-
1
-
-
84994860357
-
Revealing the vectors of cellular identity with single-cell genomics
-
Wagner, A., Regev, A. & Yosef, N. Revealing the vectors of cellular identity with single-cell genomics. Nat. Biotechnol. 34, 1145-1160 (2016).
-
(2016)
Nat. Biotechnol
, vol.34
, pp. 1145-1160
-
-
Wagner, A.1
Regev, A.2
Yosef, N.3
-
2
-
-
84984677948
-
Disentangling neural cell diversity using single-cell transcriptomics
-
Poulin, J.-F., Tasic, B., Hjerling-Leffler, J., Trimarchi, J.M. & Awatramani, R. Disentangling neural cell diversity using single-cell transcriptomics. Nat. Neurosci. 19, 1131-1141 (2016).
-
(2016)
Nat. Neurosci
, vol.19
, pp. 1131-1141
-
-
Poulin, J.-F.1
Tasic, B.2
Hjerling-Leffler, J.3
Trimarchi, J.M.4
Awatramani, R.5
-
3
-
-
85019078781
-
Challenges and emerging directions in single-cell analysis
-
Yuan, G.-C. et al. Challenges and emerging directions in single-cell analysis. Genome Biol. 18, 84 (2017).
-
(2017)
Genome Biol
, vol.18
, pp. 84
-
-
Yuan, G.-C.1
-
4
-
-
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
-
5
-
-
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
-
6
-
-
85012271992
-
Seq-Well: Portable, low-cost RNA sequencing of single cells at high throughput
-
Gierahn, T.M. et al. Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput. Nat. Methods 14, 395-398 (2017).
-
(2017)
Nat. Methods
, vol.14
, pp. 395-398
-
-
Gierahn, T.M.1
-
7
-
-
85028303209
-
Comprehensive single-cell transcriptional profiling of a multicellular organism
-
Cao, J. et al. Comprehensive single-cell transcriptional profiling of a multicellular organism. Science 357, 661-667 (2017).
-
(2017)
Science
, vol.357
, pp. 661-667
-
-
Cao, J.1
-
8
-
-
85031046570
-
Massively parallel single-nucleus RNA-seq with DroNc-seq
-
Habib, N. et al. Massively parallel single-nucleus RNA-seq with DroNc-seq. Nat. Methods 14, 955-958 (2017).
-
(2017)
Nat. Methods
, vol.14
, pp. 955-958
-
-
Habib, N.1
-
9
-
-
84983741021
-
Comprehensive classification of retinal bipolar neurons by singlecell transcriptomics
-
Shekhar, K. et al. Comprehensive classification of retinal bipolar neurons by singlecell transcriptomics. Cell 166, 1308-1323.e30 (2016).
-
(2016)
Cell
, vol.166
, pp. 1308-1308e30
-
-
Shekhar, K.1
-
10
-
-
84924565530
-
Cell types in the mouse cortex and hippocampus revealed by singlecell RNA-seq
-
Zeisel, A. et al. Cell types in the mouse cortex and hippocampus revealed by singlecell RNA-seq. Science 347, 1138-1142 (2015).
-
(2015)
Science
, vol.347
, pp. 1138-1142
-
-
Zeisel, A.1
-
11
-
-
84975165639
-
Oligodendrocyte heterogeneity in the mouse juvenile and adult central nervous system
-
Marques, S. et al. Oligodendrocyte heterogeneity in the mouse juvenile and adult central nervous system. Science 352, 1326-1329 (2016).
-
(2016)
Science
, vol.352
, pp. 1326-1329
-
-
Marques, S.1
-
12
-
-
84941201582
-
Single-cell messenger RNA sequencing reveals rare intestinal cell types
-
Grün, D. et al. Single-cell messenger RNA sequencing reveals rare intestinal cell types. Nature 525, 251-255 (2015).
