-
1
-
-
84891102589
-
Mutational signatures: The patterns of somatic mutations hidden in cancer genomes
-
L.B. Alexandrov, and M.R. Stratton Mutational signatures: the patterns of somatic mutations hidden in cancer genomes Curr. Opin. Genet. Dev. 24 2014 52 60
-
(2014)
Curr. Opin. Genet. Dev.
, vol.24
, pp. 52-60
-
-
Alexandrov, L.B.1
Stratton, M.R.2
-
2
-
-
77958471357
-
Differential expression analysis for sequence count data
-
S. Anders, and W. Huber Differential expression analysis for sequence count data Genome Biol. 11 2010 R106
-
(2010)
Genome Biol.
, vol.11
, pp. R106
-
-
Anders, S.1
Huber, W.2
-
3
-
-
27144548491
-
The External RNA Controls Consortium: A progress report
-
S.C. Baker, S.R. Bauer, R.P. Beyer, J.D. Brenton, B. Bromley, J. Burrill, H. Causton, M.P. Conley, R. Elespuru, M. Fero, et al. External RNA Controls Consortium The External RNA Controls Consortium: a progress report Nat. Methods 2 2005 731 734
-
(2005)
Nat. Methods
, vol.2
, pp. 731-734
-
-
Baker, S.C.1
Bauer, S.R.2
Beyer, R.P.3
Brenton, J.D.4
Bromley, B.5
Burrill, J.6
Causton, H.7
Conley, M.P.8
Elespuru, R.9
Fero, M.10
-
4
-
-
84861033754
-
Genome-wide copy number analysis of single cells
-
T. Baslan, J. Kendall, L. Rodgers, H. Cox, M. Riggs, A. Stepansky, J. Troge, K. Ravi, D. Esposito, B. Lakshmi, and et al. Genome-wide copy number analysis of single cells Nat. Protoc. 7 2012 1024 1041
-
(2012)
Nat. Protoc.
, vol.7
, pp. 1024-1041
-
-
Baslan, T.1
Kendall, J.2
Rodgers, L.3
Cox, H.4
Riggs, M.5
Stepansky, A.6
Troge, J.7
Ravi, K.8
Esposito, D.9
Lakshmi, B.10
-
5
-
-
84876592083
-
A genomic view of mosaicism and human disease
-
L.G. Biesecker, and N.B. Spinner A genomic view of mosaicism and human disease Nat. Rev. Genet. 14 2013 307 320
-
(2013)
Nat. Rev. Genet.
, vol.14
, pp. 307-320
-
-
Biesecker, L.G.1
Spinner, N.B.2
-
6
-
-
84887109584
-
Accounting for technical noise in single-cell RNA-seq experiments
-
P. Brennecke, S. Anders, J.K. Kim, A.A. Kołodziejczyk, X. Zhang, V. Proserpio, B. Baying, V. Benes, S.A. Teichmann, J.C. Marioni, and M.G. Heisler Accounting for technical noise in single-cell RNA-seq experiments Nat. Methods 10 2013 1093 1095
-
(2013)
Nat. Methods
, vol.10
, pp. 1093-1095
-
-
Brennecke, P.1
Anders, S.2
Kim, J.K.3
Kołodziejczyk, A.A.4
Zhang, X.5
Proserpio, V.6
Baying, B.7
Benes, V.8
Teichmann, S.A.9
Marioni, J.C.10
Heisler, M.G.11
-
7
-
-
84923292191
-
Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells
-
F. Buettner, K.N. Natarajan, F.P. Casale, V. Proserpio, A. Scialdone, F.J. Theis, S.A. Teichmann, J.C. Marioni, and O. Stegle Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells Nat. Biotechnol. 33 2015 155 160
-
(2015)
Nat. Biotechnol.
