-
1
-
-
84884829249
-
Mapping human epigenomes
-
Rivera, C.M., Ren, B. Mapping human epigenomes. Cell 155, 39-55 (2013).
-
(2013)
Cell
, vol.155
, pp. 39-55
-
-
Rivera, C.M.1
Ren, B.2
-
2
-
-
80053144962
-
A decade of exploring the cancer epigenome-biological and translational implications
-
Baylin, S.B., Jones, P.A. A decade of exploring the cancer epigenome-biological and translational implications. Nat. Rev. Cancer 11, 726-734 (2011).
-
(2011)
Nat. Rev. Cancer
, vol.11
, pp. 726-734
-
-
Baylin, S.B.1
Jones, P.A.2
-
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
-
-
79955583542
-
Mapping and analysis of chromatin state dynamics in nine human cell types
-
Ernst, J. et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473, 43-49 (2011).
-
(2011)
Nature
, vol.473
, pp. 43-49
-
-
Ernst, J.1
-
5
-
-
84878997106
-
Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells
-
Shalek, A.K. et al. Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells. Nature 498, 236-240 (2013).
-
(2013)
Nature
, vol.498
, pp. 236-240
-
-
Shalek, A.K.1
-
7
-
-
84859641038
-
Using gene expression noise to understand gene regulation
-
Munsky, B., Neuert, G., van Oudenaarden, A. Using gene expression noise to understand gene regulation. Science 336, 183-187 (2012).
-
(2012)
Science
, vol.336
, pp. 183-187
-
-
Munsky, B.1
Neuert, G.2
Van Oudenaarden, A.3
-
8
-
-
84885617426
-
Single-cell Hi-C reveals cell-to-cell variability in chromosome structure
-
Nagano, T. et al. Single-cell Hi-C reveals cell-to-cell variability in chromosome structure. Nature 502, 59-64 (2013).
-
(2013)
Nature
, vol.502
, pp. 59-64
-
-
Nagano, T.1
-
9
-
-
84883138228
-
Linking stochastic fluctuations in chromatin structure and gene expression
-
Brown, C.R., Mao, C., Falkovskaia, E., Jurica, M.S., Boeger, H. Linking stochastic fluctuations in chromatin structure and gene expression. PLoS Biol. 11, e1001621 (2013).
-
(2013)
PLoS Biol
, vol.11
, pp. e1001621
-
-
Brown, C.R.1
Mao, C.2
Falkovskaia, E.3
Jurica, M.S.4
Boeger, H.5
-
10
-
-
84930006926
-
Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing
-
Cusanovich, D.A. et al. Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing. Science 348, 910-914 (2015).
-
(2015)
Science
, vol.348
, pp. 910-914
-
-
Cusanovich, D.A.1
-
11
-
-
84877318097
-
Single-molecule analysis of combinatorial epigenomic states in normal and tumor cells
-
Murphy, P.J. et al. Single-molecule analysis of combinatorial epigenomic states in normal and tumor cells. Proc. Natl. Acad. Sci. USA 110, 7772-7777 (2013).
-
(2013)
Proc. Natl. Acad. Sci. USA
, vol.110
, pp. 7772-7777
-
-
Murphy, P.J.1
-
12
-
-
84900529199
-
Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq
-
Treutlein, B. et al. Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq. Nature 509, 371-375 (2014).
-
(2014)
Nature
, vol.509
, pp. 371-375
-
-
Treutlein, B.1
-
13
-
-
84902668801
-
Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma
-
Patel, A.P. et al. Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma. Science 344, 1396-1401 (2014).
-
(2014)
Science
, vol.344
, pp. 1396-1401
-
-
Patel, A.P.1
-
14
-
-
84863230091
-
Single-cell exome sequencing reveals single-nucleotide mutation characteristics of a kidney tumor
-
Xu, X. et al. Single-cell exome sequencing reveals single-nucleotide mutation characteristics of a kidney tumor. Cell 148, 886-895 (2012).
-
(2012)
Cell
, vol.148
, pp. 886-895
-
-
Xu, X.1
-
15
-
-
84906238686
-
Clonal evolution in breast cancer revealed by single nucleus genome sequencing
-
Wang, Y. et al. Clonal evolution in breast cancer revealed by single nucleus genome sequencing. Nature 512, 155-160 (2014).
-
(2014)
Nature
, vol.512
, pp. 155-160
-
-
Wang, Y.1
-
16
-
-
84896284039
-
The present and future role of microfluidics in biomedical research
-
Sackmann, E.K., Fulton, A.L., Beebe, D.J. The present and future role of microfluidics in biomedical research. Nature 507, 181-189 (2014).
