-
1
-
-
48249114344
-
Evolution of the clock from yeast to man by period-doubling folds in the cellular oscillator
-
Klevecz RR, &, Li CM, (2007) Evolution of the clock from yeast to man by period-doubling folds in the cellular oscillator. Cold Spring Harb Symp Quant Biol 72, 421-429.
-
(2007)
Cold Spring Harb Symp Quant Biol
, vol.72
, pp. 421-429
-
-
Klevecz, R.R.1
Li, C.M.2
-
2
-
-
84862793209
-
The ultradian clock (∼40 min) in yeast (Saccharomyces cerevisiae)
-
In (Lloyd D. & Rossi E.L. eds), Springer, Berlin
-
Lloyd D, Murray DB, Klevecz RR, Wolf J, &, Kuriyama H, (2008) The ultradian clock (∼40 min) in yeast (Saccharomyces cerevisiae). In Ultradian Rhythms from Molecules to Mind: A New Vision of Life (, Lloyd D, &, Rossi EL, eds), pp. 11-42. Springer, Berlin.
-
(2008)
Ultradian Rhythms from Molecules to Mind: A New Vision of Life
, pp. 11-42
-
-
Lloyd, D.1
Murray, D.B.2
Klevecz, R.R.3
Wolf, J.4
Kuriyama, H.5
-
3
-
-
0842342616
-
A genomewide oscillation in transcription gates DNA replication and cell cycle
-
DOI 10.1073/pnas.0306490101
-
Klevecz RR, Bolen J, Forrest G, &, Murray DB, (2004) A genomewide oscillation in transcription gates DNA replication and cell cycle. Proc Natl Acad Sci USA 101, 1200-1205. (Pubitemid 38182666)
-
(2004)
Proceedings of the National Academy of Sciences of the United States of America
, vol.101
, Issue.5
, pp. 1200-1205
-
-
Klevecz, R.R.1
Bolen, J.2
Forrest, G.3
Murray, D.B.4
-
4
-
-
33750823409
-
A rapid genome-scale response of the transcriptional oscillator to perturbation reveals a period-doubling path to phenotypic change
-
DOI 10.1073/pnas.0604860103
-
Li CM, &, Klevecz RR, (2006) A rapid genome-scale response of the transcriptional oscillator to perturbation reveals a period-doubling path to phenotypic change. Proc Natl Acad Sci USA 103, 16254-16259. (Pubitemid 44715183)
-
(2006)
Proceedings of the National Academy of Sciences of the United States of America
, vol.103
, Issue.44
, pp. 16254-16259
-
-
Li, C.M.1
Klevecz, R.R.2
-
5
-
-
33847778663
-
Regulation of yeast oscillatory dynamics
-
DOI 10.1073/pnas.0606677104
-
Murray DB, Beckmann M, &, Kitano H, (2007) Regulation of yeast oscillatory dynamics. Proc Natl Acad Sci USA 104, 2241-2246. (Pubitemid 46391382)
-
(2007)
Proceedings of the National Academy of Sciences of the United States of America
, vol.104
, Issue.7
, pp. 2241-2246
-
-
Murray, D.B.1
Beckmann, M.2
Kitano, H.3
-
6
-
-
27944487902
-
Cell biology: Logic of the yeast metabolic cycle: Temporal compartmentalization of cellular processes
-
DOI 10.1126/science.1120499
-
Tu BP, Kudlicki A, Rowicka M, &, McKnight SL, (2005) Logic of the yeast metabolic cycle: temporal compartmentalization of cellular processes. Science 310, 1152-1158. (Pubitemid 41681736)
-
(2005)
Science
, vol.310
, Issue.5751
, pp. 1152-1158
-
-
Tu, B.P.1
Kudlicki, A.2
Rowicka, M.3
McKnight, S.L.4
-
7
-
-
36749067297
-
Cyclic changes in metabolic state during the life of a yeast cell
-
Tu BP, Mohler RE, Liu JC, Dombek KM, Young ET, Synovec RE, &, McKnight SL, (2007) Cyclic changes in metabolic state during the life of a yeast cell. Proc Natl Acad Sci USA 104, 16886-168891.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 16886-168891
