-
1
-
-
84929684998
-
Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells
-
pmid: 26000487
-
A. M. Klein et al., Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells. Cell 161, 1187–1201 (2015). doi: 10.1016/j.cell.2015.04.044; pmid: 26000487
-
(2015)
Cell
, vol.161
, pp. 1187-1201
-
-
Klein, A.M.1
-
2
-
-
0020407569
-
A major developmental transition in early Xenopus embryos: I. Characterization and timing of cellular changes at the midblastula stage
-
pmid: 6183003
-
J. Newport, M. Kirschner, A major developmental transition in early Xenopus embryos: I. characterization and timing of cellular changes at the midblastula stage. Cell 30, 675–686 (1982). doi: 10.1016/0092-8674(82)90272-0; pmid: 6183003
-
(1982)
Cell
, vol.30
, pp. 675-686
-
-
Newport, J.1
Kirschner, M.2
-
3
-
-
0020460737
-
A major developmental transition in early Xenopus embryos: II. Control of the onset of transcription
-
pmid: 7139712
-
J. Newport, M. Kirschner, A major developmental transition in early Xenopus embryos: II. Control of the onset of transcription. Cell 30, 687–696 (1982). doi: 10.1016/ 0092-8674(82)90273-2; pmid: 7139712
-
(1982)
Cell
, vol.30
, pp. 687-696
-
-
Newport, J.1
Kirschner, M.2
-
4
-
-
33646133209
-
Patterning the early Xenopus embryo
-
pmid: 16527985
-
J. Heasman, Patterning the early Xenopus embryo. Development 133, 1205–1217 (2006). doi: 10.1242/dev.02304 pmid: 16527985
-
(2006)
Development
, vol.133
, pp. 1205-1217
-
-
Heasman, J.1
-
5
-
-
85040921934
-
Xenbase: A genomic, epigenomic and transcriptomic model organism database
-
pmid: 29059324
-
K. Karimi et al., Xenbase: A genomic, epigenomic and transcriptomic model organism database. Nucleic Acids Res. 46, D861–D868 (2018). pmid: 29059324
-
(2018)
Nucleic Acids Res
, vol.46
, pp. D861-D868
-
-
Karimi, K.1
-
6
-
-
0033961916
-
The fate of cells in the tailbud of Xenopus laevis
-
pmid: 10603344
-
R. L. Davis, M. W. Kirschner, The fate of cells in the tailbud of Xenopus laevis. Development 127, 255–267 (2000). pmid: 10603344
-
(2000)
Development
, vol.127
, pp. 255-267
-
-
Davis, R.L.1
Kirschner, M.W.2
-
7
-
-
85046550550
-
Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo
-
D. E. Wagner et al., Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo. Science 360, aar4362 (2018).
-
(2018)
Science
, vol.360
, pp. aar4362
-
-
Wagner, D.E.1
-
8
-
-
84907962027
-
Enhanced XAO: The ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase
-
pmid: 24139024
-
E. Segerdell et al., Enhanced XAO: The ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase. J. Biomed. Semantics 4, 31 (2013). doi: 10.1186/ 2041-1480-4-31; pmid: 24139024
-
(2013)
J. Biomed. Semantics
, vol.4
, pp. 31
-
-
Segerdell, E.1
-
9
-
-
53249127138
-
An ontology Xenopus anatomy and development
-
pmid: 18817563
-
E. Segerdell, J. B. Bowes, N. Pollet, P. D. Vize, An ontology Xenopus anatomy and development. BMC Dev. Biol. 8, 92 (2008). doi: 10.1186/1471-213X-8-92; pmid: 18817563
-
(2008)
BMC Dev. Biol.
, vol.8
, pp. 92
-
-
Segerdell, E.1
Bowes, J.B.2
Pollet, N.3
Vize, P.D.4
-
10
-
-
84900873950
-
The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of singl cells
-
pmid: 24658644
-
C. Trapnell et al., The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of singl cells. Nat. Biotechnol. 32, 381–386 (2014). doi: 10.1038/ nbt.2859; pmid: 24658644
-
(2014)
Nat. Biotechnol.
