-
1
-
-
84878997106
-
Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells
-
Shalek, A.K., Satija, R., Adiconis, X., Gertner, R.S., Gaublomme, J.T., Raychowdhury, R., Schwartz, S., Yosef, N., Malboeuf, C., Lu, D. et al. (2013) Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells. Nature, 498, 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
-
2
-
-
79953267923
-
Profiling metabolites, and peptides in single cells
-
Rubakhin, S.S., Romanova, E.V., Nemes, P. and Sweedler, J.V. (2011) Profiling metabolites and peptides in single cells. Nat. Methods, 8, S20-S29.
-
(2011)
Nat. Methods
, vol.8
-
-
Rubakhin, S.S.1
Romanova, E.V.2
Nemes, P.3
Sweedler, J.V.4
-
3
-
-
77749323185
-
RNA-Seq analysis to capture the transcriptome landscape of a single cell
-
Tang, F.C., Barbacioru, C., Nordman, E., Li, B., Xu, N.L., Bashkirov, V.I., Lao, K.Q., and Surani, M.A. (2010) RNA-Seq analysis to capture the transcriptome landscape of a single cell. Nat. Protoc., 5, 516-535.
-
(2010)
Nat. Protoc.
, vol.5
, pp. 516-535
-
-
Tang, F.C.1
Barbacioru, C.2
Nordman, E.3
Li, B.4
Xu, N.L.5
Bashkirov, V.I.6
Lao, K.Q.7
Surani, M.A.8
-
4
-
-
84863697677
-
From single cells to deep phenotypes in cancer
-
Bendall, S.C., and Nolan, G.P. (2012) From single cells to deep phenotypes in cancer. Nat. Biotechnol., 30, 639-647.
-
(2012)
Nat. Biotechnol.
, vol.30
, pp. 639-647
-
-
Bendall, S.C.1
Nolan, G.P.2
-
5
-
-
80052174976
-
High-throughput microfluidic single-cell RT-qPCR
-
White, A.K., VanInsberghe, M., Petriv, O.I., Hamidi, M., Sikorski, D., Marra, M.A., Piret, J., Aparicio, S., and Hansen, C.L. (2011) High-throughput microfluidic single-cell RT-qPCR. Proc. Natl Acad. Sci. USA, 108, 13999- 14004.
-
(2011)
Proc. Natl Acad. Sci. USA
, vol.108
-
-
White, A.K.1
VanInsberghe, M.2
Petriv, O.I.3
Hamidi, M.4
Sikorski, D.5
Marra, M.A.6
Piret, J.7
Aparicio, S.8
Hansen, C.L.9
-
6
-
-
84872690870
-
An Oct4-Sall4-Nanog network controls developmental progression in the pre-implantation mouse embryo
-
Tan, M.H., Au, K.F., Leong, D.E., Foygel, K., Wong, W.H., and Yao, M.W. (2013) An Oct4-Sall4-Nanog network controls developmental progression in the pre-implantation mouse embryo. Mol. Syst. Biol., 9, 632.
-
(2013)
Mol. Syst. Biol.
, vol.9
, pp. 632
-
-
Tan, M.H.1
Au, K.F.2
Leong, D.E.3
Foygel, K.4
Wong, W.H.5
Yao, M.W.6
-
7
-
-
84882582801
-
Single-cell gene expression analysis revealsgenetic associations masked in whole-tissue experiments
-
doi:10.1038/nbt.2642.
-
Wills, Q.F., Livak, K.J., Tipping, A.J., Enver, T., Goldson, A.J., Sexton, D.W., and Holmes, C. (2013) Single-cell gene expression analysis revealsgenetic associations masked in whole-tissue experiments. Nat. Biotechnol., doi:10.1038/nbt.2642.
-
(2013)
Nat. Biotechnol.
-
-
Wills, Q.F.1
Livak, K.J.2
Tipping, A.J.3
Enver, T.4
Goldson, A.J.5
Sexton, D.W.6
Holmes, C.7
-
8
-
-
84856499339
-
Single-cell protein analysis
-
Wu, M., and Singh, A.K. (2012) Single-cell protein analysis. Curr. Opin. Biotech., 23, 83-88.
-
(2012)
Curr. Opin. Biotech.
, vol.23
, pp. 83-88
-
-
Wu, M.1
Singh, A.K.2
-
9
-
-
84880937170
-
Quantitative single cell, and single molecule proteomics for clinical studies
-
Willison, K.R., and Klug, D.R. (2013) Quantitative single cell, and single molecule proteomics for clinical studies. Curr. Opin. Biotechnol., http://dx.doi.org/10.1016/j.copbio.2013.06.001.
