-
1
-
-
15744394192
-
Transcriptional regulation by the numbers: Models
-
Bintu, L., Buchler, N.E., Garcia, H.G., Gerland, U., Hwa, T., Kondev, J., and Phillips, R. 2005. Transcriptional regulation by the numbers: Models. Curr. Opin. Genet. Dev. 15: 116-124.
-
(2005)
Curr. Opin. Genet. Dev.
, vol.15
, pp. 116-124
-
-
Bintu, L.1
Buchler, N.E.2
Garcia, H.G.3
Gerland, U.4
Hwa, T.5
Kondev, J.6
Phillips, R.7
-
2
-
-
1442306129
-
Evolutionary comparisons suggest many novel cAMP response protein binding sites in Escherichia coli
-
Brown, C.T. and Callan Jr., C.G. 2004. Evolutionary comparisons suggest many novel cAMP response protein binding sites in Escherichia coli. Proc. Natl. Acad. Sci. 101: 2404-2409.
-
(2004)
Proc. Natl. Acad. Sci.
, vol.101
, pp. 2404-2409
-
-
Brown, C.T.1
Callan Jr., C.G.2
-
3
-
-
0035135420
-
Regulatory element detection using correlation with expression
-
Bussemaker, H.J., Li, H., and Siggia, E.D. 2001. Regulatory element detection using correlation with expression. Nat. Genet. 27: 167-171.
-
(2001)
Nat. Genet.
, vol.27
, pp. 167-171
-
-
Bussemaker, H.J.1
Li, H.2
Siggia, E.D.3
-
4
-
-
10744226888
-
Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs
-
Cawley, S., Bekiranov, S., Ng, H.H., Kapranov, P., Sekinger, E.A., Kampa, D., Piccolboni, A., Sementchenko, V., Cheng, J., Williams, A.J., et al. 2004. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 116: 499-509.
-
(2004)
Cell
, vol.116
, pp. 499-509
-
-
Cawley, S.1
Bekiranov, S.2
Ng, H.H.3
Kapranov, P.4
Sekinger, E.A.5
Kampa, D.6
Piccolboni, A.7
Sementchenko, V.8
Cheng, J.9
Williams, A.J.10
-
5
-
-
0038724989
-
Finding functional features in Saccharomyces genomes by phylogenetic footprinting
-
Cliften, P., Sudarsanam, P., Desikan, A., Fulton, L., Fulton, B., Majors, J., Waterston, R., Cohen, B.A., and Johnston, M. 2003. Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301: 71-76.
-
(2003)
Science
, vol.301
, pp. 71-76
-
-
Cliften, P.1
Sudarsanam, P.2
Desikan, A.3
Fulton, L.4
Fulton, B.5
Majors, J.6
Waterston, R.7
Cohen, B.A.8
Johnston, M.9
-
6
-
-
0027200714
-
The DAL82 protein of Saccharomyces cerevisiae binds to the DAL upstream induction sequence (UIS)
-
Dorrington, R.A. and Cooper, T.G. 1993. The DAL82 protein of Saccharomyces cerevisiae binds to the DAL upstream induction sequence (UIS). Nucleic Acids Res. 21: 3777-3784.
-
(1993)
Nucleic Acids Res.
, vol.21
, pp. 3777-3784
-
-
Dorrington, R.A.1
Cooper, T.G.2
-
7
-
-
0037119587
-
Stochastic gene expression in a single cell
-
Elowitz, M.B., Levine, A.J., Siggia, E.D., and Swain, P.S. 2002. Stochastic gene expression in a single cell. Science 297: 1183-1186.
-
(2002)
Science
, vol.297
, pp. 1183-1186
-
-
Elowitz, M.B.1
Levine, A.J.2
Siggia, E.D.3
Swain, P.S.4
-
8
-
-
0037126028
-
Physical constraints and functional characteristics of transcription factor-DNA interaction
-
Gerland, U., Moroz, J.D., and Hwa, T. 2002. Physical constraints and functional characteristics of transcription factor-DNA interaction. Proc. Natl. Acad. Sci. 99: 12015-12020.
