-
1
-
-
0037438387
-
Transcriptional accessibility for genes of multiple tissues and hematopoietic lineages is hierarchically controlled during early hematopoiesis
-
K. Akashi, X. He, J. Chen, H. Iwasaki, C. Niu, B. Steenhard, J. Zhang, J. Haug and L. Li (2003) Transcriptional accessibility for genes of multiple tissues and hematopoietic lineages is hierarchically controlled during early hematopoiesis. Blood 101 383-389.
-
(2003)
Blood
, vol.101
, pp. 383-389
-
-
Akashi, K.1
He, X.2
Chen, J.3
Iwasaki, H.4
Niu, C.5
Steenhard, B.6
Zhang, J.7
Haug, J.8
Li, L.9
-
2
-
-
0032616683
-
Identification of genetic networks from a small number of gene expression patterns under the Boolean network model
-
T. Akutsu, S. Miyano and S. Kuhara (1999) Identification of genetic networks from a small number of gene expression patterns under the Boolean network model. Pac. Symp. Biocomput. 17-28.
-
(1999)
Pac. Symp. Biocomput.
, pp. 17-28
-
-
Akutsu, T.1
Miyano, S.2
Kuhara, S.3
-
3
-
-
0003880161
-
-
3d ed., New York: Garland Publishing
-
B. Alberts, D. Bray, J. Lewis, M. Raff, K. Roberts and J. Watson (1994) Molecular Biology of the Cell. 3d ed. New York: Garland Publishing
-
(1994)
Molecular Biology of the Cell
-
-
Alberts, B.1
Bray, D.2
Lewis, J.3
Raff, M.4
Roberts, K.5
Watson, J.6
-
6
-
-
1242274449
-
Detection of multistability, bifurcations, and hysteresis in a large class of biological positive-feedback systems
-
D. Angeli, J.E. Ferrell Jr. and E.D. Sontag (2004) Detection of multistability, bifurcations, and hysteresis in a large class of biological positive-feedback systems. Proc. Natl. Acad. Sci. USA 101 1822-1827.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 1822-1827
-
-
Angeli, D.1
Ferrell, J.E.2
Sontag, E.D.3
-
7
-
-
5444263735
-
Epigenetic aspects of differentiation
-
K.L. Arney and A.G. Fisher (2004) Epigenetic aspects of differentiation. J. Cell Sci. 117 4355-4363.
-
(2004)
J. Cell Sci.
, vol.117
, pp. 4355-4363
-
-
Arney, K.L.1
Fisher, A.G.2
-
8
-
-
0030574422
-
Counting and classifying attractors in high dimensional dynamical systems
-
R.J. Bagley and L. Glass (1996) Counting and classifying attractors in high dimensional dynamical systems. J. Theo. Biol. 183 269-284.
-
(1996)
J. Theo. Biol.
, vol.183
, pp. 269-284
-
-
Bagley, R.J.1
Glass, L.2
-
9
-
-
0038483826
-
Emergence of scaling in random networks
-
A.L. Barabasi and R. Albert (1999) Emergence of scaling in random networks. Science 286 509-512.
-
(1999)
Science
, vol.286
, pp. 509-512
-
-
Barabasi, A.L.1
Albert, R.2
-
11
-
-
17144456808
-
Positive feedback in eukaryotic gene networks: Cell differentiation by graded to binary response conversion
-
A. Becksei, B. Seraphin and L. Serrano (2001) Positive feedback in eukaryotic gene networks: Cell differentiation by graded to binary response conversion. EMBO J. 20 2528-2535.
-
(2001)
EMBO J.
, vol.20
, pp. 2528-2535
-
-
Becksei, A.1
Seraphin, B.2
Serrano, L.3
-
12
-
-
12444301754
-
Structure and evolution of protein interaction networks: A statistical model for link dynamics and gene duplications
-
J. Berg, M. Lassig and A. Wagner (2004) Structure and evolution of protein interaction networks: A statistical model for link dynamics and gene duplications. BMC Evol. Biol. 4 51.
-
(2004)
BMC Evol. Biol.
