-
2
-
-
84929661801
-
Advances and applications of single-cell sequencing technologies
-
Wang, Y. & Navin, N. E. Advances and applications of single-cell sequencing technologies. Mol. Cell 58, 598-609 (2015).
-
(2015)
Mol. Cell
, vol.58
, pp. 598-609
-
-
Wang, Y.1
Navin, N.E.2
-
3
-
-
85020555541
-
-
(ed The Stem Cell Research Community) (Stembook
-
Grapin-Botton, A. in StemBook (ed. The Stem Cell Research Community) (Stembook, 2008); http://www.stembook.org/node/524
-
(2008)
StemBook
-
-
Grapin-Botton, A.1
-
4
-
-
84881609101
-
Mesodermal and hematopoietic differentiation from ES and iPS cells
-
Inoue-Yokoo, T., Tani, K. & Sugiyama, D. Mesodermal and hematopoietic differentiation from ES and iPS cells. Stem Cell Rev. 9, 422-434 (2013).
-
(2013)
Stem Cell Rev
, vol.9
, pp. 422-434
-
-
Inoue-Yokoo, T.1
Tani, K.2
Sugiyama, D.3
-
5
-
-
84923384631
-
Intrinsic regulations in neural fate commitment
-
Tang, K., Peng, G., Qiao, Y., Song, L. & Jing, N. Intrinsic regulations in neural fate commitment. Dev. Growth Differ. 57, 109-120 (2015).
-
(2015)
Dev. Growth Differ
, vol.57
, pp. 109-120
-
-
Tang, K.1
Peng, G.2
Qiao, Y.3
Song, L.4
Jing, N.5
-
6
-
-
79951664674
-
Vertebrate intestinal endoderm development
-
Spence, J. R., Lauf, R. & Shroyer, N. F. Vertebrate intestinal endoderm development. Dev. Dyn. 240, 501-520 (2011).
-
(2011)
Dev. Dyn
, vol.240
, pp. 501-520
-
-
Spence, J.R.1
Lauf, R.2
Shroyer, N.F.3
-
7
-
-
84984643819
-
Diffusion pseudotime robustly reconstructs lineage branching
-
Haghverdi, L., Buttner, M., Wolf, F. A., Buettner, F. & Theis, F. J. Diffusion pseudotime robustly reconstructs lineage branching. Nat. Methods 13, 845-848 (2016).
-
(2016)
Nat. Methods
, vol.13
, pp. 845-848
-
-
Haghverdi, L.1
Buttner, M.2
Wolf, F.A.3
Buettner, F.4
Theis, F.J.5
-
8
-
-
84900822715
-
The formation of proximal and distal definitive endoderm populations in culture requires p38 MAPK activity
-
Yap, C., Goh, H. N., Familari, M., Rathjen, P. D. & Rathjen, J. The formation of proximal and distal definitive endoderm populations in culture requires p38 MAPK activity. J. Cell Sci. 127, 2204-2216 (2014).
-
(2014)
J. Cell Sci
, vol.127
, pp. 2204-2216
-
-
Yap, C.1
Goh, H.N.2
Familari, M.3
Rathjen, P.D.4
Rathjen, J.5
-
9
-
-
34548154025
-
A systematic screen for genes expressed in definitive endoderm by Serial Analysis of Gene Expression (SAGE)
-
Hou, J. et al. A systematic screen for genes expressed in definitive endoderm by Serial Analysis of Gene Expression (SAGE). BMC Dev. Biol. 7, 92 (2007).
-
(2007)
BMC Dev. Biol
, vol.7
, pp. 92
-
-
Hou, J.1
-
10
-
-
76249102739
-
Organogenesis and development of the liver
-
Si-Tayeb, K., Lemaigre, F. P. & Duncan, S. A. Organogenesis and development of the liver. Dev. Cell 18, 175-189 (2010).
-
(2010)
Dev. Cell
, vol.18
, pp. 175-189
-
-
Si-Tayeb, K.1
Lemaigre, F.P.2
Duncan, S.A.3
-
11
-
-
0034918945
-
Irx1 and Irx2 expression in early lung development
-
Becker, M. B., Zulch, A., Bosse, A. & Gruss, P. Irx1 and Irx2 expression in early lung development. Mech. Dev. 106, 155-158 (2001).
-
(2001)
Mech. Dev
, vol.106
, pp. 155-158
-
-
Becker, M.B.1
Zulch, A.2
Bosse, A.3
Gruss, P.4
-
12
-
-
84859557287
-
Generation of multipotent lung and airway progenitors from mouse ESCs and patient-specific cystic fibrosis iPSCs
-
Mou, H. et al. Generation of multipotent lung and airway progenitors from mouse ESCs and patient-specific cystic fibrosis iPSCs. Cell Stem Cell 10, 385-397 (2012).