-
(2002)
Proc. Natl. Acad. Sci.
, vol.99
, pp. 12015-12020
-
-
Gerland, U.1
Moroz, J.D.2
Hwa, T.3
-
9
-
-
34548087820
-
Explicit equilibrium modeling of transcription-factor binding and gene regulation
-
Granek, J.A. and Clarke, N.D. 2005. Explicit equilibrium modeling of transcription-factor binding and gene regulation. Genome Biol. 6: R87.
-
(2005)
Genome Biol.
, vol.6
-
-
Granek, J.A.1
Clarke, N.D.2
-
10
-
-
4544352942
-
Transcriptional regulatory code of a eukaryotic genome
-
Harbison, C.T., Gordon, D.B., Lee, T.I., Rinaldi, N.J., Macisaac, K.D., Danford, T.W., Hannett, N.M., Tagne, J.B., Reynolds, D.B., Yoo, J., et al. 2004. Transcriptional regulatory code of a eukaryotic genome. Nature 431: 99-104.
-
(2004)
Nature
, vol.431
, pp. 99-104
-
-
Harbison, C.T.1
Gordon, D.B.2
Lee, T.I.3
Rinaldi, N.J.4
Macisaac, K.D.5
Danford, T.W.6
Hannett, N.M.7
Tagne, J.B.8
Reynolds, D.B.9
Yoo, J.10
-
11
-
-
0034616930
-
Functional discovery via a compendium of expression profiles
-
Hughes, T.R., Marton, M.J., Jones, A.R., Roberts, C.J., Stoughton, R., Armour, C.D., Bennett, H.A., Coffey, E., Dai, H., He, Y.D., et al. 2000. Functional discovery via a compendium of expression profiles. Cell 102: 109-126.
-
(2000)
Cell
, vol.102
, pp. 109-126
-
-
Hughes, T.R.1
Marton, M.J.2
Jones, A.R.3
Roberts, C.J.4
Stoughton, R.5
Armour, C.D.6
Bennett, H.A.7
Coffey, E.8
Dai, H.9
He, Y.D.10
-
12
-
-
0035945567
-
Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF
-
Iyer, V.R., Horak, C.E., Scafe, C.S., Botstein, D., Snyder, M., and Brown, P.O. 2001. Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 409: 533-538.
-
(2001)
Nature
, vol.409
, pp. 533-538
-
-
Iyer, V.R.1
Horak, C.E.2
Scafe, C.S.3
Botstein, D.4
Snyder, M.5
Brown, P.O.6
-
13
-
-
0031027203
-
A basic helix-loop-helix-leucine zipper transcription complex in yeast functions in a signaling pathway from mitochondria to the nucleus. Mol
-
Jia, Y., Rothermel, B., Thornton, J., and Butow, R.A. 1997. A basic helix-loop-helix-leucine zipper transcription complex in yeast functions in a signaling pathway from mitochondria to the nucleus. Mol. Cell. Biol. 17: 1110-1117.
-
(1997)
Cell. Biol.
, vol.17
, pp. 1110-1117
-
-
Jia, Y.1
Rothermel, B.2
Thornton, J.3
Butow, R.A.4
-
14
-
-
0343924289
-
Repression by Ume6 involves recruitment of a complex containing Sin3 corepressor and Rpd3 histone deacetylase to target promoters
-
Kadosh, D. and Struhl, K. 1997. Repression by Ume6 involves recruitment of a complex containing Sin3 corepressor and Rpd3 histone deacetylase to target promoters. Cell 89: 365-371.
-
(1997)
Cell
, vol.89
, pp. 365-371
-
-
Kadosh, D.1
Struhl, K.2
-
15
-
-
0038349948
-
Sequencing and comparison of yeast species to identify genes and regulatory elements
-
Kellis, M., Patterson, N., Endrizzi, M., Birren, B., and Lander, E.S. 2003. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423: 241-254.
