-
1
-
-
0037471175
-
Zipf's law in gene expression
-
Furusawa, C. & Kaneko, K. Zipf's law in gene expression. Phys Rev Lett 90, 088102 (2003).
-
(2003)
Phys Rev Lett
, vol.90
, pp. 088102
-
-
Furusawa, C.1
Kaneko, K.2
-
2
-
-
1642287458
-
Universality and flexibility in gene expression from bacteria to human
-
Ueda, H. R. et al. Universality and flexibility in gene expression from bacteria to human. Proc Natl Acad Sci U S A 101, 3765-3769 (2004).
-
(2004)
Proc Natl Acad Sci U S A
, vol.101
, pp. 3765-3769
-
-
Ueda, H.R.1
-
3
-
-
57749195712
-
RNA-Seq: A revolutionary tool for transcriptomics
-
Wang, Z., Gerstein, M. & Snyder, M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10, 57-63 (2009).
-
(2009)
Nat Rev Genet
, vol.10
, pp. 57-63
-
-
Wang, Z.1
Gerstein, M.2
Snyder, M.3
-
4
-
-
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
-
5
-
-
84869014474
-
Acomprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: A case study in Saccharomyces cerevisiae
-
Nookaew, I. et al. Acomprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae. Nucleic Acids Res 40, 10084-10097 (2012).
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 10084-10097
-
-
Nookaew, I.1
-
6
-
-
84866953427
-
CEL-Seq: Single-cell RNA-Seq by multiplexed linear amplification
-
Hashimshony, T., Wagner, F., Sher, N. & Yanai, I. CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification. Cell Rep 2, 666-673 (2012).
-
(2012)
Cell Rep
, vol.2
, pp. 666-673
-
-
Hashimshony, T.1
Wagner, F.2
Sher, N.3
Yanai, I.4
-
7
-
-
84855331824
-
Transposase mediated construction of RNA-seq libraries
-
Gertz, J. et al. Transposase mediated construction of RNA-seq libraries. Genome Res 22, 134-141 (2012).
-
(2012)
Genome Res
, vol.22
, pp. 134-141
-
-
Gertz, J.1
-
8
-
-
84864880991
-
Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells
-
Ramskold, D. et al. Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells. Nat Biotechnol 30, 777-782 (2012).
-
(2012)
Nat Biotechnol
, vol.30
, pp. 777-782
-
-
Ramskold, D.1
-
9
-
-
84876085773
-
Quartz-Seq: A highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity
-
Sasagawa, Y. et al.Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity. Genome Biol 14, R31 (2013).
-
(2013)
Genome Biol
, vol.14
, pp. R31
-
-
Sasagawa, Y.1
-
10
-
-
84872194966
-
Two methods for full-length RNA sequencing for low quantities of cells and single cells
-
Pan, X. et al. Two methods for full-length RNA sequencing for low quantities of cells and single cells. Proc Natl Acad Sci U S A 110, 594-599 (2013).
-
(2013)
Proc Natl Acad Sci u S a
, vol.110
, pp. 594-599
-
-
Pan, X.1
-
11
-
-
84877751402
-
Quantitative transcriptomics using designed primer-based amplification
-
Bhargava, V., Ko, P., Willems, E., Mercola, M. & Subramaniam, S. Quantitative transcriptomics using designed primer-based amplification. Sci Rep 3, 1740 (2013).
-
(2013)
Sci Rep
, vol.3
, pp. 1740
-
-
Bhargava, V.1
Ko, P.2
Willems, E.3
Mercola, M.4
Subramaniam, S.5
-
12
-
-
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
-
13
-
-
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
-
14
-
-
79953288433
-
Development and applications of single-cell transcriptome analysis
-
Tang, F., Lao, K. & Surani, M. A. Development and applications of single-cell transcriptome analysis. Nat Methods 8, S6-11 (2011).
-
(2011)
Nat Methods
, vol.8
, pp. S6-S11
-
-
Tang, F.1
Lao, K.2
Surani, M.A.3
-
15
-
-
84872196159
-
Single-neuron RNA-Seq: Technical feasibility and reproducibility
-
Qiu, S. et al. Single-neuron RNA-Seq: technical feasibility and reproducibility. Front Genet 3, 124 (2012).