-
(2013)
Curr. Opin. Biotechnol.
-
-
Willison, K.R.1
Klug, D.R.2
-
10
-
-
84872270965
-
Progress toward single cell metabolomics
-
Rubakhin, S.S., Lanni, E.J., and Sweedler, J.V. (2013) Progress toward single cell metabolomics. Curr. Opin. Biotechnol., 24, 95-104.
-
(2013)
Curr. Opin. Biotechnol.
, vol.24
, pp. 95-104
-
-
Rubakhin, S.S.1
Lanni, E.J.2
Sweedler, J.V.3
-
11
-
-
79960070912
-
Preparation of next-generation sequencing libraries using Nextera technology: simultaneous DNA fragmentation, and adaptor tagging by in vitro transposition
-
Caruccio, N. (2011) Preparation of next-generation sequencing libraries using Nextera technology: simultaneous DNA fragmentation, and adaptor tagging by in vitro transposition. Methods Mol. Biol., 733, 241-255.
-
(2011)
Methods Mol. Biol.
, vol.733
, pp. 241-255
-
-
Caruccio, N.1
-
12
-
-
79953288433
-
Development, and applications of single-cell transcriptome analysis
-
Tang, F., Lao, K., and Surani, M.A. (2011) Development, and applications of single-cell transcriptome analysis. Nat. Methods, 8, S6-S11.
-
(2011)
Nat. Methods
, vol.8
-
-
Tang, F.1
Lao, K.2
Surani, M.A.3
-
13
-
-
84872264658
-
Investigating transcriptional states at single-cell-resolution
-
Tischler, J., and Surani, M.A. (2013) Investigating transcriptional states at single-cell-resolution. Curr. Opin. Biotechnol., 24, 69-78.
-
(2013)
Curr. Opin. Biotechnol.
, vol.24
, pp. 69-78
-
-
Tischler, J.1
Surani, M.A.2
-
14
-
-
84864880991
-
Full-length mRNA-Seq from single-cell levels ofRNAand individual circulating tumor cells
-
Ramskold, D., Luo, S.,Wang,Y.C., Li, R., Deng, Q., Faridani, O.R., Daniels, G.A., Khrebtukova, I., Loring, J.F., Laurent, L.C., et al. (2012) Full-length mRNA-Seq from single-cell levels ofRNAand individual circulating tumor cells. Nat. Biotechnol., 30, 777-782.
-
(2012)
Nat. Biotechnol.
, vol.30
, pp. 777-782
-
-
Ramskold, 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
-
15
-
-
0035046755
-
Reverse transcriptase template switching: a SMART approach for full-length cDNA library construction
-
Zhu, Y.Y., Machleder, E.M., Chenchik, A., Li, R., and Siebert, P.D. (2001) Reverse transcriptase template switching: a SMART approach for full-length cDNA library construction. Biotechniques, 30, 892-897.
-
(2001)
Biotechniques
, vol.30
, pp. 892-897
-
-
Zhu, Y.Y.1
Machleder, E.M.2
Chenchik, A.3
Li, R.4
Siebert, P.D.5
-
16
-
-
0038006781
-
Gene expression differences in quiescent versus regenerating hair cells of avian sensory epithelia: implications forhumanhearing, and balance disorders
-
Hawkins, R.D., Bashiardes, S., Helms, C.A., Hu, L., Saccone, N.L., Warchol, M.E., and Lovett, M. (2003) Gene expression differences in quiescent versus regenerating hair cells of avian sensory epithelia: implications forhumanhearing, and balance disorders.Hum.Mol. Genet., 12, 1261-1272.
-
(2003)
Hum.Mol. Genet.
, vol.12
, pp. 1261-1272
-
-
Hawkins, R.D.1
Bashiardes, S.2
Helms, C.A.3
Hu, L.4
Saccone, N.L.5
Warchol, M.E.6
Lovett, M.7
-
17
-
-
35048862372
-
Toward a systems biology of mouse inner ear organogenesis: gene expression pathways, patterns, and network analysis
-
Sajan, S.A., Warchol, M.E., and Lovett, M. (2007) Toward a systems biology of mouse inner ear organogenesis: gene expression pathways, patterns, and network analysis. Genetics, 177, 631-653.
