-
1
-
-
46249106990
-
Mapping and quantifying mammalian transcriptomes by RNA-Seq
-
Mortazavi A, Williams BA, McCue K, et al. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 2008;5:621-8
-
(2008)
Nat Methods
, vol.5
, pp. 621-628
-
-
Mortazavi, A.1
Williams, B.A.2
McCue, K.3
-
2
-
-
45549088326
-
The transcriptional landscape of the yeast genome defined by RNA sequencing
-
Nagalakshmi U, Wang Z, Waern K, et al. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 2008;320:1344-9
-
(2008)
Science
, vol.320
, pp. 1344-1349
-
-
Nagalakshmi, U.1
Wang, Z.2
Waern, K.3
-
3
-
-
33847052127
-
Identification of pancreatic cancer stem cells
-
Li C, Heidt DG, Dalerba P, et al. Identification of pancreatic cancer stem cells. Cancer Res 2007;67:1030-7
-
(2007)
Cancer Res
, vol.67
, pp. 1030-1037
-
-
Li, C.1
Heidt, D.G.2
Dalerba, P.3
-
5
-
-
34547193404
-
Phenotypic characterization of human colorectal cancer stem cells
-
Dalerba P, Dylla SJ, Park I-K, et al. Phenotypic characterization of human colorectal cancer stem cells. Proc Natl Acad Sci USA 2007;104:10158-63
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 10158-10163
-
-
Dalerba, P.1
Dylla, S.J.2
Park, I.-K.3
-
6
-
-
33846512398
-
Identification of a subpopulation of cells with cancer stem cell properties in head and neck squamous cell carcinoma
-
Prince ME, Sivanandan R, Kaczorowski A, et al. Identification of a subpopulation of cells with cancer stem cell properties in head and neck squamous cell carcinoma. Proc Natl Acad Sci USA 2007;104:973-8
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 973-978
-
-
Prince, M.E.1
Sivanandan, R.2
Kaczorowski, A.3
-
7
-
-
84871940855
-
The isolation and characterization of renal cancer initiating cells from human Wilms' tumour xenografts unveils new therapeutic targets
-
Pode-Shakked N, Shukrun R, Mark-Danieli M, et al. The isolation and characterization of renal cancer initiating cells from human Wilms' tumour xenografts unveils new therapeutic targets. EMBO Mol Med 2013;5:18-37
-
(2013)
EMBO Mol Med
, vol.5
, pp. 18-37
-
-
Pode-Shakked, N.1
Shukrun, R.2
Mark-Danieli, M.3
-
8
-
-
9244241576
-
Identification of human brain tumour initiating cells
-
Singh SK, Hawkins C, Clarke ID, et al. Identification of human brain tumour initiating cells. Nature 2004;432:396-401
-
(2004)
Nature
, vol.432
, pp. 396-401
-
-
Singh, S.K.1
Hawkins, C.2
Clarke, I.D.3
-
9
-
-
0030789242
-
Human acute myeloid leukemia is organized as a hierarchy that originates from a primitive hematopoietic cell
-
Bonnet D, Dick JE. Human acute myeloid leukemia is organized as a hierarchy that originates from a primitive hematopoietic cell. Nat Med 1997;3:730-7
-
(1997)
Nat Med
, vol.3
, pp. 730-737
-
-
Bonnet, D.1
Dick, J.E.2
-
11
-
-
30144433093
-
Generation of a functional mammary gland from a single stem cell
-
Shackleton M, Vaillant F, Simpson KJ, et al. Generation of a functional mammary gland from a single stem cell. Nature 2006;439:84-8
-
(2006)
Nature
, vol.439
, pp. 84-88
-
-
Shackleton, M.1
Vaillant, F.2
Simpson, K.J.3
-
12
-
-
30144432901
-
Purification and unique properties of mammary epithelial stem cells
-
Stingl J, Eirew P, Ricketson I, et al. Purification and unique properties of mammary epithelial stem cells. Nature 2006; 439:993-7
-
(2006)
Nature
, vol.439
, pp. 993-997
-
-
Stingl, J.1
Eirew, P.2
Ricketson, I.3
-
13
-
-
35548974423
-
Identification of stem cells in small intestine and colon by marker gene Lgr5
-
Barker N, van Es JH, Kuipers J, et al. Identification of stem cells in small intestine and colon by marker gene Lgr5. Nature 2007;449:1003-7
-
(2007)
Nature
, vol.449
, pp. 1003-1007
-
-
Barker, N.1
van Es, J.H.2
Kuipers, J.3
-
14
-
-
48149095359
-
Six2 Defines and Regulates a Multipotent Self-Renewing Nephron Progenitor Population throughout Mammalian Kidney Development
-
Kobayashi A, Valerius MT, Mugford JW, et al. Six2 Defines and Regulates a Multipotent Self-Renewing Nephron Progenitor Population throughout Mammalian Kidney Development. Cell Stem Cell 2008;3:169-81
