-
1
-
-
67349146589
-
mRNA-Seq whole-transcriptome analysis of a single cell
-
Tang, F. et al. mRNA-Seq whole-transcriptome analysis of a single cell. Nat. Methods 6, 377-382 (2009).
-
(2009)
Nat. Methods
, vol.6
, pp. 377-382
-
-
Tang, F.1
-
2
-
-
84882455458
-
Single-cell sequencing-based technologies will revolutionize whole-organism science
-
Shapiro, E., Biezuner, T., Linnarsson, S. Single-cell sequencing-based technologies will revolutionize whole-organism science. Nat. Rev. Genet. 14, 618-630 (2013).
-
(2013)
Nat. Rev. Genet.
, vol.14
, pp. 618-630
-
-
Shapiro, E.1
Biezuner, T.2
Linnarsson, S.3
-
3
-
-
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
-
4
-
-
84906228597
-
Single-cell RNA-seq: Advances and future challenges
-
Saliba, A.-E., Westermann, A.J., Gorski, S.A., Vogel, J. Single-cell RNA-seq: Advances and future challenges. Nucleic Acids Res. 42, 8845-8860 (2014).
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. 8845-8860
-
-
Saliba, A.-E.1
Westermann, A.J.2
Gorski, S.A.3
Vogel, J.4
-
5
-
-
84958606331
-
Single-cell genome sequencing: Current state of the science
-
Gawad, C., Koh, W., Quake, S.R. Single-cell genome sequencing: Current state of the science. Nat. Rev. Genet. 17, 175-188 (2016).
-
(2016)
Nat. Rev. Genet.
, vol.17
, pp. 175-188
-
-
Gawad, C.1
Koh, W.2
Quake, S.R.3
-
6
-
-
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
-
7
-
-
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
-
8
-
-
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
-
9
-
-
84955706109
-
ZIFA: Dimensionality reduction for zero-inflated single-cell gene expression analysis
-
Pierson, E., Yau, C. ZIFA: Dimensionality reduction for zero-inflated single-cell gene expression analysis. Genome Biol. 16, 241 (2015).
-
(2015)
Genome Biol.
, vol.16
, pp. 241
-
-
Pierson, E.1
Yau, C.2
-
10
-
-
84962658087
-
Design and computational analysis of single-cell RNA-sequencing experiments
-
Bacher, R., Kendziorski, C. Design and computational analysis of single-cell RNA-sequencing experiments. Genome Biol. 17, 63 (2016).
-
(2016)
Genome Biol.
, vol.17
, pp. 63
-
-
Bacher, R.1
Kendziorski, C.2
-
11
-
-
84962861088
-
Beyond comparisons of means: Understanding changes in gene expression at the single-cell level
-
Vallejos, C.A., Richardson, S., Marioni, J.C. Beyond comparisons of means: Understanding changes in gene expression at the single-cell level. Genome Biol. 17, 70 (2016).
-
(2016)
Genome Biol.
, vol.17
, pp. 70
-
-
Vallejos, C.A.1
Richardson, S.2
Marioni, J.C.3
-
12
-
-
80052521697
-
Synthetic spike-in standards for RNA-seq experiments
-
Jiang, L. et al. Synthetic spike-in standards for RNA-seq experiments. Genome Res. 21, 1543-1551 (2011).
-
(2011)
Genome Res.
, vol.21
, pp. 1543-1551
-
-
Jiang, L.1
-
13
-
-
84929687805
-
The technology and biology of single-cell RNA sequencing
-
Kolodziejczyk, A.A., Kim, J.K., Svensson, V., Marioni, J.C., Teichmann, S.A. The technology and biology of single-cell RNA sequencing. Mol. Cell 58, 610-620 (2015).
-
(2015)
Mol. Cell
, vol.58
, pp. 610-620
-
-
Kolodziejczyk, A.A.1
Kim, J.K.2
Svensson, V.3
Marioni, J.C.4
Teichmann, S.A.5
-
14
-
-
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
-
15
-
-
0242333835
-
Normalization of cDNA microarray data
-
Smyth, G.K., Speed, T. Normalization of cDNA microarray data. Methods 31, 265-273 (2003).