, vol.4
, pp. 51
-
-
Berg, J.1
Lassig, M.2
Wagner, A.3
-
13
-
-
0037047611
-
MAP kinase phosphatase as a locus of flexibility in a mitogen-activated protein kinase signaling network
-
U.S. Bhalla, P.T. Ram and R. Iyengar (2002) MAP kinase phosphatase as a locus of flexibility in a mitogen-activated protein kinase signaling network. Science 297 1018-1023.
-
(2002)
Science
, vol.297
, pp. 1018-1023
-
-
Bhalla, U.S.1
Ram, P.T.2
Iyengar, R.3
-
14
-
-
0025182223
-
Cross-talk between second messengers
-
M. Bouvier (1990) Cross-talk between second messengers. Ann. NY Acad. Sci. 594 120-129.
-
(1990)
Ann. NY Acad. Sci.
, vol.594
, pp. 120-129
-
-
Bouvier, M.1
-
15
-
-
0141596113
-
Molecular networks: The top-down view
-
D. Bray (2003) Molecular networks: The top-down view. Science 301 1864-1865.
-
(2003)
Science
, vol.301
, pp. 1864-1865
-
-
Bray, D.1
-
16
-
-
9144226389
-
Molecular signatures of self-renewal, differentiation, and lineage choice in multipotential hemopoietic progenitor cells in vitro
-
L. Bruno, R. Hoffmann, F. McBlane, J. Brown, R. Gupta, C. Joshi, S. Pearson, T. Seidl, C. Heyworth and T. Enver (2004) Molecular signatures of self-renewal, differentiation, and lineage choice in multipotential hemopoietic progenitor cells in vitro. Mol. Cell Biol. 24 741-756.
-
(2004)
Mol. Cell Biol.
, vol.24
, pp. 741-756
-
-
Bruno, L.1
Hoffmann, R.2
McBlane, F.3
Brown, J.4
Gupta, R.5
Joshi, C.6
Pearson, S.7
Seidl, T.8
Heyworth, C.9
Enver, T.10
-
17
-
-
0035474697
-
Are randomly grown graphs really random?
-
D.S. Callaway, J.E. Hopcroft, J.M. Kleinberg, M.E. Newman and S.H. Strogatz (2001) Are randomly grown graphs really random? Phys. Rev. E. Stat. Nonlin. Soft Matter Phys. 64 041902.
-
(2001)
Phys. Rev. E. Stat. Nonlin. Soft Matter Phys.
, vol.64
, pp. 041902
-
-
Callaway, D.S.1
Hopcroft, J.E.2
Kleinberg, J.M.3
Newman, M.E.4
Strogatz, S.H.5
-
18
-
-
0036790977
-
Diversity, topographic differentiation, and positional memory in human fibroblasts
-
H.Y. Chang, J.T. Chi, S. Dudoit, C. Bondre, M. van de Rijn, D. Botstein and P.O. Brown (2002) Diversity, topographic differentiation, and positional memory in human fibroblasts. Proc. Natl. Acad. Sci. USA 99 12877-12882.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 12877-12882
-
-
Chang, H.Y.1
Chi, J.T.2
Dudoit, S.3
Bondre, C.4
van de Rijn, M.5
Botstein, D.6
Brown, P.O.7
-
19
-
-
0028826488
-
PU.1 (Spi-1) autoregulates its expression in myeloid cells
-
H. Chen, D. Ray-Gallet, P. Zhang, C.J. Hetherington, D.A. Gonzalez, D.E. Zhang, F. Moreau-Gachelin and D.G. Tenen (1995) PU.1 (Spi-1) autoregulates its expression in myeloid cells. Oncogene 11 1549-1560.
-
(1995)
Oncogene
, vol.11
, pp. 1549-1560
-
-
Chen, H.1
Ray-Gallet, D.2
Zhang, P.3
Hetherington, C.J.4
Gonzalez, D.A.5
Zhang, D.E.6
Moreau-Gachelin, F.7
Tenen, D.G.8
-
20
-
-
0034696445
-
How to make a biological switch
-
J.L. Cherry and F.R. Adler (2000) How to make a biological switch. J. Theo. Biol. 203 117-133.
