-
1
-
-
84865130689
-
NLRP6 negatively regulates innate immunity and host defence against bacterial pathogens
-
Anand, P.K., Malireddi, R.K.S., Lukens, J.R., Vogel, P., Bertin, J., Lamkanfi, M., Kanneganti, T.-D., NLRP6 negatively regulates innate immunity and host defence against bacterial pathogens. Nature 488 (2012), 389–393.
-
(2012)
Nature
, vol.488
, pp. 389-393
-
-
Anand, P.K.1
Malireddi, R.K.S.2
Lukens, J.R.3
Vogel, P.4
Bertin, J.5
Lamkanfi, M.6
Kanneganti, T.-D.7
-
2
-
-
84926178081
-
Bursty gene expression in the intact mammalian liver
-
Bahar Halpern, K., Tanami, S., Landen, S., Chapal, M., Szlak, L., Hutzler, A., Nizhberg, A., Itzkovitz, S., Bursty gene expression in the intact mammalian liver. Mol. Cell 58 (2015), 147–156.
-
(2015)
Mol. Cell
, vol.58
, pp. 147-156
-
-
Bahar Halpern, K.1
Tanami, S.2
Landen, S.3
Chapal, M.4
Szlak, L.5
Hutzler, A.6
Nizhberg, A.7
Itzkovitz, S.8
-
3
-
-
85044040461
-
Single molecule approaches for quantifying transcription and degradation rates in intact mammalian tissues
-
Bahar Halpern, K., Itzkovitz, S., Single molecule approaches for quantifying transcription and degradation rates in intact mammalian tissues. Methods 15 (2015), 30155–30159.
-
(2015)
Methods
, vol.15
, pp. 30155-30159
-
-
Bahar Halpern, K.1
Itzkovitz, S.2
-
4
-
-
84950278078
-
Control of transcript variability in single mammalian cells
-
Battich, N., Stoeger, T., Pelkmans, L., Control of transcript variability in single mammalian cells. Cell 163 (2015), 1596–1610.
-
(2015)
Cell
, vol.163
, pp. 1596-1610
-
-
Battich, N.1
Stoeger, T.2
Pelkmans, L.3
-
5
-
-
84864251757
-
Transcript dynamics of proinflammatory genes revealed by sequence analysis of subcellular RNA fractions
-
Bhatt, D.M., Pandya-Jones, A., Tong, A.-J., Barozzi, I., Lissner, M.M., Natoli, G., Black, D.L., Smale, S.T., Transcript dynamics of proinflammatory genes revealed by sequence analysis of subcellular RNA fractions. Cell 150 (2012), 279–290.
-
(2012)
Cell
, vol.150
, pp. 279-290
-
-
Bhatt, D.M.1
Pandya-Jones, A.2
Tong, A.-J.3
Barozzi, I.4
Lissner, M.M.5
Natoli, G.6
Black, D.L.7
Smale, S.T.8
-
6
-
-
0242416539
-
Noise in eukaryotic gene expression
-
Blake, W.J., Kaern, M., Cantor, C.R., Collins, J.J., Noise in eukaryotic gene expression. Nature 422 (2003), 633–637.
-
(2003)
Nature
, vol.422
, pp. 633-637
-
-
Blake, W.J.1
Kaern, M.2
Cantor, C.R.3
Collins, J.J.4
-
7
-
-
84920460444
-
Detained introns are a novel, widespread class of post-transcriptionally spliced introns
-
Boutz, P.L., Bhutkar, A., Sharp, P.A., Detained introns are a novel, widespread class of post-transcriptionally spliced introns. Genes Dev. 29 (2015), 63–80.
-
(2015)
Genes Dev.
, vol.29
, pp. 63-80
-
-
Boutz, P.L.1
Bhutkar, A.2
Sharp, P.A.3
-
8
-
-
84860257802
-
Interplay between gene expression noise and regulatory network architecture
-
Chalancon, G., Ravarani, C.N.J., Balaji, S., Martinez-Arias, A., Aravind, L., Jothi, R., Babu, M.M., Interplay between gene expression noise and regulatory network architecture. Trends Genet. 28 (2012), 221–232.