, vol.33
, pp. 155-160
-
-
Buettner, F.1
Natarajan, K.N.2
Casale, F.P.3
Proserpio, V.4
Scialdone, A.5
Theis, F.J.6
Teichmann, S.A.7
Marioni, J.C.8
Stegle, O.9
-
8
-
-
84865592340
-
Cytometry: Today's technology and tomorrow's horizons
-
P.K. Chattopadhyay, and M. Roederer Cytometry: today's technology and tomorrow's horizons Methods 57 2012 251 258
-
(2012)
Methods
, vol.57
, pp. 251-258
-
-
Chattopadhyay, P.K.1
Roederer, M.2
-
9
-
-
0029966845
-
Whole genome amplification using a degenerate oligonucleotide primer allows hundreds of genotypes to be performed on less than one nanogram of genomic DNA
-
V.G. Cheung, and S.F. Nelson Whole genome amplification using a degenerate oligonucleotide primer allows hundreds of genotypes to be performed on less than one nanogram of genomic DNA Proc. Natl. Acad. Sci. USA 93 1996 14676 14679
-
(1996)
Proc. Natl. Acad. Sci. USA
, vol.93
, pp. 14676-14679
-
-
Cheung, V.G.1
Nelson, S.F.2
-
10
-
-
84946037477
-
Ensembl 2015
-
F. Cunningham, M.R. Amode, D. Barrell, K. Beal, K. Billis, S. Brent, D. Carvalho-Silva, P. Clapham, G. Coates, S. Fitzgerald, and et al. Ensembl 2015 Nucleic Acids Res. 43 2015 D662 D669
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. D662-D669
-
-
Cunningham, F.1
Amode, M.R.2
Barrell, D.3
Beal, K.4
Billis, K.5
Brent, S.6
Carvalho-Silva, D.7
Clapham, P.8
Coates, G.9
Fitzgerald, S.10
-
11
-
-
18344396798
-
Comprehensive human genome amplification using multiple displacement amplification
-
F.B. Dean, S. Hosono, L. Fang, X. Wu, A.F. Faruqi, P. Bray-Ward, Z. Sun, Q. Zong, Y. Du, J. Du, and et al. Comprehensive human genome amplification using multiple displacement amplification Proc. Natl. Acad. Sci. USA 99 2002 5261 5266
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 5261-5266
-
-
Dean, F.B.1
Hosono, S.2
Fang, L.3
Wu, X.4
Faruqi, A.F.5
Bray-Ward, P.6
Sun, Z.7
Zong, Q.8
Du, Y.9
Du, J.10
-
12
-
-
84892179132
-
Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells
-
Q. Deng, D. Ramsköld, B. Reinius, and R. Sandberg Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells Science 343 2014 193 196
-
(2014)
Science
, vol.343
, pp. 193-196
-
-
Deng, Q.1
Ramsköld, D.2
Reinius, B.3
Sandberg, R.4
-
13
-
-
0026588147
-
Analysis of gene expression in single live neurons
-
J. Eberwine, H. Yeh, K. Miyashiro, Y. Cao, S. Nair, R. Finnell, M. Zettel, and P. Coleman Analysis of gene expression in single live neurons Proc. Natl. Acad. Sci. USA 89 1992 3010 3014
-
(1992)
Proc. Natl. Acad. Sci. USA
, vol.89
, pp. 3010-3014
-
-
Eberwine, J.1
Yeh, H.2
Miyashiro, K.3
Cao, Y.4
Nair, S.5
Finnell, R.6
Zettel, M.7
Coleman, P.8
-
14
-
-
77956520011
-
Functional roles for noise in genetic circuits
-
A. Eldar, and M.B. Elowitz Functional roles for noise in genetic circuits Nature 467 2010 167 173
-
(2010)
Nature
, vol.467
, pp. 167-173
-
-
Eldar, A.1
Elowitz, M.B.2
-
15
-
-
84869096434
-
DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution
-
E. Falconer, M. Hills, U. Naumann, S.S.S. Poon, E.A. Chavez, A.D. Sanders, Y. Zhao, M. Hirst, and P.M. Lansdorp DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution Nat. Methods 9 2012 1107 1112
-
(2012)
Nat. Methods
, vol.9
, pp. 1107-1112
-
-
Falconer, E.1
Hills, M.2
Naumann, U.3
Poon, S.S.S.4
Chavez, E.A.5
Sanders, A.D.6
Zhao, Y.7
Hirst, M.8
Lansdorp, P.M.9
-
17
-
-
79957842166
-
Computational methods for transcriptome annotation and quantification using RNA-seq
-
M. Garber, M.G. Grabherr, M. Guttman, and C. Trapnell Computational methods for transcriptome annotation and quantification using RNA-seq Nat. Methods 8 2011 469 477
-
(2011)
Nat. Methods
, vol.8
, pp. 469-477
-
-
Garber, M.1
Grabherr, M.G.2
Guttman, M.3
Trapnell, C.4
-
18
-
-
84890055556
-
Massively parallel polymerase cloning and genome sequencing of single cells using nanoliter microwells
-
J. Gole, A. Gore, A. Richards, Y.-J. Chiu, H.-L. Fung, D. Bushman, H.-I. Chiang, J. Chun, Y.-H. Lo, and K. Zhang Massively parallel polymerase cloning and genome sequencing of single cells using nanoliter microwells Nat. Biotechnol. 31 2013 1126 1132
-
(2013)
Nat. Biotechnol.