-
(2003)
Methods
, vol.31
, pp. 265-273
-
-
Smyth, G.K.1
Speed, T.2
-
16
-
-
77949481052
-
Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments
-
Bullard, J.H., Purdom, E., Hansen, K.D., Dudoit, S. Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics 11, 94 (2010).
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 94
-
-
Bullard, J.H.1
Purdom, E.2
Hansen, K.D.3
Dudoit, S.4
-
17
-
-
84887791432
-
A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis
-
Dillies, M.-A. et al. A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis. Brief. Bioinform. 14, 671-683 (2013).
-
(2013)
Brief. Bioinform.
, vol.14
, pp. 671-683
-
-
Dillies, M.-A.1
-
19
-
-
84909644283
-
Normalization of RNA-seq data using factor analysis of control genes or samples
-
Risso, D., Ngai, J., Speed, T.P., Dudoit, S. Normalization of RNA-seq data using factor analysis of control genes or samples. Nat. Biotechnol. 32, 896-902 (2014).
-
(2014)
Nat. Biotechnol.
, vol.32
, pp. 896-902
-
-
Risso, D.1
Ngai, J.2
Speed, T.P.3
Dudoit, S.4
-
20
-
-
84925226706
-
Svaseq: Removing batch effects and other unwanted noise from sequencing data
-
Leek, J.T. svaseq: Removing batch effects and other unwanted noise from sequencing data. Nucleic Acids Res. 42, e161 (2014).
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. e161
-
-
Leek, J.T.1
-
21
-
-
84895069488
-
Quantitative single-cell RNA-seq with unique molecular identifiers
-
Islam, S. et al. Quantitative single-cell RNA-seq with unique molecular identifiers. Nat. Methods 11, 163-166 (2014).
-
(2014)
Nat. Methods
, vol.11
, pp. 163-166
-
-
Islam, S.1
-
22
-
-
84946226911
-
Design and analysis of single-cell sequencing experiments
-
Grün, D., van Oudenaarden, A. Design and analysis of single-cell sequencing experiments. Cell 163, 799-810 (2015).
-
(2015)
Cell
, vol.163
, pp. 799-810
-
-
Grün, D.1
Van Oudenaarden, A.2
-
23
-
-
84953226880
-
BASiCS: Bayesian analysis of single-cell sequencing data
-
Vallejos, C.A., Marioni, J.C., Richardson, S. BASiCS: Bayesian analysis of single-cell sequencing data. PLoS Comput. Biol. 11, e1004333 (2015).
-
(2015)
PLoS Comput. Biol.
, vol.11
, pp. e1004333
-
-
Vallejos, C.A.1
Marioni, J.C.2
Richardson, S.3
-
24
-
-
46249106990
-
Mapping and quantifying mammalian transcriptomes by RNA-Seq
-
Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L., Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5, 621-628 (2008).
-
(2008)
Nat. Methods
, vol.5
, pp. 621-628
-
-
Mortazavi, A.1
Williams, B.A.2
McCue, K.3
Schaeffer, L.4
Wold, B.5
-
25
-
-
77949507153
-
RNA-Seq gene expression estimation with read mapping uncertainty
-
Li, B., Ruotti, V., Stewart, R.M., Thomson, J.A., Dewey, C.N. RNA-Seq gene expression estimation with read mapping uncertainty. Bioinformatics 26, 493-500 (2010).
-
(2010)
Bioinformatics
, vol.26
, pp. 493-500
-
-
Li, B.1
Ruotti, V.2
Stewart, R.M.3
Thomson, J.A.4
Dewey, C.N.5
-
26
-
-
77958471357
-
Differential expression analysis for sequence count data
-
Anders, S., Huber, W. Differential expression analysis for sequence count data. Genome Biol. 11, R106 (2010).
-
(2010)
Genome Biol.
, vol.11
, pp. R106
-
-
Anders, S.1
Huber, W.2
-
27
-
-
77953176036
-
A scaling normalization method for differential expression analysis of RNA-seq data
-
Robinson, M.D., Oshlack, A. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol. 11, R25 (2010).
-
(2010)
Genome Biol.
