-
1
-
-
84865755978
-
The accessible chromatin landscape of the human genome
-
Thurman, R.E., et al. The accessible chromatin landscape of the human genome. Nature 489, 75-82 (2012).
-
(2012)
Nature
, vol.489
, pp. 75-82
-
-
Thurman, R.E.1
-
2
-
-
58049217860
-
-
Hindorff, L.A., Junkins, H.A., Mehta, J.P., Manolio, T.A. A Catalog of Published Genome-Wide Association Studies. http://www.genome.gov/gwastudies (2009).
-
(2009)
A Catalog of Published Genome-Wide Association Studies
-
-
Hindorff, L.A.1
Junkins, H.A.2
Mehta, J.P.3
Manolio, T.A.4
-
3
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
ENCODE Project Consortium
-
ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74 (2012).
-
(2012)
Nature
, vol.489
, pp. 57-74
-
-
-
4
-
-
77957940722
-
The NIH Roadmap Epigenomics Mapping Consortium
-
Bernstein, B.E., et al. The NIH Roadmap Epigenomics Mapping Consortium. Nat. Biotechnol. 28, 1045-1048 (2010).
-
(2010)
Nat. Biotechnol.
, vol.28
, pp. 1045-1048
-
-
Bernstein, B.E.1
-
5
-
-
84874381107
-
Genome-wide quantitative enhancer activity maps identified by STARR-seq
-
Arnold, C.D., et al. Genome-wide quantitative enhancer activity maps identified by STARR-seq. Science 339, 1074-1077 (2013).
-
(2013)
Science
, vol.339
, pp. 1074-1077
-
-
Arnold, C.D.1
-
6
-
-
84938876935
-
Massively parallel quantification of the regulatory effects of noncoding genetic variation in a human cohort
-
Vockley, C.M., et al. Massively parallel quantification of the regulatory effects of noncoding genetic variation in a human cohort. Genome Res. 25, 1206-1214 (2015).
-
(2015)
Genome Res.
, vol.25
, pp. 1206-1214
-
-
Vockley, C.M.1
-
7
-
-
84983801995
-
Direct GR binding sites potentiate clusters of TF binding across the human genome
-
Vockley, C.M., et al. Direct GR binding sites potentiate clusters of TF binding across the human genome. Cell 166, 1269-1281 (2016).
-
(2016)
Cell
, vol.166
, pp. 1269-1281
-
-
Vockley, C.M.1
-
8
-
-
84986898390
-
Applications of CRISPR technologies in research and beyond
-
Barrangou, R., Doudna, J.A. Applications of CRISPR technologies in research and beyond. Nat. Biotechnol. 34, 933-941 (2016).
-
(2016)
Nat. Biotechnol.
, vol.34
, pp. 933-941
-
-
Barrangou, R.1
Doudna, J.A.2
-
9
-
-
84865070369
-
A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity
-
Jinek, M., et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816-821 (2012).
-
(2012)
Science
, vol.337
, pp. 816-821
-
-
Jinek, M.1
-
10
-
-
84873729095
-
Multiplex genome engineering using CRISPR/Cas systems
-
Cong, L., et al. Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819-823 (2013).
-
(2013)
Science
, vol.339
, pp. 819-823
-
-
Cong, L.1
-
11
-
-
84873734105
-
RNA-guided human genome engineering via Cas9
-
Mali, P., et al. RNA-guided human genome engineering via Cas9. Science 339, 823-826 (2013).
-
(2013)
Science
, vol.339
, pp. 823-826
-
-
Mali, P.1
-
12
-
-
84874624936
-
Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease
-
Cho, S.W., Kim, S., Kim, J.M., Kim, J.-S. Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease. Nat. Biotechnol. 31, 230-232 (2013).
-
(2013)
Nat. Biotechnol.
, vol.31
, pp. 230-232
-
-
Cho, S.W.1
Kim, S.2
Kim, J.M.3
Kim, J.-S.4
-
13
-
-
84892765883
-
Genome-scale CRISPR-Cas9 knockout screening in human cells
-
Shalem, O., et al. Genome-scale CRISPR-Cas9 knockout screening in human cells. Science 343, 84-87 (2014).
