-
1
-
-
0034303585
-
Neuronal specification in the spinal cord: Inductive signals and transcriptional codes
-
Jessell, T.M. Neuronal specification in the spinal cord: Inductive signals and transcriptional codes. Nat. Rev. Genet. 1, 20-29 (2000).
-
(2000)
Nat. Rev. Genet.
, vol.1
, pp. 20-29
-
-
Jessell, T.M.1
-
2
-
-
0037047320
-
Directed differentiation of embryonic stem cells into motor neurons
-
Wichterle, H., Lieberam, I., Porter, J.A., Jessell, T.M. Directed differentiation of embryonic stem cells into motor neurons. Cell 110, 385-397 (2002).
-
(2002)
Cell
, vol.110
, pp. 385-397
-
-
Wichterle, H.1
Lieberam, I.2
Porter, J.A.3
Jessell, T.M.4
-
3
-
-
85010870303
-
Modeling ALS with motor neurons derived from human induced pluripotent stem cells
-
Sances, S., et al. Modeling ALS with motor neurons derived from human induced pluripotent stem cells. Nat. Neurosci. 19, 542-553 (2016).
-
(2016)
Nat. Neurosci.
, vol.19
, pp. 542-553
-
-
Sances, S.1
-
4
-
-
84874255781
-
Intricate interplay between astrocytes and motor neurons in ALS
-
Phatnani, H.P., et al. Intricate interplay between astrocytes and motor neurons in ALS. Proc. Natl. Acad. Sci. USA 110, E756-E765 (2013).
-
(2013)
Proc. Natl. Acad. Sci. USA
, vol.110
, pp. E756-E765
-
-
Phatnani, H.P.1
-
5
-
-
60849086260
-
Engineering the embryoid body microenvironment to direct embryonic stem cell differentiation
-
Bratt-Leal, A.M., Carpenedo, R.L., McDevitt, T.C. Engineering the embryoid body microenvironment to direct embryonic stem cell differentiation. Biotechnol. Prog. 25, 43-51 (2009).
-
(2009)
Biotechnol. Prog.
, vol.25
, pp. 43-51
-
-
Bratt-Leal, A.M.1
Carpenedo, R.L.2
McDevitt, T.C.3
-
6
-
-
84984643819
-
Diffusion pseudotime robustly reconstructs lineage branching
-
Haghverdi, L., Büttner, 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
Büttner, M.2
Wolf, F.A.3
Buettner, F.4
Theis, F.J.5
-
7
-
-
84974587998
-
Wishbone identifies bifurcating developmental trajectories from single-cell data
-
Setty, M., et al. Wishbone identifies bifurcating developmental trajectories from single-cell data. Nat. Biotechnol. 34, 637-645 (2016).
-
(2016)
Nat. Biotechnol.
, vol.34
, pp. 637-645
-
-
Setty, M.1
-
8
-
-
84969505817
-
SLICER: Inferring branched, nonlinear cellular trajectories from single cell RNA-seq data
-
Welch, J.D., Hartemink, A.J., Prins, J.F. SLICER: Inferring branched, nonlinear cellular trajectories from single cell RNA-seq data. Genome Biol. 17, 106 (2016).
-
(2016)
Genome Biol.
, vol.17
, pp. 106
-
-
Welch, J.D.1
Hartemink, A.J.2
Prins, J.F.3
-
9
-
-
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
-
10
-
-
84900873950
-
The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells
-
Trapnell, C., et al. The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nat. Biotechnol. 32, 381-386 (2014).
-
(2014)
Nat. Biotechnol.
, vol.32
, pp. 381-386
-
-
Trapnell, C.1
-
11
-
-
84924365758
-
Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape
-
Marco, E., et al. Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape. Proc. Natl. Acad. Sci. USA 111, E5643-E5650 (2014).
-
(2014)
Proc. Natl. Acad. Sci. USA
, vol.111
, pp. E5643-E5650
-
-
Marco, E.1
-
12
-
-
84887457901
-
Topology of viral evolution
-
Chan, J.M., Carlsson, G., Rabadan, R. Topology of viral evolution. Proc. Natl. Acad. Sci. USA 110, 18566-18571 (2013).
-
(2013)
Proc. Natl. Acad. Sci. USA
, vol.110
, pp. 18566-18571
-
-
Chan, J.M.1
Carlsson, G.2
Rabadan, R.3
-
13
-
-
84988911029
-
Inference of ancestral recombination graphs through topological data analysis
-
Cámara, P.G., Levine, A.J., Rabadán, R. Inference of Ancestral Recombination Graphs through Topological Data Analysis. PLoS Comput. Biol. 12, e1005071 (2016).