-
(2000)
J. Theo. Biol.
, vol.203
, pp. 117-133
-
-
Cherry, J.L.1
Adler, F.R.2
-
21
-
-
0141814720
-
Endothelial cell diversity revealed by global expression profiling
-
J.T. Chi, H.Y. Chang, G. Haraldsen, F.L. Jahnsen, O.G. Troyanskaya, D.S. Chang, Z. Wang, S.G. Rockson, M. van de Rijn, D. Botstein, et al. (2003) Endothelial cell diversity revealed by global expression profiling. Proc. Natl. Acad. Sci. USA 100 10623-10628.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 10623-10628
-
-
Chi, J.T.1
Chang, H.Y.2
Haraldsen, G.3
Jahnsen, F.L.4
Troyanskaya, O.G.5
Chang, D.S.6
Wang, Z.7
Rockson, S.G.8
van de Rijn, M.9
Botstein, D.10
-
22
-
-
0036306859
-
Positive and negative feedback: striking a balance between necessary antagonists
-
O. Cinquin and J. Demongeot (2002) Positive and negative feedback: striking a balance between necessary antagonists. J. Theo. Biol. 216 229-241.
-
(2002)
J. Theo. Biol.
, vol.216
, pp. 229-241
-
-
Cinquin, O.1
Demongeot, J.2
-
23
-
-
0023605430
-
The HL-60 promyelocytic leukemia cell line: Proliferation, differentiation, and cellular oncogene expression
-
S.J. Collins (1987) The HL-60 promyelocytic leukemia cell line: Proliferation, differentiation, and cellular oncogene expression. Blood 70 1233-1244.
-
(1987)
Blood
, vol.70
, pp. 1233-1244
-
-
Collins, S.J.1
-
25
-
-
0034574602
-
The establishment of Spemann's organizer and patterning of the vertebrate embryo
-
E.M. De Robertis, J. Larrain, M. Oelgeschlager and O. Wessely (2000) The establishment of Spemann's organizer and patterning of the vertebrate embryo. Nat. Rev. Genet. 1 171-181.
-
(2000)
Nat. Rev. Genet.
, vol.1
, pp. 171-181
-
-
De Robertis, E.M.1
Larrain, J.2
Oelgeschlager, M.3
Wessely, O.4
-
26
-
-
84956252965
-
Random networks of automata: A simple annealed approximation
-
B. Derrida and Y. Pomeau (1986) Random networks of automata: A simple annealed approximation. Europhys. Lett. 1 45-49.
-
(1986)
Europhys. Lett.
, vol.1
, pp. 45-49
-
-
Derrida, B.1
Pomeau, Y.2
-
27
-
-
0033736476
-
Genetic network inference: From co-expression clustering to reverse engineering
-
P. D'Haeseleer, S. Liang and R. Somogyi (2000) Genetic network inference: From co-expression clustering to reverse engineering. Bioinformatics 16 707-726.
-
(2000)
Bioinformatics
, vol.16
, pp. 707-726
-
-
D'Haeseleer, P.1
Liang, S.2
Somogyi, R.3
-
28
-
-
0242659156
-
Systems biology is taking off
-
M. Ehrenberg, J. Elf, E. Aurell, R. Sandberg and J. Tegner (2003) Systems biology is taking off. Genome Res. 13 2377-2380.
-
(2003)
Genome Res.
, vol.13
, pp. 2377-2380
-
-
Ehrenberg, M.1
Elf, J.2
Aurell, E.3
Sandberg, R.4
Tegner, J.5
-
29
-
-
0038692119
-
Human housekeeping genes are compact
-
E. Eisenberg and E.Y. Levanon (2003) Human housekeeping genes are compact. Trends Genet. 19 362-365.
-
(2003)
Trends Genet.