-
(2015)
Nature
, vol.525
, pp. 251-255
-
-
Grün, D.1
-
13
-
-
85018582872
-
Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors
-
Villani, A.-C. et al. Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors. Science 356, eaah4573 (2017).
-
(2017)
Science
, vol.356
, pp. eaah4573
-
-
Villani, A.-C.1
-
14
-
-
85016148799
-
Single-cell spatial reconstruction reveals global division of labour in the mammalian liver
-
Halpern, K.B. et al. Single-cell spatial reconstruction reveals global division of labour in the mammalian liver. Nature 542, 352-356 (2017).
-
(2017)
Nature
, vol.542
, pp. 352-356
-
-
Halpern, K.B.1
-
15
-
-
84990876505
-
Molecular diversity of midbrain development in mouse, human, and stem cells
-
La Manno, G. et al. Molecular diversity of midbrain development in mouse, human, and stem cells. Cell 167, 566-580. e19 (2016).
-
(2016)
Cell
, vol.167
, pp. 566-566e19
-
-
La Manno, G.1
-
16
-
-
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
-
17
-
-
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
-
18
-
-
85020483426
-
Single-cell topological RNA-seq analysis reveals insights into cellular differentiation and development
-
Rizvi, A.H. et al. Single-cell topological RNA-seq analysis reveals insights into cellular differentiation and development. Nat. Biotechnol. 35, 551-560 (2017).
-
(2017)
Nat. Biotechnol
, vol.35
, pp. 551-560
-
-
Rizvi, A.H.1
-
19
-
-
84941010341
-
Single-cell RNA-Seq with waterfall reveals molecular cascades underlying adult neurogenesis
-
Shin, J. et al. Single-cell RNA-Seq with waterfall reveals molecular cascades underlying adult neurogenesis. Cell Stem Cell 17, 360-372 (2015).
-
(2015)
Cell Stem Cell
, vol.17
, pp. 360-372
-
-
Shin, J.1
-
20
-
-
85015680018
-
Discovering sparse transcription factor codes for cell states and state transitions during development
-
Furchtgott, L.A., Melton, S., Menon, V. & Ramanathan, S. Discovering sparse transcription factor codes for cell states and state transitions during development. eLife 6, e20488 (2017).
-
(2017)
ELife
, vol.6
, pp. e20488
-
-
Furchtgott, L.A.1
Melton, S.2
Menon, V.3
Ramanathan, S.4
-
21
-
-
84856090845
-
Lineage tracing
-
Kretzschmar, K. & Watt, F.M. Lineage tracing. Cell 148, 33-45 (2012).
-
(2012)
Cell
, vol.148
, pp. 33-45
-
-
Kretzschmar, K.1
Watt, F.M.2
-
22
-
-
85010220036
-
Building a lineage from single cells: Genetic techniques for cell lineage tracking
-
Woodworth, M.B., Girskis, K.M. & Walsh, C.A. Building a lineage from single cells: genetic techniques for cell lineage tracking. Nat. Rev. Genet. 18, 230-244 (2017).
-
(2017)
Nat. Rev. Genet
, vol.18
, pp. 230-244
-
-
Woodworth, M.B.1
Girskis, K.M.2
Walsh, C.A.3
-
23
-
-
84974576984
-
Whole-organism lineage tracing by combinatorial and cumulative genome editing
-
McKenna, A. et al. Whole-organism lineage tracing by combinatorial and cumulative genome editing. Science 353, aaf7907 (2016).
-
(2016)
Science
, vol.353
, pp. aaf7907
-
-
McKenna, A.1
-
24
-
-
85011341602
-
Massively parallel clonal analysis using CRISPR/Cas9 induced genetic scars
-
Preprint at
-
Junker, J.P. et al. Massively parallel clonal analysis using CRISPR/Cas9 induced genetic scars. Preprint at bioRxiv https://dx.doi.org/10.1101/056499 (2017).