-
(2008)
Cell Stem Cell
, vol.3
, pp. 169-181
-
-
Kobayashi, A.1
Valerius, M.T.2
Mugford, J.W.3
-
15
-
-
84968883790
-
Single-cell analysis of CD4+ T-cell differentiation reveals three major cell states and progressive acceleration of proliferation
-
Proserpio V, Piccolo A, Haim-Vilmovsky L, et al. Single-cell analysis of CD4+ T-cell differentiation reveals three major cell states and progressive acceleration of proliferation. Genome Biol 2016;17:103
-
(2016)
Genome Biol
, vol.17
, pp. 103
-
-
Proserpio, V.1
Piccolo, A.2
Haim-Vilmovsky, L.3
-
16
-
-
83255177150
-
Single-cell dissection of transcriptional heterogeneity in human colon tumors
-
Dalerba P, Kalisky T, Sahoo D, et al. Single-cell dissection of transcriptional heterogeneity in human colon tumors. Nat Biotechnol 2011;29:1120-7
-
(2011)
Nat Biotechnol
, vol.29
, pp. 1120-1127
-
-
Dalerba, P.1
Kalisky, T.2
Sahoo, D.3
-
17
-
-
84904624915
-
Single cell dissection of early kidney development: multilineage priming
-
Brunskill EW, Park J-S, Chung E, et al. Single cell dissection of early kidney development: multilineage priming. Development 2014;141:3093-101
-
(2014)
Development
, vol.141
, pp. 3093-3101
-
-
Brunskill, E.W.1
Park, J.-S.2
Chung, E.3
-
18
-
-
84860124795
-
Identification of a cKit(+) colonic crypt base secretory cell that supports Lgr5(+) stem cells in mice
-
Rothenberg ME, Nusse Y, Kalisky T, et al. Identification of a cKit(+) colonic crypt base secretory cell that supports Lgr5(+) stem cells in mice. Gastroenterology 2012;142: 1195-1205.e6
-
(2012)
Gastroenterology
, vol.142
, pp. 1195-1205
-
-
Rothenberg, M.E.1
Nusse, Y.2
Kalisky, T.3
-
19
-
-
84900529199
-
Reconstructing lineage hierarchies of the distal lung epithelium using singlecell RNA-seq
-
Treutlein B, Brownfield DG, Wu AR, et al. Reconstructing lineage hierarchies of the distal lung epithelium using singlecell RNA-seq. Nature 2014;509:371-5
-
(2014)
Nature
, vol.509
, pp. 371-375
-
-
Treutlein, B.1
Brownfield, D.G.2
Wu, A.R.3
-
20
-
-
77951912210
-
Resolution of Cell Fate Decisions Revealed by Single-Cell Gene Expression Analysis from Zygote to Blastocyst
-
Guo G, Huss M, Tong GQ, et al. Resolution of Cell Fate Decisions Revealed by Single-Cell Gene Expression Analysis from Zygote to Blastocyst. Dev Cell 2010;18:675-85
-
(2010)
Dev Cell
, vol.18
, pp. 675-685
-
-
Guo, G.1
Huss, M.2
Tong, G.Q.3
-
21
-
-
84893910301
-
Quantitative assessment of single-cell RNA-sequencing methods
-
Wu AR, Neff NF, Kalisky T, et al. Quantitative assessment of single-cell RNA-sequencing methods. Nat Methods 2014;11: 41-6
-
(2014)
Nat Methods
, vol.11
, pp. 41-46
-
-
Wu, A.R.1
Neff, N.F.2
Kalisky, T.3
-
22
-
-
84900517167
-
Microfluidic single-cell whole-transcriptome sequencing
-
Streets AM, Zhang X, Cao C, et al. Microfluidic single-cell whole-transcriptome sequencing. Proc Natl Acad Sci USA 2014;111:7048-53
-
(2014)
Proc Natl Acad Sci USA
, vol.111
, pp. 7048-7053
-
-
Streets, A.M.1
Zhang, X.2
Cao, C.3
-
23
-
-
84922311090
-
Combinatorial labeling of single cells for gene expression cytometry
-
Fan HC, Fu GK, Fodor SP a. Combinatorial labeling of single cells for gene expression cytometry. Science 2015;347: 1258367
-
(2015)
Science
, vol.347
-
-
Fan, H.C.1
Fu, G.K.2
Fodor, S.P.3
-
24
-
-
84988884535
-
An Automated Microwell Platform for Large-Scale Single Cell RNA-Seq
-
Yuan J, Sims PA. An Automated Microwell Platform for Large-Scale Single Cell RNA-Seq. Sci Rep 2016;6:33883
-
(2016)
Sci Rep
, vol.6
, pp. 33883
-
-
Yuan, J.1
Sims, P.A.2
-
25
-
-
84939162152
-
Scalable microfluidics for singlecell RNA printing and sequencing
-
Bose S, Wan Z, Carr A, et al. Scalable microfluidics for singlecell RNA printing and sequencing. Genome Biol 2015;16:120
-
(2015)
Genome Biol
, vol.16
, pp. 120
-
-
Bose, S.1
Wan, Z.2
Carr, A.3
-
26
-
-
84929684999
-
Highly Parallel Genomewide Expression Profiling of Individual Cells Using Nanoliter Droplets