, vol.11
, pp. R25
-
-
Robinson, M.D.1
Oshlack, A.2
-
28
-
-
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
-
29
-
-
84922321862
-
Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex
-
Pollen, A.A. et al. Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex. Nat. Biotechnol. 32, 1053-1058 (2014).
-
(2014)
Nat. Biotechnol.
, vol.32
, pp. 1053-1058
-
-
Pollen, A.A.1
-
30
-
-
84924565530
-
Brain structure. Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq
-
Zeisel, A. et al. Brain structure. Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq. Science 347, 1138-1142 (2015).
-
(2015)
Science
, vol.347
, pp. 1138-1142
-
-
Zeisel, A.1
-
31
-
-
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
-
32
-
-
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
-
33
-
-
84923292191
-
Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells
-
Buettner, F. et al. Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells. Nat. Biotechnol. 33, 155-160 (2015).
-
(2015)
Nat. Biotechnol.
, vol.33
, pp. 155-160
-
-
Buettner, F.1
-
34
-
-
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
-
35
-
-
84936803955
-
Normalization and noise reduction for single cell RNA-seq experiments
-
Ding, B. et al. Normalization and noise reduction for single cell RNA-seq experiments. Bioinformatics 31, 2225-2227 (2015).
-
(2015)
Bioinformatics
, vol.31
, pp. 2225-2227
-
-
Ding, B.1
-
36
-
-
84890060756
-
SAMstrt: Statistical test for differential expression in single-cell transcriptome with spike-in normalization
-
Katayama, S., Töhönen, V., Linnarsson, S., Kere, J. SAMstrt: Statistical test for differential expression in single-cell transcriptome with spike-in normalization. Bioinformatics 29, 2943-2945 (2013).
-
(2013)
Bioinformatics
, vol.29
, pp. 2943-2945
-
-
Katayama, S.1
Töhönen, V.2
Linnarsson, S.3
Kere, J.4
-
37
-
-
85017522016
-
SCnorm: A quantile-regression based approach for robust normalization of single-cell RNA-seq data
-
Bacher, R. et al. SCnorm: A quantile-regression based approach for robust normalization of single-cell RNA-seq data. Nat. Methods http://dx.doi.org/10.1038/nmeth.4263 (2017).
-
(2017)
Nat. Methods
-
-
Bacher, R.1
-
38
-
-
85010878111
-
Single-cell mRNA quantification and differential analysis with Census
-
Qiu, X. et al. Single-cell mRNA quantification and differential analysis with Census. Nat. Methods 14, 309-315 (2017).
-
(2017)
Nat. Methods
, vol.14
, pp. 309-315
-
-
Qiu, X.1
-
39
-
-
79959403670
-
Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq
-
Islam, S. et al. Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq. Genome Res. 21, 1160-1167 (2011).
-
(2011)
Genome Res.
, vol.21
, pp. 1160-1167
-
-
Islam, S.1
-
40
-
-
84923358731
-
Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures
-
Munro, S.A. et al. Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures. Nat. Commun. 5, 5125 (2014).
-
(2014)
Nat. Commun.
, vol.5
, pp. 5125
-
-
Munro, S.A.1
-
41
-
-
84961775163
-
Heterogeneity in Oct4 and Sox2 targets biases cell fate in 4-cell mouse embryos
-
Goolam, M. et al. Heterogeneity in Oct4 and Sox2 targets biases cell fate in 4-cell mouse embryos. Cell 165, 61-74 (2016).
-
(2016)
Cell
, vol.165
, pp. 61-74
-
-
Goolam, M.1
-
42
-
-
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
-
43
-
-
84981274155
-
Spliced synthetic genes as internal controls in RNA sequencing experiments
-
Hardwick, S.A. et al. Spliced synthetic genes as internal controls in RNA sequencing experiments. Nat. Methods 13, 792-798 (2016).
-
(2016)
Nat. Methods
, vol.13
, pp. 792-798
-
-
Hardwick, S.A.1
-
44
-
-
84868010349
-
Revisiting global gene expression analysis
-
Lovén, J. et al. Revisiting global gene expression analysis. Cell 151, 476-482 (2012).
-
(2012)
Cell
, vol.151
, pp. 476-482
-
-
Lovén, J.1
-
46
-
-
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
|