-
(2012)
Trends Genet.
, vol.28
, pp. 221-232
-
-
Chalancon, G.1
Ravarani, C.N.J.2
Balaji, S.3
Martinez-Arias, A.4
Aravind, L.5
Jothi, R.6
Babu, M.M.7
-
9
-
-
68949212914
-
Altered nuclear retention of mRNAs containing inverted repeats in human embryonic stem cells: functional role of a nuclear noncoding RNA
-
Chen, L.-L., Carmichael, G.G., Altered nuclear retention of mRNAs containing inverted repeats in human embryonic stem cells: functional role of a nuclear noncoding RNA. Mol. Cell 35 (2009), 467–478.
-
(2009)
Mol. Cell
, vol.35
, pp. 467-478
-
-
Chen, L.-L.1
Carmichael, G.G.2
-
10
-
-
84867914780
-
Transcriptional burst frequency and burst size are equally modulated across the human genome
-
Dar, R.D., Razooky, B.S., Singh, A., Trimeloni, T.V., McCollum, J.M., Cox, C.D., Simpson, M.L., Weinberger, L.S., Transcriptional burst frequency and burst size are equally modulated across the human genome. Proc. Natl. Acad. Sci. USA 109 (2012), 17454–17459.
-
(2012)
Proc. Natl. Acad. Sci. USA
, vol.109
, pp. 17454-17459
-
-
Dar, R.D.1
Razooky, B.S.2
Singh, A.3
Trimeloni, T.V.4
McCollum, J.M.5
Cox, C.D.6
Simpson, M.L.7
Weinberger, L.S.8
-
11
-
-
34548507690
-
In vivo dynamics of RNA polymerase II transcription
-
Darzacq, X., Shav-Tal, Y., de Turris, V., Brody, Y., Shenoy, S.M., Phair, R.D., Singer, R.H., In vivo dynamics of RNA polymerase II transcription. Nat. Struct. Mol. Biol. 14 (2007), 796–806.
-
(2007)
Nat. Struct. Mol. Biol.
, vol.14
, pp. 796-806
-
-
Darzacq, X.1
Shav-Tal, Y.2
de Turris, V.3
Brody, Y.4
Shenoy, S.M.5
Phair, R.D.6
Singer, R.H.7
-
12
-
-
84865757142
-
Landscape of transcription in human cells
-
Djebali, S., Davis, C.A., Merkel, A., Dobin, A., Lassmann, T., Mortazavi, A., Tanzer, A., Lagarde, J., Lin, W., Schlesinger, F., et al. Landscape of transcription in human cells. Nature 489 (2012), 101–108.
-
(2012)
Nature
, vol.489
, pp. 101-108
-
-
Djebali, S.1
Davis, C.A.2
Merkel, A.3
Dobin, A.4
Lassmann, T.5
Mortazavi, A.6
Tanzer, A.7
Lagarde, J.8
Lin, W.9
Schlesinger, F.10
-
13
-
-
77956520011
-
Functional roles for noise in genetic circuits
-
Eldar, A., Elowitz, M.B., 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
-
14
-
-
79957576718
-
NLRP6 inflammasome regulates colonic microbial ecology and risk for colitis
-
Elinav, E., Strowig, T., Kau, A.L., Henao-Mejia, J., Thaiss, C.A., Booth, C.J., Peaper, D.R., Bertin, J., Eisenbarth, S.C., Gordon, J.I., Flavell, R.A., NLRP6 inflammasome regulates colonic microbial ecology and risk for colitis. Cell 145 (2011), 745–757.
-
(2011)
Cell
, vol.145
, pp. 745-757
-
-
Elinav, E.1
Strowig, T.2
Kau, A.L.3
Henao-Mejia, J.4
Thaiss, C.A.5
Booth, C.J.6
Peaper, D.R.7
Bertin, J.8
Eisenbarth, S.C.9
Gordon, J.I.10
Flavell, R.A.11
-
15
-
-
33847771442
-
The highways and byways of mRNA decay
-
Garneau, N.L., Wilusz, J., Wilusz, C.J., The highways and byways of mRNA decay. Nat. Rev. Mol. Cell Biol. 8 (2007), 113–126.