-
-
Tu, B.P.1
Mohler, R.E.2
Liu, J.C.3
Dombek, K.M.4
Young, E.T.5
Synovec, R.E.6
McKnight, S.L.7
-
8
-
-
0037867771
-
Generation and maintenance of synchrony in Saccharomyces cerevisiae continuous culture
-
DOI 10.1016/S0014-4827(03)00068-5
-
Murray DB, Klevecz RR, &, Lloyd D, (2003) Generation and maintenance of synchrony in Saccharomyces cerevisiae continuous culture. Exp Cell Res 287, 10-15. (Pubitemid 36683196)
-
(2003)
Experimental Cell Research
, vol.287
, Issue.1
, pp. 10-15
-
-
Murray, D.B.1
Klevecz, R.R.2
Lloyd, D.3
-
9
-
-
0034734908
-
Ultradian oscillation of Saccharomyces cerevisiae during aerobic continuous culture: Hydrogen sulphide mediates population synchrony
-
Sohn HY, Murray DB, &, Kuriyama H, (2000) Ultradian oscillation of Saccharomyces cerevisiae during aerobic continuous culture: hydrogen sulphide mediates population synchrony. Yeast 16, 1185-1190.
-
(2000)
Yeast
, vol.16
, pp. 1185-1190
-
-
Sohn, H.Y.1
Murray, D.B.2
Kuriyama, H.3
-
10
-
-
0024278876
-
Oscillations in continuous cultures of budding yeast: A segregated parameter analysis
-
Porro D, Martegani E, Ranzi BM, &, Alberghina L, (1988) Oscillations in continuous cultures of budding yeast: a segregated parameter analysis. Biotechnol Bioeng 32, 411-417.
-
(1988)
Biotechnol Bioeng
, vol.32
, pp. 411-417
-
-
Porro, D.1
Martegani, E.2
Ranzi, B.M.3
Alberghina, L.4
-
11
-
-
0037648781
-
The Gts1 protein stabilizes the autonomous oscillator in yeast
-
DOI 10.1002/yea.976
-
Adams CA, Kuriyama H, Lloyd D, &, Murray DB, (2003) The Gts1 protein stabilizes the autonomous oscillator in yeast. Yeast 20, 463-470. (Pubitemid 36582283)
-
(2003)
Yeast
, vol.20
, Issue.6
, pp. 463-470
-
-
Adams, C.A.1
Kuriyama, H.2
Lloyd, D.3
Murray, D.B.4
-
12
-
-
0036651116
-
+, monoamine oxidase type A inhibitors) perturb the ultradian clock in Saccharomyces cerevisiae
-
DOI 10.1076/brhm.33.3.351.8256
-
Salgado E, Murray DB, &, Lloyd D, (2002) Some antidepressant agents (Li, monoamine oxidase type A inhibitors) perturb the ultradian clock in Saccharomyces cerevisiae. Biol Rhythm Res 33, 351-361. (Pubitemid 34969780)
-
(2002)
Biological Rhythm Research
, vol.33
, Issue.3
, pp. 351-361
-
-
Salgado, E.1
Murray, D.B.2
Lloyd, D.3
-
13
-
-
34547701946
-
Destabilization of energy-metabolism oscillation in the absence of trehalose synthesis in the chemostat culture of yeast
-
DOI 10.1016/j.abb.2007.04.029, PII S0003986107002275
-
Xu Z, &, Tsurugi K, (2007) Destabilization of energy-metabolism oscillation in the absence of trehalose synthesis in the chemostat culture of yeast. Arch Biochem Biophys 464, 350-358. (Pubitemid 47210931)
-
(2007)
Archives of Biochemistry and Biophysics
, vol.464
, Issue.2
, pp. 350-358
-
-
Xu, Z.1
Tsurugi, K.2
-
14
-
-
34347387832
-
Restriction of DNA replication to the reductive phase of the metabolic cycle protects genome integrity
-
DOI 10.1126/science.1140958
-
Chen Z, Odstrcil EA, Tu BP, &, McKnight SL, (2007) Restriction of DNA replication to the reductive phase of the metabolic cycle protects genome integrity. Science 316, 1916-1919. (Pubitemid 47025794)