-
Macosko EZ, Basu A, Satija R, et al. Highly Parallel Genomewide Expression Profiling of Individual Cells Using Nanoliter Droplets. Cell 2015;161:1202-14
-
(2015)
Cell
, vol.161
, pp. 1202-1214
-
-
Macosko, E.Z.1
Basu, A.2
Satija, R.3
-
27
-
-
84929684998
-
Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells
-
Klein AM, Mazutis L, Akartuna I, et al. Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells. Cell 2015;161:1187-201
-
(2015)
Cell
, vol.161
, pp. 1187-1201
-
-
Klein, A.M.1
Mazutis, L.2
Akartuna, I.3
-
28
-
-
84864880991
-
Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells
-
Ramsköld D, Luo S, Wang Y-C, et al. Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells. Nat Biotechnol 2012;30:777-82
-
(2012)
Nat Biotechnol
, vol.30
, pp. 777-782
-
-
Ramsköld, D.1
Luo, S.2
Wang, Y.-C.3
-
29
-
-
84891677425
-
Full-length RNAseq from single cells using Smart-seq2
-
Picelli S, Faridani OR, Björklund AK, et al. Full-length RNAseq from single cells using Smart-seq2. Nat Protoc 2014;9: 171-81
-
(2014)
Nat Protoc
, vol.9
, pp. 171-181
-
-
Picelli, S.1
Faridani, O.R.2
Björklund, A.K.3
-
30
-
-
84893905629
-
Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types
-
Jaitin DA, Kenigsberg E, Keren-Shaul H, et al. Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types. Science 2014;343:776-9
-
(2014)
Science
, vol.343
, pp. 776-779
-
-
Jaitin, D.A.1
Kenigsberg, E.2
Keren-Shaul, H.3
-
31
-
-
84964452502
-
CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq
-
Hashimshony T, Senderovich N, Avital G, et al. CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq. Genome Biol 2016;17:77
-
(2016)
Genome Biol
, vol.17
, pp. 77
-
-
Hashimshony, T.1
Senderovich, N.2
Avital, G.3
-
32
-
-
25844433114
-
Gene expression profiling in single cells from the pancreatic islets of Langerhans reveals lognormal distribution of mRNA levels
-
Bengtsson M, Ståhlberg A, Rorsman P, et al. Gene expression profiling in single cells from the pancreatic islets of Langerhans reveals lognormal distribution of mRNA levels. Genome Res 2005;15:1388-92
-
(2005)
Genome Res
, vol.15
, pp. 1388-1392
-
-
Bengtsson, M.1
Ståhlberg, A.2
Rorsman, P.3
-
33
-
-
84859602728
-
Microfluidic single-cell real-time PCR for comparative analysis of gene expression patterns
-
Sanchez-Freire V, Ebert AD, Kalisky T, et al. Microfluidic single-cell real-time PCR for comparative analysis of gene expression patterns. Nat Protoc 2012;7:829-38
-
(2012)
Nat Protoc
, vol.7
, pp. 829-838
-
-
Sanchez-Freire, V.1
Ebert, A.D.2
Kalisky, T.3
-
34
-
-
84882582801
-
Single-cell gene expression analysis reveals genetic associations masked in wholetissue experiments
-
Wills QF, Livak KJ, Tipping AJ, et al. Single-cell gene expression analysis reveals genetic associations masked in wholetissue experiments. Nat Biotechnol 2013;31:748-52
-
(2013)
Nat Biotechnol
, vol.31
, pp. 748-752
-
-
Wills, Q.F.1
Livak, K.J.2
Tipping, A.J.3
-
35
-
-
84885172419
-
Mapping cellular hierarchy by single-cell analysis of the cell surface repertoire
-
Guo G, Luc S, Marco E, et al. Mapping cellular hierarchy by single-cell analysis of the cell surface repertoire. Cell Stem Cell 2013;13:492-505
-
(2013)
Cell Stem Cell
, vol.13
, pp. 492-505
-
-
Guo, G.1
Luc, S.2
Marco, E.3
-
36
-
-
79958171563
-
The GUDMAP database-an online resource for genitourinary research
-
Harding SD, Armit C, Armstrong J, et al. The GUDMAP database-an online resource for genitourinary research. Development 2011;138:2845-53
-
(2011)
Development
, vol.138
, pp. 2845-2853
-
-
Harding, S.D.1
Armit, C.2
Armstrong, J.3
-
38
-
-
65449136284
-
TopHat: Discovering splice junctions with RNA-Seq
-
Trapnell C, Pachter L, Salzberg SL. TopHat: Discovering splice junctions with RNA-Seq. Bioinformatics 2009;25: 1105-11
-
(2009)
Bioinformatics
, vol.25
, pp. 1105-1111
-
-
Trapnell, C.1
Pachter, L.2
Salzberg, S.L.3
-
39
-
-
84876996918
-
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