-
(2016)
PLoS Comput. Biol.
, vol.12
, pp. e1005071
-
-
Cámara, P.G.1
Levine, A.J.2
Rabadán, R.3
-
14
-
-
84995421882
-
Topological data analysis generates high-resolution, genome-wide maps of human recombination
-
Camara, P.G., Rosenbloom, D.I., Emmett, K.J., Levine, A.J., Rabadan, R. Topological data analysis generates high-resolution, genome-wide maps of human recombination. Cell Syst. 3, 83-94 (2016).
-
(2016)
Cell Syst.
, vol.3
, pp. 83-94
-
-
Camara, P.G.1
Rosenbloom, D.I.2
Emmett, K.J.3
Levine, A.J.4
Rabadan, R.5
-
15
-
-
79955561607
-
Topology based data analysis identifies a subgroup of breast cancers with a unique mutational profile and excellent survival
-
Nicolau, M., Levine, A.J., Carlsson, G. Topology based data analysis identifies a subgroup of breast cancers with a unique mutational profile and excellent survival. Proc. Natl. Acad. Sci. USA 108, 7265-7270 (2011).
-
(2011)
Proc. Natl. Acad. Sci. USA
, vol.108
, pp. 7265-7270
-
-
Nicolau, M.1
Levine, A.J.2
Carlsson, G.3
-
16
-
-
84946040296
-
Identification of type 2 diabetes subgroups through topological analysis of patient similarity
-
Li, L., et al. Identification of type 2 diabetes subgroups through topological analysis of patient similarity. Sci. Transl. Med. 7, 311ra174 (2015).
-
(2015)
Sci. Transl. Med.
, vol.7
, pp. 311ra174
-
-
Li, L.1
-
17
-
-
84899574465
-
Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell development
-
Bendall, S.C., et al. Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell development. Cell 157, 714-725 (2014).
-
(2014)
Cell
, vol.157
, pp. 714-725
-
-
Bendall, S.C.1
-
18
-
-
84929151009
-
Spatial reconstruction of single-cell gene expression data
-
Satija, R., Farrell, J.A., Gennert, D., Schier, A.F., Regev, A. Spatial reconstruction of single-cell gene expression data. Nat. Biotechnol. 33, 495-502 (2015).
-
(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
-
19
-
-
85076471198
-
-
Citeseer
-
Singh, G., Mémoli, F., Carlsson, G.E. in SPBG 91-100 (Citeseer, 2007).
-
(2007)
SPBG
, pp. 91-100
-
-
Singh, G.1
Mémoli, F.2
Carlsson, G.E.3
-
20
-
-
84866953427
-
CEL-Seq: Single-cell RNA-Seq by multiplexed linear amplification
-
Hashimshony, T., Wagner, F., Sher, N., Yanai, I. CEL-Seq: Single-cell RNA-Seq by multiplexed linear amplification. Cell Rep. 2, 666-673 (2012).
-
(2012)
Cell Rep.
, vol.2
, pp. 666-673
-
-
Hashimshony, T.1
Wagner, F.2
Sher, N.3
Yanai, I.4
-
21
-
-
84951574149
-
MAST: A flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data
-
Finak, G., et al. MAST: A flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data. Genome Biol. 16, 278 (2015).
-
(2015)
Genome Biol.
, vol.16
, pp. 278
-
-
Finak, G.1
-
22
-
-
84974625379
-
The contribution of cell cycle to heterogeneity in single-cell RNA-seq data
-
McDavid, A., Finak, G., Gottardo, R. The contribution of cell cycle to heterogeneity in single-cell RNA-seq data. Nat. Biotechnol. 34, 591-593 (2016).
-
(2016)
Nat. Biotechnol.
, vol.34
, pp. 591-593
-
-
McDavid, A.1
Finak, G.2
Gottardo, R.3
-
23
-
-
84892511644
-
Large-scale gene function analysis with the PANTHER classification system
-
Mi, H., Muruganujan, A., Casagrande, J.T., Thomas, P.D. Large-scale gene function analysis with the PANTHER classification system. Nat. Protoc. 8, 1551-1566 (2013).
-
(2013)
Nat. Protoc.
, vol.8
, pp. 1551-1566
-
-
Mi, H.1
Muruganujan, A.2
Casagrande, J.T.3
Thomas, P.D.4
-
24
-
-
0036847229
-
Gene expression regulation by retinoic acid
-
Balmer, J.E., Blomhoff, R. Gene expression regulation by retinoic acid. J. Lipid Res. 43, 1773-1808 (2002).