-
(2007)
Nat. Rev. Mol. Cell Biol.
, vol.8
, pp. 113-126
-
-
Garneau, N.L.1
Wilusz, J.2
Wilusz, C.J.3
-
16
-
-
33645429016
-
Exact stochastic simulation of coupled chemical reactions
-
Gillespie, D.T., Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81 (1977), 2340–2361.
-
(1977)
J. Phys. Chem.
, vol.81
, pp. 2340-2361
-
-
Gillespie, D.T.1
-
17
-
-
28944434119
-
Real-time kinetics of gene activity in individual bacteria
-
Golding, I., Paulsson, J., Zawilski, S.M., Cox, E.C., Real-time kinetics of gene activity in individual bacteria. Cell 123 (2005), 1025–1036.
-
(2005)
Cell
, vol.123
, pp. 1025-1036
-
-
Golding, I.1
Paulsson, J.2
Zawilski, S.M.3
Cox, E.C.4
-
18
-
-
84859921736
-
A novel ChREBP isoform in adipose tissue regulates systemic glucose metabolism
-
Herman, M.A., Peroni, O.D., Villoria, J., Schön, M.R., Abumrad, N.A., Blüher, M., Klein, S., Kahn, B.B., A novel ChREBP isoform in adipose tissue regulates systemic glucose metabolism. Nature 484 (2012), 333–338.
-
(2012)
Nature
, vol.484
, pp. 333-338
-
-
Herman, M.A.1
Peroni, O.D.2
Villoria, J.3
Schön, M.R.4
Abumrad, N.A.5
Blüher, M.6
Klein, S.7
Kahn, B.B.8
-
19
-
-
84355162740
-
Single-molecule transcript counting of stem-cell markers in the mouse intestine
-
Itzkovitz, S., Lyubimova, A., Blat, I.C., Maynard, M., van Es, J., Lees, J., Jacks, T., Clevers, H., van Oudenaarden, A., Single-molecule transcript counting of stem-cell markers in the mouse intestine. Nat. Cell Biol. 14 (2011), 106–114.
-
(2011)
Nat. Cell Biol.
, vol.14
, pp. 106-114
-
-
Itzkovitz, S.1
Lyubimova, A.2
Blat, I.C.3
Maynard, M.4
van Es, J.5
Lees, J.6
Jacks, T.7
Clevers, H.8
van Oudenaarden, A.9
-
20
-
-
19544379881
-
Stochasticity in gene expression: from theories to phenotypes
-
Kaern, M., Elston, T.C., Blake, W.J., Collins, J.J., Stochasticity in gene expression: from theories to phenotypes. Nat. Rev. Genet. 6 (2005), 451–464.
-
(2005)
Nat. Rev. Genet.
, vol.6
, pp. 451-464
-
-
Kaern, M.1
Elston, T.C.2
Blake, W.J.3
Collins, J.J.4
-
21
-
-
79955407832
-
Real-time observation of transcription initiation and elongation on an endogenous yeast gene
-
Larson, D.R., Zenklusen, D., Wu, B., Chao, J.A., Singer, R.H., Real-time observation of transcription initiation and elongation on an endogenous yeast gene. Science 332 (2011), 475–478.
-
(2011)
Science
, vol.332
, pp. 475-478
-
-
Larson, D.R.1
Zenklusen, D.2
Wu, B.3
Chao, J.A.4
Singer, R.H.5
-
22
-
-
84883434699
-
Single-molecule mRNA detection and counting in mammalian tissue
-
Lyubimova, A., Itzkovitz, S., Junker, J.P., Fan, Z.P., Wu, X., van Oudenaarden, A., Single-molecule mRNA detection and counting in mammalian tissue. Nat. Protoc. 8 (2013), 1743–1758.
-
(2013)
Nat. Protoc.