, vol.19
, pp. 362-365
-
-
Eisenberg, E.1
Levanon, E.Y.2
-
30
-
-
0035905782
-
Modelling cellular behaviour
-
D. Endy and R. Brent (2001) Modelling cellular behaviour. Nature 409 391-395.
-
(2001)
Nature
, vol.409
, pp. 391-395
-
-
Endy, D.1
Brent, R.2
-
31
-
-
0032504051
-
Loops, lineage, and leukemia
-
T. Enver and M. Greaves (1998) Loops, lineage, and leukemia. Cell 94 9-12.
-
(1998)
Cell
, vol.94
, pp. 9-12
-
-
Enver, T.1
Greaves, M.2
-
34
-
-
0033001953
-
Diverse signaling pathways activated by growth factor receptors induce broadly overlapping, rather than independent, sets of genes
-
D. Fambrough, K. McClure, A. Kazlauskas and E.S. Lander (1999) Diverse signaling pathways activated by growth factor receptors induce broadly overlapping, rather than independent, sets of genes. Cell 97 727-741.
-
(1999)
Cell
, vol.97
, pp. 727-741
-
-
Fambrough, D.1
McClure, K.2
Kazlauskas, A.3
Lander, E.S.4
-
35
-
-
0035650176
-
From topology to dynamics in biochemical networks
-
J.J. Fox and C.C. Hill (2001) From topology to dynamics in biochemical networks. Chaos 11 809-815.
-
(2001)
Chaos
, vol.11
, pp. 809-815
-
-
Fox, J.J.1
Hill, C.C.2
-
37
-
-
11244264337
-
Loss of gata1 but not gata2 converts erythropoiesis to myelopoiesis in zebrafish embryos
-
J.L. Galloway, R.A. Wingert, C. Thisse, B. Thisse and L.I. Zon (2005) Loss of gata1 but not gata2 converts erythropoiesis to myelopoiesis in zebrafish embryos. Dev. Cell 8 109-116.
-
(2005)
Dev. Cell
, vol.8
, pp. 109-116
-
-
Galloway, J.L.1
Wingert, R.A.2
Thisse, C.3
Thisse, B.4
Zon, L.I.5
-
38
-
-
36949041214
-
Connectance of large dynamic (cybernetic) systems: Critical values for stability
-
M.R. Gardner and W.R. Ashby (1970) Connectance of large dynamic (cybernetic) systems: Critical values for stability. Nature 228 784.
-
(1970)
Nature
, vol.228
, pp. 784
-
-
Gardner, M.R.1
Ashby, W.R.2
-
39
-
-
0034688174
-
Construction of a genetic toggle switch in Escherichia coli
-
T.S. Gardner, C.R. Cantor and J.J. Collins (2000) Construction of a genetic toggle switch in Escherichia coli. Nature 403 339-342.
-
(2000)
Nature
, vol.403
, pp. 339-342
-
-
Gardner, T.S.1
Cantor, C.R.2
Collins, J.J.3
-
40
-
-
0038048325
-
Inferring genetic networks and identifying compound mode of action via expression profiling
-
T.S. Gardner, D. di Bernardo, D. Lorenz and J.J. Collins (2003) Inferring genetic networks and identifying compound mode of action via expression profiling. Science 301 102-105.
-
(2003)
Science
, vol.301
, pp. 102-105
-
-
Gardner, T.S.1
di Bernardo, D.2
Lorenz, D.3
Collins, J.J.4
-
41
-
-
0036519296
-
Haematopoietic cell-fate decisions, chromatin regulation and ikaros
-
K. Georgopoulos (2002) Haematopoietic cell-fate decisions, chromatin regulation and ikaros. Nat. Rev. Immunol. 2 162-174.
-
(2002)
Nat. Rev. Immunol.
, vol.2
, pp. 162-174
-
-
Georgopoulos, K.1
-
42
-
-
4444258534
-
Chromatin architecture of the human genome: Gene-rich domains are enriched in open chromatin fibers
-
N. Gilbert, S. Boyle, H. Fiegler, K. Woodfine, N.P. Carter and W.A. Bickmore (2004) Chromatin architecture of the human genome: Gene-rich domains are enriched in open chromatin fibers. Cell 118 555-566.