-
(2003)
Nature
, vol.423
, pp. 241-254
-
-
Kellis, M.1
Patterson, N.2
Endrizzi, M.3
Birren, B.4
Lander, E.S.5
-
16
-
-
0035912781
-
Carbon- and nitrogen-quality signaling to translation are mediated by distinct GATA-type transcription factors
-
Kuruvilla, F.G., Shamji, A.F., and Schreiber, S.L. 2001. Carbon- and nitrogen-quality signaling to translation are mediated by distinct GATA-type transcription factors. Proc. Natl. Acad. Sci. 98: 7283-7288.
-
(2001)
Proc. Natl. Acad. Sci.
, vol.98
, pp. 7283-7288
-
-
Kuruvilla, F.G.1
Shamji, A.F.2
Schreiber, S.L.3
-
17
-
-
0037174671
-
Transcriptional regulatory networks in Saccharomyces cerevisiae
-
Lee, T.I., Rinaldi, N.J., Robert, F., Odom, D.T., Bar-Joseph, Z., Gerber, G.K., Hannett, N.M., Harbison, C.T., Thompson, C.M., Simon, I., et al. 2002. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298: 799-804.
-
(2002)
Science
, vol.298
, pp. 799-804
-
-
Lee, T.I.1
Rinaldi, N.J.2
Robert, F.3
Odom, D.T.4
Bar-Joseph, Z.5
Gerber, G.K.6
Hannett, N.M.7
Harbison, C.T.8
Thompson, C.M.9
Simon, I.10
-
18
-
-
0038492517
-
A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells
-
Li, Z., Van Calcar, S., Qu, C., Cavenee, W.K., Zhang, M.Q., and Ren, B. 2003. A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells. Proc. Natl. Acad. Sci. 100: 8164-8169.
-
(2003)
Proc. Natl. Acad. Sci.
, vol.100
, pp. 8164-8169
-
-
Li, Z.1
Van Calcar, S.2
Qu, C.3
Cavenee, W.K.4
Zhang, M.Q.5
Ren, B.6
-
19
-
-
0036396542
-
Rationalization of gene regulation by a eukaryotic transcription factor: Calculation of regulatory region occupancy from predicted binding affinities
-
Liu, X. and Clarke, N.D. 2002. Rationalization of gene regulation by a eukaryotic transcription factor: Calculation of regulatory region occupancy from predicted binding affinities. J. Mol. Biol. 323: 1-8.
-
(2002)
J. Mol. Biol.
, vol.323
, pp. 1-8
-
-
Liu, X.1
Clarke, N.D.2
-
20
-
-
0030868697
-
Xbp1, a stress-induced transcriptional repressor of the Saccharomyces cerevisiae Swi4/Mbp1 family
-
Mai, B. and Breeden, L. 1997. Xbp1, a stress-induced transcriptional repressor of the Saccharomyces cerevisiae Swi4/Mbp1 family. Mol. Cell. Biol. 17: 6491-6501.
-
(1997)
Mol. Cell. Biol.
, vol.17
, pp. 6491-6501
-
-
Mai, B.1
Breeden, L.2
-
21
-
-
0035023140
-
Xbp1-mediated repression of CLB gene expression contributes to the modifications of yeast cell morphology and cell cycle seen during nitrogen-limited growth
-
Miled, C., Mann, C., and Faye, G. 2001. Xbp1-mediated repression of CLB gene expression contributes to the modifications of yeast cell morphology and cell cycle seen during nitrogen-limited growth. Mol. Cell. Biol. 21: 3714-3724.
-
(2001)
Mol. Cell. Biol.
, vol.21
, pp. 3714-3724
-
-
Miled, C.1
Mann, C.2
Faye, G.3
-
22
-
-
0642368358
-
Position specific variation in the rate of evolution in transcription factor binding sites
-
Moses, A.M., Chiang, D.Y., Kellis, M., Lander, E.S., and Eisen, M.B. 2003. Position specific variation in the rate of evolution in transcription factor binding sites. BMC Evol. Biol. 3: 19.