-
(2007)
Science
, vol.316
, Issue.5833
, pp. 1916-1919
-
-
Chen, Z.1
Odstrcil, E.A.2
Tu, B.P.3
McKnight, S.L.4
-
15
-
-
4544352942
-
Transcriptional regulatory code of a eukaryotic genome
-
DOI 10.1038/nature02800
-
Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW, Hannett NM, Tagne JB, Reynolds DB, Yoo J, et al. (2004) Transcriptional regulatory code of a eukaryotic genome. Nature 431, 99-104. (Pubitemid 39215116)
-
(2004)
Nature
, vol.430
, Issue.7004
, pp. 99-104
-
-
Harbison, C.T.1
Gordon, D.B.2
Lee, T.I.3
Rinaldl, 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
Jennings, E.G.11
Zeitlinger, J.12
Pokholok, D.K.13
Kellis, M.14
Rolfe, P.A.15
Takusagawa, K.T.16
Lander, E.S.17
Gilford, D.K.18
Fraenkel, E.19
Young, R.A.20
more..
-
16
-
-
0027501142
-
A role for the transcription factors Mbp1 and Swi4 in progression from G1 to S phase
-
Koch C, Moll T, Neuberg M, Ahorn H, &, Nasmyth K, (1993) A role for the transcription factors Mbp1 and Swi4 in progression from G1 to S phase. Science 261, 1551-1557. (Pubitemid 23319597)
-
(1993)
Science
, vol.261
, Issue.5128
, pp. 1551-1557
-
-
Koch, C.1
Moll, T.2
Neuberg, M.3
Ahorn, H.4
Nasmyth, K.5
-
17
-
-
0034973590
-
Transcriptional profiling shows that Gcn4p is a master regulator of gene expression during amino acid starvation in yeast
-
DOI 10.1128/MCB.21.13.4347-4368.2001
-
Natarajan K, Meyer MR, Jackson BM, Slade D, Roberts C, Hinnebusch AG, &, Marton MJ, (2001) Transcriptional profiling shows that Gcn4p is a master regulator of gene expression during amino acid starvation in yeast. Mol Cell Biol 21, 4347-4368. (Pubitemid 32565316)
-
(2001)
Molecular and Cellular Biology
, vol.21
, Issue.13
, pp. 4347-4368
-
-
Natarajan, K.1
Meyer, M.R.2
Jackson, B.M.3
Slade, D.4
Roberts, C.5
Hinnebusch, A.G.6
Marton, M.J.7
-
18
-
-
0021168682
-
5' untranslated sequences are required for the translational control of a yeast regulatory gene
-
DOI 10.1073/pnas.81.16.5096
-
Thireos G, Penn MD, &, Greer H, (1984) 5â untranslated sequences are required for the translational control of a yeast regulatory gene. Proc Natl Acad Sci USA 81, 5096-5100. (Pubitemid 14008887)
-
(1984)
Proceedings of the National Academy of Sciences of the United States of America
, vol.81
, Issue.16
, pp. 5096-5100
-
-
Thireos, G.1
Penn, M.D.2
Greer, H.3
-
19
-
-
0029879360
-
The Saccharomyces cerevisiae zinc finger proteins Msn2p and Msn4p are required for transcriptional induction through the stress-response element (STRE)
-
Martinez-Pastor MT, Marchler G, Schuller C, Marchler-Bauer A, Ruis H, &, Estruch F, (1996) The Saccharomyces cerevisiae zinc finger proteins Msn2p and Msn4p are required for transcriptional induction through the stress response element (STRE). EMBO J 15, 2227-2235. (Pubitemid 26141139)
-
(1996)
EMBO Journal
, vol.15
, Issue.9
, pp. 2227-2235
-
-
Martinez-Pastor, M.T.1
Marchler, G.2
Schuller, C.3
Marchler-Bauer, A.4
Ruis, H.5
Estruch, F.6
-
20
-
-
0037080980
-
Acute glucose starvation activates the nuclear localization signal of a stress-specific yeast transcription factor
-
DOI 10.1093/emboj/21.1.135
-