-
(2004)
Cell
, vol.118
, pp. 555-566
-
-
Gilbert, N.1
Boyle, S.2
Fiegler, H.3
Woodfine, K.4
Carter, N.P.5
Bickmore, W.A.6
-
43
-
-
0345600247
-
A protein interaction map of Drosophila melanogaster
-
L. Giot, J.S. Bader, C. Brouwer, A. Chaudhuri, B. Kuang, Y. Li, Y.L. Hao, C.E. Ooi, B. Godwin, E. Vitols, et al. (2003) A protein interaction map of Drosophila melanogaster. Science 302 1727-1736.
-
(2003)
Science
, vol.302
, pp. 1727-1736
-
-
Giot, L.1
Bader, J.S.2
Brouwer, C.3
Chaudhuri, A.4
Kuang, B.5
Li, Y.6
Hao, Y.L.7
Ooi, C.E.8
Godwin, B.9
Vitols, E.10
-
44
-
-
0015609281
-
The logical analysis of continuous, non-linear biochemical control networks
-
L. Glass and S.A. Kauffman (1973) The logical analysis of continuous, non-linear biochemical control networks. J. Theo. Biol. 39 103-129.
-
(1973)
J. Theo. Biol.
, vol.39
, pp. 103-129
-
-
Glass, L.1
Kauffman, S.A.2
-
45
-
-
0003343268
-
The strategy of growth
-
H. Teir, T. Rytaumaa (Eds), London: Academic Press
-
R.J. Goss (1967) The strategy of growth. H. Teir, T. Rytaumaa (Eds) Control of Cellular Growth in the Adult Organism London: Academic Press 3-27.
-
(1967)
Control of Cellular Growth in the Adult Organism
, pp. 3-27
-
-
Goss, R.J.1
-
46
-
-
0036566226
-
Differentiation plasticity of hematopoietic cells
-
T. Graf (2002) Differentiation plasticity of hematopoietic cells. Blood 99 3089-3101.
-
(2002)
Blood
, vol.99
, pp. 3089-3101
-
-
Graf, T.1
-
47
-
-
0041806587
-
GATA-1-dependent transcriptional repression of GATA-2 via disruption of positive autoregulation and domain-wide chromatin remodeling
-
J.A. Grass, M.E. Boyer, S. Pal, J. Wu, M.J. Weiss and E.H. Bresnick (2003) GATA-1-dependent transcriptional repression of GATA-2 via disruption of positive autoregulation and domain-wide chromatin remodeling. Proc. Natl. Acad. Sci. USA 100 8811-8816.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 8811-8816
-
-
Grass, J.A.1
Boyer, M.E.2
Pal, S.3
Wu, J.4
Weiss, M.J.5
Bresnick, E.H.6
-
48
-
-
85040473565
-
A model of transcriptional regulatory networks based on biases in the observed regulation rules
-
S.E. Harris, B.K. Sawhill, A. Wuensche and S.A. Kauffman (2002) A model of transcriptional regulatory networks based on biases in the observed regulation rules. Complexity 7 23-40.
-
(2002)
Complexity
, vol.7
, pp. 23-40
-
-
Harris, S.E.1
Sawhill, B.K.2
Wuensche, A.3
Kauffman, S.A.4
-
49
-
-
0035931072
-
A compendium of gene expression in normal human tissues
-
L.L. Hsiao, F. Dangond, T. Yoshida, R. Hong, R.V. Jensen, J. Misra, W. Dillon, K.F. Lee, K.E. Clark, P. Haverty, et al. (2001) A compendium of gene expression in normal human tissues. Physiol. Genomics 7 97-104.
-
(2001)
Physiol. Genomics
, vol.7
, pp. 97-104
-
-
Hsiao, L.L.1
Dangond, F.2
Yoshida, T.3
Hong, R.4
Jensen, R.V.5
Misra, J.6
Dillon, W.7
Lee, K.F.8
Clark, K.E.9
Haverty, P.10
-
50
-
-
0030954167
-
Multilineage gene expression precedes commitment in the hemopoietic system
-
M. Hu, D. Krause, M. Greaves, S. Sharkis, M. Dexter, C. Heyworth and T. Enver (1997) Multilineage gene expression precedes commitment in the hemopoietic system. Genes Dev. 11 774-785.