-
(2003)
BMC Evol. Biol.
, vol.3
, pp. 19
-
-
Moses, A.M.1
Chiang, D.Y.2
Kellis, M.3
Lander, E.S.4
Eisen, M.B.5
-
23
-
-
27644482258
-
Evolutionary population genetics of promoters: Predicting binding sites and functional phylogenies
-
Mustonen, V. and Lassig, M. 2005. Evolutionary population genetics of promoters: Predicting binding sites and functional phylogenies. Proc. Natl. Acad. Sci. 102: 15936-15941.
-
(2005)
Proc. Natl. Acad. Sci.
, vol.102
, pp. 15936-15941
-
-
Mustonen, V.1
Lassig, M.2
-
24
-
-
14844307159
-
Inferring quantitative models of regulatory networks from expression data
-
Nachman, I., Regev, A., and Friedman, N. 2004. Inferring quantitative models of regulatory networks from expression data. Bioinformatics (Suppl 1) 20: I248-I256.
-
(2004)
Bioinformatics (Suppl 1)
, vol.20
-
-
Nachman, I.1
Regev, A.2
Friedman, N.3
-
25
-
-
10744227070
-
Control of pancreas and liver gene expression by HNF transcription factors
-
Odom, D.T., Zizlsperger, N., Gordon, D.B., Bell, G.W., Rinaldi, N.J., Murray, H.L., Volkert, T.L., Schreiber, J., Rolfe, P.A., Gifford, D.K., et al. 2004. Control of pancreas and liver gene expression by HNF transcription factors. Science 303: 1378-1381.
-
(2004)
Science
, vol.303
, pp. 1378-1381
-
-
Odom, D.T.1
Zizlsperger, N.2
Gordon, D.B.3
Bell, G.W.4
Rinaldi, N.J.5
Murray, H.L.6
Volkert, T.L.7
Schreiber, J.8
Rolfe, P.A.9
Gifford, D.K.10
-
26
-
-
0842285841
-
Summing up the noise in gene networks
-
Paulsson, J. 2004. Summing up the noise in gene networks. Nature 427: 415-418.
-
(2004)
Nature
, vol.427
, pp. 415-418
-
-
Paulsson, J.1
-
27
-
-
2942576308
-
Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo
-
Rajewsky, N., Vergassola, M., Gaul, U., and Siggia, E.D. 2002. Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo. BMC Bioinformatics 3: 30.
-
(2002)
BMC Bioinformatics
, vol.3
, pp. 30
-
-
Rajewsky, N.1
Vergassola, M.2
Gaul, U.3
Siggia, E.D.4
-
28
-
-
25444468618
-
Noise in gene expression: Origins, consequences, and control
-
Raser, J.M. and O'Shea, E.K. 2005. Noise in gene expression: Origins, consequences, and control. Science 309: 2010-2013.
-
(2005)
Science
, vol.309
, pp. 2010-2013
-
-
Raser, J.M.1
O'Shea, E.K.2
-
29
-
-
1042288539
-
Use of chromatin immunoprecipitation assays in genome-wide location analysis of mammalian transcription factors
-
Ren, B. and Dynlacht, B.D. 2004. Use of chromatin immunoprecipitation assays in genome-wide location analysis of mammalian transcription factors. Methods Enzymol. 376: 304-315.
-
(2004)
Methods Enzymol.
, vol.376
, pp. 304-315
-
-
Ren, B.1
Dynlacht, B.D.2
-
30
-
-
0034704248
-
Genome-wide location and function of DNA binding proteins
-
Ren, B., Robert, F., Wyrick, J.J., Aparicio, O., Jennings, E.G., Simon, I., Zeitlinger, J., Schreiber, J., Hannett, N., Kanin, E., et al. 2000. Genome-wide location and function of DNA binding proteins. Science 290: 2306-2309.