, vol.31
, pp. 1126-1132
-
-
Gole, J.1
Gore, A.2
Richards, A.3
Chiu, Y.-J.4
Fung, H.-L.5
Bushman, D.6
Chiang, H.-I.7
Chun, J.8
Lo, Y.-H.9
Zhang, K.10
-
19
-
-
84901831004
-
Validation of noise models for single-cell transcriptomics
-
D. Grün, L. Kester, and A. van Oudenaarden Validation of noise models for single-cell transcriptomics Nat. Methods 11 2014 637 640
-
(2014)
Nat. Methods
, vol.11
, pp. 637-640
-
-
Grün, D.1
Kester, L.2
Van Oudenaarden, A.3
-
20
-
-
84941201582
-
Single-cell messenger RNA sequencing reveals rare intestinal cell types
-
D. Grün, A. Lyubimova, L. Kester, K. Wiebrands, O. Basak, N. Sasaki, H. Clevers, and A. van Oudenaarden Single-cell messenger RNA sequencing reveals rare intestinal cell types Nature 525 2015 251 255 10.1038/nature14966
-
(2015)
Nature
, vol.525
, pp. 251-255
-
-
Grün, D.1
Lyubimova, A.2
Kester, L.3
Wiebrands, K.4
Basak, O.5
Sasaki, N.6
Clevers, H.7
Van Oudenaarden, A.8
-
21
-
-
84941753288
-
Diffusion maps for high-dimensional single-cell analysis of differentiation data
-
L. Haghverdi, F. Buettner, and F.J. Theis Diffusion maps for high-dimensional single-cell analysis of differentiation data Bioinformatics 31 2015 2989 2998 10.1093/bioinformatics/btv325
-
(2015)
Bioinformatics
, vol.31
, pp. 2989-2998
-
-
Haghverdi, L.1
Buettner, F.2
Theis, F.J.3
-
22
-
-
84866953427
-
CEL-Seq: Single-cell RNA-Seq by multiplexed linear amplification
-
T. Hashimshony, F. Wagner, N. Sher, and I. Yanai CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification Cell Rep. 2 2012 666 673
-
(2012)
Cell Rep.
, vol.2
, pp. 666-673
-
-
Hashimshony, T.1
Wagner, F.2
Sher, N.3
Yanai, I.4
-
23
-
-
84925497456
-
Spatiotemporal transcriptomics reveals the evolutionary history of the endoderm germ layer
-
T. Hashimshony, M. Feder, M. Levin, B.K. Hall, and I. Yanai Spatiotemporal transcriptomics reveals the evolutionary history of the endoderm germ layer Nature 519 2015 219 222
-
(2015)
Nature
, vol.519
, pp. 219-222
-
-
Hashimshony, T.1
Feder, M.2
Levin, M.3
Hall, B.K.4
Yanai, I.5
-
24
-
-
0036713497
-
Representation is faithfully preserved in global cDNA amplified exponentially from sub-picogram quantities of mRNA
-
N.N. Iscove, M. Barbara, M. Gu, M. Gibson, C. Modi, and N. Winegarden Representation is faithfully preserved in global cDNA amplified exponentially from sub-picogram quantities of mRNA Nat. Biotechnol. 20 2002 940 943
-
(2002)
Nat. Biotechnol.
, vol.20
, pp. 940-943
-
-
Iscove, N.N.1
Barbara, M.2
Gu, M.3
Gibson, M.4
Modi, C.5
Winegarden, N.6
-
25
-
-
79959403670
-
Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq
-
S. Islam, U. Kjällquist, A. Moliner, P. Zajac, J.-B. Fan, P. Lönnerberg, and S. Linnarsson Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq Genome Res. 21 2011 1160 1167
-
(2011)
Genome Res.
, vol.21
, pp. 1160-1167
-
-
Islam, S.1
Kjällquist, U.2
Moliner, A.3
Zajac, P.4
Fan, J.-B.5
Lönnerberg, P.6
Linnarsson, S.7
-
26
-
-
84895069488
-
Quantitative single-cell RNA-seq with unique molecular identifiers
-
S. Islam, A. Zeisel, S. Joost, G. La Manno, P. Zajac, M. Kasper, P. Lönnerberg, and S. Linnarsson Quantitative single-cell RNA-seq with unique molecular identifiers Nat. Methods 11 2014 163 166
-
(2014)
Nat. Methods
, vol.11
, pp. 163-166
-
-
Islam, S.1
Zeisel, A.2
Joost, S.3
La Manno, G.4
Zajac, P.5
Kasper, M.6
Lönnerberg, P.7
Linnarsson, S.8
-
27
-
-
84893905629
-
Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types
-
D.A. Jaitin, E. Kenigsberg, H. Keren-Shaul, N. Elefant, F. Paul, I. Zaretsky, A. Mildner, N. Cohen, S. Jung, A. Tanay, and I. Amit Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types Science 343 2014 776 779
-
(2014)
Science
, vol.343
, pp. 776-779
-
-
Jaitin, D.A.1
Kenigsberg, E.2
Keren-Shaul, H.3
Elefant, N.4
Paul, F.5
Zaretsky, I.6
Mildner, A.7
Cohen, N.8
Jung, S.9
Tanay, A.10
Amit, I.11
-
28
-
-
84908338722
-
Genome-wide RNA Tomography in the zebrafish embryo
-
J.P. Junker, E.S. Noël, V. Guryev, K.A. Peterson, G. Shah, J. Huisken, A.P. McMahon, E. Berezikov, J. Bakkers, and A. van Oudenaarden Genome-wide RNA Tomography in the zebrafish embryo Cell 159 2014 662 675
-
(2014)
Cell
, vol.159
, pp. 662-675
-
-
Junker, J.P.1
Noël, E.S.2
Guryev, V.3
Peterson, K.A.4
Shah, G.5
Huisken, J.6
McMahon, A.P.7
Berezikov, E.8
Bakkers, J.9
Van Oudenaarden, A.10
-
29
-
-
84903574951
-
Bayesian approach to single-cell differential expression analysis
-
P.V. Kharchenko, L. Silberstein, and D.T. Scadden Bayesian approach to single-cell differential expression analysis Nat. Methods 11 2014 740 742
-
(2014)
Nat. Methods
, vol.11
, pp. 740-742
-
-
