-
1
-
-
0036532201
-
Deciphering gene expression regulatory networks
-
10.1016/S0959-437X(02)00277-0, 11893484
-
Wyrick JJ, Young RA. Deciphering gene expression regulatory networks. Curr Opin Genet Dev 2002, 12:130-136. 10.1016/S0959-437X(02)00277-0, 11893484.
-
(2002)
Curr Opin Genet Dev
, vol.12
, pp. 130-136
-
-
Wyrick, J.J.1
Young, R.A.2
-
2
-
-
7744225947
-
Transcriptional networks: reverse-engineering gene regulation on a global scale
-
10.1016/j.mib.2004.10.009, 15556037
-
Chua G, Robinson MD, Morris Q, Hughes TR. Transcriptional networks: reverse-engineering gene regulation on a global scale. Curr Opin Microbiol 2004, 7:638-646. 10.1016/j.mib.2004.10.009, 15556037.
-
(2004)
Curr Opin Microbiol
, vol.7
, pp. 638-646
-
-
Chua, G.1
Robinson, M.D.2
Morris, Q.3
Hughes, T.R.4
-
3
-
-
0037174671
-
Transcriptional regulatory networks in Saccharomyces cerevisiae
-
10.1126/science.1075090, 12399584
-
Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, Zeitlinger J, Jennings EG, Murray HL, Gordon DB, Ren B, Wyrick JJ, Tagne JB, Volkert TL, Fraenkel E, Gifford DK, Young RA. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 2002, 298:799-804. 10.1126/science.1075090, 12399584.
-
(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
Zeitlinger, J.11
Jennings, E.G.12
Murray, H.L.13
Gordon, D.B.14
Ren, B.15
Wyrick, J.J.16
Tagne, J.B.17
Volkert, T.L.18
Fraenkel, E.19
Gifford, D.K.20
Young, R.A.21
more..
-
4
-
-
2442537233
-
Gene regulatory network growth by duplication
-
10.1038/ng1340, 15107850
-
Teichmann SA, Babu MM. Gene regulatory network growth by duplication. Nat Genet 2004, 36:492-496. 10.1038/ng1340, 15107850.
-
(2004)
Nat Genet
, vol.36
, pp. 492-496
-
-
Teichmann, S.A.1
Babu, M.M.2
-
5
-
-
0029058555
-
Transcriptional regulation in the yeast GAL gene family: a complex genetic network
-
Lohr D, Venkov P, Zlatanova J. Transcriptional regulation in the yeast GAL gene family: a complex genetic network. FASEB J 1995, 9:777-787.
-
(1995)
FASEB J
, vol.9
, pp. 777-787
-
-
Lohr, D.1
Venkov, P.2
Zlatanova, J.3
-
6
-
-
27744450664
-
A comparative analysis of the GAL genetic switch between not-so distant cousins: Saccharomyces cerevisiae versus Kluyveromyces lactis
-
10.1016/j.femsyr.2005.05.003, 16014343
-
Rubio-Texeira M. A comparative analysis of the GAL genetic switch between not-so distant cousins: Saccharomyces cerevisiae versus Kluyveromyces lactis. FEMS Yeast Res 2005, 5:1115-1128. 10.1016/j.femsyr.2005.05.003, 16014343.
-
(2005)
FEMS Yeast Res
, vol.5
, pp. 1115-1128
-
-
Rubio-Texeira, M.1
-
7
-
-
33745195271
-
Yeast Gal4: a transcriptional paradigm revisited
-
10.1038/sj.embor.7400679, 1479557, 16670683
-
Traven A, Jelicic B, Sopta M. Yeast Gal4: a transcriptional paradigm revisited. EMBO Rep 2006, 7:496-499. 10.1038/sj.embor.7400679, 1479557, 16670683.