Gorner W, Durchschlag E, Wolf J, Brown EL, Ammerer G, Ruis H, &, Schuller C, (2002) Acute glucose starvation activates the nuclear localization signal of a stress-specific yeast transcription factor. EMBO J 21, 135-144. (Pubitemid 34087082)
-
(2002)
EMBO Journal
, vol.21
, Issue.1-2
, pp. 135-144
-
-
Gorner, W.1
Durchschlag, E.2
Wolf, J.3
Brown, E.L.4
Ammerer, G.5
Ruis, H.6
Schuller, C.7
-
21
-
-
0033004441
-
Rpn4p acts as a transcription factor by binding to PACE, a nonamer box found upstream of 26S proteasomal and other genes in yeast
-
DOI 10.1016/S0014-5793(99)00467-6, PII S0014579399004676
-
Mannhaupt G, Schnall R, Karpov V, Vetter I, &, Feldmann H, (1999) Rpn4p acts as a transcription factor by binding to PACE, a nonamer box found upstream of 26S proteasomal and other genes in yeast. FEBS Lett 450, 27-34. (Pubitemid 29206706)
-
(1999)
FEBS Letters
, vol.450
, Issue.1-2
, pp. 27-34
-
-
Mannhaupt, G.1
Schnall, R.2
Karpov, V.3
Vetter, I.4
Feldmann, H.5
-
22
-
-
0034730140
-
Singular value decomposition for genome-wide expression data processing and modeling
-
Alter O, Brown PO, &, Botstein D, (2000) Singular value decomposition for genome-wide expression data processing and modeling. Proc Natl Acad Sci USA 97, 10101-10106.
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, pp. 10101-10106
-
-
Alter, O.1
Brown, P.O.2
Botstein, D.3
-
23
-
-
0005914137
-
Effect of the dilution rate on the mode of oscillation in continuous cultures of Saccharomyces cerevisiae
-
Beuse M, Bartling R, Kopmann A, Diekmann H, &, Thoma M, (1998) Effect of the dilution rate on the mode of oscillation in continuous cultures of Saccharomyces cerevisiae. J Biotechnol 61, 15-31.
-
(1998)
J Biotechnol
, vol.61
, pp. 15-31
-
-
Beuse, M.1
Bartling, R.2
Kopmann, A.3
Diekmann, H.4
Thoma, M.5
-
24
-
-
0035209295
-
Clock control of ultradian respiratory oscillation found during yeast continuous culture
-
DOI 10.1128/JB.183.24.7253-7259.2001
-
Murray DB, Roller S, Kuriyama H, &, Lloyd D, (2001) Clock control of ultradian respiratory oscillation found during yeast continuous culture. J Bacteriol 183, 7253-7259. (Pubitemid 33121860)
-
(2001)
Journal of Bacteriology
, vol.183
, Issue.24
, pp. 7253-7259
-
-
Murray, D.B.1
Roller, S.2
Kuriyama, H.3
Lloyd, D.4
-
25
-
-
34248993889
-
Gene expression waves: Cell cycle independent collective dynamics in cultured cells
-
DOI 10.1111/j.1742-4658.2007.05822.x
-
Tsuchiya M, Wong ST, Yeo ZX, Colosimo A, Palumbo MC, Farina L, Crescenzi M, Mazzola A, Negri R, Bianchi MM, et al. (2007) Gene expression waves. Cell cycle independent collective dynamics in cultured cells. FEBS J 274, 2878-2886. (Pubitemid 46800554)
-
(2007)
FEBS Journal
, vol.274
, Issue.11
, pp. 2878-2886
-
-
Tsuchyia, M.1
Wong, S.T.2
Yeo, Z.X.3
Colosimo, A.4
Palumbo, M.C.5
Farina, L.6
Crescenzi, M.7
Mazzola, A.8
Negri, R.9
Bianchi, M.M.10
Selvarajoo, K.11
Tomita, M.12
Giuliani, A.13
-
26
-
-
78649675624
-
Evaluating gene expression dynamics using pairwise RNA FISH data
-
Wyart M, Botstein D, &, Wingreen NS, (2010) Evaluating gene expression dynamics using pairwise RNA FISH data. PLoS Comput Biol 6, e1000979.