, vol.8
, pp. 1743-1758
-
-
Lyubimova, A.1
Itzkovitz, S.2
Junker, J.P.3
Fan, Z.P.4
Wu, X.5
van Oudenaarden, A.6
-
23
-
-
34347260600
-
Living with noisy genes: how cells function reliably with inherent variability in gene expression
-
Maheshri, N., O'Shea, E.K., Living with noisy genes: how cells function reliably with inherent variability in gene expression. Annu. Rev. Biophys. Biomol. Struct. 36 (2007), 413–434.
-
(2007)
Annu. Rev. Biophys. Biomol. Struct.
, vol.36
, pp. 413-434
-
-
Maheshri, N.1
O'Shea, E.K.2
-
24
-
-
84881506759
-
Nascent-Seq reveals novel features of mouse circadian transcriptional regulation
-
Menet, J.S., Rodriguez, J., Abruzzi, K.C., Rosbash, M., Nascent-Seq reveals novel features of mouse circadian transcriptional regulation. eLife, 1, 2012, e00011.
-
(2012)
eLife
, vol.1
, pp. e00011
-
-
Menet, J.S.1
Rodriguez, J.2
Abruzzi, K.C.3
Rosbash, M.4
-
25
-
-
0025281303
-
Establishment of a pancreatic β cell line that retains glucose-inducible insulin secretion: special reference to expression of glucose transporter isoforms
-
Miyazaki, J., Araki, K., Yamato, E., Ikegami, H., Asano, T., Shibasaki, Y., Oka, Y., Yamamura, K., Establishment of a pancreatic β cell line that retains glucose-inducible insulin secretion: special reference to expression of glucose transporter isoforms. Endocrinology 127 (1990), 126–132.
-
(1990)
Endocrinology
, vol.127
, pp. 126-132
-
-
Miyazaki, J.1
Araki, K.2
Yamato, E.3
Ikegami, H.4
Asano, T.5
Shibasaki, Y.6
Oka, Y.7
Yamamura, K.8
-
26
-
-
84860450204
-
To the pore and through the pore: a story of mRNA export kinetics
-
Oeffinger, M., Zenklusen, D., To the pore and through the pore: a story of mRNA export kinetics. Biochim. Biophys. Acta 1819 (2012), 494–506.
-
(2012)
Biochim. Biophys. Acta
, vol.1819
, pp. 494-506
-
-
Oeffinger, M.1
Zenklusen, D.2
-
27
-
-
84878044937
-
Splicing kinetics and transcript release from the chromatin compartment limit the rate of Lipid A-induced gene expression
-
Pandya-Jones, A., Bhatt, D.M., Lin, C.-H., Tong, A.-J., Smale, S.T., Black, D.L., Splicing kinetics and transcript release from the chromatin compartment limit the rate of Lipid A-induced gene expression. RNA 19 (2013), 811–827.
-
(2013)
RNA
, vol.19
, pp. 811-827
-
-
Pandya-Jones, A.1
Bhatt, D.M.2
Lin, C.-H.3
Tong, A.-J.4
Smale, S.T.5
Black, D.L.6
-
28
-
-
0842285841
-
Summing up the noise in gene networks
-
Paulsson, J., Summing up the noise in gene networks. Nature 427 (2004), 415–418.
-
(2004)
Nature
, vol.427
, pp. 415-418
-
-
Paulsson, J.1
-
29
-
-
84904820636
-
RBPmap: a web server for mapping binding sites of RNA-binding proteins
-
Paz, I., Kosti, I., Ares, M. Jr., Cline, M., Mandel-Gutfreund, Y., RBPmap: a web server for mapping binding sites of RNA-binding proteins. Nucleic Acids Res. 42 (2014), W361–W367.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. W361-W367
-
-
Paz, I.1
Kosti, I.2
Ares, M.3
Cline, M.4
Mandel-Gutfreund, Y.5
-
30
-
-
38449087713
-
ChREBP, a transcriptional regulator of glucose and lipid metabolism
-
Postic, C., Dentin, R., Denechaud, P.-D., Girard, J., ChREBP, a transcriptional regulator of glucose and lipid metabolism. Annu. Rev. Nutr. 27 (2007), 179–192.