-
Kim D, Pertea G, Trapnell C, et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 2013;14:R36
-
(2013)
Genome Biol
, vol.14
, pp. R36
-
-
Kim, D.1
Pertea, G.2
Trapnell, C.3
-
40
-
-
62349130698
-
Ultrafast and memoryefficient alignment of short DNA sequences to the human genome
-
Langmead B, Trapnell C, Pop M, et al. Ultrafast and memoryefficient alignment of short DNA sequences to the human genome. Genome Biol 2009;10:R25
-
(2009)
Genome Biol
, vol.10
, pp. R25
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
-
42
-
-
84928987900
-
HTSeq-A Python framework to work with high-throughput sequencing data
-
Anders S, Pyl PT, Huber W. HTSeq-A Python framework to work with high-throughput sequencing data. Bioinformatics 2015;31:166-69
-
(2015)
Bioinformatics
, vol.31
, pp. 166-169
-
-
Anders, S.1
Pyl, P.T.2
Huber, W.3
-
43
-
-
84883364264
-
Count-based differential expression analysis of RNA sequencing data using R and Bioconductor
-
Anders S, McCarthy DJ, Chen Y, et al. Count-based differential expression analysis of RNA sequencing data using R and Bioconductor. Nat Protoc 2013;8:1765-86
-
(2013)
Nat Protoc
, vol.8
, pp. 1765-1786
-
-
Anders, S.1
McCarthy, D.J.2
Chen, Y.3
-
45
-
-
77958471357
-
Differential expression analysis for sequence count data
-
Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol 2010;11:R106
-
(2010)
Genome Biol
, vol.11
, pp. R106
-
-
Anders, S.1
Huber, W.2
-
46
-
-
79959327151
-
Counting individual DNA molecules by the stochastic attachment of diverse labels
-
Fu GK, Hu J, Wang P-H, et al. Counting individual DNA molecules by the stochastic attachment of diverse labels. Proc Natl Acad Sci USA 2011;108:9026-31
-
(2011)
Proc Natl Acad Sci USA
, vol.108
, pp. 9026-9031
-
-
Fu, G.K.1
Hu, J.2
Wang, P.-H.3
-
47
-
-
84895069488
-
Quantitative single-cell RNAseq with unique molecular identifiers
-
Islam S, Zeisel A, Joost S, et al. Quantitative single-cell RNAseq with unique molecular identifiers. Nat Methods 2014;11: 163-6
-
(2014)
Nat Methods
, vol.11
, pp. 163-166
-
-
Islam, S.1
Zeisel, A.2
Joost, S.3
-
48
-
-
84856484968
-
Counting absolute numbers of molecules using unique molecular identifiers
-
Kivioja T, Vähärautio A, Karlsson K, et al. Counting absolute numbers of molecules using unique molecular identifiers. Nat Methods 2011;9:72-4
-
(2011)
Nat Methods
, vol.9
, pp. 72-74
-
-
Kivioja, T.1
Vähärautio, A.2
Karlsson, K.3
-
49
-
-
84878997106
-
Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells
-
Shalek AK, Satija R, Adiconis X, et al. Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells. Nature 2013;498:236-40
-
(2013)
Nature
, vol.498
, pp. 236-240
-
-
Shalek, A.K.1
Satija, R.2
Adiconis, X.3
-
50
-
-
84865527768
-
Detecting differential usage of exons from RNA-seq data
-
Anders S, Reyes A, Huber W. Detecting differential usage of exons from RNA-seq data. Genome Res 2012;22:2008-17
-
(2012)
Genome Res
, vol.22
, pp. 2008-2017
-
-
Anders, S.1
Reyes, A.2
Huber, W.3
-
51
-
-
78649714014
-
Analysis and design of RNA sequencing experiments for identifying isoform regulation
-
Katz Y, Wang ET, Airoldi EM, et al. Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nat Methods 2010;7:1009-15
-
(2010)
Nat Methods
, vol.7
, pp. 1009-1015
-
-
Katz, Y.1
Wang, E.T.2
Airoldi, E.M.3
-
52
-
-
84919936245
-
rMATS: robust and flexible detection of differential alternative splicing from replicate RNASeq data
-
Shen S, Park JW, Lu Z, et al. rMATS: robust and flexible detection of differential alternative splicing from replicate RNASeq data. Proc Natl Acad Sci USA 2014;111:E5593-601
-
(2014)
Proc Natl Acad Sci USA
, vol.111
, pp. E5593-E5601
-
-
Shen, S.1
Park, J.W.2
Lu, Z.3
-
53
-
-
84892179132
-
Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells
-
Deng Q, Ramsköld D, Reinius B, et al. Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells. Science 2014;343:193-6
-
(2014)
Science
, vol.343
, pp. 193-196
-
-
Deng, Q.1
Ramsköld, D.2
Reinius, B.3
-
54
-
-