, vol.32
, pp. 381-386
-
-
Trapnell, C.1
-
11
-
-
85042766930
-
Fundamental limits on dynamic inference from single-cell snapshots
-
pmid: 29463712
-
C. Weinreb, S. Wolock, B. K. Tusi, M. Socolovsky, A. M. Klei Fundamental limits on dynamic inference from single-cell snapshots. Proc. Natl. Acad. Sci. U.S.A. 115, E2467–E2476 (2018). doi: 10.1073/pnas.1714723115; pmid: 29463712
-
(2018)
Proc. Natl. Acad. Sci. U.S.A.
, vol.115
, pp. E2467-E2476
-
-
Weinreb, C.1
Wolock, S.2
Tusi, B.K.3
Socolovsky, M.4
Klei, A.M.5
-
12
-
-
85045308562
-
Reconstruction of developmental landscapes by optimal-transport analysis of single-cell gene expression sheds light on cellular reprogramming
-
preprint. 27 September
-
G. Schiebinger et al., Reconstruction of developmental landscapes by optimal-transport analysis of single-cell gene expression sheds light on cellular reprogramming. bioRxiv 191056 [preprint]. 27 September 2017. doi: 10.1101/191056
-
(2017)
bioRxiv 191056
-
-
Schiebinger, G.1
-
13
-
-
0036932031
-
Adult and embryonic blood and endothelium derive from distinct precursor populations which are differentially programmed by BMP in Xenopus
-
pmid: 12421708
-
M. Walmsley, A. Ciau-Uitz, R. Patient, Adult and embryonic blood and endothelium derive from distinct precursor populations which are differentially programmed by BMP in Xenopus. Development 129, 5683–5695 (2002). doi: 10.124 dev.00169; pmid: 12421708
-
(2002)
Development
, vol.129
, pp. 5683-5695
-
-
Walmsley, M.1
Ciau-Uitz, A.2
Patient, R.3
-
14
-
-
49649086600
-
Fli1 acts at the t of the transcriptional network driving blood and endothelial development
-
pmid: 18718762
-
F. Liu, M. Walmsley, A. Rodaway, R. Patient, Fli1 acts at the t of the transcriptional network driving blood and endothelial development. Curr. Biol. 18, 1234–1240 (2008). doi: 10.1016 j.cub.2008.07.048; pmid: 18718762
-
(2008)
Curr. Biol.
, vol.18
, pp. 1234-1240
-
-
Liu, F.1
Walmsley, M.2
Rodaway, A.3
Patient, R.4
-
15
-
-
84973864190
-
Evolutionary Changes in the Developmen Origin of Hatching Gland Cells in Basal Ray-Finned Fishes
-
pmid: 27268981
-
T. Nagasawa et al., Evolutionary Changes in the Developmen Origin of Hatching Gland Cells in Basal Ray-Finned Fishes. Zool. Sci. 33, 272–281 (2016). doi: 10.2108/zs150183; pmid: 27268981
-
(2016)
Zool. Sci.
, vol.33
, pp. 272-281
-
-
Nagasawa, T.1
-
16
-
-
0015308017
-
Electron microscopic study on the xanthophore differentiation in Xenopus laevis, with special reference to their pterinosomes
-
pmid: 4335114
-
M. Yasutomi, T. Hama, Electron microscopic study on the xanthophore differentiation in Xenopus laevis, with special reference to their pterinosomes. J. Ultrastruct. Res. 38, 421–432 (1972). doi: 10.1016/0022-5320(72)90080-9; pmid: 4335114
-
(1972)