Kharchenko, P.V.1
Silberstein, L.2
Scadden, D.T.3
-
30
-
-
84856484968
-
Counting absolute numbers of molecules using unique molecular identifiers
-
T. Kivioja, A. Vähärautio, K. Karlsson, M. Bonke, M. Enge, S. Linnarsson, and J. Taipale Counting absolute numbers of molecules using unique molecular identifiers Nat. Methods 9 2012 72 74
-
(2012)
Nat. Methods
, vol.9
, pp. 72-74
-
-
Kivioja, T.1
Vähärautio, A.2
Karlsson, K.3
Bonke, M.4
Enge, M.5
Linnarsson, S.6
Taipale, J.7
-
31
-
-
0033551238
-
Comparative genomic hybridization, loss of heterozygosity, and DNA sequence analysis of single cells
-
C.A. Klein, O. Schmidt-Kittler, J.A. Schardt, K. Pantel, M.R. Speicher, and G. Riethmüller Comparative genomic hybridization, loss of heterozygosity, and DNA sequence analysis of single cells Proc. Natl. Acad. Sci. USA 96 1999 4494 4499
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 4494-4499
-
-
Klein, C.A.1
Schmidt-Kittler, O.2
Schardt, J.A.3
Pantel, K.4
Speicher, M.R.5
Riethmüller, G.6
-
32
-
-
84929684998
-
Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells
-
A.M. Klein, L. Mazutis, I. Akartuna, N. Tallapragada, A. Veres, V. Li, L. Peshkin, D.A. Weitz, and M.W. Kirschner Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells Cell 161 2015 1187 1201
-
(2015)
Cell
, vol.161
, pp. 1187-1201
-
-
Klein, A.M.1
Mazutis, L.2
Akartuna, I.3
Tallapragada, N.4
Veres, A.5
Li, V.6
Peshkin, L.7
Weitz, D.A.8
Kirschner, M.W.9
-
34
-
-
77949587649
-
Fast and accurate long-read alignment with Burrows-Wheeler transform
-
H. Li, and R. Durbin Fast and accurate long-read alignment with Burrows-Wheeler transform Bioinformatics 26 2010 589 595
-
(2010)
Bioinformatics
, vol.26
, pp. 589-595
-
-
Li, H.1
Durbin, R.2
-
35
-
-
84896739948
-
Single cell genomics: Advances and future perspectives
-
I.C. Macaulay, and T. Voet Single cell genomics: advances and future perspectives PLoS Genet. 10 2014 e1004126
-
(2014)
PLoS Genet.
, vol.10
, pp. e1004126
-
-
MacAulay, I.C.1
Voet, T.2
-
36
-
-
84929684999
-
Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets
-
E.Z. Macosko, A. Basu, R. Satija, J. Nemesh, K. Shekhar, M. Goldman, I. Tirosh, A.R. Bialas, N. Kamitaki, E.M. Martersteck, and et al. Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets Cell 161 2015 1202 1214
-
(2015)
Cell
, vol.161
, pp. 1202-1214
-
-
MacOsko, E.Z.1
Basu, A.2
Satija, R.3
Nemesh, J.4
Shekhar, K.5
Goldman, M.6
Tirosh, I.7
Bialas, A.R.8
Kamitaki, N.9
Martersteck, E.M.10
-
37
-
-
77956295988
-
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
-
A. McKenna, M. Hanna, E. Banks, A. Sivachenko, K. Cibulskis, A. Kernytsky, K. Garimella, D. Altshuler, S. Gabriel, M. Daly, and M.A. DePristo The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data Genome Res. 20 2010 1297 1303
-
(2010)
Genome Res.
, vol.20
, pp. 1297-1303
-
-
McKenna, A.1
Hanna, M.2
Banks, E.3
Sivachenko, A.4
Cibulskis, K.5
Kernytsky, A.6
Garimella, K.7
Altshuler, D.8
Gabriel, S.9
Daly, M.10
Depristo, M.A.11
-
38
-
-
84875404794
-
The UCSC Genome Browser database: Extensions and updates 2013
-
L.R. Meyer, A.S. Zweig, A.S. Hinrichs, D. Karolchik, R.M. Kuhn, M. Wong, C.A. Sloan, K.R. Rosenbloom, G. Roe, B. Rhead, and et al. The UCSC Genome Browser database: extensions and updates 2013 Nucleic Acids Res. 41 2013 D64 D69
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D64-D69
-
-
Meyer, L.R.1
Zweig, A.S.2
Hinrichs, A.S.3
Karolchik, D.4
Kuhn, R.M.5
Wong, M.6
Sloan, C.A.7
Rosenbloom, K.R.8
Roe, G.9
Rhead, B.10
-
39
-
-
84879346704
-
A robust method to analyze copy number alterations of less than 100 kb in single cells using oligonucleotide array CGH
-
B. Möhlendick, C. Bartenhagen, B. Behrens, E. Honisch, K. Raba, W.T. Knoefel, and N.H. Stoecklein A robust method to analyze copy number alterations of less than 100 kb in single cells using oligonucleotide array CGH PLoS ONE 8 2013 e67031
-
(2013)
PLoS ONE
, vol.8
, pp. e67031
-
-
Möhlendick, B.1
Bartenhagen, C.2
Behrens, B.3
Honisch, E.4
Raba, K.5
Knoefel, W.T.6
Stoecklein, N.H.7
-
40
-
-
84859641038
-
Using gene expression noise to understand gene regulation
-
B. Munsky, G. Neuert, and A. van Oudenaarden Using gene expression noise to understand gene regulation Science 336 2012 183 187
-
(2012)
Science
, vol.336
, pp. 183-187
-
-
Munsky, B.1
Neuert, G.2
Van Oudenaarden, A.3
-
41
-
-
84863892710
-
Human aneuploidy: Mechanisms and new insights into an age-old problem
-
S.I. Nagaoka, T.J. Hassold, and P.A. Hunt Human aneuploidy: mechanisms and new insights into an age-old problem Nat. Rev. Genet. 13 2012 493 504
-
(2012)
Nat. Rev. Genet.