-
(2012)
Cell Stem Cell
, vol.10
, pp. 385-397
-
-
Mou, H.1
-
13
-
-
43949093759
-
Regionalisation of the endoderm progenitors and morphogenesis of the gut portals of the mouse embryo
-
Franklin, V. et al. Regionalisation of the endoderm progenitors and morphogenesis of the gut portals of the mouse embryo. Mech. Dev. 125, 587-600 (2008).
-
(2008)
Mech. Dev
, vol.125
, pp. 587-600
-
-
Franklin, V.1
-
14
-
-
34248545437
-
Lack of the murine homeobox gene Hesx1 leads to a posterior transformation of the anterior forebrain
-
Andoniadou, C. L. et al. Lack of the murine homeobox gene Hesx1 leads to a posterior transformation of the anterior forebrain. Development 134, 1499-1508 (2007).
-
(2007)
Development
, vol.134
, pp. 1499-1508
-
-
Andoniadou, C.L.1
-
15
-
-
84939772971
-
Computational assignment of cell-cycle stage from single-cell transcriptome data
-
Scialdone, A. et al. Computational assignment of cell-cycle stage from single-cell transcriptome data. Methods 85, 54-61 (2015).
-
(2015)
Methods
, vol.85
, pp. 54-61
-
-
Scialdone, A.1
-
16
-
-
84856165921
-
Patterning embryos with oscillations: Structure, function and dynamics of the vertebrate segmentation clock
-
Oates, A. C., Morelli, L. G. & Ares, S. Patterning embryos with oscillations: structure, function and dynamics of the vertebrate segmentation clock. Development 139, 625-639 (2012).
-
(2012)
Development
, vol.139
, pp. 625-639
-
-
Oates, A.C.1
Morelli, L.G.2
Ares, S.3
-
17
-
-
0032033316
-
Msg1 and Mrg1, founding members of a gene family, show distinct patterns of gene expression during mouse embryogenesis
-
Dunwoodie, S. L., Rodriguez, T. A. & Beddington, R. S. Msg1 and Mrg1, founding members of a gene family, show distinct patterns of gene expression during mouse embryogenesis. Mech. Dev. 72, 27-40 (1998).
-
(1998)
Mech. Dev
, vol.72
, pp. 27-40
-
-
Dunwoodie, S.L.1
Rodriguez, T.A.2
Beddington, R.S.3
-
18
-
-
26244444282
-
Cited1 is a bifunctional transcriptional cofactor that regulates early nephronic patterning
-
Plisov, S. et al. Cited1 is a bifunctional transcriptional cofactor that regulates early nephronic patterning. J. Am. Soc. Nephrol. 16, 1632-1644 (2005).
-
(2005)
J. Am. Soc. Nephrol
, vol.16
, pp. 1632-1644
-
-
Plisov, S.1
-
19
-
-
78650360161
-
Boundary formation and maintenance in tissue development
-
Dahmann, C., Oates, A. C. & Brand, M. Boundary formation and maintenance in tissue development. Nat. Rev. Genet. 12, 43-55 (2011).
-
(2011)
Nat. Rev. Genet
, vol.12
, pp. 43-55
-
-
Dahmann, C.1
Oates, A.C.2
Brand, M.3
-
20
-
-
59649110012
-
Transcriptional control of endothelial cell development
-
De Val, S. & Black, B. L. Transcriptional control of endothelial cell development. Dev. Cell 16, 180-195 (2009).
-
(2009)
Dev. Cell
, vol.16
, pp. 180-195
-
-
De Val, S.1
Black, B.L.2
-
21
-
-
84856179584
-
Recruitment of 5 Hoxa genes in the allantois is essential for proper extra-embryonic function in placental mammals
-
Scotti, M. & Kmita, M. Recruitment of 5 Hoxa genes in the allantois is essential for proper extra-embryonic function in placental mammals. Development 139, 731-739 (2012).
-
(2012)
Development
, vol.139
, pp. 731-739
-
-
Scotti, M.1
Kmita, M.2
-
22
-
-
0034161361
-
Vasculogenesis in the day 6 5 to 9.5 mouse embryo
-
Drake, C. J. & Fleming, P. A. Vasculogenesis in the day 6.5 to 9.5 mouse embryo. Blood 95, 1671-1679 (2000).
-
(2000)
Blood
, vol.95
, pp. 1671-1679
-
-
Drake, C.J.1
Fleming, P.A.2
-
23
-
-
84996802157
-
LYVE1 marks the divergence of yolk sac definitive hemogenic endothelium from the primitive erythroid lineage
-
Lee, L. K. et al. LYVE1 marks the divergence of yolk sac definitive hemogenic endothelium from the primitive erythroid lineage. Cell Rep. 17, 2286-2298 (2016).