-
(2006)
EMBO Rep
, vol.7
, pp. 496-499
-
-
Traven, A.1
Jelicic, B.2
Sopta, M.3
-
8
-
-
0035805255
-
Integrated genomic and proteomic analyses of a systematically perturbed metabolic network
-
10.1126/science.292.5518.929, 11340206
-
Ideker T, Thorsson V, Ranish JA, Christmas R, Buhler J, Eng JK, Bumgarner R, Goodlett DR, Aebersold R, Hood L. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 2001, 292:929-934. 10.1126/science.292.5518.929, 11340206.
-
(2001)
Science
, vol.292
, pp. 929-934
-
-
Ideker, T.1
Thorsson, V.2
Ranish, J.A.3
Christmas, R.4
Buhler, J.5
Eng, J.K.6
Bumgarner, R.7
Goodlett, D.R.8
Aebersold, R.9
Hood, L.10
-
9
-
-
18744361871
-
Enhancement of cellular memory by reducing stochastic transitions
-
10.1038/nature03524, 15889097
-
Acar M, Becskei A, van Oudenaarden A. Enhancement of cellular memory by reducing stochastic transitions. Nature 2005, 435:228-232. 10.1038/nature03524, 15889097.
-
(2005)
Nature
, vol.435
, pp. 228-232
-
-
Acar, M.1
Becskei, A.2
van Oudenaarden, A.3
-
10
-
-
4944252431
-
Autoregulation of regulatory proteins is key for dynamic operation of GAL switch in Saccharomyces cerevisiae
-
10.1016/j.febslet.2004.09.001, 15474022
-
Ruhela A, Verma M, Edwards JS, Bhat PJ, Bhartiya S, Venkatesh KV. Autoregulation of regulatory proteins is key for dynamic operation of GAL switch in Saccharomyces cerevisiae. FEBS Lett 2004, 576:119-126. 10.1016/j.febslet.2004.09.001, 15474022.
-
(2004)
FEBS Lett
, vol.576
, pp. 119-126
-
-
Ruhela, A.1
Verma, M.2
Edwards, J.S.3
Bhat, P.J.4
Bhartiya, S.5
Venkatesh, K.V.6
-
11
-
-
33748311990
-
Dual feedback loops in the GAL regulon suppress cellular heterogeneity in yeast
-
10.1038/ng1869, 16936734
-
Ramsey SA, Smith JJ, Orrell D, Marelli M, Petersen TW, deAtauri P, Bolouri H, Aitchison JD. Dual feedback loops in the GAL regulon suppress cellular heterogeneity in yeast. Nat Genet 2006, 38:1082-1087. 10.1038/ng1869, 16936734.
-
(2006)
Nat Genet
, vol.38
, pp. 1082-1087
-
-
Ramsey, S.A.1
Smith, J.J.2
Orrell, D.3
Marelli, M.4
Petersen, T.W.5
deAtauri, P.6
Bolouri, H.7
Aitchison, J.D.8
-
12
-
-
77950863293
-
Remarkably ancient balanced polymorphisms in a multi-locus gene network
-
10.1038/nature08791, 2834422, 20164837
-
Hittinger CT, Goncalves P, Sampaio JP, Dover J, Johnston M, Rokas A. Remarkably ancient balanced polymorphisms in a multi-locus gene network. Nature 2010, 464:54-58. 10.1038/nature08791, 2834422, 20164837.
-
(2010)
Nature
, vol.464
, pp. 54-58
-
-
Hittinger, C.T.1
Goncalves, P.2
Sampaio, J.P.3
Dover, J.4
Johnston, M.5
Rokas, A.6
-
13
-
-
34250204870
-
Transcriptional rewiring of fungal galactose-metabolism circuitry
-
10.1016/j.cub.2007.05.017, 17540568
-
Martchenko M, Levitin A, Hogues H, Nantel A, Whiteway M. Transcriptional rewiring of fungal galactose-metabolism circuitry. Curr Biol 2007, 17:1007-1013. 10.1016/j.cub.2007.05.017, 17540568.