-
(2002)
J. Lipid Res.
, vol.43
, pp. 1773-1808
-
-
Balmer, J.E.1
Blomhoff, R.2
-
25
-
-
84856745520
-
Retinoic acid signalling during development
-
Rhinn, M., Dollé, P. Retinoic acid signalling during development. Development 139, 843-858 (2012).
-
(2012)
Development
, vol.139
, pp. 843-858
-
-
Rhinn, M.1
Dollé, P.2
-
26
-
-
0030002762
-
Temporal colinearity in expression of anterior Hox genes in developing chick embryos
-
Gaunt, S.J., Strachan, L. Temporal colinearity in expression of anterior Hox genes in developing chick embryos. Dev. Dyn. 207, 270-280 (1996).
-
(1996)
Dev. Dyn.
, vol.207
, pp. 270-280
-
-
Gaunt, S.J.1
Strachan, L.2
-
27
-
-
84906351069
-
Long intergenic non-coding RNA HOTAIRM1 regulates cell cycle progression during myeloid maturation in NB4 human promyelocytic leukemia cells
-
Zhang, X., Weissman, S.M., Newburger, P.E. Long intergenic non-coding RNA HOTAIRM1 regulates cell cycle progression during myeloid maturation in NB4 human promyelocytic leukemia cells. RNA Biol. 11, 777-787 (2014).
-
(2014)
RNA Biol.
, vol.11
, pp. 777-787
-
-
Zhang, X.1
Weissman, S.M.2
Newburger, P.E.3
-
28
-
-
80052536392
-
RNA-Seq of human neurons derived from iPS cells reveals candidate long non-coding RNAs involved in neurogenesis and neuropsychiatric disorders
-
Lin, M., et al. RNA-Seq of human neurons derived from iPS cells reveals candidate long non-coding RNAs involved in neurogenesis and neuropsychiatric disorders. PLoS One 6, e23356 (2011).
-
(2011)
PLoS One
, vol.6
, pp. e23356
-
-
Lin, M.1
-
29
-
-
84884269699
-
The regulation of Hox gene expression during animal development
-
Mallo, M., Alonso, C.R. The regulation of Hox gene expression during animal development. Development 140, 3951-3963 (2013).
-
(2013)
Development
, vol.140
, pp. 3951-3963
-
-
Mallo, M.1
Alonso, C.R.2
-
30
-
-
50649118350
-
Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation
-
Dinger, M.E., et al. Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res. 18, 1433-1445 (2008).
-
(2008)
Genome Res.
, vol.18
, pp. 1433-1445
-
-
Dinger, M.E.1
-
31
-
-
0030268113
-
Neurogenins, a novel family of atonal-related bHLH transcription factors, are putative mammalian neuronal determination genes that reveal progenitor cell heterogeneity in the developing CNS and PNS
-
Sommer, L., Ma, Q., Anderson, D.J. neurogenins, a novel family of atonal-related bHLH transcription factors, are putative mammalian neuronal determination genes that reveal progenitor cell heterogeneity in the developing CNS and PNS. Mol. Cell. Neurosci. 8, 221-241 (1996).
-
(1996)
Mol. Cell. Neurosci.
, vol.8
, pp. 221-241
-
-
Sommer, L.1
Ma, Q.2
Anderson, D.J.3
-
32
-
-
84880312659
-
RNA protein interaction in neurons
-
Darnell, R.B. RNA protein interaction in neurons. Annu. Rev. Neurosci. 36, 243-270 (2013).
-
(2013)
Annu. Rev. Neurosci.
, vol.36
, pp. 243-270
-
-
Darnell, R.B.1
-
33
-
-
84926386137
-
Essential roles for the splicing regulator nSR100/SRRM4 during nervous system development
-
Quesnel-Vallières, M., Irimia, M., Cordes, S.P., Blencowe, B.J. Essential roles for the splicing regulator nSR100/SRRM4 during nervous system development. Genes Dev. 29, 746-759 (2015).
-
(2015)
Genes Dev.
, vol.29
, pp. 746-759
-
-
Quesnel-Vallières, M.1
Irimia, M.2
Cordes, S.P.3
Blencowe, B.J.4
-
34
-
-
69449093703
-
Regulation of vertebrate nervous system alternative splicing and development by an SR-related protein
-
Calarco, J.A., et al. Regulation of vertebrate nervous system alternative splicing and development by an SR-related protein. Cell 138, 898-910 (2009).