-
(2016)
Cell Rep
, vol.17
, pp. 2286-2298
-
-
Lee, L.K.1
-
24
-
-
84933677570
-
Distinct sources of hematopoietic progenitors emerge before HSCs and provide functional blood cells in the mammalian embryo
-
McGrath, K. E. et al. Distinct sources of hematopoietic progenitors emerge before HSCs and provide functional blood cells in the mammalian embryo. Cell Rep. 11, 1892-1904 (2015).
-
(2015)
Cell Rep
, vol.11
, pp. 1892-1904
-
-
McGrath, K.E.1
-
25
-
-
84978761773
-
Resolving early mesoderm diversification through single-cell expression profiling
-
Scialdone, A. et al. Resolving early mesoderm diversification through single-cell expression profiling. Nature 535, 289-293 (2016).
-
(2016)
Nature
, vol.535
, pp. 289-293
-
-
Scialdone, A.1
-
26
-
-
34247529381
-
Germ cell specification in mice
-
Hayashi, K., de Sousa Lopes, S. M. & Surani, M. A. Germ cell specification in mice. Science 316, 394-396 (2007).
-
(2007)
Science
, vol.316
, pp. 394-396
-
-
Hayashi, K.1
De Sousa Lopes, S.M.2
Surani, M.A.3
-
27
-
-
84979076996
-
Generating human hematopoietic stem cells in vitro-exploring endothelial to hematopoietic transition as a portal for stemness acquisition
-
Slukvin, I. Generating human hematopoietic stem cells in vitro-exploring endothelial to hematopoietic transition as a portal for stemness acquisition. FEBS Lett. 590, 4126-4143 (2016).
-
(2016)
FEBS Lett
, vol.590
, pp. 4126-4143
-
-
Slukvin, I.1
-
28
-
-
84979995627
-
New insights into the regulation by RUNX1 and GFI1(s) proteins of the endothelial to hematopoietic transition generating primordial hematopoietic cells
-
Thambyrajah, R. et al. New insights into the regulation by RUNX1 and GFI1(s) proteins of the endothelial to hematopoietic transition generating primordial hematopoietic cells. Cell Cycle 15, 2108-2114 (2016).
-
(2016)
Cell Cycle
, vol.15
, pp. 2108-2114
-
-
Thambyrajah, R.1
-
29
-
-
85026232977
-
Let-7 microRNA-dependent control of leukotriene signaling regulates the transition of hematopoietic niche in mice
-
Jiang, X. et al. Let-7 microRNA-dependent control of leukotriene signaling regulates the transition of hematopoietic niche in mice. Nat. Commun. 8, 128 (2017).
-
(2017)
Nat. Commun
, vol.8
, pp. 128
-
-
Jiang, X.1
-
30
-
-
84937820643
-
Epoxyeicosatrienoic acids enhance embryonic haematopoiesis and adult marrow engraftment
-
Li, P. et al. Epoxyeicosatrienoic acids enhance embryonic haematopoiesis and adult marrow engraftment. Nature 523, 468-471 (2015).
-
(2015)
Nature
, vol.523
, pp. 468-471
-
-
Li, P.1
-
31
-
-
34250883337
-
Prostaglandin E2 regulates vertebrate haematopoietic stem cell homeostasis
-
North, T. E. et al. Prostaglandin E2 regulates vertebrate haematopoietic stem cell homeostasis. Nature 447, 1007-1011 (2007).
-
(2007)
Nature
, vol.447
, pp. 1007-1011
-
-
North, T.E.1
-
32
-
-
84888273208
-
Prostaglandin-modulated umbilical cord blood hematopoietic stem cell transplantation
-
Cutler, C. et al. Prostaglandin-modulated umbilical cord blood hematopoietic stem cell transplantation. Blood 122, 3074-3081 (2013).
-
(2013)
Blood
, vol.122
, pp. 3074-3081
-
-
Cutler, C.1
-
33
-
-
84964556059
-
Pooling across cells to normalize single-cell RNA sequencing data with many zero counts
-
Lun, A. T., Bach, K. & Marioni, J. C. Pooling across cells to normalize single-cell RNA sequencing data with many zero counts. Genome Biol. 17, 75 (2016).
-
(2016)
Genome Biol
, vol.17
, pp. 75
-
-
Lun, A.T.1
Bach, K.2
Marioni, J.C.3
-
34
-
-
85010931059
-
A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor
-
Lun, A. T., McCarthy, D. J. & Marioni, J. C. A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor. F1000Res. 5, 2122 (2016).