-
(2000)
Science
, vol.290
, pp. 2306-2309
-
-
Ren, B.1
Robert, F.2
Wyrick, J.J.3
Aparicio, O.4
Jennings, E.G.5
Simon, I.6
Zeitlinger, J.7
Schreiber, J.8
Hannett, N.9
Kanin, E.10
-
31
-
-
0034603061
-
Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles
-
Roberts, C.J., Nelson, B., Marton, M.J., Stoughton, R., Meyer, M.R., Bennett, H.A., He, Y.D., Dai, H., Walker, W.L., Hughes, T.R., et al. 2000. Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. Science 287: 873-880.
-
(2000)
Science
, vol.287
, pp. 873-880
-
-
Roberts, C.J.1
Nelson, B.2
Marton, M.J.3
Stoughton, R.4
Meyer, M.R.5
Bennett, H.A.6
He, Y.D.7
Dai, H.8
Walker, W.L.9
Hughes, T.R.10
-
32
-
-
0036678794
-
Assigning numbers to the arrows: Parameterizing a gene regulation network by using accurate expression kinetics
-
Ronen, M., Rosenberg, R., Shraiman, B.I., and Alon, U. 2002. Assigning numbers to the arrows: Parameterizing a gene regulation network by using accurate expression kinetics. Proc. Natl. Acad. Sci. 99: 10555-10560.
-
(2002)
Proc. Natl. Acad. Sci.
, vol.99
, pp. 10555-10560
-
-
Ronen, M.1
Rosenberg, R.2
Shraiman, B.I.3
Alon, U.4
-
33
-
-
11144244771
-
Growth-regulated recruitment of the essential yeast ribosomal protein gene activator Ifh1
-
Schawalder, S.B., Kabani, M., Howald, I., Choudhury, U., Werner, M., and Shore, D. 2004. Growth-regulated recruitment of the essential yeast ribosomal protein gene activator Ifh1. Nature 432: 1058-1061.
-
(2004)
Nature
, vol.432
, pp. 1058-1061
-
-
Schawalder, S.B.1
Kabani, M.2
Howald, I.3
Choudhury, U.4
Werner, M.5
Shore, D.6
-
34
-
-
1542510106
-
Phylogenetic estimation of context-dependent substitution rates by maximum likelihood
-
Siepel, A. and Haussler, D. 2004. Phylogenetic estimation of context-dependent substitution rates by maximum likelihood. Mol. Biol. Evol. 21: 468-488.
-
(2004)
Mol. Biol. Evol.
, vol.21
, pp. 468-488
-
-
Siepel, A.1
Haussler, D.2
-
35
-
-
17944372930
-
Serial regulation of transcriptional regulators in the yeast cell cycle
-
Simon, I., Barnett, J., Hannett, N., Harbison, C.T., Rinaldi, N.J., Volkert, T.L., Wyrick, J.J., Zeitlinger, J., Gifford, D.K., Jaakkola, T.S., et al. 2001. Serial regulation of transcriptional regulators in the yeast cell cycle. Cell 106: 697-708.
-
(2001)
Cell
, vol.106
, pp. 697-708
-
-
Simon, I.1
Barnett, J.2
Hannett, N.3
Harbison, C.T.4
Rinaldi, N.J.5
Volkert, T.L.6
Wyrick, J.J.7
Zeitlinger, J.8
Gifford, D.K.9
Jaakkola, T.S.10
-
36
-
-
0031742022
-
Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization
-
Spellman, P.T., Sherlock, G., Zhang, M.Q., Iyer, V.R., Anders, K., Eisen, M.B., Brown, P.O., Botstein, D., and Futcher, B. 1998. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell 9: 3273-3297.
-
(1998)
Mol. Biol. Cell
, vol.9
, pp. 3273-3297
-
-
Spellman, P.T.1
Sherlock, G.2
Zhang, M.Q.3
Iyer, V.R.4
Anders, K.5
Eisen, M.B.6
Brown, P.O.7
Botstein, D.8
Futcher, B.9
-
37
-
-
0000133199
-
Identifying protein-binding sites from unaligned DNA fragments
-
Stormo, G.D. and Hartzell III, G.W. 1989. Identifying protein-binding sites from unaligned DNA fragments. Proc. Natl. Acad. Sci. 86: 1183-1187.