J. Ultrastruct. Res.
, vol.38
, pp. 421-432
-
-
Yasutomi, M.1
Hama, T.2
-
17
-
-
85036538773
-
Mouse embryonic stem cells can differentiate via multiple paths to the same state
-
pmid: 28990928
-
J. A. Briggs et al., Mouse embryonic stem cells can differentiate via multiple paths to the same state. eLife 6, e26945 (2017). doi: 10.7554/eLife.26945; pmid: 28990928
-
(2017)
eLife
, vol.6
, pp. e26945
-
-
Briggs, J.A.1
-
18
-
-
0033749652
-
A role for GATA5 in Xenopus endoderm specification
-
pmid: 11003835
-
H. Weber, C. E. Symes, M. E. Walmsley, A. R. Rodaway, R. K. Patient, A role for GATA5 in Xenopus endoderm specification. Development 127, 4345–4360 (2000). pmid: 11003835
-
(2000)
Development
, vol.127
, pp. 4345-4360
-
-
Weber, H.1
Symes, C.E.2
Walmsley, M.E.3
Rodaway, A.R.4
Patient, R.K.5
-
19
-
-
0032756903
-
Gata5 is required for the development of the heart and endoderm in zebrafish
-
pmid: 10580005
-
J. F. Reiter et al., Gata5 is required for the development of the heart and endoderm in zebrafish. Genes Dev. 13, 2983–2995 (1999). doi: 10.1101/gad.13.22.2983; pmid: 10580005
-
(1999)
Genes Dev
, vol.13
, pp. 2983-2995
-
-
Reiter, J.F.1
-
20
-
-
0027738464
-
The MyoD family and myogenesis: Redundancy, networks, and thresholds
-
pmid: 8269506
-
H. Weintraub, The MyoD family and myogenesis: Redundancy, networks, and thresholds. Cell 75, 1241–1244 (1993). doi: 10.1016/0092-8674(93)90610-3; pmid: 8269506
-
(1993)
Cell
, vol.75
, pp. 1241-1244
-
-
Weintraub, H.1
-
21
-
-
77649299348
-
An atlas of combinatorial transcriptional regulation in mouse and man
-
pmid: 20211142
-
T. Ravasi et al., An atlas of combinatorial transcriptional regulation in mouse and man. Cell 140, 744–752 (2010). doi: 10.1016/j.cell.2010.01.044; pmid: 20211142
-
(2010)
Cell
, vol.140
, pp. 744-752
-
-
Ravasi, T.1
-
22
-
-
73049167504
-
Teleonomic mechanisms in cellular metabolism, growth, and differentiation
-
pmid: 14475415
-
J. Monod, F. Jacob, Teleonomic mechanisms in cellular metabolism, growth, and differentiation. Cold Spring Harb. Symp. Quant. Biol. 26, 389–401 (1961). doi: 10.1101/ SQB.1961.026.01.048; pmid: 14475415
-
(1961)
Cold Spring Harb. Symp. Quant. Biol.
, vol.26
, pp. 389-401
-
-
Monod, J.1
Jacob, F.2
-
23
-
-
79952900560
-
Turning straw into gold: Directing cell fate for regenerative medicine
-
pmid: 21386864
-
D. E. Cohen, D. Melton, Turning straw into gold: Directing cell fate for regenerative medicine. Nat. Rev. Genet. 12, 243–252 (2011). doi: 10.1038/nrg2938; pmid: 21386864
-
(2011)
Nat. Rev. Genet.
, vol.12
, pp. 243-252
-
-
Cohen, D.E.1
Melton, D.2
-
24
-
-
0030954167
-
Multilineage gene expression precedes commitment in the hemopoietic system
-
pmid: 9087431
-
M. Hu et al., Multilineage gene expression precedes commitment in the hemopoietic system. Genes Dev. 11, 774–785 (1997). doi: 10.1101/gad.11.6.774; pmid: 9087431
-
(1997)
Genes Dev
, vol.11
, pp. 774-785
-
-
Hu, M.1
-
25
-
-
79958263080
-
Pluripotency factors in embryonic stem cells regulate differentiation into germ layers
-
pmid: 21663792
-
M. Thomson et al., Pluripotency factors in embryonic stem cells regulate differentiation into germ layers. Cell 145, 875–889 (2011). doi: 10.1016/j.cell.2011.05.017; pmid: 21663792
-
(2011)
Cell
, vol.145
, pp. 875-889
-
-
Thomson, M.1
-
26
-
-
85015695567
-
Human haematopoietic stem cell lineage commitment is a continuous process
-
pmid: 28319093
-
L. Velten et al., Human haematopoietic stem cell lineage commitment is a continuous process. Nat. Cell Biol. 19, 271–281 (2017). doi: 10.1038/ncb3493; pmid: 28319093
-
(2017)
Nat. Cell Biol.