, vol.13
, pp. 493-504
-
-
Nagaoka, S.I.1
Hassold, T.J.2
Hunt, P.A.3
-
42
-
-
79953766940
-
Tumour evolution inferred by single-cell sequencing
-
N. Navin, J. Kendall, J. Troge, P. Andrews, L. Rodgers, J. McIndoo, K. Cook, A. Stepansky, D. Levy, D. Esposito, and et al. Tumour evolution inferred by single-cell sequencing Nature 472 2011 90 94
-
(2011)
Nature
, vol.472
, pp. 90-94
-
-
Navin, N.1
Kendall, J.2
Troge, J.3
Andrews, P.4
Rodgers, L.5
McIndoo, J.6
Cook, K.7
Stepansky, A.8
Levy, D.9
Esposito, D.10
-
44
-
-
84931084251
-
Reconstructing gene regulatory dynamics from high-dimensional single-cell snapshot data
-
A. Ocone, L. Haghverdi, N.S. Mueller, and F.J. Theis Reconstructing gene regulatory dynamics from high-dimensional single-cell snapshot data Bioinformatics 31 2015 i89 i96
-
(2015)
Bioinformatics
, vol.31
, pp. i89-i96
-
-
Ocone, A.1
Haghverdi, L.2
Mueller, N.S.3
Theis, F.J.4
-
45
-
-
84933054617
-
Genome-wide maps of recombination and chromosome segregation in human oocytes and embryos show selection for maternal recombination rates
-
C.S. Ottolini, L.J. Newnham, A. Capalbo, S.A. Natesan, H.A. Joshi, D. Cimadomo, D.K. Griffin, K. Sage, M.C. Summers, A.R. Thornhill, and et al. Genome-wide maps of recombination and chromosome segregation in human oocytes and embryos show selection for maternal recombination rates Nat. Genet. 47 2015 727 735
-
(2015)
Nat. Genet.
, vol.47
, pp. 727-735
-
-
Ottolini, C.S.1
Newnham, L.J.2
Capalbo, A.3
Natesan, S.A.4
Joshi, H.A.5
Cimadomo, D.6
Griffin, D.K.7
Sage, K.8
Summers, M.C.9
Thornhill, A.R.10
-
46
-
-
84872194966
-
Two methods for full-length RNA sequencing for low quantities of cells and single cells
-
X. Pan, R.E. Durrett, H. Zhu, Y. Tanaka, Y. Li, X. Zi, S.L. Marjani, G. Euskirchen, C. Ma, R.H. Lamotte, and et al. Two methods for full-length RNA sequencing for low quantities of cells and single cells Proc. Natl. Acad. Sci. USA 110 2013 594 599
-
(2013)
Proc. Natl. Acad. Sci. USA
, vol.110
, pp. 594-599
-
-
Pan, X.1
Durrett, R.E.2
Zhu, H.3
Tanaka, Y.4
Li, Y.5
Zi, X.6
Marjani, S.L.7
Euskirchen, G.8
Ma, C.9
Lamotte, R.H.10
-
47
-
-
84902668801
-
Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma
-
A.P. Patel, I. Tirosh, J.J. Trombetta, A.K. Shalek, S.M. Gillespie, H. Wakimoto, D.P. Cahill, B.V. Nahed, W.T. Curry, R.L. Martuza, and et al. Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma Science 344 2014 1396 1401
-
(2014)
Science
, vol.344
, pp. 1396-1401
-
-
Patel, A.P.1
Tirosh, I.2
Trombetta, J.J.3
Shalek, A.K.4
Gillespie, S.M.5
Wakimoto, H.6
Cahill, D.P.7
Nahed, B.V.8
Curry, W.T.9
Martuza, R.L.10
-
48
-
-
84887101406
-
Smart-seq2 for sensitive full-length transcriptome profiling in single cells
-
S. Picelli, Å.K. Björklund, O.R. Faridani, S. Sagasser, G. Winberg, and R. Sandberg Smart-seq2 for sensitive full-length transcriptome profiling in single cells Nat. Methods 10 2013 1096 1098
-
(2013)
Nat. Methods
, vol.10
, pp. 1096-1098
-
-
Picelli, S.1
Björklund, Å.K.2
Faridani, O.R.3
Sagasser, S.4
Winberg, G.5
Sandberg, R.6
-
49
-
-
84922321862
-
Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex
-
A.A. Pollen, T.J. Nowakowski, J. Shuga, X. Wang, A.A. Leyrat, J.H. Lui, N. Li, L. Szpankowski, B. Fowler, P. Chen, and et al. Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex Nat. Biotechnol. 32 2014 1053 1058
-
(2014)
Nat. Biotechnol.