85016091925
-
Large-scale singlecell RNA-seq reveals a developmental hierarchy in human oligodendroglioma
-
Tirosh I, Venteicher AS, Hebert C, et al. Large-scale singlecell RNA-seq reveals a developmental hierarchy in human oligodendroglioma. Nature 2016;539:309-13
-
(2016)
Nature
, vol.539
, pp. 309-313
-
-
Tirosh, I.1
Venteicher, A.S.2
Hebert, C.3
-
55
-
-
85020615271
-
Single-cell RNA-sequencing: The future of genome biology is now
-
Picelli S. Single-cell RNA-sequencing: The future of genome biology is now. RNA Biol 2016;6286:1-14
-
(2016)
RNA Biol
, vol.6286
, pp. 1-14
-
-
Picelli, S.1
-
56
-
-
84929687805
-
The Technology and Biology of Single-Cell RNA Sequencing
-
Kolodziejczyk AA, Kim JK, Svensson V, et al. The Technology and Biology of Single-Cell RNA Sequencing. Mol Cell 2015;58: 610-20
-
(2015)
Mol Cell
, vol.58
, pp. 610-620
-
-
Kolodziejczyk, A.A.1
Kim, J.K.2
Svensson, V.3
-
59
-
-
84872195205
-
Methods for qPCR gene expression profiling applied to 1440 lymphoblastoid single cells
-
Livak KJ, Wills QF, Tipping AJ, et al. Methods for qPCR gene expression profiling applied to 1440 lymphoblastoid single cells. Methods 2013;59:71-9
-
(2013)
Methods
, vol.59
, pp. 71-79
-
-
Livak, K.J.1
Wills, Q.F.2
Tipping, A.J.3
-
60
-
-
0141816971
-
Solving the 'World-to-Chip' interface problem with a microfluidic matrix
-
Liu J, Hansen C, Quake SR. Solving the 'World-to-Chip' interface problem with a microfluidic matrix. Anal Chem 2003;75: 4718-23
-
(2003)
Anal Chem
, vol.75
, pp. 4718-4723
-
-
Liu, J.1
Hansen, C.2
Quake, S.R.3
-
62
-
-
55549089660
-
Accurate whole human genome sequencing using reversible terminator chemistry
-
Bentley DR, Gormley NA, Balasubramanian S, et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 2008;456:53-9
-
(2008)
Nature
, vol.456
, pp. 53-59
-
-
Bentley, D.R.1
Gormley, N.A.2
Balasubramanian, S.3
-
63
-
-
77749323185
-
RNA-Seq analysis to capture the transcriptome landscape of a single cell
-
Tang F, Barbacioru C, Nordman E, et al. RNA-Seq analysis to capture the transcriptome landscape of a single cell. Nat Protoc 2010;5:516-35
-
(2010)
Nat Protoc
, vol.5
, pp. 516-535
-
-
Tang, F.1
Barbacioru, C.2
Nordman, E.3
-
64
-
-
0035046755
-
Reverse transcriptase template switching: A SMART approach for full-length cDNA library construction
-
Zhu YY, Machleder EM, Chenchik A, et al. Reverse transcriptase template switching: A SMART approach for full-length cDNA library construction. Biotechniques 2001;30:892-97
-
(2001)
Biotechniques
, vol.30
, pp. 892-897
-
-
Zhu, Y.Y.1
Machleder, E.M.2
Chenchik, A.3
-
65
-
-
0033559113
-
Amplification of cDNA ends based on template-switching effect and step-out PCR
-
Matz M, Shagin D, Bogdanova E, et al. Amplification of cDNA ends based on template-switching effect and step-out PCR. Nucleic Acids Res 1999;27:1558-60
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 1558-1560
-
-
Matz, M.1
Shagin, D.2
Bogdanova, E.3
-
66
-
-
78649773164
-
Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition
-
Adey A, Morrison HG, Asan, et al. Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition. Genome Biol 2010;11:R119
-
(2010)
Genome Biol
, vol.11
, pp. R119
-
-
Adey, A.1
Morrison, H.G.2
Asan3
-
67
-
-
0037336665
-
Tn 5 as a model for understanding DNA transposition
-
Reznikoff WS. Tn 5 as a model for understanding DNA transposition. Mol Biol 2003;47:1199-206
-
(2003)
Mol Biol
, vol.47
, pp. 1199-1206
-
-
Reznikoff, W.S.1
-
68
-
-
84913593681
-
Tn5 transposase and tagmentation procedures for massively scaled sequencing projects
-
Picelli S, Björklund AK, Reinius B, et al. Tn5 transposase and tagmentation procedures for massively scaled sequencing projects. Genome Res 2014;24:2033-40
-
(2014)
Genome Res
, vol.24
, pp. 2033-2040
-
-
Picelli, S.1
Björklund, A.K.2
Reinius, B.3
-
70
-
-
84887101406
-
Smart-seq2 for sensitive full-length transcriptome profiling in single cells
-