-
(2007)
Genetics
, vol.177
, pp. 631-653
-
-
Sajan, S.A.1
Warchol, M.E.2
Lovett, M.3
-
18
-
-
33744957995
-
Molecular properties of adult mouse gastric, and intestinal epithelial progenitors in their niches
-
Giannakis, M., Stappenbeck, T.S., Mills, J.C., Leip, D.G., Lovett, M., Clifton, S.W., Ippolito, J.E., Glasscock, J.I., Arumugam, M., Brent, M.R., et al. (2006) Molecular properties of adult mouse gastric, and intestinal epithelial progenitors in their niches. J. Biol. Chem., 281, 11292-11300.
-
(2006)
J. Biol. Chem.
, vol.281
, pp. 11292-11300
-
-
Giannakis, M.1
Stappenbeck, T.S.2
Mills, J.C.3
Leip, D.G.4
Lovett, M.5
Clifton, S.W.6
Ippolito, J.E.7
Glasscock, J.I.8
Arumugam, M.9
Brent, M.R.10
-
19
-
-
79952607358
-
Identification of direct downstream targets of Dlx5 during early inner ear development
-
Sajan, S.A., Rubenstein, J.L., Warchol, M.E., and Lovett, M. (2011) Identification of direct downstream targets of Dlx5 during early inner ear development. Hum. Mol. Genet., 20, 1262-1273.
-
(2011)
Hum. Mol. Genet.
, vol.20
, pp. 1262-1273
-
-
Sajan, S.A.1
Rubenstein, J.L.2
Warchol, M.E.3
Lovett, M.4
-
20
-
-
9444254040
-
SMART amplification combined with cDNA size fractionation in order to obtain large full-length clones
-
The German cDNA Consortium,
-
Wellenreuther, R., Schupp, I., Poustka, A., and Wiemann, S., and The German cDNA Consortium (2004) SMART amplification combined with cDNA size fractionation in order to obtain large full-length clones. BMC Genomics, 5, 36.
-
(2004)
BMC Genomics
, vol.5
, pp. 36
-
-
Wellenreuther, R.1
Schupp, I.2
Poustka, A.3
Wiemann, S.4
-
21
-
-
77951643590
-
Identifying single-cell molecular programs by stochastic profiling
-
Janes, K.A., Wang, C.C., Holmberg, K.J., Cabral, K., and Brugge, J.S. (2010) Identifying single-cell molecular programs by stochastic profiling. Nat. Methods, 7, 311-317.
-
(2010)
Nat. Methods
, vol.7
, pp. 311-317
-
-
Janes, K.A.1
Wang, C.C.2
Holmberg, K.J.3
Cabral, K.4
Brugge, J.S.5
-
22
-
-
79951551684
-
Genomewide characterization of non-polyadenylated RNAs
-
Yang, L., Duff, M.O., Graveley, B.R., Carmichael, G.G., and Chen, L.L. (2011) Genomewide characterization of non-polyadenylated RNAs. Genome Biol., 12, R16.
-
(2011)
Genome Biol.
, vol.12
-
-
Yang, L.1
Duff, M.O.2
Graveley, B.R.3
Carmichael, G.G.4
Chen, L.L.5
-
23
-
-
32644439132
-
MicroRNA expression profiling of single whole embryonic stem cells
-
Tang, F.C., Hajkova, P., Barton, S.C., Lao, K.Q., and Surani, M.A. (2006) MicroRNA expression profiling of single whole embryonic stem cells. Nucl. Acid. Res., 34, e9.
-
(2006)
Nucl. Acid. Res.
, vol.34
-
-
Tang, F.C.1
Hajkova, P.2
Barton, S.C.3
Lao, K.Q.4
Surani, M.A.5
-
24
-
-
77952367798
-
Widespread transcription at neuronal activity-regulated enhancers
-
Kim, T.K., Hemberg, M., Gray, J.M., Costa, A.M., Bear, D.M., Wu, J., Harmin, D.A., Laptewicz, M., Barbara-Haley, K., Kuersten, S., et al. (2010) Widespread transcription at neuronal activity-regulated enhancers. Nature, 465, 182-187.
-
(2010)
Nature
, vol.465
, pp. 182-187
-
-
Kim, T.K.1
Hemberg, M.2
Gray, J.M.3
Costa, A.M.4
Bear, D.M.5
Wu, J.6
Harmin, D.A.7
Laptewicz, M.8
Barbara-Haley, K.9
Kuersten, S.10
-
25
-
-
18344396798
-
Comprehensive human genome amplification using multiple displacement amplification
-
Dean, F.D., Hosono, S., Fang, L., Wu, X., Faruqi, F., Bray-Ward, P., Sun, Z., Zong, Q., Du, Y., Du, J., et al. (2002) Comprehensive human genome amplification using multiple displacement amplification. Proc. Natl Acad. Sci. USA, 99, 5261-5266.