-
(2014)
Science
, vol.343
, pp. 84-87
-
-
Shalem, O.1
-
14
-
-
84892749369
-
Genetic screens in human cells using the CRISPR-Cas9 system
-
Wang, T., Wei, J.J., Sabatini, D.M., Lander, E.S. Genetic screens in human cells using the CRISPR-Cas9 system. Science 343, 80-84 (2014).
-
(2014)
Science
, vol.343
, pp. 80-84
-
-
Wang, T.1
Wei, J.J.2
Sabatini, D.M.3
Lander, E.S.4
-
15
-
-
84898665052
-
Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR-guide RNA library
-
Koike-Yusa, H., Li, Y., Tan, E.P., Del Castillo Velasco-Herrera, M., Yusa, K. Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR-guide RNA library. Nat. Biotechnol. 32, 267-273 (2014).
-
(2014)
Nat. Biotechnol
, vol.32
, pp. 267-273
-
-
Koike-Yusa, H.1
Li, Y.2
Tan, E.P.3
Del Castillo Velasco-Herrera, M.4
Yusa, K.5
-
16
-
-
84946925193
-
BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis
-
Canver, M.C., et al. BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis. Nature 527, 192-197 (2015).
-
(2015)
Nature
, vol.527
, pp. 192-197
-
-
Canver, M.C.1
-
17
-
-
84957590341
-
Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9
-
Korkmaz, G., et al. Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9. Nat. Biotechnol. 34, 192-198 (2016).
-
(2016)
Nat. Biotechnol.
, vol.34
, pp. 192-198
-
-
Korkmaz, G.1
-
18
-
-
84957602988
-
High-throughput mapping of regulatory DNA
-
Rajagopal, N., et al. High-throughput mapping of regulatory DNA. Nat. Biotechnol. 34, 167-174 (2016).
-
(2016)
Nat. Biotechnol.
, vol.34
, pp. 167-174
-
-
Rajagopal, N.1
-
19
-
-
84960387483
-
A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening
-
Diao, Y., et al. A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening. Genome Res. 26, 397-405 (2016).
-
(2016)
Genome Res.
, vol.26
, pp. 397-405
-
-
Diao, Y.1
-
20
-
-
84988985113
-
High-resolution interrogation of functional elements in the noncoding genome
-
Sanjana, N.E., et al. High-resolution interrogation of functional elements in the noncoding genome. Science 353, 1545-1549 (2016).
-
(2016)
Science
, vol.353
, pp. 1545-1549
-
-
Sanjana, N.E.1
-
21
-
-
84959104222
-
Functional footprinting of regulatory DNA
-
Vierstra, J., et al. Functional footprinting of regulatory DNA. Nat. Methods 12, 927-930 (2015).
-
(2015)
Nat. Methods
, vol.12
, pp. 927-930
-
-
Vierstra, J.1
-
22
-
-
84992753525
-
Loss-of-function genetic tools for animal models: Cross-species and cross-platform differences
-
Housden, B.E., et al. Loss-of-function genetic tools for animal models: Cross-species and cross-platform differences. Nat. Rev. Genet. 18, 24-40 (2017).
-
(2017)
Nat. Rev. Genet.
, vol.18
, pp. 24-40
-
-
Housden, B.E.1
-
23
-
-
84961290066
-
Editing the epigenome: Technologies for programmable transcription and epigenetic modulation
-
Thakore, P.I., Black, J.B., Hilton, I.B., Gersbach, C.A. Editing the epigenome: Technologies for programmable transcription and epigenetic modulation. Nat. Methods 13, 127-137 (2016).
-
(2016)
Nat. Methods
, vol.13
, pp. 127-137
-
-
Thakore, P.I.1
Black, J.B.2
Hilton, I.B.3
Gersbach, C.A.4
-
24
-
-
84874687019
-
Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression
-
Qi, L.S., et al. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152, 1173-1183 (2013).