Picelli S, BjörklundAK, Faridani OR, et al. Smart-seq2 for sensitive full-length transcriptome profiling in single cells. Nat Methods 2013;10:1096-8
-
(2013)
Nat Methods
, vol.10
, pp. 1096-1098
-
-
Picelli, S.1
Björklund, A.K.2
Faridani, O.R.3
-
71
-
-
84902668801
-
Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma
-
Patel AP, Tirosh I, Trombetta JJ, et al. Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma. Science 2014;344:1396-401
-
(2014)
Science
, vol.344
, pp. 1396-1401
-
-
Patel, A.P.1
Tirosh, I.2
Trombetta, J.J.3
-
72
-
-
84945256616
-
Intrinsic Age-Dependent Changes and Cell-Cell Contacts Regulate Nephron Progenitor Lifespan
-
Chen S, Brunskill EW, Potter SS, et al. Intrinsic Age-Dependent Changes and Cell-Cell Contacts Regulate Nephron Progenitor Lifespan. Dev Cell 2015;35:49-62
-
(2015)
Dev Cell
, vol.35
, pp. 49-62
-
-
Chen, S.1
Brunskill, E.W.2
Potter, S.S.3
-
73
-
-
84896525250
-
Digital encoding of cellular mRNAs enabling precise and absolute gene expression measurement by single-molecule counting
-
Fu GK, Wilhelmy J, Stern D, et al. Digital encoding of cellular mRNAs enabling precise and absolute gene expression measurement by single-molecule counting. Anal Chem 2014; 86:2867-70
-
(2014)
Anal Chem
, vol.86
, pp. 2867-2870
-
-
Fu, G.K.1
Wilhelmy, J.2
Stern, D.3
-
74
-
-
84862212456
-
Droplet microfluidics for high-throughput biological assays
-
Guo MT, Rotem A, Heyman JA, et al. Droplet microfluidics for high-throughput biological assays. Lab Chip 2012;12:2146-55
-
(2012)
Lab Chip
, vol.12
, pp. 2146-2155
-
-
Guo, M.T.1
Rotem, A.2
Heyman, J.A.3
-
75
-
-
79959403670
-
Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq
-
Islam S, Kjällquist U, Moliner A, et al. Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq. Genome Res 2011;21:1160-67
-
(2011)
Genome Res
, vol.21
, pp. 1160-1167
-
-
Islam, S.1
Kjällquist, U.2
Moliner, A.3
-
76
-
-
84856398949
-
Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes
-
Shiroguchi K, Jia TZ, Sims PA, et al. Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes. Proc Natl Acad Sci USA 2012;109:1347-52
-
(2012)
Proc Natl Acad Sci USA
, vol.109
, pp. 1347-1352
-
-
Shiroguchi, K.1
Jia, T.Z.2
Sims, P.A.3
-
77
-
-
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 2014;11: 637-40
-
(2014)
Nat Methods
, vol.11
, pp. 637-640
-
-
Grün, D.1
Kester, L.2
van Oudenaarden, A.3
-
79
-
-
85044635843
-
Comprehensive single cell transcriptional profiling of a multicellular organism by combinatorial indexing
-
Heitland I, Hermann A, Kuhn M, et al. Comprehensive single cell transcriptional profiling of a multicellular organism by combinatorial indexing. bioRxiv 2017; 1-90
-
(2017)
BioRxiv
, pp. 1-90
-
-
Heitland, I.1
Hermann, A.2
Kuhn, M.3
-
81
-
-
80052521697
-
Synthetic spike-in standards for RNA-seq experiments
-
Jiang L, Schlesinger F, Davis CA, et al. Synthetic spike-in standards for RNA-seq experiments. Genome Res 2011;21: 1543-51
-
(2011)
Genome Res
, vol.21
, pp. 1543-1551
-
-
Jiang, L.1
Schlesinger, F.2
Davis, C.A.3
-
82
-
-
84981274155
-
Spliced synthetic genes as internal controls in RNA sequencing experiments
-
Hardwick SA, Chen WY, Wong T, et al. Spliced synthetic genes as internal controls in RNA sequencing experiments. Nat Meth 2016;13:792-98
-
(2016)
Nat Meth
, vol.13
, pp. 792-798
-
-
Hardwick, S.A.1
Chen, W.Y.2
Wong, T.3
-
83
-
-
84887109584
-
Accounting for technical noise in single-cell RNA-seq experiments
-
Brennecke P, Anders S, Kim JK, et al. Accounting for technical noise in single-cell RNA-seq experiments. Nat Methods 2013; 10:1093-5
-
(2013)
Nat Methods
, vol.10
, pp. 1093-1095
-
-
Brennecke, P.1
Anders, S.2
Kim, J.K.3
-
84
-
-
84924565530
-
Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq
-
Zeisel A, Manchado a. BM, Codeluppi S, et al. Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq. Science 2015;347:1138-42
-
(2015)
Science
, vol.347
, pp. 1138-1142
-
-
-
85
-
-
84976883162
-
Microglia development follows a stepwise program to regulate brain homeostasis
-