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.99
, pp. 5261-5266
-
-
Dean, F.D.1
Hosono, S.2
Fang, L.3
Wu, X.4
Faruqi, F.5
Bray-Ward, P.6
Sun, Z.7
Zong, Q.8
Du, Y.9
Du, J.10
-
26
-
-
84875160584
-
Single-cell sequencing in its prime
-
Lasken, R.S. (2013) Single-cell sequencing in its prime. Nat. Biotechnol., 31, 211-212.
-
(2013)
Nat. Biotechnol.
, vol.31
, pp. 211-212
-
-
Lasken, R.S.1
-
27
-
-
48349105094
-
Impact of whole genome amplification on analysis of copy number variants
-
Pugh, T.J., Delaney, A.D., Farnoud, N., Flibotte, S., Griffith, M., Li, H.I., Qian, H., Farinha, P., Gascoyne, R.D., and Marra, M.A. (2008) Impact of whole genome amplification on analysis of copy number variants. Nucleic Acids Res., 36, e80.
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Pugh, T.J.1
Delaney, A.D.2
Farnoud, N.3
Flibotte, S.4
Griffith, M.5
Li, H.I.6
Qian, H.7
Farinha, P.8
Gascoyne, R.D.9
Marra, M.A.10
-
28
-
-
79953766940
-
Tumour evolution inferred by single-cell sequencing
-
Navin, N., Kendall, J., Troge, J., Andrews, P., Rodgers, L., McIndoo, J., Cook, K., Stepansky, A., Levy, D., Esposito, D., et al. (2011) Tumour evolution inferred by single-cell sequencing. Nature, 472, 90-119.
-
(2011)
Nature
, vol.472
, pp. 90-119
-
-
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
-
29
-
-
84871461434
-
Genome-wide detection of single-nucleotide, and copy-number variations of a singlehuman cell
-
Zong, C., Lu, S., Chapman, A.R., and Xie, X.S. (2012) Genome-wide detection of single-nucleotide, and copy-number variations of a singlehuman cell. Science, 338, 1622-1626.
-
(2012)
Science
, vol.338
, pp. 1622-1626
-
-
Zong, C.1
Lu, S.2
Chapman, A.R.3
Xie, X.S.4
-
30
-
-
79954614277
-
A high-throughput DNA methylation analysis of a single cell
-
Kantlehner, M., Kirchner, R., Hartmann, P., Ellwart, J.W., Alunni-Fabbroni, M., and Schumacher, A. (2011) A high-throughput DNA methylation analysis of a single cell. Nucleic Acids Res., 39, e44.
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Kantlehner, M.1
Kirchner, R.2
Hartmann, P.3
Ellwart, J.W.4
Alunni-Fabbroni, M.5
Schumacher, A.6
-
31
-
-
34047116826
-
Distribution, silencing potential, and evolutionary impact of promoterDNAmethylation in the human genome
-
Weber, M. (2007) Distribution, silencing potential, and evolutionary impact of promoterDNAmethylation in the human genome. Nat. Genet., 39, 457-466.
-
(2007)
Nat. Genet.
, vol.39
, pp. 457-466
-
-
Weber, M.1
-
32
-
-
84878915819
-
A systematic evaluation of whole genome amplification of bisulfite-modified DNA
-
Bundo, M., Sunaga, F., Ueda, J., Kasai, K., Kato, T., and Iwamoto, K. (2012) A systematic evaluation of whole genome amplification of bisulfite-modified DNA. Clin. Epigenetics, 4, 22.
-
(2012)
Clin. Epigenetics
, vol.4
, pp. 22
-
-
Bundo, M.1
Sunaga, F.2
Ueda, J.3
Kasai, K.4
Kato, T.5
Iwamoto, K.6
-
33
-
-
78751470921
-
Structure, and function of mammalian DNA methyltransferases
-
Jurkowska, R.Z., Jurkowski, T.P., and Jeltsch, A. (2011) Structure, and function of mammalian DNA methyltransferases. Chembiochem, 12, 206- 222.
-
(2011)
Chembiochem
, vol.12
-
-
Jurkowska, R.Z.1
Jurkowski, T.P.2
Jeltsch, A.3
-
34
-
-
54949091170
-
Interaction between DNMT1 and DNA replication reactions in the SV40 in vitro replication system
-
Shimamura, S., and Ishikawa, F. (2008) Interaction between DNMT1, and DNA replication reactions in the SV40 in vitro replication system. Cancer Sci., 99, 1960-1966.