-
(2017)
BioRxiv
-
-
Junker, J.P.1
-
25
-
-
85016160400
-
Synthetic recording and in situ readout of lineage information in single cells
-
Frieda, K.L. et al. Synthetic recording and in situ readout of lineage information in single cells. Nature 541, 107-111 (2017).
-
(2017)
Nature
, vol.541
, pp. 107-111
-
-
Frieda, K.L.1
-
26
-
-
85015591616
-
Continuous genetic recording with self-targeting CRISPR-Cas in human cells
-
Perli, S.D., Cui, C.H. & Lu, T.K. Continuous genetic recording with self-targeting CRISPR-Cas in human cells. Science 353, aag0511 (2016).
-
(2016)
Science
, vol.353
, pp. aag0511
-
-
Perli, S.D.1
Cui, C.H.2
Lu, T.K.3
-
27
-
-
85002263454
-
Rapidly evolving homing CRISPR barcodes
-
Kalhor, R., Mali, P. & Church, G.M. Rapidly evolving homing CRISPR barcodes. Nat. Methods 14, 195-200 (2017).
-
(2017)
Nat. Methods
, vol.14
, pp. 195-200
-
-
Kalhor, R.1
Mali, P.2
Church, G.M.3
-
28
-
-
85019143041
-
Quantitative analysis of synthetic cell lineage tracing using nuclease barcoding
-
Schmidt, S.T., Zimmerman, S.M., Wang, J., Kim, S.K. & Quake, S.R. Quantitative analysis of synthetic cell lineage tracing using nuclease barcoding. ACS Synth. Biol. 6, 936-942 (2017).
-
(2017)
ACS Synth. Biol
, vol.6
, pp. 936-942
-
-
Schmidt, S.T.1
Zimmerman, S.M.2
Wang, J.3
Kim, S.K.4
Quake, S.R.5
-
29
-
-
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
-
30
-
-
84876528441
-
ZFIN, the Zebrafish Model Organism Database: Increased support for mutants and transgenics
-
Howe, D.G. et al. ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics. Nucleic Acids Res. 41, D854-D860 (2013).
-
(2013)
Nucleic Acids Res
, vol.41
, pp. D854-D860
-
-
Howe, D.G.1
-
31
-
-
0036356430
-
Patterning the zebrafish central nervous system
-
Wilson, S.W., Brand, M. & Eisen, J.S. Patterning the zebrafish central nervous system. Results Probl. Cell Differ. 40, 181-215 (2002).
-
(2002)
Results Probl. Cell Differ
, vol.40
, pp. 181-215
-
-
Wilson, S.W.1
Brand, M.2
Eisen, J.S.3
-
32
-
-
85019721514
-
A novel perivascular cell population in the zebrafish brain
-
Venero Galanternik, M. et al. A novel perivascular cell population in the zebrafish brain. eLife 6, e24369 (2017).
-
(2017)
ELife
, vol.6
, pp. e24369
-
-
Venero Galanternik, M.1
-
33
-
-
84874007223
-
Neurogenesis in zebrafish-from embryo to adult
-
Schmidt, R., Strähle, U. & Scholpp, S. Neurogenesis in zebrafish-from embryo to adult. Neural Dev. 8, 3 (2013).
-
(2013)
Neural Dev
, vol.8
, pp. 3
-
-
Schmidt, R.1
Strähle, U.2
Scholpp, S.3
-
34
-
-
33847201433
-
Apelin and its receptor control heart field formation during zebrafish gastrulation
-
Zeng, X.-X.I., Wilm, T.P., Sepich, D.S. & Solnica-Krezel, L. Apelin and its receptor control heart field formation during zebrafish gastrulation. Dev. Cell 12, 391-402 (2007).