-
(1997)
Genes Dev.
, vol.11
, pp. 774-785
-
-
Hu, M.1
Krause, D.2
Greaves, M.3
Sharkis, S.4
Dexter, M.5
Heyworth, C.6
Enver, T.7
-
51
-
-
0032809387
-
Gene expression profiling, genetic networks, and cellular states: An integrating concept for tumorigenesis and drug discovery
-
S. Huang (1999) Gene expression profiling, genetic networks, and cellular states: An integrating concept for tumorigenesis and drug discovery. J. Mol. Med. 77 469-480.
-
(1999)
J. Mol. Med.
, vol.77
, pp. 469-480
-
-
Huang, S.1
-
52
-
-
0034850921
-
Genomics, complexity and drug discovery: Insights from Boolean network models of cellular regulation
-
S. Huang (2001) Genomics, complexity and drug discovery: Insights from Boolean network models of cellular regulation. Pharmacogenomics 2 203-222.
-
(2001)
Pharmacogenomics
, vol.2
, pp. 203-222
-
-
Huang, S.1
-
53
-
-
2442583455
-
Regulation of cellular states in mammalian cells from a genome-wide view
-
J. Collado-Vides, R.C. Hofestadt (Eds), Cambridge, MA: MIT Press
-
S. Huang (2002) Regulation of cellular states in mammalian cells from a genome-wide view. J. Collado-Vides, R.C. Hofestadt (Eds) Gene Regulation and Metabolism: Post-Genomic Computational Approach Cambridge, MA: MIT Press 181-220.
-
(2002)
Gene Regulation and Metabolism: Post-Genomic Computational Approach
, pp. 181-220
-
-
Huang, S.1
-
54
-
-
3042721988
-
Back to the biology in systems biology: What can we learn from biomolecular networks
-
S. Huang (2004) Back to the biology in systems biology: What can we learn from biomolecular networks. Brief Funct. Genomics Proteomics 2 279-297.
-
(2004)
Brief Funct. Genomics Proteomics
, vol.2
, pp. 279-297
-
-
Huang, S.1
-
55
-
-
0034715919
-
Shape-dependent control of cell growth, differentiation, and apoptosis: Switching between attractors in cell regulatory networks
-
S. Huang and D.E. Ingber (2000) Shape-dependent control of cell growth, differentiation, and apoptosis: Switching between attractors in cell regulatory networks. Exp. Cell Res. 261 91-103.
-
(2000)
Exp. Cell Res.
, vol.261
, pp. 91-103
-
-
Huang, S.1
Ingber, D.E.2
-
56
-
-
18144408736
-
Cell fate as high-dimensional attractor of a complex gene regulatory network
-
S. Huang, G.S. Eichler, Y. Bar-Yam and D.E. Ingber (2005) Cell fate as high-dimensional attractor of a complex gene regulatory network. Phys. Rev. Lett. (in press)
-
(2005)
Phys. Rev. Lett.
-
-
Huang, S.1
Eichler, G.S.2
Bar-Yam, Y.3
Ingber, D.E.4
-
57
-
-
0034307684
-
Probability in transcriptional regulation and its implications for leukocyte differentiation and inducible gene expression
-
D.A. Hume (2000) Probability in transcriptional regulation and its implications for leukocyte differentiation and inducible gene expression. Blood 96 2323-2328.
-
(2000)
Blood
, vol.96
, pp. 2323-2328
-
-
Hume, D.A.1
-
58
-
-
0036960243
-
The changing concept of epigenetics
-
E. Jablonka and M.J. Lamb (2002) The changing concept of epigenetics. Ann. N. Y Acad. Sci. 981 82-96.
-
(2002)
Ann. N. Y Acad. Sci.