Matcovitch-Natan O, Winter DR, Giladi A, et al. Microglia development follows a stepwise program to regulate brain homeostasis. Science 2016;353:aad8670
-
(2016)
Science
, vol.353
-
-
Matcovitch-Natan, O.1
Winter, D.R.2
Giladi, A.3
-
86
-
-
0034710876
-
Coupled two-way clustering of DNA microarray data
-
Getz G, Levine E, Domany E. Coupled two-way clustering of DNA microarray data. Proc Natl Acad Sci USA 2000;97: 12079-84
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, pp. 12079-12084
-
-
Getz, G.1
Levine, E.2
Domany, E.3
-
87
-
-
84990876505
-
Molecular diversity of midbrain development in mouse, human and stem cells
-
La Manno G, Gyllborg D, Codeluppi S, et al. Molecular diversity of midbrain development in mouse, human and stem cells. Cell 2016;167:566-580.e19
-
(2016)
Cell
, vol.167
, pp. 566-580
-
-
La Manno, G.1
Gyllborg, D.2
Codeluppi, S.3
-
88
-
-
33847172327
-
Clustering by passing messages between data points
-
Frey BJ, Dueck D. Clustering by passing messages between data points. Science 2007;315:972-76
-
(2007)
Science
, vol.315
, pp. 972-976
-
-
Frey, B.J.1
Dueck, D.2
-
89
-
-
85170282443
-
A Density-Based Algorithm for Discovering Clusters in Large Spatial Databases with Noise
-
Ester M, Kriegel HP, Sander J, et al. A Density-Based Algorithm for Discovering Clusters in Large Spatial Databases with Noise. Proc 2nd Int Conf Knowl Discov DataMin 1996; 226-31
-
(1996)
Proc 2nd Int Conf Knowl Discov DataMin
, pp. 226-231
-
-
Ester, M.1
Kriegel, H.P.2
Sander, J.3
-
90
-
-
66649115648
-
Automated high-dimensional flow cytometric data analysis
-
Pyne S, Hu X, Wang K, et al. Automated high-dimensional flow cytometric data analysis. Proc Natl Acad Sci USA 2009; 106:8519-24
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 8519-8524
-
-
Pyne, S.1
Hu, X.2
Wang, K.3
-
91
-
-
84903722445
-
Joint modeling and registration of cell populations in cohorts of high-dimensional flow cytometric data
-
Pyne S, Lee SX, Wang K, et al. Joint modeling and registration of cell populations in cohorts of high-dimensional flow cytometric data. PLoS One 2014;9
-
(2014)
PLoS One
, pp. 9
-
-
Pyne, S.1
Lee, S.X.2
Wang, K.3
-
92
-
-
84934442835
-
Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis
-
Levine JH, Simonds EF, Bendall SC, et al. Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis. Cell 2015;162:184-97
-
(2015)
Cell
, vol.162
, pp. 184-197
-
-
Levine, J.H.1
Simonds, E.F.2
Bendall, S.C.3
-
94
-
-
84938632823
-
Geometry of the Gene Expression Space of Individual Cells
-
Korem Y, Szekely P, Hart Y, et al. Geometry of the Gene Expression Space of Individual Cells. PLOS Comput Biol 2015; 11:e1004224
-
(2015)
PLOS Comput Biol
, vol.11
-
-
Korem, Y.1
Szekely, P.2
Hart, Y.3
-
95
-
-
84900873950
-
The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells
-
Trapnell C, Cacchiarelli D, Grimsby J, et al. The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nat Biotechnol 2014;32: 381-6
-
(2014)
Nat Biotechnol
, vol.32
, pp. 381-386
-
-
Trapnell, C.1
Cacchiarelli, D.2
Grimsby, J.3
-
96
-
-
84929151009
-
Spatial reconstruction of single-cell gene expression data
-
Satija R, Farrell JA, Gennert D, et al. Spatial reconstruction of single-cell gene expression data. Nat Biotechnol 2015;33: 495-502
-
(2015)
Nat Biotechnol
, vol.33
, pp. 495-502
-
-
Satija, R.1
Farrell, J.A.2
Gennert, D.3
-
97
-
-
84897090228
-
Highly Multiplexed Subcellular RNA Sequencing in Situ
-
Lee JHJH, Daugharthy ER, Scheiman J, et al. Highly Multiplexed Subcellular RNA Sequencing in Situ. Science 2014;343:1360-63
-
(2014)
Science
, vol.343
, pp. 1360-1363
-
-
Lee, J.H.J.H.1
Daugharthy, E.R.2
Scheiman, J.3
-
98
-
-
84923799606
-
Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues
-
Lee JH, Daugharthy ER, Scheiman J, et al. Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues. Nat Protoc 2015;10:442-58
-
(2015)
Nat Protoc
, vol.10
, pp. 442-458
-
-
Lee, J.H.1
Daugharthy, E.R.2
Scheiman, J.3
-
99
-
-
67349146589
-