-
(2010)
PLoS Comput Biol
, vol.6
-
-
Wyart, M.1
Botstein, D.2
Wingreen, N.S.3
-
27
-
-
77951081705
-
Metabolic cycling in single yeast cells from unsynchronized steady-state populations limited on glucose or phosphate
-
et al
-
Silverman SJ, Petti AA, Slavov N, Parsons L, Briehof R, Thiberge SY, Zenklusen D, Gandhi SJ, Larson DR, Singer RH, et al. (2010) Metabolic cycling in single yeast cells from unsynchronized steady-state populations limited on glucose or phosphate. Proc Natl Acad Sci USA 107, 6946-6951.
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, pp. 6946-6951
-
-
Silverman, S.J.1
Petti, A.A.2
Slavov, N.3
Parsons, L.4
Briehof, R.5
Thiberge, S.Y.6
Zenklusen, D.7
Gandhi, S.J.8
Larson, D.R.9
Singer, R.H.10
-
28
-
-
78651390996
-
True or false: All genes are rhythmic
-
Ptitsyn AA, &, Gimble JM, (2011) True or false: all genes are rhythmic. Ann Med 43, 1-12.
-
(2011)
Ann Med
, vol.43
, pp. 1-12
-
-
Ptitsyn, A.A.1
Gimble, J.M.2
-
29
-
-
34347341785
-
Digital signal processing reveals circadian baseline oscillation in majority of mammalian genes
-
Ptitsyn AA, Zvonic S, &, Gimble JM, (2007) Digital signal processing reveals circadian baseline oscillation in majority of mammalian genes. PLOS Comput Biol 3, e120.
-
(2007)
PLOS Comput Biol
, vol.3
-
-
Ptitsyn, A.A.1
Zvonic, S.2
Gimble, J.M.3
-
30
-
-
33646886193
-
A potential mechanism of energy-metabolism oscillation in an aerobic chemostat culture of the yeast Saccharomyces cerevisiae
-
DOI 10.1111/j.1742-4658.2006.05201.x
-
Xu Z, &, Tsurugi K, (2006) A potential mechanism of energy-metabolism oscillation in an aerobic chemostat culture of the yeast Saccharomyces cerevisiae. FEBS J 273, 1696-1709. (Pubitemid 43779823)
-
(2006)
FEBS Journal
, vol.273
, Issue.8
, pp. 1696-1709
-
-
Xu, Z.1
Tsurugi, K.2
-
31
-
-
0026492327
-
Oscillatory metabolism of Saccharomyces cerevisiae in continuous culture
-
Satroutdinov AD, Kuriyama H, &, Kobayashi H, (1992) Oscillatory metabolism of Saccharomyces cerevisiae in continuous culture. FEMS Microbiol Lett 77, 261-267.
-
(1992)
FEMS Microbiol Lett
, vol.77
, pp. 261-267
-
-
Satroutdinov, A.D.1
Kuriyama, H.2
Kobayashi, H.3
-
32
-
-
77953027564
-
Driving ribosome assembly
-
Kressler D, Hurt E, &, Bassler J, (2010) Driving ribosome assembly. Biochimica Et Biophysica Acta-Mol Cell Res 1803, 673-683.
-
(2010)
Biochimica et Biophysica Acta - Mol Cell Res
, vol.1803
, pp. 673-683
-
-
Kressler, D.1
Hurt, E.2
Bassler, J.3
-
33
-
-
73249132431
-
Powering through ribosome assembly
-
Strunk BS, &, Karbstein K, (2009) Powering through ribosome assembly. RNA 15, 2083-2104.
