nature
, vol.467
, pp. 849-853
-
-
Chi, P.1
-
25
-
-
53849146020
-
Model-based analysis of ChIP-Seq (MACS)
-
Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).
-
(2008)
Genome Biol.
, vol.9
, pp. R137
-
-
Zhang, Y.1
-
26
-
-
84886812425
-
Detecting somatic genetic alterations in tumor specimens by exon capture and massively parallel sequencing
-
Won,H.H., Scott, S. N., Brannon, A. R., Shah, R. H.& Berger, M. F. Detecting somatic genetic alterations in tumor specimens by exon capture and massively parallel sequencing. J. Vis. Exp. e50710 (2013).
-
(2013)
J. Vis. Exp.
-
-
Won, H.H.1
Scott, S.N.2
Brannon, A.R.3
Shah, R.H.4
Berger, M.F.5
-
27
-
-
67649884743
-
Fast and accurate short read alignment with Burrows-Wheeler transform
-
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
28
-
-
79955483667
-
A framework for variation discovery and genotyping using next-generation DNA sequencing data
-
DePristo, M. A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature Genet. 43, 491-498 (2011).
-
(2011)
Nature Genet.
, vol.43
, pp. 491-498
-
-
DePristo, M.A.1
-
29
-
-
84874025843
-
Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples
-
Cibulskis, K. et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nature Biotechnol. 31, 213-219 (2013).
-
(2013)
Nature Biotechnol.
, vol.31
, pp. 213-219
-
-
Cibulskis, K.1
-
30
-
-
84866440781
-
DELLY: Structural variant discovery by integrated paired-end and split-read analysis
-
Rausch, T. et al. DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics 28, i333-i339 (2012).
-
(2012)
Bioinformatics
, vol.28
, pp. i333-i339
-
-
Rausch, T.1
-
31
-
-
79957868920
-
Bismark: A flexible aligner and methylation caller for Bisulfite-Seq applications
-
Krueger, F. & Andrews, S. R. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 27, 1571-1572 (2011).
-
(2011)
Bioinformatics
, vol.27
, pp. 1571-1572
-
-
Krueger, F.1
Andrews, S.R.2
-
32
-
-
78651430230
-
Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization
-
Boeva, V. et al. Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization. Bioinformatics 27, 268-269 (2011).
-
(2011)
Bioinformatics
, vol.27
, pp. 268-269
-
-
Boeva, V.1
-
33
-
-
79961007031
-
CREST maps somatic structural variation in cancer genomes with base-pair resolution
-
Wang, J. et al. CREST maps somatic structural variation in cancer genomes with base-pair resolution. Nature Methods 8, 652-654 (2011).
-
(2011)
Nature Methods
, vol.8
, pp. 652-654
-
-
Wang, J.1
-
34
-
-
77955405475
-
Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor
-
McLaren, W. et al. Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics 26, 2069-2070 (2010).
-
(2010)
Bioinformatics
, vol.26
, pp. 2069-2070
-
-
McLaren, W.1
-
35
-
-
69649109364
-
Circos: An information aesthetic for comparative genomics
-
Krzywinski, M. et al. Circos: an information aesthetic for comparative genomics. Genome Res. 19, 1639-1645 (2009).
-
(2009)
Genome Res.
, vol.19
, pp. 1639-1645
-
-
Krzywinski, M.1
-
36
-
-
40449100030
-
Direct multiplexed measurement of gene expression with colorcoded probe pairs
-
Geiss, G. K. et al. Direct multiplexed measurement of gene expression with colorcoded probe pairs. Nature Biotechnol. 26, 317-325 (2008).
-
(2008)
Nature Biotechnol.
, vol.26
, pp. 317-325
-
-
Geiss, G.K.1
-
37
-
-
0023145290
-
A line of non-tumorigenic mouse melanocytes, syngeneic with the B16 melanoma and requiring a tumour promoter for growth
-
Bennett, D. C., Cooper, P. J. & Hart, I. R. A line of non-tumorigenic mouse melanocytes, syngeneic with the B16 melanoma and requiring a tumour promoter for growth. Int. J. Cancer 39, 414-418 (1987).
-
(1987)
Int. J. Cancer
, vol.39
, pp. 414-418
-
-
Bennett, D.C.1
Cooper, P.J.2
Hart, I.R.3
-
38
-
-
0037037582
-
Interferongamma is required for activation-induced death of T lymphocytes
-
Refaeli, Y., Van Parijs, L., Alexander, S. I.&Abbas, A. K. Interferongamma is required for activation-induced death of T lymphocytes. J. Exp. Med. 196, 999-1005 (2002).
-
(2002)
J. Exp. Med.
, vol.196
, pp. 999-1005
-
-
Refaeli, Y.1
Van Parijs, L.2
Alexander, S.I.3
Abbas, A.K.4
-
39
-
-
2442562277
-
A novel triple-modality reporter gene for whole-body fluorescent, bioluminescent, and nuclear noninvasive imaging
-
Ponomarev, V. et al. A novel triple-modality reporter gene for whole-body fluorescent, bioluminescent, and nuclear noninvasive imaging. Eur. J. Nucl. Med. Mol. Imaging 31, 740-751 (2004).
-
(2004)
Eur. J. Nucl. Med. Mol. Imaging
, vol.31
, pp. 740-751
-
-
Ponomarev, V.1
|