mRNA-Seq whole-transcriptome analysis of a single cell
-
Tang F, Barbacioru C, Wang Y, et al. mRNA-Seq whole-transcriptome analysis of a single cell. Nat Methods 2009;6: 377-82
-
(2009)
Nat Methods
, vol.6
, pp. 377-382
-
-
Tang, F.1
Barbacioru, C.2
Wang, Y.3
-
100
-
-
77956412152
-
Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNA-seq analysis
-
Tang F, Barbacioru C, Bao S, et al. Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNA-seq analysis. Cell Stem Cell 2010;6:468-78
-
(2010)
Cell Stem Cell
, vol.6
, pp. 468-478
-
-
Tang, F.1
Barbacioru, C.2
Bao, S.3
-
101
-
-
84855331824
-
Transposase mediated construction of RNA-seq libraries
-
Gertz J, Varley KE, Davis NS, et al. Transposase mediated construction of RNA-seq libraries. Genome Res 2012;22:134-41
-
(2012)
Genome Res
, vol.22
, pp. 134-141
-
-
Gertz, J.1
Varley, K.E.2
Davis, N.S.3
-
102
-
-
84922321862
-
Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex
-
Pollen AA, Nowakowski TJ, Shuga J, et al. Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex. Nat Biotechnol 2014;32:1053-8
-
(2014)
Nat Biotechnol
, vol.32
, pp. 1053-1058
-
-
Pollen, A.A.1
Nowakowski, T.J.2
Shuga, J.3
-
103
-
-
85016584336
-
Aging increases cell-to-cell transcriptional variability upon immune stimulation
-
Martinez-jimenez CP, Eling N, Chen H, et al. Aging increases cell-to-cell transcriptional variability upon immune stimulation. Science 2017;1436:1433-36
-
(2017)
Science
, vol.1436
, pp. 1433-1436
-
-
Martinez-jimenez, C.P.1
Eling, N.2
Chen, H.3
-
104
-
-
85018582872
-
Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors
-
Villani A-C, Satija R, Reynolds G, et al. Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors. Science 2017;356:eaah4573
-
(2017)
Science
, vol.356
-
-
Villani, A.-C.1
Satija, R.2
Reynolds, G.3
-
105
-
-
85016574289
-
Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq
-
Venteicher AS, Tirosh I, Hebert C, et al. Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq. Science 2017;355:eaai8478
-
(2017)
Science
, vol.355
-
-
Venteicher, A.S.1
Tirosh, I.2
Hebert, C.3
-
106
-
-
85009809647
-
Effective detection of variation in single-cell transcriptomes using MATQ-seq
-
Sheng K, Cao W, Niu Y, et al. Effective detection of variation in single-cell transcriptomes using MATQ-seq. Nat Methods 2017;14:267-70
-
(2017)
Nat Methods
, vol.14
, pp. 267-270
-
-
Sheng, K.1
Cao, W.2
Niu, Y.3
-
107
-
-
84859621573
-
Highly multiplexed and strand-specific single-cell RNA 5' end sequencing
-
Islam S, Kjällquist U, Moliner A, et al. Highly multiplexed and strand-specific single-cell RNA 5' end sequencing. Nat Protoc 2012;7:813-28
-
(2012)
Nat Protoc
, vol.7
, pp. 813-828
-
-
Islam, S.1
Kjällquist, U.2
Moliner, A.3
-
108
-
-
84866953427
-
CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification
-
Hashimshony T, Wagner F, Sher N, et al. CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification. Cell Rep 2012; 2:666-73
-
(2012)
Cell Rep
, vol.2
, pp. 666-673
-
-
Hashimshony, T.1
Wagner, F.2
Sher, N.3
-
110
-
-
85012271992
-
Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput
-
Gierahn TM, Wadsworth MH, Hughes TK, et al. Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput. Nat Methods 2017;14:395-98
-
(2017)
Nat Methods
, vol.14
, pp. 395-398
-
-
Gierahn, T.M.1
Wadsworth, M.H.2
Hughes, T.K.3
-
111
-
-
85006454169
-
Massively parallel digital transcriptional profiling of single cells
-
Zheng GXY, Terry JM, Belgrader P, et al. Massively parallel digital transcriptional profiling of single cells. bioRxiv 2016; 8:65912
-
(2016)
BioRxiv
, vol.8
, pp. 65912
-
-
Zheng, G.X.Y.1
Terry, J.M.2
Belgrader, P.3
-
112
-
-
85021995058
-
Massively parallel nanowell-based single-cell gene expression profiling
-
Goldstein LD, Chen Y-JJ, Dunne J, et al. Massively parallel nanowell-based single-cell gene expression profiling. BMC Bioinformatics 2017; 1-10
-
(2017)
BMC Bioinformatics
, pp. 1-10
-
-
Goldstein, L.D.1
Chen, Y.-J.J.2
Dunne, J.3
|