-
(2013)
Cell
, vol.152
, pp. 1173-1183
-
-
Qi, L.S.1
-
25
-
-
84880571335
-
CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes
-
Gilbert, L.A., et al. CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell 154, 442-451 (2013).
-
(2013)
Cell
, vol.154
, pp. 442-451
-
-
Gilbert, L.A.1
-
26
-
-
84881336110
-
Reprogramming to pluripotency using designer TALE transcription factors targeting enhancers
-
Gao, X., et al. Reprogramming to pluripotency using designer TALE transcription factors targeting enhancers. Stem Cell Reports 1, 183-197 (2013).
-
(2013)
Stem Cell Reports
, vol.1
, pp. 183-197
-
-
Gao, X.1
-
27
-
-
84964313405
-
Comparison of TALE designer transcription factors and the CRISPR/dCas9 in regulation of gene expression by targeting enhancers
-
Gao, X., et al. Comparison of TALE designer transcription factors and the CRISPR/dCas9 in regulation of gene expression by targeting enhancers. Nucleic Acids Res. 42, e155 (2014).
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. e155
-
-
Gao, X.1
-
28
-
-
84908352138
-
Genome-scale CRISPR-mediated control of gene repression and activation
-
Gilbert, L.A., et al. Genome-scale CRISPR-mediated control of gene repression and activation. Cell 159, 647-661 (2014).
-
(2014)
Cell
, vol.159
, pp. 647-661
-
-
Gilbert, L.A.1
-
29
-
-
84923096541
-
Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex
-
Konermann, S., et al. Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex. Nature 517, 583-588 (2015).
-
(2015)
Nature
, vol.517
, pp. 583-588
-
-
Konermann, S.1
-
30
-
-
84929135130
-
Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers
-
Hilton, I.B., et al. Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers. Nat. Biotechnol. 33, 510-517 (2015).
-
(2015)
Nat. Biotechnol.
, vol.33
, pp. 510-517
-
-
Hilton, I.B.1
-
31
-
-
84928924333
-
Functional annotation of native enhancers with a Cas9-histone demethylase fusion
-
Kearns, N.A., et al. Functional annotation of native enhancers with a Cas9-histone demethylase fusion. Nat. Methods 12, 401-403 (2015).
-
(2015)
Nat. Methods
, vol.12
, pp. 401-403
-
-
Kearns, N.A.1
-
32
-
-
84949100864
-
Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements
-
Thakore, P.I., et al. Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements. Nat. Methods 12, 1143-1149 (2015).
-
(2015)
Nat. Methods
, vol.12
, pp. 1143-1149
-
-
Thakore, P.I.1
-
33
-
-
84988607070
-
A CRISPR-based approach for targeted DNA demethylation
-
Xu, X., et al. A CRISPR-based approach for targeted DNA demethylation. Cell Discov. 2, 16009 (2016).
-
(2016)
Cell Discov.
, vol.2
, pp. 16009
-
-
Xu, X.1
-
34
-
-
84979911627
-
CRISPR-dCas9 mediated TET1 targeting for selective DNA demethylation at BRCA1 promoter
-
Choudhury, S.R., Cui, Y., Lubecka, K., Stefanska, B., Irudayaraj, J. CRISPR-dCas9 mediated TET1 targeting for selective DNA demethylation at BRCA1 promoter. Oncotarget 7, 46545-46556 (2016).
-
(2016)
Oncotarget
, vol.7
, pp. 46545-46556
-
-
Choudhury, S.R.1
Cui, Y.2
Lubecka, K.3
Stefanska, B.4
Irudayaraj, J.5
-
35
-
-
84979034770
-
Repurposing the CRISPR-Cas9 system for targeted DNA methylation
-
Vojta, A., et al. Repurposing the CRISPR-Cas9 system for targeted DNA methylation. Nucleic Acids Res. 44, 5615-5628 (2016).
-
(2016)
Nucleic Acids Res.