, vol.32
, pp. 1053-1058
-
-
Pollen, A.A.1
Nowakowski, T.J.2
Shuga, J.3
Wang, X.4
Leyrat, A.A.5
Lui, J.H.6
Li, N.7
Szpankowski, L.8
Fowler, B.9
Chen, P.10
-
50
-
-
33748994704
-
Stochastic mRNA synthesis in mammalian cells
-
A. Raj, C.S. Peskin, D. Tranchina, D.Y. Vargas, and S. Tyagi Stochastic mRNA synthesis in mammalian cells PLoS Biol. 4 2006 e309
-
(2006)
PLoS Biol.
, vol.4
, pp. e309
-
-
Raj, A.1
Peskin, C.S.2
Tranchina, D.3
Vargas, D.Y.4
Tyagi, S.5
-
51
-
-
53349161901
-
Imaging individual mRNA molecules using multiple singly labeled probes
-
A. Raj, P. van den Bogaard, S.A. Rifkin, A. van Oudenaarden, and S. Tyagi Imaging individual mRNA molecules using multiple singly labeled probes Nat. Methods 5 2008 877 879
-
(2008)
Nat. Methods
, vol.5
, pp. 877-879
-
-
Raj, A.1
Van Den Bogaard, P.2
Rifkin, S.A.3
Van Oudenaarden, A.4
Tyagi, S.5
-
52
-
-
84864880991
-
Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells
-
D. Ramsköld, S. Luo, Y.-C. Wang, R. Li, Q. Deng, O.R. Faridani, G.A. Daniels, I. Khrebtukova, J.F. Loring, L.C. Laurent, and et al. Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells Nat. Biotechnol. 30 2012 777 782
-
(2012)
Nat. Biotechnol.
, vol.30
, pp. 777-782
-
-
Ramsköld, D.1
Luo, S.2
Wang, Y.-C.3
Li, R.4
Deng, Q.5
Faridani, O.R.6
Daniels, G.A.7
Khrebtukova, I.8
Loring, J.F.9
Laurent, L.C.10
-
53
-
-
2942718723
-
Control of stochasticity in eukaryotic gene expression
-
J.M. Raser, and E.K. O'Shea Control of stochasticity in eukaryotic gene expression Science 304 2004 1811 1814
-
(2004)
Science
, vol.304
, pp. 1811-1814
-
-
Raser, J.M.1
O'Shea, E.K.2
-
55
-
-
84876085773
-
Quartz-Seq: A highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity
-
Y. Sasagawa, I. Nikaido, T. Hayashi, H. Danno, K.D. Uno, T. Imai, and H.R. Ueda Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity Genome Biol. 14 2013 R31
-
(2013)
Genome Biol.
, vol.14
, pp. R31
-
-
Sasagawa, Y.1
Nikaido, I.2
Hayashi, T.3
Danno, H.4
Uno, K.D.5
Imai, T.6
Ueda, H.R.7
-
56
-
-
84878997106
-
Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells
-
A.K. Shalek, R. Satija, X. Adiconis, R.S. Gertner, J.T. Gaublomme, R. Raychowdhury, S. Schwartz, N. Yosef, C. Malboeuf, D. Lu, and et al. Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells Nature 498 2013 236 240
-
(2013)
Nature
, vol.498
, pp. 236-240
-
-
Shalek, A.K.1
Satija, R.2
Adiconis, X.3
Gertner, R.S.4
Gaublomme, J.T.5
Raychowdhury, R.6
Schwartz, S.7
Yosef, N.8
Malboeuf, C.9
Lu, D.10
-
57
-
-
84903185013
-
Single-cell RNA-seq reveals dynamic paracrine control of cellular variation
-
A.K. Shalek, R. Satija, J. Shuga, J.J. Trombetta, D. Gennert, D. Lu, P. Chen, R.S. Gertner, J.T. Gaublomme, N. Yosef, and et al. Single-cell RNA-seq reveals dynamic paracrine control of cellular variation Nature 510 2014 363 369
-
(2014)
Nature
, vol.510
, pp. 363-369
-
-
Shalek, A.K.1
Satija, R.2
Shuga, J.3
Trombetta, J.J.4
Gennert, D.5
Lu, D.6
Chen, P.7
Gertner, R.S.8
Gaublomme, J.T.9
Yosef, N.10
-
58
-
-
78951470515
-
Origins of regulated cell-to-cell variability
-
B. Snijder, and L. Pelkmans Origins of regulated cell-to-cell variability Nat. Rev. Mol. Cell Biol. 12 2011 119 125
-
(2011)
Nat. Rev. Mol. Cell Biol.