-
(2014)
Nature
, vol.507
, pp. 181-189
-
-
Sackmann, E.K.1
Fulton, A.L.2
Beebe, D.J.3
-
17
-
-
84862212456
-
Droplet microfluidics for high-throughput biological assays
-
Guo, M.T., Rotem, A., Heyman, J.A., Weitz, D.A. Droplet microfluidics for high-throughput biological assays. Lab Chip 12, 2146-2155 (2012).
-
(2012)
Lab Chip
, vol.12
, pp. 2146-2155
-
-
Guo, M.T.1
Rotem, A.2
Heyman, J.A.3
Weitz, D.A.4
-
18
-
-
84929684998
-
Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells
-
Klein, A.M. et al. Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells. Cell 161, 1187-1201 (2015).
-
(2015)
Cell
, vol.161
, pp. 1187-1201
-
-
Klein, A.M.1
-
19
-
-
84929684999
-
Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets
-
Macosko, E.Z. et al. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell 161, 1202-1214 (2015).
-
(2015)
Cell
, vol.161
, pp. 1202-1214
-
-
Macosko, E.Z.1
-
20
-
-
84930685084
-
High-throughput single-cell labeling (Hi-SCL) for RNA-Seq using drop-based microfluidics
-
Rotem, A. et al. High-throughput single-cell labeling (Hi-SCL) for RNA-Seq using drop-based microfluidics. PLoS ONE 10, e0116328 (2015).
-
(2015)
PLoS ONE
, vol.10
, pp. e0116328
-
-
Rotem, A.1
-
21
-
-
77955172885
-
Genome-wide chromatin maps derived from limited numbers of hematopoietic progenitors
-
Adli, M., Zhu, J., Bernstein, B.E. Genome-wide chromatin maps derived from limited numbers of hematopoietic progenitors. Nat. Methods 7, 615-618 (2010).
-
(2010)
Nat. Methods
, vol.7
, pp. 615-618
-
-
Adli, M.1
Zhu, J.2
Bernstein, B.E.3
-
22
-
-
65649130015
-
Automated microfluidic chromatin immunoprecipitation from 2,000 cells
-
Wu, A.R. et al. Automated microfluidic chromatin immunoprecipitation from 2,000 cells. Lab Chip 9, 1365-1370 (2009).
-
(2009)
Lab Chip
, vol.9
, pp. 1365-1370
-
-
Wu, A.R.1
-
23
-
-
84907419194
-
Immunogenetics Chromatin state dynamics during blood formation
-
Lara-Astiaso, D. et al. Immunogenetics. Chromatin state dynamics during blood formation. Science 345, 943-949 (2014).
-
(2014)
Science
, vol.345
, pp. 943-949
-
-
Lara-Astiaso, D.1
-
24
-
-
33745549658
-
Epigenetic characterization of the early embryo with a chromatin immunoprecipitation protocol applicable to small cell populations
-
O'Neill, L.P., VerMilyea, M.D., Turner, B.M. Epigenetic characterization of the early embryo with a chromatin immunoprecipitation protocol applicable to small cell populations. Nat. Genet. 38, 835-841 (2006).
-
(2006)
Nat. Genet
, vol.38
, pp. 835-841
-
-
O'Neill, L.P.1
VerMilyea, M.D.2
Turner, B.M.3
-
25
-
-
84918528600
-
Regulatory principles of pluripotency: From the ground state up
-
Hackett, J.A., Surani, M.A. Regulatory principles of pluripotency: from the ground state up. Cell Stem Cell 15, 416-430 (2014).
-
(2014)
Cell Stem Cell
, vol.15
, pp. 416-430
-
-
Hackett, J.A.1
Surani, M.A.2
-
26
-
-
84902259602
-
Single-cell gene expression profiles define self-renewing, pluripotent, and lineage primed states of human pluripotent stem cells
-
Hough, S.R. et al. Single-cell gene expression profiles define self-renewing, pluripotent, and lineage primed states of human pluripotent stem cells. Stem Cell Rep. 2, 881-895 (2014).
-
(2014)
Stem Cell Rep
, vol.2
, pp. 881-895
-
-
Hough, S.R.1
-
27
-
-
84904460344
-
Dynamic heterogeneity and DNA methylation in embryonic stem cells
-
Singer, Z.S. et al. Dynamic heterogeneity and DNA methylation in embryonic stem cells. Mol. Cell 55, 319-331 (2014).
-
(2014)
Mol. Cell
, vol.55
, pp. 319-331
-
-
Singer, Z.S.1
-
28
-
-
84905405443
-
Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity
-
Smallwood, S.A. et al. Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity. Nat. Methods 11, 817-820 (2014).
-
(2014)
Nat. Methods
, vol.11
, pp. 817-820
-
-
Smallwood, S.A.1
-
29
-
-
37549002155
-
Nanog safeguards pluripotency and mediates germline development
-
Chambers, I. et al. Nanog safeguards pluripotency and mediates germline development. Nature 450, 1230-1234 (2007).