, vol.44
, pp. 5615-5628
-
-
Vojta, A.1
-
36
-
-
84884160273
-
CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering
-
Mali, P., et al. CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat. Biotechnol. 31, 833-838 (2013).
-
(2013)
Nat. Biotechnol.
, vol.31
, pp. 833-838
-
-
Mali, P.1
-
37
-
-
84988569121
-
Editing DNA methylation in the mammalian genome
-
Liu, X.S., et al. Editing DNA methylation in the mammalian genome. Cell 167, 233-247 (2016).
-
(2016)
Cell
, vol.167
, pp. 233-247
-
-
Liu, X.S.1
-
38
-
-
38649099445
-
High-resolution mapping and characterization of open chromatin across the genome
-
Boyle, A.P., et al. High-resolution mapping and characterization of open chromatin across the genome. Cell 132, 311-322 (2008).
-
(2008)
Cell
, vol.132
, pp. 311-322
-
-
Boyle, A.P.1
-
39
-
-
33745416080
-
Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays
-
Sabo, P.J., et al. Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays. Nat. Methods 3, 511-518 (2006).
-
(2006)
Nat. Methods
, vol.3
, pp. 511-518
-
-
Sabo, P.J.1
-
40
-
-
0031593199
-
Locus control regions of mammalian ?-globin gene clusters: Combining phylogenetic analyses and experimental results to gain functional insights
-
Hardison, R., et al. Locus control regions of mammalian ?-globin gene clusters: Combining phylogenetic analyses and experimental results to gain functional insights. Gene 205, 73-94 (1997).
-
(1997)
Gene
, vol.205
, pp. 73-94
-
-
Hardison, R.1
-
41
-
-
0030340142
-
Developmental regulation of the vertebrate globin multigene family
-
Baron, M.H. Developmental regulation of the vertebrate globin multigene family. Gene Expr. 6, 129-137 (1996).
-
(1996)
Gene Expr.
, vol.6
, pp. 129-137
-
-
Baron, M.H.1
-
42
-
-
0021057680
-
Inducible transcription of five globin genes in K562 human leukemia cells
-
Dean, A., Ley, T.J., Humphries, R.K., Fordis, M., Schechter, A.N. Inducible transcription of five globin genes in K562 human leukemia cells. Proc. Natl. Acad. Sci. USA 80, 5515-5519 (1983).
-
(1983)
Proc. Natl. Acad. Sci. USA
, vol.80
, pp. 5515-5519
-
-
Dean, A.1
Ley, T.J.2
Humphries, R.K.3
Fordis, M.4
Schechter, A.N.5
-
43
-
-
80053539409
-
Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity
-
Song, L., et al. Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Genome Res. 21, 1757-1767 (2011).
-
(2011)
Genome Res.
, vol.21
, pp. 1757-1767
-
-
Song, L.1
-
44
-
-
84871229995
-
Trastuzumab: Updated mechanisms of action and resistance in breast cancer
-
Vu, T., Claret, F.X. Trastuzumab: Updated mechanisms of action and resistance in breast cancer. Front. Oncol. 2, 62 (2012).
-
(2012)
Front. Oncol.
, vol.2
, pp. 62
-
-
Vu, T.1
Claret, F.X.2
-
45
-
-
0035869407
-
Use of chemotherapy plus a monoclonal antibody against HER2 for metastatic breast cancer that overexpresses HER2
-
Slamon, D.J., et al. Use of chemotherapy plus a monoclonal antibody against HER2 for metastatic breast cancer that overexpresses HER2. N. Engl. J. Med. 344, 783-792 (2001).
-
(2001)
N. Engl. J. Med.
, vol.344
, pp. 783-792
-
-
Slamon, D.J.1
-
46
-
-
79952162826
-
HER2-amplified breast cancer: Mechanisms of trastuzumab resistance and novel targeted therapies
-
Gajria, D., Chandarlapaty, S. HER2-amplified breast cancer: Mechanisms of trastuzumab resistance and novel targeted therapies. Expert Rev. Anticancer Ther. 11, 263-275 (2011).
-
(2011)
Expert Rev. Anticancer Ther.