-
(2009)
Cell
, vol.138
, pp. 898-910
-
-
Calarco, J.A.1
-
35
-
-
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
-
36
-
-
84962688754
-
Single-cell RNA-Seq reveals lineage and X chromosome dynamics in human preimplantation embryos
-
Petropoulos, S., et al. Single-cell RNA-Seq reveals lineage and X chromosome dynamics in human preimplantation embryos. Cell 165, 1012-1026 (2016).
-
(2016)
Cell
, vol.165
, pp. 1012-1026
-
-
Petropoulos, S.1
-
37
-
-
84960110736
-
Sequential transcriptional waves direct the differentiation of newborn neurons in the mouse neocortex
-
Telley, L., et al. Sequential transcriptional waves direct the differentiation of newborn neurons in the mouse neocortex. Science 351, 1443-1446 (2016).
-
(2016)
Science
, vol.351
, pp. 1443-1446
-
-
Telley, L.1
-
38
-
-
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
-
39
-
-
84928987900
-
HTSeq-A Python framework to work with high-throughput sequencing data
-
Anders, S., Pyl, P.T., Huber, W. HTSeq-a Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166-169 (2015).
-
(2015)
Bioinformatics
, vol.31
, pp. 166-169
-
-
Anders, S.1
Pyl, P.T.2
Huber, W.3
-
40
-
-
84923647450
-
Computational and analytical challenges in single-cell transcriptomics
-
Stegle, O., Teichmann, S.A., Marioni, J.C. Computational and analytical challenges in single-cell transcriptomics. Nat. Rev. Genet. 16, 133-145 (2015).
-
(2015)
Nat. Rev. Genet.
, vol.16
, pp. 133-145
-
-
Stegle, O.1
Teichmann, S.A.2
Marioni, J.C.3
-
41
-
-
84901831004
-
Validation of noise models for single-cell transcriptomics
-
Grün, D., Kester, L., van Oudenaarden, A. Validation of noise models for single-cell transcriptomics. Nat. Methods 11, 637-640 (2014).
-
(2014)
Nat. Methods
, vol.11
, pp. 637-640
-
-
Grün, D.1
Kester, L.2
Van Oudenaarden, A.3
-
42
-
-
84903574951
-
Bayesian approach to single-cell differential expression analysis
-
Kharchenko, P.V., Silberstein, L., Scadden, D.T. Bayesian approach to single-cell differential expression analysis. Nat. Methods 11, 740-742 (2014).
-
(2014)
Nat. Methods
, vol.11
, pp. 740-742
-
-
Kharchenko, P.V.1
Silberstein, L.2
Scadden, D.T.3
-
43
-
-
84903185013
-
Single-cell RNA-seq reveals dynamic paracrine control of cellular variation
-
Shalek, A.K., et al. Single-cell RNA-seq reveals dynamic paracrine control of cellular variation. Nature 510, 363-369 (2014).
-
(2014)
Nature
, vol.510
, pp. 363-369
-
-
Shalek, A.K.1
-
44
-
-
84887109584
-
Accounting for technical noise in single-cell RNA-seq experiments
-
Brennecke, P., et al. Accounting for technical noise in single-cell RNA-seq experiments. Nat. Methods 10, 1093-1095 (2013).
-
(2013)
Nat. Methods
, vol.10
, pp. 1093-1095
-
-
Brennecke, P.1
-
45
-
-
0036883297
-
Topological persistence and simplification
-
Edelsbrunner, H., Letscher, D., Zomorodian, A. Topological persistence and simplification. Discrete Comput. Geom. 28, 511-533 (2002).
-
(2002)
Discrete Comput. Geom.
, vol.28
, pp. 511-533
-
-
Edelsbrunner, H.1
Letscher, D.2
Zomorodian, A.3
-
47
-
-
70449356774
-
QuickGO: A web-based tool for Gene Ontology searching
-
Binns, D., et al. QuickGO: A web-based tool for Gene Ontology searching. Bioinformatics 25, 3045-3046 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 3045-3046
-
-
Binns, D.1
-
48
-
-
84946069451
-
UniProt: A hub for protein information
-
UniProt Consortium.
-
UniProt Consortium. UniProt: A hub for protein information. Nucleic Acids Res. 43, D204-D212 (2015).
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. D204-D212
-
-
-
49
-
-
84976892806
-
NONCODE 2016: An informative and valuable data source of long non-coding RNAs
-
Zhao, Y., et al. NONCODE 2016: An informative and valuable data source of long non-coding RNAs. Nucleic Acids Res. 44, D203-D208 (2016).
-
(2016)
Nucleic Acids Res.
, vol.44
, pp. D203-D208
-
-
Zhao, Y.1
|