-
(2007)
Curr Biol
, vol.17
, pp. 1007-1013
-
-
Martchenko, M.1
Levitin, A.2
Hogues, H.3
Nantel, A.4
Whiteway, M.5
-
14
-
-
77953399342
-
Multiple GAL pathway gene clusters evolved independently and by different mechanisms in fungi
-
10.1073/pnas.0914418107, 2890473, 20479238
-
Slot JC, Rokas A. Multiple GAL pathway gene clusters evolved independently and by different mechanisms in fungi. Proc Natl Acad Sci USA 2010, 107:10136-10141. 10.1073/pnas.0914418107, 2890473, 20479238.
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, pp. 10136-10141
-
-
Slot, J.C.1
Rokas, A.2
-
15
-
-
4644304792
-
Parallel inactivation of multiple GAL pathway genes and ecological diversification in yeasts
-
10.1073/pnas.0404319101, 521130, 15381776
-
Hittinger CT, Rokas A, Carroll SB. Parallel inactivation of multiple GAL pathway genes and ecological diversification in yeasts. Proc Natl Acad Sci USA 2004, 101:14144-14149. 10.1073/pnas.0404319101, 521130, 15381776.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 14144-14149
-
-
Hittinger, C.T.1
Rokas, A.2
Carroll, S.B.3
-
16
-
-
0030947344
-
Molecular evidence for an ancient duplication of the entire yeast genome
-
10.1038/42711, 9192896
-
Wolfe KH, Shields DC. Molecular evidence for an ancient duplication of the entire yeast genome. Nature 1997, 387:708-713. 10.1038/42711, 9192896.
-
(1997)
Nature
, vol.387
, pp. 708-713
-
-
Wolfe, K.H.1
Shields, D.C.2
-
17
-
-
1942452749
-
Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae
-
10.1038/nature02424, 15004568
-
Kellis M, Birren BW, Lander ES. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 2004, 428:617-624. 10.1038/nature02424, 15004568.
-
(2004)
Nature
, vol.428
, pp. 617-624
-
-
Kellis, M.1
Birren, B.W.2
Lander, E.S.3
-
18
-
-
0025997532
-
Galactokinase encoded by GAL1 is a bifunctional protein required for induction of the GAL genes in Kluyveromyces lactis and is able to suppress the gal3 phenotype in Saccharomyces cerevisiae
-
361914, 1922058
-
Meyer J, Walker-Jonah A, Hollenberg CP. Galactokinase encoded by GAL1 is a bifunctional protein required for induction of the GAL genes in Kluyveromyces lactis and is able to suppress the gal3 phenotype in Saccharomyces cerevisiae. Mol Cell Biol 1991, 11:5454-5461. 361914, 1922058.
-
(1991)
Mol Cell Biol
, vol.11
, pp. 5454-5461
-
-
Meyer, J.1
Walker-Jonah, A.2
Hollenberg, C.P.3
-
19
-
-
0021471049
-
Sequences that regulate the divergent GAL1-GAL10 promoter in Saccharomyces cerevisiae
-
368932, 6092912
-
Johnston M, Davis RW. Sequences that regulate the divergent GAL1-GAL10 promoter in Saccharomyces cerevisiae. Mol Cell Biol 1984, 4:1440-1448. 368932, 6092912.
-
(1984)
Mol Cell Biol
, vol.4
, pp. 1440-1448
-
-
Johnston, M.1
Davis, R.W.2
-
20
-
-
0024066720
-
Yeast regulatory gene GAL3: carbon regulation; UASGal elements in common with GAL1, GAL2, GAL7, GAL10, GAL80, and MEL1; encoded protein strikingly similar to yeast and Escherichia coli galactokinases
-
363581, 3062381
-
Bajwa W, Torchia TE, Hopper JE. Yeast regulatory gene GAL3: carbon regulation; UASGal elements in common with GAL1, GAL2, GAL7, GAL10, GAL80, and MEL1; encoded protein strikingly similar to yeast and Escherichia coli galactokinases. Mol Cell Biol 1988, 8:3439-3447. 363581, 3062381.