, vol.11
, pp. 263-275
-
-
Gajria, D.1
Chandarlapaty, S.2
-
47
-
-
57349113761
-
Regulation of ERBB2 by oestrogen receptor-PAX2 determines response to tamoxifen
-
Hurtado, A., et al. Regulation of ERBB2 by oestrogen receptor-PAX2 determines response to tamoxifen. Nature 456, 663-666 (2008).
-
(2008)
Nature
, vol.456
, pp. 663-666
-
-
Hurtado, A.1
-
48
-
-
77956556826
-
EGF-induced Grb7 recruits and promotes Ras activity essential for the tumorigenicity of Sk-Br3 breast cancer cells
-
Chu, P.-Y., Li, T.-K., Ding, S.-T., Lai, I.R., Shen, T.-L. EGF-induced Grb7 recruits and promotes Ras activity essential for the tumorigenicity of Sk-Br3 breast cancer cells. J. Biol. Chem. 285, 29279-29285 (2010).
-
(2010)
J. Biol. Chem.
, vol.285
, pp. 29279-29285
-
-
Chu, P.-Y.1
Li, T.-K.2
Ding, S.-T.3
Lai, I.R.4
Shen, T.-L.5
-
49
-
-
84990852918
-
Systematic mapping of functional enhancer-promoter connections with CRISPR interference
-
Fulco, C.P., et al. Systematic mapping of functional enhancer-promoter connections with CRISPR interference. Science 354, 769-773 (2016).
-
(2016)
Science
, vol.354
, pp. 769-773
-
-
Fulco, C.P.1
-
50
-
-
84907257107
-
Saturation editing of genomic regions by multiplex homology-directed repair
-
Findlay, G.M., Boyle, E.A., Hause, R.J., Klein, J.C., Shendure, J. Saturation editing of genomic regions by multiplex homology-directed repair. Nature 513, 120-123 (2014).
-
(2014)
Nature
, vol.513
, pp. 120-123
-
-
Findlay, G.M.1
Boyle, E.A.2
Hause, R.J.3
Klein, J.C.4
Shendure, J.5
-
51
-
-
84905262730
-
Improved vectors and genome-wide libraries for CRISPR screening
-
Sanjana, N.E., Shalem, O., Zhang, F. Improved vectors and genome-wide libraries for CRISPR screening. Nat. Methods 11, 783-784 (2014).
-
(2014)
Nat. Methods
, vol.11
, pp. 783-784
-
-
Sanjana, N.E.1
Shalem, O.2
Zhang, F.3
-
52
-
-
77956276383
-
DNase-seq: A high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells
-
pdb.prot5384
-
Song, L., Crawford, G.E. DNase-seq: A high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells. Cold Spring Harb. Protoc. 2010, pdb.prot5384 (2010).
-
(2010)
Cold Spring Harb. Protoc.
, vol.2010
-
-
Song, L.1
Crawford, G.E.2
-
53
-
-
84907486023
-
GT-Scan: Identifying unique genomic targets
-
O'Brien, A., Bailey, T.L. GT-Scan: Identifying unique genomic targets. Bioinformatics 30, 2673-2675 (2014).
-
(2014)
Bioinformatics
, vol.30
, pp. 2673-2675
-
-
O'Brien, A.1
Bailey, T.L.2
-
54
-
-
44449120988
-
Production and titration of lentiviral vectors
-
Chapter 4, Unit 4.21
-
Salmon, P., Trono, D. Production and titration of lentiviral vectors. Curr. Protoc. Neurosci. Chapter 4, Unit 4.21 (2006).
-
(2006)
Curr. Protoc. Neurosci.
-
-
Salmon, P.1
Trono, D.2
-
55
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
Langmead, B., Salzberg, S.L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357-359 (2012).
-
(2012)
Nat. Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
56
-
-
84924629414
-
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
-
Love, M.I., Huber, W., Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).
-
(2014)
Genome Biol.
, vol.15
, pp. 550
-
-
Love, M.I.1
Huber, W.2
Anders, S.3
|