, vol.19
, pp. 271-281
-
-
Velten, L.1
-
27
-
-
84878273239
-
Induction of pluripotency in mouse somatic cells with lineage specifiers
-
pmid: 23706735
-
J. Shu et al., Induction of pluripotency in mouse somatic cells with lineage specifiers. Cell 153, 963–975 (2013). doi: 10.1016/ j.cell.2013.05.001; pmid: 23706735
-
(2013)
Cell
, vol.153
, pp. 963-975
-
-
Shu, J.1
-
28
-
-
33747196725
-
Multilineage transcriptional priming and determination of alternate hematopoietic cell fates
-
pmid: 16923394
-
P. Laslo et al., Multilineage transcriptional priming and determination of alternate hematopoietic cell fates. Cell 126, 755–766 (2006). doi: 10.1016/j.cell.2006.06.052; pmid: 16923394
-
(2006)
Cell
, vol.126
, pp. 755-766
-
-
Laslo, P.1
-
29
-
-
7244226383
-
Refinement of gene expression patterns in the early Xenopus embryo
-
pmid: 15329341
-
F. C. Wardle, J. C. Smith, Refinement of gene expression patterns in the early Xenopus embryo. Development 131, 4687–4696 (2004). doi: 10.1242/dev.01340; pmid: 15329341
-
(2004)
Development
, vol.131
, pp. 4687-4696
-
-
Wardle, F.C.1
Smith, J.C.2
-
30
-
-
84933544651
-
Shared regulatory programs suggest retention of blastula-stage potential in neural crest cells
-
pmid: 25931449
-
E. Buitrago-Delgado, K. Nordin, A. Rao, L. Geary, C. LaBonne, Shared regulatory programs suggest retention of blastula-stage potential in neural crest cells. Science 348, 1332–1335 (2015). doi: 10.1126/science.aaa3655; pmid: 25931449
-
(2015)
Science
, vol.348
, pp. 1332-1335
-
-
Buitrago-Delgado, E.1
Nordin, K.2
Rao, A.3
Geary, L.4
LaBonne, C.5
-
31
-
-
84897452794
-
Single-cell in situ RNA profiling by sequential hybridization
-
pmid: 24681720
-
E. Lubeck, A. F. Coskun, T. Zhiyentayev, M. Ahmad, L. Cai, Single-cell in situ RNA profiling by sequential hybridization. Nat. Methods 11, 360–361 (2014). doi: 10.1038/nmeth.2892; pmid: 24681720
-
(2014)
Nat. Methods
, vol.11
, pp. 360-361
-
-
Lubeck, E.1
Coskun, A.F.2
Zhiyentayev, T.3
Ahmad, M.4
Cai, L.5
-
32
-
-
84928395184
-
Spatially resolved, highly multiplexed RNA profiling in single cells
-
pmid: 25858977
-
K. H. Chen, A. N. Boettiger, J. R. Moffitt, S. Wang, X. Zhuang, Spatially resolved, highly multiplexed RNA profiling in single cells. Science 348, aaa6090 (2015). doi: 10.1126/science. aaa6090; pmid: 25858977
-
(2015)
Science
, vol.348
, pp. aaa6090
-
-
Chen, K.H.1
Boettiger, A.N.2
Moffitt, J.R.3
Wang, S.4
Zhuang, X.5
-
33
-
-
84929684999
-
Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets
-
pmid: 26000488
-
E. Z. Macosko et al., Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. Cell 161, 1202–1214 (2015). doi: 10.1016/j.cell.2015.05.002; pmid: 26000488
-
(2015)
Cell
, vol.161
, pp. 1202-1214
-
-
Macosko, E.Z.1
-
34
-
-
85028864573
-
The Drosophila embryo at single-cell transcriptome resolution
-
pmid: 28860209
-
N. Karaiskos et al., The Drosophila embryo at single-cell transcriptome resolution. Science 358, 194–199 (2017). doi: 10.1126/science.aan3235; pmid: 28860209
-
(2017)
Science
, vol.358
, pp. 194-199
-
-
Karaiskos, N.1
-
35
-
-
85028303209
-
Comprehensive single-cell transcriptional profiling of a multicellular organism
-
pmid: 28818938
-
J. Cao et al., Comprehensive single-cell transcriptional profiling of a multicellular organism. Science 357, 661–667 (2017). doi: 10.1126/science.aam8940; pmid: 28818938
-
(2017)
Science
, vol.357
, pp. 661-667
-
-
Cao, J.1
-
36
-
-
84929166604
-
High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin
-
pmid: 25867922
-
K. Achim et al., High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin. Nat. Biotechnol. 33, 503–509 (2015). doi: 10.1038/nbt.3209; pmid: 25867922
-
(2015)
Nat. Biotechnol.