-
(1988)
Mol Cell Biol
, vol.8
, pp. 3439-3447
-
-
Bajwa, W.1
Torchia, T.E.2
Hopper, J.E.3
-
21
-
-
35148863240
-
Gene duplication and the adaptive evolution of a classic genetic switch
-
10.1038/nature06151, 17928853
-
Hittinger CT, Carroll SB. Gene duplication and the adaptive evolution of a classic genetic switch. Nature 2007, 449:677-681. 10.1038/nature06151, 17928853.
-
(2007)
Nature
, vol.449
, pp. 677-681
-
-
Hittinger, C.T.1
Carroll, S.B.2
-
22
-
-
0022429106
-
The OR control system of bacteriophage lambda. A physical chemical model for gene regulation
-
10.1016/0022-2836(85)90086-5, 3157005
-
Shea MA, Ackers GK. The OR control system of bacteriophage lambda. A physical chemical model for gene regulation. J Mol Biol 1985, 181:211-230. 10.1016/0022-2836(85)90086-5, 3157005.
-
(1985)
J Mol Biol
, vol.181
, pp. 211-230
-
-
Shea, M.A.1
Ackers, G.K.2
-
23
-
-
0037965981
-
On schemes of combinatorial transcription logic
-
10.1073/pnas.0930314100, 404558, 12702751
-
Buchler NE, Gerland U, Hwa T. On schemes of combinatorial transcription logic. Proc Natl Acad Sci USA 2003, 100:5136-5141. 10.1073/pnas.0930314100, 404558, 12702751.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 5136-5141
-
-
Buchler, N.E.1
Gerland, U.2
Hwa, T.3
-
25
-
-
33749511375
-
Exact simulation of hybrid stochastic and deterministic models for biochemical systems
-
Alfonsi A, Cances E, Turinici G, Ventura BD, Huisinga W. Exact simulation of hybrid stochastic and deterministic models for biochemical systems. ESAIM Proc 2005, 14:113.
-
(2005)
ESAIM Proc
, vol.14
, pp. 113
-
-
Alfonsi, A.1
Cances, E.2
Turinici, G.3
Ventura, B.D.4
Huisinga, W.5
-
26
-
-
1342309249
-
Hybrid simulation of cellular behavior
-
10.1093/bioinformatics/btg409, 14960457
-
Kiehl TR, Mattheyses RM, Simmons MK. Hybrid simulation of cellular behavior. Bioinformatics 2004, 20:316-322. 10.1093/bioinformatics/btg409, 14960457.
-
(2004)
Bioinformatics
, vol.20
, pp. 316-322
-
-
Kiehl, T.R.1
Mattheyses, R.M.2
Simmons, M.K.3
-
27
-
-
34548788551
-
Hybrid stochastic and deterministic simulations of calcium blips
-
10.1529/biophysj.106.099879, 1959544, 17496042
-
Rudiger S, Shuai JW, Huisinga W, Nagaiah C, Warnecke G, Parker I, Falcke M. Hybrid stochastic and deterministic simulations of calcium blips. Biophys J 2007, 93:1847-1857. 10.1529/biophysj.106.099879, 1959544, 17496042.
-
(2007)
Biophys J
, vol.93
, pp. 1847-1857
-
-
Rudiger, S.1
Shuai, J.W.2
Huisinga, W.3
Nagaiah, C.4
Warnecke, G.5
Parker, I.6
Falcke, M.7
-
28
-
-
22944451159
-
Accurate hybrid stochastic simulation of a system of coupled chemical or biochemical reactions
-
10.1063/1.1835951, 15740306
-
Salis H, Kaznessis Y. Accurate hybrid stochastic simulation of a system of coupled chemical or biochemical reactions. J Chem Phys 2005, 122:54103. 10.1063/1.1835951, 15740306.