-
(2007)
Dev. Cell
, vol.12
, pp. 391-402
-
-
Zeng, X.-X.I.1
Wilm, T.P.2
Sepich, D.S.3
Solnica-Krezel, L.4
-
35
-
-
84967006891
-
Polq-mediated end joining is essential for surviving DNA double-strand breaks during early zebrafish development
-
Thyme, S.B. & Schier, A.F. Polq-mediated end joining is essential for surviving DNA double-strand breaks during early zebrafish development. Cell Rep. 15, 1611-1613 (2016).
-
(2016)
Cell Rep
, vol.15
, pp. 1611-1613
-
-
Thyme, S.B.1
Schier, A.F.2
-
36
-
-
84992755580
-
DNA repair profiling reveals nonrandom outcomes at Cas9-mediated breaks
-
van Overbeek, M. et al. DNA repair profiling reveals nonrandom outcomes at Cas9-mediated breaks. Mol. Cell 63, 633-646 (2016).
-
(2016)
Mol. Cell
, vol.63
, pp. 633-646
-
-
Van Overbeek, M.1
-
37
-
-
0029046703
-
Order and coherence in the fate map of the zebrafish nervous system
-
Woo, K. & Fraser, S.E. Order and coherence in the fate map of the zebrafish nervous system. Development 121, 2595-2609 (1995).
-
(1995)
Development
, vol.121
, pp. 2595-2609
-
-
Woo, K.1
Fraser, S.E.2
-
38
-
-
85020436520
-
Lineage tracing of dlx1a/2a and dlx5a/6a expressing cells in the developing zebrafish brain
-
Solek, C.M., Feng, S., Perin, S., Weinschutz Mendes, H. & Ekker, M. Lineage tracing of dlx1a/2a and dlx5a/6a expressing cells in the developing zebrafish brain. Dev. Biol. 427, 131-147 (2017).
-
(2017)
Dev. Biol
, vol.427
, pp. 131-147
-
-
Solek, C.M.1
Feng, S.2
Perin, S.3
Weinschutz Mendes, H.4
Ekker, M.5
-
39
-
-
85024109028
-
Genetic targeting and anatomical registration of neuronal populations in the zebrafish brain with a new set of BAC transgenic tools
-
Förster, D. et al. Genetic targeting and anatomical registration of neuronal populations in the zebrafish brain with a new set of BAC transgenic tools. Sci. Rep. 7, 5230 (2017).
-
(2017)
Sci. Rep
, vol.7
, pp. 5230
-
-
Förster, D.1
-
40
-
-
84923289368
-
Coexpression analysis of nine neuropeptides in the neurosecretory preoptic area of larval zebrafish
-
Herget, U. & Ryu, S. Coexpression analysis of nine neuropeptides in the neurosecretory preoptic area of larval zebrafish. Front. Neuroanat. 9, 2 (2015).
-
(2015)
Front. Neuroanat
, vol.9
, pp. 2
-
-
Herget, U.1
Ryu, S.2
-
41
-
-
33745881367
-
Neural stem cells and neurogenesis in the adult zebrafish brain: Origin, proliferation dynamics, migration and cell fate
-
Grandel, H., Kaslin, J., Ganz, J., Wenzel, I. & Brand, M. Neural stem cells and neurogenesis in the adult zebrafish brain: origin, proliferation dynamics, migration and cell fate. Dev. Biol. 295, 263-277 (2006).
-
(2006)
Dev. Biol
, vol.295
, pp. 263-277
-
-
Grandel, H.1
Kaslin, J.2
Ganz, J.3
Wenzel, I.4
Brand, M.5
-
42
-
-
85016318044
-
Single-cell RNA-Seq reveals hypothalamic cell diversity
-
Chen, R., Wu, X., Jiang, L. & Zhang, Y. Single-cell RNA-Seq reveals hypothalamic cell diversity. Cell Rep. 18, 3227-3241 (2017).