-
(2007)
Annu. Rev. Nutr.
, vol.27
, pp. 179-192
-
-
Postic, C.1
Dentin, R.2
Denechaud, P.-D.3
Girard, J.4
-
31
-
-
26844440157
-
Regulating gene expression through RNA nuclear retention
-
Prasanth, K.V., Prasanth, S.G., Xuan, Z., Hearn, S., Freier, S.M., Bennett, C.F., Zhang, M.Q., Spector, D.L., Regulating gene expression through RNA nuclear retention. Cell 123 (2005), 249–263.
-
(2005)
Cell
, vol.123
, pp. 249-263
-
-
Prasanth, K.V.1
Prasanth, S.G.2
Xuan, Z.3
Hearn, S.4
Freier, S.M.5
Bennett, C.F.6
Zhang, M.Q.7
Spector, D.L.8
-
32
-
-
53549123008
-
Nature, nurture, or chance: stochastic gene expression and its consequences
-
Raj, A., van Oudenaarden, A., Nature, nurture, or chance: stochastic gene expression and its consequences. Cell 135 (2008), 216–226.
-
(2008)
Cell
, vol.135
, pp. 216-226
-
-
Raj, A.1
van Oudenaarden, A.2
-
33
-
-
33748994704
-
Stochastic mRNA synthesis in mammalian cells
-
Raj, A., Peskin, C.S., Tranchina, D., Vargas, D.Y., Tyagi, S., 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
-
34
-
-
79959637365
-
Quantification of biological interactions with particle image cross-correlation spectroscopy (PICCS)
-
Semrau, S., Holtzer, L., González-Gaitán, M., Schmidt, T., Quantification of biological interactions with particle image cross-correlation spectroscopy (PICCS). Biophys. J. 100 (2011), 1810–1818.
-
(2011)
Biophys. J.
, vol.100
, pp. 1810-1818
-
-
Semrau, S.1
Holtzer, L.2
González-Gaitán, M.3
Schmidt, T.4
-
35
-
-
84904037679
-
Transcription factors modulate c-Fos transcriptional bursts
-
Senecal, A., Munsky, B., Proux, F., Ly, N., Braye, F.E., Zimmer, C., Mueller, F., Darzacq, X., Transcription factors modulate c-Fos transcriptional bursts. Cell Rep. 8 (2014), 75–83.
-
(2014)
Cell Rep.
, vol.8
, pp. 75-83
-
-
Senecal, A.1
Munsky, B.2
Proux, F.3
Ly, N.4
Braye, F.E.5
Zimmer, C.6
Mueller, F.7
Darzacq, X.8
-
36
-
-
84902334317
-
Widespread inhibition of posttranscriptional splicing shapes the cellular transcriptome following heat shock
-
Shalgi, R., Hurt, J.A., Lindquist, S., Burge, C.B., Widespread inhibition of posttranscriptional splicing shapes the cellular transcriptome following heat shock. Cell Rep. 7 (2014), 1362–1370.
-
(2014)
Cell Rep.
, vol.7
, pp. 1362-1370
-
-
Shalgi, R.1
Hurt, J.A.2
Lindquist, S.3
Burge, C.B.4
-
37
-
-
2942733310
-
Dynamics of single mRNPs in nuclei of living cells
-
Shav-Tal, Y., Darzacq, X., Shenoy, S.M., Fusco, D., Janicki, S.M., Spector, D.L., Singer, R.H., Dynamics of single mRNPs in nuclei of living cells. Science 304 (2004), 1797–1800.
-
(2004)
Science
, vol.304
, pp. 1797-1800
-
-
Shav-Tal, Y.1
Darzacq, X.2
Shenoy, S.M.3
Fusco, D.4
Janicki, S.M.5
Spector, D.L.6
Singer, R.H.7
-
38
-
-
84865788318
-
Consequences of mRNA transport on stochastic variability in protein levels
-
Singh, A., Bokes, P., Consequences of mRNA transport on stochastic variability in protein levels. Biophys. J. 103 (2012), 1087–1096.