-
(2012)
Front Genet
, vol.3
, pp. 124
-
-
Qiu, S.1
-
16
-
-
33750936779
-
Wnt and TGF-beta signaling are required for the induction of an in vitro model of primitive streak formation using embryonic stem cells
-
Gadue, P., Huber, T. L., Paddison, P. J. & Keller, G. M. Wnt and TGF-beta signaling are required for the induction of an in vitro model of primitive streak formation using embryonic stem cells. Proc Natl Acad Sci U S A 103, 16806-16811 (2006).
-
(2006)
Proc Natl Acad Sci U S A
, vol.103
, pp. 16806-16811
-
-
Gadue, P.1
Huber, T.L.2
Paddison, P.J.3
Keller, G.M.4
-
17
-
-
49749152786
-
Patterning of mouse embryonic stem cell-derived pan-mesoderm by Activin A/Nodal and Bmp4 signaling requires Fibroblast Growth Factor activity
-
Willems, E. & Leyns, L. Patterning of mouse embryonic stem cell-derived pan-mesoderm by Activin A/Nodal and Bmp4 signaling requires Fibroblast Growth Factor activity. Differentiation 76, 745-759 (2008).
-
(2008)
Differentiation
, vol.76
, pp. 745-759
-
-
Willems, E.1
Leyns, L.2
-
18
-
-
0030785446
-
The ALK-2 and ALK-4 activin receptors transduce distinct mesoderm-inducing signals during early Xenopus development but do not co-operate to establish thresholds
-
Armes, N. A. & Smith, J. C. The ALK-2 and ALK-4 activin receptors transduce distinct mesoderm-inducing signals during early Xenopus development but do not co-operate to establish thresholds. Development 124, 3797-3804 (1997).
-
(1997)
Development
, vol.124
, pp. 3797-3804
-
-
Armes, N.A.1
Smith, J.C.2
-
19
-
-
0028122987
-
Activin signalling and response to a morphogen gradient
-
Gurdon, J. B., Harger, P., Mitchell, A. & Lemaire, P. Activin signalling and response to a morphogen gradient. Nature 371, 487-492 (1994).
-
(1994)
Nature
, vol.371
, pp. 487-492
-
-
Gurdon, J.B.1
Harger, P.2
Mitchell, A.3
Lemaire, P.4
-
20
-
-
0028787260
-
Nodal-related signals induce axial mesoderm and dorsalize mesoderm during gastrulation
-
Jones, C. M., Kuehn, M. R., Hogan, B. L., Smith, J. C. & Wright, C. V. Nodal-related signals induce axial mesoderm and dorsalize mesoderm during gastrulation. Development 121, 3651-3662 (1995).
-
(1995)
Development
, vol.121
, pp. 3651-3662
-
-
Jones, C.M.1
Kuehn, M.R.2
Hogan, B.L.3
Smith, J.C.4
Wright, C.V.5
-
21
-
-
0042346340
-
Early endoderm development in vertebrates: Lineage differentiation and morphogenetic function
-
Tam, P. P., Kanai-Azuma, M. & Kanai, Y. Early endoderm development in vertebrates: lineage differentiation and morphogenetic function. Curr Opin Genet Dev 13, 393-400 (2003).
-
(2003)
Curr Opin Genet Dev
, vol.13
, pp. 393-400
-
-
Tam, P.P.1
Kanai-Azuma, M.2
Kanai, Y.3
-
22
-
-
70349600692
-
Activin A-induced differentiation of embryonic stem cells into endoderm and pancreatic progenitors-the influence of differentiation factors and culture conditions
-
Sulzbacher, S., Schroeder, I. S., Truong, T. T. & Wobus, A. M. Activin A-induced differentiation of embryonic stem cells into endoderm and pancreatic progenitors-the influence of differentiation factors and culture conditions. Stem Cell Rev 5, 159-173 (2009).
-
(2009)
Stem Cell Rev
, vol.5
, pp. 159-173
-
-
Sulzbacher, S.1
Schroeder, I.S.2
Truong, T.T.3
Wobus, A.M.4
-
23
-
-
67650567329
-
Early cell fate decisions of human embryonic stem cells and mouse epiblast stem cells are controlled by the same signalling pathways
-
Vallier, L. et al. Early cell fate decisions of human embryonic stem cells and mouse epiblast stem cells are controlled by the same signalling pathways. PLoS One 4, e6082 (2009).
-
(2009)
PLoS One
, vol.4
, pp. e6082
-
-
Vallier, L.1
-
24
-
-
77957663917
-
Alternative expression analysis by RNA sequencing
-
Griffith, M. et al. Alternative expression analysis by RNA sequencing. Nat Methods 7, 843-847 (2010).