-
(2017)
Cell Rep
, vol.18
, pp. 3227-3241
-
-
Chen, R.1
Wu, X.2
Jiang, L.3
Zhang, Y.4
-
43
-
-
85045136951
-
Simultaneous lineage tracing and cell type identification using CRISPR-Cas9-induced genetic scars
-
(the press)
-
Spanjaard, B. et al. Simultaneous lineage tracing and cell type identification using CRISPR-Cas9-induced genetic scars. Nat. Biotechnol. http://dx.doi.org/10.1038/nbt.4124 (in the press).
-
Nat. Biotechnol
-
-
Spanjaard, B.1
-
44
-
-
85045151597
-
Whole-organism clone tracing using single-cell sequencing
-
Alemany, A., Florescu, M., Baron, C.S., Peterson-Maduro, J. & van Oudenaarden, A. Whole-organism clone tracing using single-cell sequencing. Nature http://dx.doi. org/10.1038/nature25969 (2018).
-
(2018)
Nature
-
-
Alemany, A.1
Florescu, M.2
Baron, C.S.3
Peterson-Maduro, J.4
Van Oudenaarden, A.5
-
45
-
-
84928395184
-
RNA imaging. Spatially resolved highly multiplexed RNA profiling in single cells
-
Chen, K.H., Boettiger, A.N., Moffitt, J.R., Wang, S. & Zhuang, X. RNA imaging. Spatially resolved, highly multiplexed RNA profiling in single cells. Science 348, aaa6090 (2015).
-
(2015)
Science
, vol.348
, pp. aaa6090
-
-
Chen, K.H.1
Boettiger, A.N.2
Moffitt, J.R.3
Wang, S.4
Zhuang, X.5
-
46
-
-
84992437479
-
In situ transcription profiling of single cells reveals spatial organization of cells in the mouse hippocampus
-
Shah, S., Lubeck, E., Zhou, W. & Cai, L. In situ transcription profiling of single cells reveals spatial organization of cells in the mouse hippocampus. Neuron 92, 342-357 (2016).
-
(2016)
Neuron
, vol.92
, pp. 342-357
-
-
Shah, S.1
Lubeck, E.2
Zhou, W.3
Cai, L.4
-
47
-
-
85028864573
-
TheDrosophila embryo at single-cell transcriptome resolution
-
Karaiskos, N. et al. TheDrosophila embryo at single-cell transcriptome resolution. Science 358, 194-199 (2017).
-
(2017)
Science
, vol.358
, pp. 194-199
-
-
Karaiskos, N.1
-
48
-
-
84929166604
-
High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin
-
Achim, K. et al. High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin. Nat. Biotechnol. 33, 503-509 (2015).
-
(2015)
Nat. Biotechnol
, vol.33
, pp. 503-509
-
-
Achim, K.1
-
49
-
-
85028346710
-
Polylox barcoding reveals haematopoietic stem cell fates realized in vivo
-
Pei, W. et al. Polylox barcoding reveals haematopoietic stem cell fates realized in vivo. Nature 548, 456-460 (2017).
-
(2017)
Nature
, vol.548
, pp. 456-460
-
-
Pei, W.1
-
50
-
-
0041857925
-
Germ-line transmission of a myocardium-specific GFP transgene reveals critical regulatory elements in the cardiac myosin light chain 2 promoter of zebrafish
-
Huang, C.-J., Tu, C.-T., Hsiao, C.-D., Hsieh, F.-J. & Tsai, H.-J. Germ-line transmission of a myocardium-specific GFP transgene reveals critical regulatory elements in the cardiac myosin light chain 2 promoter of zebrafish. Dev. Dyn. 228, 30-40 (2003).
-
(2003)
Dev. Dyn
, vol.228
, pp. 30-40
-
-
Huang, C.-J.1
Tu, C.-T.2
Hsiao, C.-D.3
Hsieh, F.-J.4
Tsai, H.-J.5
-
51
-
-
84931315589
-
Multiplex conditional mutagenesis using transgenic expression of Cas9 and sgRNAs
-
Yin, L. et al. Multiplex conditional mutagenesis using transgenic expression of Cas9 and sgRNAs. Genetics 200, 431-441 (2015).