-
(2005)
J Chem Phys
, vol.122
, pp. 54103
-
-
Salis, H.1
Kaznessis, Y.2
-
29
-
-
0031029852
-
Stochastic mechanisms in gene expression
-
10.1073/pnas.94.3.814, 19596, 9023339
-
McAdams HH, Arkin A. Stochastic mechanisms in gene expression. Proc Natl Acad Sci USA 1997, 94:814-819. 10.1073/pnas.94.3.814, 19596, 9023339.
-
(1997)
Proc Natl Acad Sci USA
, vol.94
, pp. 814-819
-
-
McAdams, H.H.1
Arkin, A.2
-
30
-
-
0031879114
-
Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells
-
1460268, 9691025
-
Arkin A, Ross J, McAdams HH. Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells. Genetics 1998, 149:1633-1648. 1460268, 9691025.
-
(1998)
Genetics
, vol.149
, pp. 1633-1648
-
-
Arkin, A.1
Ross, J.2
McAdams, H.H.3
-
31
-
-
84959747425
-
Toward defining the course of evolution: minimum change for a specific tree topology
-
Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Systematic Zoology 1971, 20(4):406-416.
-
(1971)
Systematic Zoology
, vol.20
, Issue.4
, pp. 406-416
-
-
Fitch, W.M.1
-
32
-
-
23144432213
-
Optimality and evolutionary tuning of the expression level of a protein
-
10.1038/nature03842, 16049495
-
Dekel E, Alon U. Optimality and evolutionary tuning of the expression level of a protein. Nature 2005, 436:588-592. 10.1038/nature03842, 16049495.
-
(2005)
Nature
, vol.436
, pp. 588-592
-
-
Dekel, E.1
Alon, U.2
-
33
-
-
0035811161
-
In vivo dynamics of galactose metabolism in Saccharomyces cerevisiae: metabolic fluxes and metabolite levels
-
10.1002/bit.1075, 11320512
-
Ostergaard S, Olsson L, Nielsen J. In vivo dynamics of galactose metabolism in Saccharomyces cerevisiae: metabolic fluxes and metabolite levels. Biotechnol Bioeng 2001, 73:412-425. 10.1002/bit.1075, 11320512.
-
(2001)
Biotechnol Bioeng
, vol.73
, pp. 412-425
-
-
Ostergaard, S.1
Olsson, L.2
Nielsen, J.3
-
34
-
-
51649124324
-
The roles of galactitol, galactose-1-phosphate, and phosphoglucomutase in galactose-induced toxicity in Saccharomyces cerevisiae
-
10.1002/bit.21890, 18421797
-
de Jongh WA, Bro C, Ostergaard S, Regenberg B, Olsson L, Nielsen J. The roles of galactitol, galactose-1-phosphate, and phosphoglucomutase in galactose-induced toxicity in Saccharomyces cerevisiae. Biotechnol Bioeng 2008, 101:317-326. 10.1002/bit.21890, 18421797.
-
(2008)
Biotechnol Bioeng
, vol.101
, pp. 317-326
-
-
de Jongh, W.A.1
Bro, C.2
Ostergaard, S.3
Regenberg, B.4
Olsson, L.5
Nielsen, J.6
-
35
-
-
0022684387
-
A GAL family of upstream activating sequences in yeast: roles in both induction and repression of transcription
-
1166805, 3011415
-
Bram RJ, Lue NF, Kornberg RD. A GAL family of upstream activating sequences in yeast: roles in both induction and repression of transcription. EMBO J 1986, 5:603-608. 1166805, 3011415.
-
(1986)
EMBO J
, vol.5
, pp. 603-608
-
-
Bram, R.J.1
Lue, N.F.2
Kornberg, R.D.3
-
36
-
-
34547881101
-
Transcriptional rewiring: the proof is in the eating
-
10.1016/j.cub.2007.06.025, 17714646
-
Rokas A, Hittinger CT. Transcriptional rewiring: the proof is in the eating. Curr Biol 2007, 17:R626-628. 10.1016/j.cub.2007.06.025, 17714646.