-
(2010)
Nat Methods
, vol.7
, pp. 843-847
-
-
Griffith, M.1
-
25
-
-
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
-
26
-
-
79957882567
-
RNA-seq: Technical variability and sampling
-
McIntyre, L. M. et al. RNA-seq: technical variability and sampling. BMCGenomics 12, 293 (2011).
-
(2011)
BMCGenomics
, vol.12
, pp. 293
-
-
McIntyre, L.M.1
-
27
-
-
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
-
28
-
-
50649089207
-
RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays
-
Marioni, J. C., Mason, C. E., Mane, S. M., Stephens, M. & Gilad, Y. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 18, 1509-1517 (2008).
-
(2008)
Genome Res
, vol.18
, pp. 1509-1517
-
-
Marioni, J.C.1
Mason, C.E.2
Mane, S.M.3
Stephens, M.4
Gilad, Y.5
-
29
-
-
84878997106
-
Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells
-
Shalek, A. K. et al. Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells. Nature 498, 236-240 (2013).
-
(2013)
Nature
, vol.498
, pp. 236-240
-
-
Shalek, A.K.1
-
30
-
-
27144548491
-
The External RNA Controls Consortium: A progress report
-
Baker, S. C. et al. The External RNA Controls Consortium: a progress report. Nat Methods 2, 731-734 (2005).
-
(2005)
Nat Methods
, vol.2
, pp. 731-734
-
-
Baker, S.C.1
-
31
-
-
0037119587
-
Stochastic gene expression in a single cell
-
Elowitz, M. B., Levine, A. J., Siggia, E. D. & Swain, P. S. Stochastic gene expression in a single cell. Science 297, 1183-1186 (2002).
-
(2002)
Science
, vol.297
, pp. 1183-1186
-
-
Elowitz, M.B.1
Levine, A.J.2
Siggia, E.D.3
Swain, P.S.4
-
32
-
-
33745287724
-
Noise in protein expression scales with natural protein abundance
-
Bar-Even, A. et al. Noise in protein expression scales with natural protein abundance. Nat Genet 38, 636-643 (2006).
-
(2006)
Nat Genet
, vol.38
, pp. 636-643
-
-
Bar-Even, A.1
-
33
-
-
84954396263
-
Inferring the kinetics of stochastic gene expression from single-cell RNA-sequencing data
-
Kim, J. K. & Marioni, J. C. Inferring the kinetics of stochastic gene expression from single-cell RNA-sequencing data. Genome Biol 14, R7 (2013).
-
(2013)
Genome Biol
, vol.14
, pp. R7
-
-
Kim, J.K.1
Marioni, J.C.2
-
34
-
-
0027391640
-
Characterization of a DNA polymerase from the hyperthermophile archaea Thermococcus litoralis. Vent DNA polymerase, steady state kinetics, thermal stability, processivity, strand displacement, and exonuclease activities
-
Kong, H., Kucera, R. B. & Jack, W. E. Characterization of a DNA polymerase from the hyperthermophile archaea Thermococcus litoralis. Vent DNA polymerase, steady state kinetics, thermal stability, processivity, strand displacement, and exonuclease activities. J Biol Chem 268, 1965-1975 (1993).
-
(1993)
J Biol Chem
, vol.268
, pp. 1965-1975
-
-
Kong, H.1
Kucera, R.B.2
Jack, W.E.3
-
35
-
-
0030446799
-
Thermodynamic and kinetic measurements of promoter binding by T7 RNA polymerase
-
Ujvari, A. & Martin, C. T. Thermodynamic and kinetic measurements of promoter binding by T7 RNA polymerase. Biochemistry 35, 14574-14582 (1996).
-
(1996)
Biochemistry
, vol.35
, pp. 14574-14582
-
-
Ujvari, A.1
Martin, C.T.2
-
36
-
-
33645241407
-
The RIN: An RNA integrity number for assigning integrity values to RNA measurements
-
Schroeder, A. et al. The RIN: an RNA integrity number for assigning integrity values to RNA measurements. BMC Mol Biol 7, 3 (2006).
-
(2006)
BMC Mol Biol
, vol.7
, pp. 3
-
-
Schroeder, A.1
-
37
-
-
79953177468
-
Aligning short sequencing reads with Bowtie
-
Chapter 11, Unit 11 17
-
Langmead, B. Aligning short sequencing reads with Bowtie. Curr Protoc Bioinformatics Chapter 11, Unit 11 17 (2010).
-
(2010)
Curr Protoc Bioinformatics
-
-
Langmead, B.1
|