-
(2007)
Nature
, vol.450
, pp. 1230-1234
-
-
Chambers, I.1
-
30
-
-
42649112047
-
An embryonic stem cell-like gene expression signature in poorly differentiated aggressive human tumors
-
Ben-Porath, I. et al. An embryonic stem cell-like gene expression signature in poorly differentiated aggressive human tumors. Nat. Genet. 40, 499-507 (2008).
-
(2008)
Nat. Genet
, vol.40
, pp. 499-507
-
-
Ben-Porath, I.1
-
31
-
-
84882837534
-
Signatures of mutational processes in human cancer
-
Alexandrov, L.B. et al. Signatures of mutational processes in human cancer. Nature 500, 415-421 (2013).
-
(2013)
Nature
, vol.500
, pp. 415-421
-
-
Alexandrov, L.B.1
-
32
-
-
33745865934
-
Chromatin in pluripotent embryonic stem cells and differentiation
-
Meshorer, E., Misteli, T. Chromatin in pluripotent embryonic stem cells and differentiation. Nat. Rev. Mol. Cell Biol. 7, 540-546 (2006).
-
(2006)
Nat. Rev. Mol. Cell Biol
, vol.7
, pp. 540-546
-
-
Meshorer, E.1
Misteli, T.2
-
33
-
-
44649117905
-
Integration of external signaling pathways with the core transcriptional network in embryonic stem cells
-
Chen, X. et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 133, 1106-1117 (2008).
-
(2008)
Cell
, vol.133
, pp. 1106-1117
-
-
Chen, X.1
-
34
-
-
84871539869
-
Foxa2 and H2A.Z mediate nucleosome depletion during embryonic stem cell differentiation
-
Li, Z. et al. Foxa2 and H2A.Z mediate nucleosome depletion during embryonic stem cell differentiation. Cell 151, 1608-1616 (2012).
-
(2012)
Cell
, vol.151
, pp. 1608-1616
-
-
Li, Z.1
-
35
-
-
33646872978
-
Chromatin signatures of pluripotent cell lines
-
Azuara, V. et al. Chromatin signatures of pluripotent cell lines. Nat. Cell Biol. 8, 532-538 (2006).
-
(2006)
Nat. Cell Biol
, vol.8
, pp. 532-538
-
-
Azuara, V.1
-
36
-
-
33646070846
-
A bivalent chromatin structure marks key developmental genes in embryonic stem cells
-
Bernstein, B.E. et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125, 315-326 (2006).
-
(2006)
Cell
, vol.125
, pp. 315-326
-
-
Bernstein, B.E.1
-
37
-
-
84873310426
-
Genome-wide chromatin state transitions associated with developmental and environmental cues
-
Zhu, J. et al. Genome-wide chromatin state transitions associated with developmental and environmental cues. Cell 152, 642-654 (2013).
-
(2013)
Cell
, vol.152
, pp. 642-654
-
-
Zhu, J.1
-
38
-
-
84924601067
-
Single-cell DNA methylome sequencing and bioinformatic inference of epigenomic cell-state dynamics
-
Farlik, M. et al. Single-cell DNA methylome sequencing and bioinformatic inference of epigenomic cell-state dynamics. Cell Rep. 10, 1386-1397 (2015).
-
(2015)
Cell Rep
, vol.10
, pp. 1386-1397
-
-
Farlik, M.1
-
39
-
-
66049117813
-
Naive and primed pluripotent states
-
Nichols, J., Smith, A. Naive and primed pluripotent states. Cell Stem Cell 4, 487-492 (2009).
-
(2009)
Cell Stem Cell
, vol.4
, pp. 487-492
-
-
Nichols, J.1
Smith, A.2
-
40
-
-
55449105221
-
Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains
-
Ku, M. et al. Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet. 4, e1000242 (2008).
-
(2008)
PLoS Genet
, vol.4
, pp. e1000242
-
-
Ku, M.1
-
41
-
-
84923188586
-
Deconstructing transcriptional heterogeneity in pluripotent stem cells
-
Kumar, R.M. et al. Deconstructing transcriptional heterogeneity in pluripotent stem cells. Nature 516, 56-61 (2014).
-
(2014)
Nature
, vol.516
, pp. 56-61
-
-
Kumar, R.M.1
-
42
-
-
84877057770
-
Single-cell analysis and sorting using droplet-based microfluidics
-
Mazutis, L. et al. Single-cell analysis and sorting using droplet-based microfluidics. Nat. Protoc. 8, 870-891 (2013).
-
(2013)
Nat. Protoc
, vol.8
, pp. 870-891
-
-
Mazutis, L.1
-
43
-
-
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
-
44
-
-
77952148742
-
Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
-
Guttman, M. et al. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat. Biotechnol. 28, 503-510 (2010).
-
(2010)
Nat. Biotechnol
, vol.28
, pp. 503-510
-
-
Guttman, M.1
|