-
(2016)
F1000Res
, vol.5
, pp. 2122
-
-
Lun, A.T.1
McCarthy, D.J.2
Marioni, J.C.3
-
35
-
-
84947748539
-
Single cell RNA-sequencing of pluripotent states unlocks modular transcriptional variation
-
Kolodziejczyk, A. A. et al. Single cell RNA-sequencing of pluripotent states unlocks modular transcriptional variation. Cell Stem Cell 17, 471-485 (2015).
-
(2015)
Cell Stem Cell
, vol.17
, pp. 471-485
-
-
Kolodziejczyk, A.A.1
-
36
-
-
85041039136
-
-
Rtsne: T-distributed stochastic neighbor embedding using Barnes-Hut implementation. R package version 0.11 (Krijthe, J., 2015)
-
Rtsne: T-distributed stochastic neighbor embedding using Barnes-Hut implementation. R package version 0.11 (Krijthe, J., 2015); https://github. com/jkrijthe/Rtsne
-
-
-
-
37
-
-
40049099114
-
Defining clusters from a hierarchical cluster tree: The Dynamic Tree Cut package for R
-
Langfelder, P., Zhang, B. & Horvath, S. Defining clusters from a hierarchical cluster tree: The Dynamic Tree Cut package for R. Bioinformatics 24, 719-720 (2008).
-
(2008)
Bioinformatics
, vol.24
, pp. 719-720
-
-
Langfelder, P.1
Zhang, B.2
Horvath, S.3
-
38
-
-
75249087100
-
EdgeR: A Bioconductor package for differential expression analysis of digital gene expression data
-
Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: A Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140 (2010).
-
(2010)
Bioinformatics
, vol.26
, pp. 139-140
-
-
Robinson, M.D.1
McCarthy, D.J.2
Smyth, G.K.3
-
39
-
-
84966667709
-
Destiny: Diffusion maps for large-scale single-cell data in R
-
Angerer, P. et al. destiny: diffusion maps for large-scale single-cell data in R. Bioinformatics 32, 1241-1243 (2016).
-
(2016)
Bioinformatics
, vol.32
, pp. 1241-1243
-
-
Angerer, P.1
-
40
-
-
85031825743
-
Model-based branching point detection in single-cell data by K-branches clustering
-
Chlis, N. K., Wolf, F. A. & Theis, F. J. Model-based branching point detection in single-cell data by K-branches clustering. Bioinformatics 33, 3211-3219 (2017).
-
(2017)
Bioinformatics
, vol.33
, pp. 3211-3219
-
-
Chlis, N.K.1
Wolf, F.A.2
Theis, F.J.3
-
41
-
-
85041076314
-
-
cluster: Cluster analysis basics and extensions. R package version 2.0.5 (Maechler, M., Rousseeuw, P., Struyf, A., Hubert, M. & Hornik, K., 2016
-
cluster: Cluster analysis basics and extensions. R package version 2.0.5 (Maechler, M., Rousseeuw, P., Struyf, A., Hubert, M. & Hornik, K., 2016).
-
-
-
-
42
-
-
84873332657
-
Production of hepatocyte-like cells from human pluripotent stem cells
-
Hannan, N. R., Segeritz, C. P., Touboul, T. & Vallier, L. Production of hepatocyte-like cells from human pluripotent stem cells. Nat. Protoc. 8, 430-437 (2013).
-
(2013)
Nat. Protoc
, vol.8
, pp. 430-437
-
-
Hannan, N.R.1
Segeritz, C.P.2
Touboul, T.3
Vallier, L.4
-
43
-
-
84876996918
-
TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
-
Kim, D. et al. TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14, R36 (2013).
-
(2013)
Genome Biol
, vol.14
, pp. R36
-
-
Kim, D.1
-
44
-
-
84897397058
-
FeatureCounts: An efficient general purpose program for assigning sequence reads to genomic features
-
Liao, Y., Smyth, G. K. & Shi, W. featureCounts: An efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923-930 (2014).
-
(2014)
Bioinformatics
, vol.30
, pp. 923-930
-
-
Liao, Y.1
Smyth, G.K.2
Shi, W.3
-
45
-
-
84891677425
-
Full-length RNA-seq from single cells using Smart-seq2
-
Picelli, S. et al. Full-length RNA-seq from single cells using Smart-seq2. Nat. Protoc. 9, 171-181 (2014).
-
(2014)
Nat. Protoc
, vol.9
, pp. 171-181
-
-
Picelli, S.1
-
46
-
-
84871809302
-
STAR: Ultrafast universal RNA-seq aligner
-
Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15-21 (2013).
-
(2013)
Bioinformatics
, vol.29
, pp. 15-21
-
-
Dobin, A.1
-
47
-
-
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
|