-
(2008)
Cancer Sci.
, vol.99
, pp. 1960-1966
-
-
Shimamura, S.1
Ishikawa, F.2
-
35
-
-
57349097152
-
Dynamic proteomics of individual cancer cells in response to a drug
-
Cohen, A.A., Geva-Zatorsky, N., Eden, E., Frenkel-Morgenstern, M., Issaeva, I., Sigal, A., Milo, R., Cohen-Saidon, C., Liron, Y., Kam, Z., et al. (2008) Dynamic proteomics of individual cancer cells in response to a drug. Science, 322, 1511-1516.
-
(2008)
Science
, vol.322
, pp. 1511-1516
-
-
Cohen, A.A.1
Geva-Zatorsky, N.2
Eden, E.3
Frenkel-Morgenstern, M.4
Issaeva, I.5
Sigal, A.6
Milo, R.7
Cohen-Saidon, C.8
Liron, Y.9
Kam, Z.10
-
36
-
-
84880357794
-
Highly multiplexed single-cell analysis of formalin-fixed, paraffin-embedded cancer tissue
-
Gerdes, M.J., Sevinsky, C.J., Sood, A., Adak, S., Bello, M.O., Bordwell, A., Can, A., Corwin, A., Dinn, S., Filkins, R.J., et al.. (2013) Highly multiplexed single-cell analysis of formalin-fixed, paraffin-embedded cancer tissue. Proc. Natl Acad. Sci. USA, 29, 11982-11987.
-
(2013)
Proc. Natl Acad. Sci. USA
, vol.29
, pp. 11982-11987
-
-
Gerdes, M.J.1
Sevinsky, C.J.2
Sood, A.3
Adak, S.4
Bello, M.O.5
Bordwell, A.6
Can, A.7
Corwin, A.8
Dinn, S.9
Filkins, R.J.10
-
37
-
-
55249090260
-
Spatially selective sampling of single cells using optically trapped fusogenic emulsion droplets: a new single-cell proteomic tool
-
Lanigan, P.M., Chan, K., Ninkovic, T., Templer, R.H., French, P.M., de Mello, A.J., Willison, K.R., Parker, P.J., Neil, M.A., Ces, O., et al. (2008) Spatially selective sampling of single cells using optically trapped fusogenic emulsion droplets: a new single-cell proteomic tool. J. R. Soc. Interface, 5, S161-S168.
-
(2008)
J. R. Soc. Interface
, vol.5
-
-
Lanigan, P.M.1
Chan, K.2
Ninkovic, T.3
Templer, R.H.4
French, P.M.5
de Mello, A.J.6
Willison, K.R.7
Parker, P.J.8
Neil, M.A.9
Ces, O.10
-
38
-
-
79952668680
-
A first step towards practical single cell proteomics: a microfluidic antibody capture chip with TIRF detection
-
Salehi-Reyhani, A., Kaplinsky, J., Burgin, E., Novakova, M., Demello, A.J., Templer, R.H., Parker, P., Neil, M.A.A., Ces, O., French, P., et al. (2011) A first step towards practical single cell proteomics: a microfluidic antibody capture chip with TIRF detection. Lab Chip, 11, 1256-1261.
-
(2011)
Lab Chip
, vol.11
, pp. 1256-1261
-
-
Salehi-Reyhani, A.1
Kaplinsky, J.2
Burgin, E.3
Novakova, M.4
Demello, A.J.5
Templer, R.H.6
Parker, P.7
Neil, M.A.A.8
Ces, O.9
French, P.10
-
39
-
-
84856004321
-
Single-cell proteomic chip for profiling intracellular signaling pathways in single tumor cells
-
Shi, Q.H., Qin, L.D., Wei, W., Geng, F., Fan, R., Shin, Y.S., Guo, D.L.,Hood, L., Mischel, P.S., and Heath, J.R. (2012) Single-cell proteomic chip for profiling intracellular signaling pathways in single tumor cells. Proc. Natl Acad. Sci. USA, 109, 419-424.
-
(2012)
Proc. Natl Acad. Sci. USA
, vol.109
, pp. 419-424
-
-
Shi, Q.H.1
Qin, L.D.2
Wei, W.3
Geng, F.4
Fan, R.5
Shin, Y.S.6
Guo, D.L.7
Hood, L.8
Mischel, P.S.9
Heath, J.R.10
|