, vol.12
, pp. 119-125
-
-
Snijder, B.1
Pelkmans, L.2
-
59
-
-
67349146589
-
MRNA-Seq whole-transcriptome analysis of a single cell
-
F. Tang, C. Barbacioru, Y. Wang, E. Nordman, C. Lee, N. Xu, X. Wang, J. Bodeau, B.B. Tuch, A. Siddiqui, and et al. mRNA-Seq whole-transcriptome analysis of a single cell Nat. Methods 6 2009 377 382
-
(2009)
Nat. Methods
, vol.6
, pp. 377-382
-
-
Tang, F.1
Barbacioru, C.2
Wang, Y.3
Nordman, E.4
Lee, C.5
Xu, N.6
Wang, X.7
Bodeau, J.8
Tuch, B.B.9
Siddiqui, A.10
-
60
-
-
77956412152
-
Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNA-Seq analysis
-
F. Tang, C. Barbacioru, S. Bao, C. Lee, E. Nordman, X. Wang, K. Lao, and M.A. Surani Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNA-Seq analysis Cell Stem Cell 6 2010 468 478
-
(2010)
Cell Stem Cell
, vol.6
, pp. 468-478
-
-
Tang, F.1
Barbacioru, C.2
Bao, S.3
Lee, C.4
Nordman, E.5
Wang, X.6
Lao, K.7
Surani, M.A.8
-
61
-
-
77952123055
-
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
-
C. Trapnell, B.A. Williams, G. Pertea, A. Mortazavi, G. Kwan, M.J. van Baren, S.L. Salzberg, B.J. Wold, and L. Pachter Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation Nat. Biotechnol. 28 2010 511 515
-
(2010)
Nat. Biotechnol.
, vol.28
, pp. 511-515
-
-
Trapnell, C.1
Williams, B.A.2
Pertea, G.3
Mortazavi, A.4
Kwan, G.5
Van Baren, M.J.6
Salzberg, S.L.7
Wold, B.J.8
Pachter, L.9
-
62
-
-
84900873950
-
The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells
-
C. Trapnell, D. Cacchiarelli, J. Grimsby, P. Pokharel, S. Li, M. Morse, N.J. Lennon, K.J. Livak, T.S. Mikkelsen, and J.L. Rinn The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells Nat. Biotechnol. 32 2014 381 386
-
(2014)
Nat. Biotechnol.
, vol.32
, pp. 381-386
-
-
Trapnell, C.1
Cacchiarelli, D.2
Grimsby, J.3
Pokharel, P.4
Li, S.5
Morse, M.6
Lennon, N.J.7
Livak, K.J.8
Mikkelsen, T.S.9
Rinn, J.L.10
-
63
-
-
84900529199
-
Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq
-
B. Treutlein, D.G. Brownfield, A.R. Wu, N.F. Neff, G.L. Mantalas, F.H. Espinoza, T.J. Desai, M.A. Krasnow, and S.R. Quake Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq Nature 509 2014 371 375
-
(2014)
Nature
, vol.509
, pp. 371-375
-
-
Treutlein, B.1
Brownfield, D.G.2
Wu, A.R.3
Neff, N.F.4
Mantalas, G.L.5
Espinoza, F.H.6
Desai, T.J.7
Krasnow, M.A.8
Quake, S.R.9
-
64
-
-
19544387813
-
Sorting points into neighborhoods (SPIN): Data analysis and visualization by ordering distance matrices
-
D. Tsafrir, I. Tsafrir, L. Ein-Dor, O. Zuk, D.A. Notterman, and E. Domany Sorting points into neighborhoods (SPIN): data analysis and visualization by ordering distance matrices Bioinformatics 21 2005 2301 2308
-
(2005)
Bioinformatics
, vol.21
, pp. 2301-2308
-
-
Tsafrir, D.1
Tsafrir, I.2
Ein-Dor, L.3
Zuk, O.4
Notterman, D.A.5
Domany, E.6
-
65
-
-
84876056588
-
Genome-wide copy number profiling of single cells in S-phase reveals DNA-replication domains
-
N. Van der Aa, J. Cheng, L. Mateiu, M. Zamani Esteki, P. Kumar, E. Dimitriadou, E. Vanneste, Y. Moreau, J.R. Vermeesch, and T. Voet Genome-wide copy number profiling of single cells in S-phase reveals DNA-replication domains Nucleic Acids Res. 41 2013 e66
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. e66
-
-
Van Der Aa, N.1
Cheng, J.2
Mateiu, L.3
Zamani Esteki, M.4
Kumar, P.5
Dimitriadou, E.6
Vanneste, E.7
Moreau, Y.8
Vermeesch, J.R.9
Voet, T.10
-
67
-
-
34147104969
-
A faster circular binary segmentation algorithm for the analysis of array CGH data
-
E.S. Venkatraman, and A.B. Olshen A faster circular binary segmentation algorithm for the analysis of array CGH data Bioinformatics 23 2007 657 663
-
(2007)
Bioinformatics
, vol.23
, pp. 657-663
-
-