, vol.33
, pp. 503-509
-
-
Achim, K.1
-
37
-
-
84929151009
-
Spatial reconstruction of single-cell gene expression data
-
pmid: 25867923
-
R. Satija, J. A. Farrell, D. Gennert, A. F. Schier, A. Regev, Spatial reconstruction of single-cell gene expression data. Nat. Biotechnol. 33, 495–502 (2015). doi: 10.1038/nbt.3192; pmid: 25867923
-
(2015)
Nat. Biotechnol.
, vol.33
, pp. 495-502
-
-
Satija, R.1
Farrell, J.A.2
Gennert, D.3
Schier, A.F.4
Regev, A.5
-
38
-
-
0019306889
-
Determination and cellular commitment in the embryonic amphibian mesoderm
-
pmid: 7402328
-
D. Forman, J. M. Slack, Determination and cellular commitment in the embryonic amphibian mesoderm. Nature 286, 492–494 (1980). doi: 10.1038/286492a0; pmid: 7402328
-
(1980)
Nature
, vol.286
, pp. 492-494
-
-
Forman, D.1
Slack, J.M.2
-
39
-
-
0021186384
-
Fates and states of determination of single vegetal pole blastomeres of X. Laevis
-
pmid: 6722871
-
J. Heasman, C. C. Wylie, P. Hausen, J. C. Smith, Fates and states of determination of single vegetal pole blastomeres of X. laevis. Cell 37, 185–194 (1984). doi: 10.1016/ 0092-8674(84)90314-3; pmid: 6722871
-
(1984)
Cell
, vol.37
, pp. 185-194
-
-
Heasman, J.1
Wylie, C.C.2
Hausen, P.3
Smith, J.C.4
-
40
-
-
84950291354
-
Embryonic transcription is controlled by maternally defined chromatin state
-
pmid: 26679111
-
S. Hontelez et al., Embryonic transcription is controlled by maternally defined chromatin state. Nat. Commun. 6, 10148 (2015). doi: 10.1038/ncomms10148; pmid: 26679111
-
(2015)
Nat. Commun.
, vol.6
, pp. 10148
-
-
Hontelez, S.1
-
41
-
-
69949156902
-
A hierarchy of H3K4me3 and H3K27me3 acquisition in spatial gene regulation in Xenopus embryos
-
pmid: 19758566
-
R. C. Akkers et al., A hierarchy of H3K4me3 and H3K27me3 acquisition in spatial gene regulation in Xenopus embryos. Dev. Cell 17, 425–434 (2009). doi: 10.1016/ j.devcel.2009.08.005; pmid: 19758566
-
(2009)
Dev. Cell
, vol.17
, pp. 425-434
-
-
Akkers, R.C.1
-
42
-
-
68049097008
-
Epigenetic dynamics of stem cells and cell lineage commitment: Digging Waddington’s canal
-
pmid: 19603040
-
M. Hemberger, W. Dean, W. Reik, Epigenetic dynamics of stem cells and cell lineage commitment: Digging Waddington’s canal. Nat. Rev. Mol. Cell Biol. 10, 526–537 (2009). doi: 10.1038/nrm2727; pmid: 19603040
-
(2009)
Nat. Rev. Mol. Cell Biol.
, vol.10
, pp. 526-537
-
-
Hemberger, M.1
Dean, W.2
Reik, W.3
-
43
-
-
79952184341
-
Chromatin accessibility pre-determines glucocorticoid receptor binding patterns
-
pmid: 21258342
-
S. John et al., Chromatin accessibility pre-determines glucocorticoid receptor binding patterns. Nat. Genet. 43, 264–268 (2011). doi: 10.1038/ng.759; pmid: 21258342
-
(2011)
Nat. Genet.
, vol.43
, pp. 264-268
-
-
John, S.1
-
44
-
-
75749101495
-
Chromatin remodelling during development
-
pmid: 20110991
-
L. Ho, G. R. Crabtree, Chromatin remodelling during development. Nature 463, 474–484 (2010). doi: 10.1038/ nature08911; pmid: 20110991
-
(2010)
Nature
, vol.463
, pp. 474-484
-
-
Ho, L.1
Crabtree, G.R.2
-
45
-
-
84994079481
-
The origin and evolution of cell types
-
pmid: 27818507
-
D. Arendt et al., The origin and evolution of cell types. Nat. Rev. Genet. 17, 744–757 (2016). doi: 10.1038/ nrg.2016.127; pmid: 27818507
-
(2016)
Nat. Rev. Genet.
, vol.17
, pp. 744-757
-
-
Arendt, D.1
|