-
(2009)
RNA
, vol.15
, pp. 2083-2104
-
-
Strunk, B.S.1
Karbstein, K.2
-
34
-
-
66149138898
-
Periodic fermentor yield and enhanced product enrichment from autonomous oscillations
-
Stowers CC, Robertson JB, Ban H, Tanner RD, &, Boczko EM, (2009) Periodic fermentor yield and enhanced product enrichment from autonomous oscillations. Appl Biochem Biotechnol 156, 59-75.
-
(2009)
Appl Biochem Biotechnol
, vol.156
, pp. 59-75
-
-
Stowers, C.C.1
Robertson, J.B.2
Ban, H.3
Tanner, R.D.4
Boczko, E.M.5
-
35
-
-
79959199873
-
Coupling among growth rate response, metabolic cycle, and cell division cycle in yeast
-
Slavov N, &, Botstein D, (2011) Coupling among growth rate response, metabolic cycle, and cell division cycle in yeast. Mol Biol Cell 22, 1997-2009.
-
(2011)
Mol Biol Cell
, vol.22
, pp. 1997-2009
-
-
Slavov, N.1
Botstein, D.2
-
36
-
-
34447271553
-
A tuneable attractor underlies yeast respiratory dynamics
-
DOI 10.1016/j.biosystems.2006.09.032, PII S0303264706001833
-
Murray DB, &, Lloyd D, (2007) A tuneable attractor underlies yeast respiratory dynamics. Biosystems 90, 287-294. (Pubitemid 47039275)
-
(2007)
BioSystems
, vol.90
, Issue.1
, pp. 287-294
-
-
Murray, D.B.1
Lloyd, D.2
-
37
-
-
33846796117
-
Observation of a chaotic multioscillatory metabolic attractor by real-time monitoring of a yeast continuous culture
-
DOI 10.1111/j.1742-4658.2007.05651.x
-
Roussel MR, &, Lloyd D, (2007) Observation of a chaotic multioscillatory metabolic attractor by real-time monitoring of a yeast continuous culture. FEBS J 274, 1011-1018. (Pubitemid 46204420)
-
(2007)
FEBS Journal
, vol.274
, Issue.4
, pp. 1011-1018
-
-
Roussel, M.R.1
Lloyd, D.2
-
38
-
-
34547667386
-
Signal processing and the design of microarray time-series experiments
-
DOI 10.1385/1-59745-390-0:75, Microarray Data Analysis: Methods and Applications
-
Klevecz RR, Li CM, &, Bolen JL, (2007) Signal processing and the design of microarray time-series experiments. Methods Mol Biol 377, 75-94. (Pubitemid 350183366)
-
(2007)
Methods in Molecular Biology
, vol.377
, pp. 75-94
-
-
Klevecz, R.R.1
Li, C.M.2
Bolen, J.L.3
-
39
-
-
0034069495
-
Gene ontology: Tool for the unification of biology
-
DOI 10.1038/75556
-
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25, 25-29. (Pubitemid 30257031)
-
(2000)
Nature Genetics
, vol.25
, Issue.1
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
Butler, H.5
Cherry, J.M.6
Davis, A.P.7
Dolinski, K.8
Dwight, S.S.9
Eppig, J.T.10
Harris, M.A.11
Hill, D.P.12
Issel-Tarver, L.13
Kasarskis, A.14
Lewis, S.15
Matese, J.C.16
Richardson, J.E.17
Ringwald, M.18
Rubin, G.M.19
Sherlock, G.20
more..
-
40
-
-
12344269924
-
GO::TermFinder - Open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes
-
DOI 10.1093/bioinformatics/bth456
-
Boyle EI, Weng S, Gollub J, Jin H, Botstein D, Cherry JM, &, Sherlock G, (2004) GO::TermFinder-open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics 20, 3710-3715. (Pubitemid 40136825)
-
(2004)
Bioinformatics
, vol.20
, Issue.18
, pp. 3710-3715
-
-
Boyle, E.I.1
Weng, S.2
Gollub, J.3
Jin, H.4
Botstein, D.5
Cherry, J.M.6
Sherlock, G.7
|