Venkatraman, E.S.1
Olshen, A.B.2
-
68
-
-
84880213158
-
Single-cell paired-end genome sequencing reveals structural variation per cell cycle
-
T. Voet, P. Kumar, P. Van Loo, S.L. Cooke, J. Marshall, M.-L. Lin, M. Zamani Esteki, N. Van der Aa, L. Mateiu, D.J. McBride, and et al. Single-cell paired-end genome sequencing reveals structural variation per cell cycle Nucleic Acids Res. 41 2013 6119 6138
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. 6119-6138
-
-
Voet, T.1
Kumar, P.2
Van Loo, P.3
Cooke, S.L.4
Marshall, J.5
Lin, M.-L.6
Zamani Esteki, M.7
Van Der Aa, N.8
Mateiu, L.9
McBride, D.J.10
-
69
-
-
84864258558
-
Genome-wide single-cell analysis of recombination activity and de novo mutation rates in human sperm
-
J. Wang, H.C. Fan, B. Behr, and S.R. Quake Genome-wide single-cell analysis of recombination activity and de novo mutation rates in human sperm Cell 150 2012 402 412
-
(2012)
Cell
, vol.150
, pp. 402-412
-
-
Wang, J.1
Fan, H.C.2
Behr, B.3
Quake, S.R.4
-
70
-
-
84906238686
-
Clonal evolution in breast cancer revealed by single nucleus genome sequencing
-
Y. Wang, J. Waters, M.L. Leung, A. Unruh, W. Roh, X. Shi, K. Chen, P. Scheet, S. Vattathil, H. Liang, and et al. Clonal evolution in breast cancer revealed by single nucleus genome sequencing Nature 512 2014 155 160
-
(2014)
Nature
, vol.512
, pp. 155-160
-
-
Wang, Y.1
Waters, J.2
Leung, M.L.3
Unruh, A.4
Roh, W.5
Shi, X.6
Chen, K.7
Scheet, P.8
Vattathil, S.9
Liang, H.10
-
71
-
-
84924565530
-
Brain structure. Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq
-
A. Zeisel, A.B. Muñoz-Manchado, S. Codeluppi, P. Lönnerberg, G. La Manno, A. Juréus, S. Marques, H. Munguba, L. He, C. Betsholtz, and et al. Brain structure. Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq Science 347 2015 1138 1142
-
(2015)
Science
, vol.347
, pp. 1138-1142
-
-
Zeisel, A.1
Muñoz-Manchado, A.B.2
Codeluppi, S.3
Lönnerberg, P.4
La Manno, G.5
Juréus, A.6
Marques, S.7
Munguba, H.8
He, L.9
Betsholtz, C.10
-
72
-
-
0026755807
-
Whole genome amplification from a single cell: Implications for genetic analysis
-
L. Zhang, X. Cui, K. Schmitt, R. Hubert, W. Navidi, and N. Arnheim Whole genome amplification from a single cell: implications for genetic analysis Proc. Natl. Acad. Sci. USA 89 1992 5847 5851
-
(1992)
Proc. Natl. Acad. Sci. USA
, vol.89
, pp. 5847-5851
-
-
Zhang, L.1
Cui, X.2
Schmitt, K.3
Hubert, R.4
Navidi, W.5
Arnheim, N.6
-
73
-
-
84872766258
-
A single cell level based method for copy number variation analysis by low coverage massively parallel sequencing
-
C. Zhang, C. Zhang, S. Chen, X. Yin, X. Pan, G. Lin, Y. Tan, K. Tan, Z. Xu, P. Hu, and et al. A single cell level based method for copy number variation analysis by low coverage massively parallel sequencing PLoS ONE 8 2013 e54236
-
(2013)
PLoS ONE
, vol.8
, pp. e54236
-
-
Zhang, C.1
Zhang, C.2
Chen, S.3
Yin, X.4
Pan, X.5
Lin, G.6
Tan, Y.7
Tan, K.8
Xu, Z.9
Hu, P.10
-
74
-
-
84886811866
-
Computational tools for copy number variation (CNV) detection using next-generation sequencing data: Features and perspectives
-
M. Zhao, Q. Wang, Q. Wang, P. Jia, and Z. Zhao Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives BMC Bioinformatics 14 Suppl 11 2013 S1
-
(2013)
BMC Bioinformatics
, vol.14
, pp. S1
-
-
Zhao, M.1
Wang, Q.2
Wang, Q.3
Jia, P.4
Zhao, Z.5
-
75
-
-
84871461434
-
Genome-wide detection of single-nucleotide and copy-number variations of a single human cell
-
C. Zong, S. Lu, A.R. Chapman, and X.S. Xie Genome-wide detection of single-nucleotide and copy-number variations of a single human cell Science 338 2012 1622 1626
-
(2012)
Science
, vol.338
, pp. 1622-1626
-
-
Zong, C.1
Lu, S.2
Chapman, A.R.3
Xie, X.S.4
|