, vol.981
, pp. 82-96
-
-
Jablonka, E.1
Lamb, M.J.2
-
59
-
-
4444311806
-
A proposal for using the ensemble approach to understand genetic regulatory networks
-
S. Kauffman (2004) A proposal for using the ensemble approach to understand genetic regulatory networks. J. Theo. Biol. 230 581-590.
-
(2004)
J. Theo. Biol.
, vol.230
, pp. 581-590
-
-
Kauffman, S.1
-
61
-
-
0014489272
-
Metabolic stability and epigenesis in randomly constructed genetic nets
-
S.A. Kauffman (1969) Metabolic stability and epigenesis in randomly constructed genetic nets. J. Theo. Biol. 22 437-467.
-
(1969)
J. Theo. Biol.
, vol.22
, pp. 437-467
-
-
Kauffman, S.A.1
-
63
-
-
0842324785
-
The nucleosome: From genomic organization to genomic regulation
-
S. Khorasanizadeh (2004) The nucleosome: From genomic organization to genomic regulation. Cell 116 259-272.
-
(2004)
Cell
, vol.116
, pp. 259-272
-
-
Khorasanizadeh, S.1
-
64
-
-
0019996706
-
Amplification and adaptation in regulatory and sensory systems
-
D.E. Koshland Jr., A. Goldbeter and J.B. Stock (1982) Amplification and adaptation in regulatory and sensory systems. Science 217 220-225.
-
(1982)
Science
, vol.217
, pp. 220-225
-
-
Koshland, D.E.1
Goldbeter, A.2
Stock, J.B.3
-
65
-
-
11144277879
-
A crack in histone lysine methylation
-
S. Kubicek and T. Jenuwein (2004) A crack in histone lysine methylation. Cell 119 903-906.
-
(2004)
Cell
, vol.119
, pp. 903-906
-
-
Kubicek, S.1
Jenuwein, T.2
-
66
-
-
0842332406
-
Dynamics of the p53-Mdm2 feedback loop in individual cells
-
G. Lahav, N. Rosenfeld, A. Sigal, N. Geva-Zatorsky, A.J. Levine, M.B. Elowitz and U. Alon (2004) Dynamics of the p53-Mdm2 feedback loop in individual cells. Nat. Genet. 36 147-150.
-
(2004)
Nat. Genet.
, vol.36
, pp. 147-150
-
-
Lahav, G.1
Rosenfeld, N.2
Sigal, A.3
Geva-Zatorsky, N.4
Levine, A.J.5
Elowitz, M.B.6
Alon, U.7
-
67
-
-
0033230728
-
Multistability: A major means of differentiation and evolution in biological systems
-
M. Laurent and N. Kellershohn (1999) Multistability: A major means of differentiation and evolution in biological systems. Trends Biochem. Sci. 24 418-422.
-
(1999)
Trends Biochem. Sci.
, vol.24
, pp. 418-422
-
-
Laurent, M.1
Kellershohn, N.2
-
68
-
-
0037174671
-
Transcriptional regulatory networks in Scccharomyces cerevisiae
-
T.I. Lee, N.J. Rinaldi, F. Robert, D.T. Odom, Z. Bar-Joseph, G.K. Gerber, N.M. Hannett, C.T. Harbison, C.M. Thompson, I. Simon, et al. (2002) Transcriptional regulatory networks in Scccharomyces 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
-
69
-
-
0037213715
-
Gene expression and the myth of the average cell
-
J.M. Levsky and R.H. Singer (2003) Gene expression and the myth of the average cell. Trends Cell Biol 13 4-6.
-
(2003)
Trends Cell Biol
, vol.13
, pp. 4-6
-
-
Levsky, J.M.1
Singer, R.H.2
-
70
-
-
9144264169
-
A map of the interactome network of the metazoan C. elegans
-
S. Li, C.M. Armstrong, N. Bertin, H. Ge, S. Milstein, M. Boxem, P.O. Vidalain, J.D. Han, A. Chesneau, T. Hao, et al. (2004) A map of the interactome network of the metazoan C. elegans. Science 303 540-543.