-
(2015)
Genetics
, vol.200
, pp. 431-441
-
-
Yin, L.1
-
52
-
-
84925351121
-
A CRISPR/Cas9 vector system for tissue-specific gene disruption in zebrafish
-
Ablain, J., Durand, E.M., Yang, S., Zhou, Y. & Zon, L.I.A. A CRISPR/Cas9 vector system for tissue-specific gene disruption in zebrafish. Dev. Cell 32, 756-764 (2015).
-
(2015)
Dev. Cell
, vol.32
, pp. 756-764
-
-
Ablain, J.1
Durand, E.M.2
Yang, S.3
Zhou, Y.4
Zon, L.I.A.5
-
53
-
-
36448963734
-
The Tol2kit: A multisite gateway-based construction kit for Tol2 transposon transgenesis constructs
-
Kwan, K.M. et al. The Tol2kit: a multisite gateway-based construction kit for Tol2 transposon transgenesis constructs. Dev. Dyn. 236, 3088-3099 (2007).
-
(2007)
Dev. Dyn
, vol.236
, pp. 3088-3099
-
-
Kwan, K.M.1
-
54
-
-
84878846928
-
Zebrabow: Multispectral cell labeling for cell tracing and lineage analysis in zebrafish
-
Pan, Y.A. et al. Zebrabow: multispectral cell labeling for cell tracing and lineage analysis in zebrafish. Development 140, 2835-2846 (2013).
-
(2013)
Development
, vol.140
, pp. 2835-2846
-
-
Pan, Y.A.1
-
55
-
-
85010710363
-
Single-cell barcoding and sequencing using droplet microfluidics
-
Zilionis, R. et al. Single-cell barcoding and sequencing using droplet microfluidics. Nat. Protoc. 12, 44-73 (2017).
-
(2017)
Nat. Protoc
, vol.12
, pp. 44-73
-
-
Zilionis, R.1
-
56
-
-
85046681739
-
Comprehensive identification and spatial mapping of habenular neuronal types using single-cell RNA-seq
-
in the press
-
Pandey, S., Shekhar, K., Regev, A. & Schier, A.F. Comprehensive identification and spatial mapping of habenular neuronal types using single-cell RNA-seq. Curr. Biol. in the press.
-
Curr. Biol
-
-
Pandey, S.1
Shekhar, K.2
Regev, A.3
Schier, A.F.4
-
57
-
-
85018435810
-
Cell diversity and network dynamics in photosensitive human brain organoids
-
Quadrato, G. et al. Cell diversity and network dynamics in photosensitive human brain organoids. Nature 545, 48-53 (2017).
-
(2017)
Nature
, vol.545
, pp. 48-53
-
-
Quadrato, G.1
-
58
-
-
85031017685
-
Reversed graph embedding resolves complex single-cell trajectories
-
Qiu, X. et al. Reversed graph embedding resolves complex single-cell trajectories. Nat. Methods 14, 979-982 (2017).
-
(2017)
Nat. Methods
, vol.14
, pp. 979-982
-
-
Qiu, X.1
-
59
-
-
0034201441
-
EMBOSS: The European Molecular Biology Open Software Suite
-
Rice, P., Longden, I. & Bleasby, A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 16, 276-277 (2000).
-
(2000)
Trends Genet
, vol.16
, pp. 276-277
-
-
Rice, P.1
Longden, I.2
Bleasby, A.3
-
60
-
-
0000122573
-
PHYLIP-Phylogeny Inference Package (Version 3.2)
-
Felsenstein, J. PHYLIP-Phylogeny Inference Package (Version 3.2). Cladistics 5, 164-166 (1989).
-
(1989)
Cladistics
, vol.5
, pp. 164-166
-
-
Felsenstein, J.1
|