-
(1989)
Proc. Natl. Acad. Sci.
, vol.86
, pp. 1183-1187
-
-
Stormo, G.D.1
Hartzell III, G.W.2
-
38
-
-
0028344546
-
UME6 is a key regulator of nitrogen repression and meiotic development
-
Strich, R., Surosky, R.T., Steber, C., Dubois, E., Messenguy, F., and Esposito, R.E. 1994. UME6 is a key regulator of nitrogen repression and meiotic development. Genes & Dev. 8: 796-810.
-
(1994)
Genes & Dev.
, vol.8
, pp. 796-810
-
-
Strich, R.1
Surosky, R.T.2
Steber, C.3
Dubois, E.4
Messenguy, F.5
Esposito, R.E.6
-
39
-
-
3142550629
-
Multilevel modeling and inference of transcription regulation
-
Tanay, A. and Shamir, R. 2004. Multilevel modeling and inference of transcription regulation. J. Comput. Biol. 11: 357-375.
-
(2004)
J. Comput. Biol.
, vol.11
, pp. 357-375
-
-
Tanay, A.1
Shamir, R.2
-
40
-
-
2442691539
-
A global view of the selection forces in the evolution of yeast cis-regulation
-
Tanay, A., Gat-Viks, I., and Shamir, R. 2004a. A global view of the selection forces in the evolution of yeast cis-regulation. Genome Res. 14: 829-834.
-
(2004)
Genome Res.
, vol.14
, pp. 829-834
-
-
Tanay, A.1
Gat-Viks, I.2
Shamir, R.3
-
41
-
-
1542357674
-
Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genome-wide data
-
Tanay, A., Sharan, R., Kupiec, M., and Shamir, R. 2004b. Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genome-wide data. Proc. Natl. Acad. Sci. 101: 2981-2986.
-
(2004)
Proc. Natl. Acad. Sci.
, vol.101
, pp. 2981-2986
-
-
Tanay, A.1
Sharan, R.2
Kupiec, M.3
Shamir, R.4
-
42
-
-
18844374522
-
Conservation and evolvability in regulatory networks: The evolution of ribosomal regulation in yeast
-
Tanay, A., Regev, A., and Shamir, R. 2005. Conservation and evolvability in regulatory networks: The evolution of ribosomal regulation in yeast. Proc. Natl. Acad. Sci. 102: 7203-7208.
-
(2005)
Proc. Natl. Acad. Sci.
, vol.102
, pp. 7203-7208
-
-
Tanay, A.1
Regev, A.2
Shamir, R.3
-
43
-
-
11144231369
-
The transcription factor Ifh1 is a key regulator of yeast ribosomal protein genes
-
Wade, J.T., Hall, D.B., and Struhl, K. 2004. The transcription factor Ifh1 is a key regulator of yeast ribosomal protein genes. Nature 432: 1054-1058.
-
(2004)
Nature
, vol.432
, pp. 1054-1058
-
-
Wade, J.T.1
Hall, D.B.2
Struhl, K.3
-
44
-
-
0037108787
-
The Ume6 regulon coordinates metabolic and meiotic gene expression in yeast
-
Williams, R.M., Primig, M., Washburn, B.K., Winzeler, E.A., Bellis, M., Sarrauste de Menthiere, C., Davis, R.W., and Esposito, R.E. 2002. The Ume6 regulon coordinates metabolic and meiotic gene expression in yeast. Proc. Natl. Acad. Sci. 99: 13431-13436.
-
(2002)
Proc. Natl. Acad. Sci.
, vol.99
, pp. 13431-13436
-
-
Williams, R.M.1
Primig, M.2
Washburn, B.K.3
Winzeler, E.A.4
Bellis, M.5
Sarrauste De Menthiere, C.6
Davis, R.W.7
Esposito, R.E.8
|