-
(2012)
Biophys. J.
, vol.103
, pp. 1087-1096
-
-
Singh, A.1
Bokes, P.2
-
39
-
-
0034851781
-
Nuclear domains
-
Spector, D.L., Nuclear domains. J. Cell Sci. 114 (2001), 2891–2893.
-
(2001)
J. Cell Sci.
, vol.114
, pp. 2891-2893
-
-
Spector, D.L.1
-
40
-
-
84855989829
-
Inflammasomes in health and disease
-
Strowig, T., Henao-Mejia, J., Elinav, E., Flavell, R., Inflammasomes in health and disease. Nature 481 (2012), 278–286.
-
(2012)
Nature
, vol.481
, pp. 278-286
-
-
Strowig, T.1
Henao-Mejia, J.2
Elinav, E.3
Flavell, R.4
-
41
-
-
79955381895
-
Mammalian genes are transcribed with widely different bursting kinetics
-
Suter, D.M., Molina, N., Gatfield, D., Schneider, K., Schibler, U., Naef, F., Mammalian genes are transcribed with widely different bursting kinetics. Science 332 (2011), 472–474.
-
(2011)
Science
, vol.332
, pp. 472-474
-
-
Suter, D.M.1
Molina, N.2
Gatfield, D.3
Schneider, K.4
Schibler, U.5
Naef, F.6
-
42
-
-
84865777822
-
Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs
-
Tilgner, H., Knowles, D.G., Johnson, R., Davis, C.A., Chakrabortty, S., Djebali, S., Curado, J., Snyder, M., Gingeras, T.R., Guigó R., Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs. Genome Res. 22 (2012), 1616–1625.
-
(2012)
Genome Res.
, vol.22
, pp. 1616-1625
-
-
Tilgner, H.1
Knowles, D.G.2
Johnson, R.3
Davis, C.A.4
Chakrabortty, S.5
Djebali, S.6
Curado, J.7
Snyder, M.8
Gingeras, T.R.9
Guigó, R.10
-
43
-
-
33746536677
-
Carbohydrate response element binding protein, ChREBP, a transcription factor coupling hepatic glucose utilization and lipid synthesis
-
Uyeda, K., Repa, J.J., Carbohydrate response element binding protein, ChREBP, a transcription factor coupling hepatic glucose utilization and lipid synthesis. Cell Metab. 4 (2006), 107–110.
-
(2006)
Cell Metab.
, vol.4
, pp. 107-110
-
-
Uyeda, K.1
Repa, J.J.2
-
44
-
-
28044451048
-
Mechanism of mRNA transport in the nucleus
-
Vargas, D.Y., Raj, A., Marras, S.A.E., Kramer, F.R., Tyagi, S., Mechanism of mRNA transport in the nucleus. Proc. Natl. Acad. Sci. USA 102 (2005), 17008–17013.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 17008-17013
-
-
Vargas, D.Y.1
Raj, A.2
Marras, S.A.E.3
Kramer, F.R.4
Tyagi, S.5
-
45
-
-
0033153297
-
Guided tours: from precursor snoRNA to functional snoRNP
-
Weinstein, L.B., Steitz, J.A., Guided tours: from precursor snoRNA to functional snoRNP. Curr. Opin. Cell Biol. 11 (1999), 378–384.
-
(1999)
Curr. Opin. Cell Biol.
, vol.11
, pp. 378-384
-
-
Weinstein, L.B.1
Steitz, J.A.2
-
46
-
-
75449105876
-
Attenuation of transcriptional bursting in mRNA transport
-
Xiong, L.P., Ma, Y.Q., Tang, L.H., Attenuation of transcriptional bursting in mRNA transport. Phys. Biol., 7, 2010, 016005.
-
(2010)
Phys. Biol.
, vol.7
, pp. 016005
-
-
Xiong, L.P.1
Ma, Y.Q.2
Tang, L.H.3
|