-
(2007)
Curr Biol
, vol.17
-
-
Rokas, A.1
Hittinger, C.T.2
-
37
-
-
77954369394
-
Experimental and steady-state analysis of the GAL regulatory system in Kluyveromyces lactis
-
10.1111/j.1742-4658.2010.07708.x, 20528923
-
Pannala VR, Bhartiya S, Venkatesh KV. Experimental and steady-state analysis of the GAL regulatory system in Kluyveromyces lactis. FEBS J 2010, 277:2987-3002. 10.1111/j.1742-4658.2010.07708.x, 20528923.
-
(2010)
FEBS J
, vol.277
, pp. 2987-3002
-
-
Pannala, V.R.1
Bhartiya, S.2
Venkatesh, K.V.3
-
38
-
-
33645429016
-
Exact stochastic simulation of coupled chemical reactions
-
Gillespie DT. Exact stochastic simulation of coupled chemical reactions. J Phys Chem 1977, 81:2340-2361.
-
(1977)
J Phys Chem
, vol.81
, pp. 2340-2361
-
-
Gillespie, D.T.1
-
39
-
-
0035865264
-
Gal80-Gal80 interaction on adjacent Gal4p binding sites is required for complete GAL gene repression
-
10.1093/emboj/20.4.841, 145427, 11179228
-
Melcher K, Xu HE. Gal80-Gal80 interaction on adjacent Gal4p binding sites is required for complete GAL gene repression. EMBO J 2001, 20:841-851. 10.1093/emboj/20.4.841, 145427, 11179228.
-
(2001)
EMBO J
, vol.20
, pp. 841-851
-
-
Melcher, K.1
Xu, H.E.2
-
40
-
-
33749395388
-
The galactose switch in Kluyveromyces lactis depends on nuclear competition between Gal4 and Gal1 for Gal80 binding
-
10.1074/jbc.M604271200, 16867978
-
Anders A, Lilie H, Franke K, Kapp L, Stelling J, Gilles ED, Breunig KD. The galactose switch in Kluyveromyces lactis depends on nuclear competition between Gal4 and Gal1 for Gal80 binding. J Biol Chem 2006, 281:29337-29348. 10.1074/jbc.M604271200, 16867978.
-
(2006)
J Biol Chem
, vol.281
, pp. 29337-29348
-
-
Anders, A.1
Lilie, H.2
Franke, K.3
Kapp, L.4
Stelling, J.5
Gilles, E.D.6
Breunig, K.D.7
-
41
-
-
0030776030
-
Nuclear pore complex number and distribution throughout the Saccharomyces cerevisiae cell cycle by three-dimensional reconstruction from electron micrographs of nuclear envelopes
-
25696, 9362057
-
Winey M, Yarar D, Giddings TH, Mastronarde DN. Nuclear pore complex number and distribution throughout the Saccharomyces cerevisiae cell cycle by three-dimensional reconstruction from electron micrographs of nuclear envelopes. Mol Biol Cell 1997, 8:2119-2132. 25696, 9362057.
-
(1997)
Mol Biol Cell
, vol.8
, pp. 2119-2132
-
-
Winey, M.1
Yarar, D.2
Giddings, T.H.3
Mastronarde, D.N.4
-
42
-
-
0023803638
-
Cooperative DNA binding of the yeast transcriptional activator GAL4
-
10.1073/pnas.85.2.382, 279552, 3124106
-
Giniger E, Ptashne M. Cooperative DNA binding of the yeast transcriptional activator GAL4. Proc Natl Acad Sci USA 1988, 85:382-386. 10.1073/pnas.85.2.382, 279552, 3124106.
-
(1988)
Proc Natl Acad Sci USA
, vol.85
, pp. 382-386
-
-
Giniger, E.1
Ptashne, M.2
|