-
(2004)
Science
, vol.303
, pp. 540-543
-
-
Li, S.1
Armstrong, C.M.2
Bertin, N.3
Ge, H.4
Milstein, S.5
Boxem, M.6
Vidalain, P.O.7
Han, J.D.8
Chesneau, A.9
Hao, T.10
-
71
-
-
0031616241
-
Reveal, a general reverse engineering algorithm for inference of genetic network architectures
-
S. Liang, S. Fuhrman and R. Somogyi (1998) Reveal, a general reverse engineering algorithm for inference of genetic network architectures. Pac. Symp. Biocomput. 18-29.
-
(1998)
Pac. Symp. Biocomput.
, pp. 18-29
-
-
Liang, S.1
Fuhrman, S.2
Somogyi, R.3
-
73
-
-
0035409444
-
The path not taken
-
E.M. Marcotte (2001) The path not taken. Nat. Biotechnol. 19 626-627.
-
(2001)
Nat. Biotechnol.
, vol.19
, pp. 626-627
-
-
Marcotte, E.M.1
-
74
-
-
0015514970
-
Will a large complex system be stable?
-
R.M. May (1972) Will a large complex system be stable? Nature 238 413-414.
-
(1972)
Nature
, vol.238
, pp. 413-414
-
-
May, R.M.1
-
75
-
-
0027375186
-
Lineage commitment in human hemopoiesis involves asymmetric cell division of multipotent progenitors and does not appear to be influenced by cytokines
-
H. Mayani, W. Dragowska and P.M. Lansdorp (1993) Lineage commitment in human hemopoiesis involves asymmetric cell division of multipotent progenitors and does not appear to be influenced by cytokines. J. Cell Physiol. 157 579-586.
-
(1993)
J. Cell Physiol.
, vol.157
, pp. 579-586
-
-
Mayani, H.1
Dragowska, W.2
Lansdorp, P.M.3
-
76
-
-
0037197962
-
Characterization of the c-MYC-regulated transcriptome by SAGE: Identification and analysis of c-MYC target genes
-
A. Menssen and H. Hermeking (2002) Characterization of the c-MYC-regulated transcriptome by SAGE: Identification and analysis of c-MYC target genes. Proc. Natl. Acad. Sci. USA 99 6274-6279.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 6274-6279
-
-
Menssen, A.1
Hermeking, H.2
-
77
-
-
0036081347
-
MIPS: A database for genomes and protein sequences
-
H.W. Mewes, D. Frishman, U. Guldener, G. Mannhaupt, K. Mayer, M. Mokrejs, B. Morgenstern, M. Munsterkotter, S. Rudd and B. Weil (2002) MIPS: A database for genomes and protein sequences. Nucleic Acids Res. 30 31-34.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 31-34
-
-
Mewes, H.W.1
Frishman, D.2
Guldener, U.3
Mannhaupt, G.4
Mayer, K.5
Mokrejs, M.6
Morgenstern, B.7
Munsterkotter, M.8
Rudd, S.9
Weil, B.10
-
78
-
-
0000702702
-
Statistical mechanics of voting
-
D.A. Meyer and T.A. Brown (1998) Statistical mechanics of voting. Phys. Rev. 81 1718-1721.
-
(1998)
Phys. Rev.
, vol.81
, pp. 1718-1721
-
-
Meyer, D.A.1
Brown, T.A.2
-
79
-
-
1542287343
-
Superfamilies of evolved and designed networks
-
R. Milo, S. Itzkovitz, N. Kashtan, R. Levitt, S. Shen-Orr, I. Ayzenshtat, M. Sheffer and U. Alon (2004) Superfamilies of evolved and designed networks. Science 303 1538-1542.
-
(2004)
Science
, vol.303
, pp. 1538-1542
-
-
Milo, R.1
Itzkovitz, S.2
Kashtan, N.3
Levitt, R.4
Shen-Orr, S.5
Ayzenshtat, I.6
Sheffer, M.7
Alon, U.8
-
80
-
-
0037174670
-
Network motifs: Simple building blocks of complex networks
-
R. Milo, S. Shen-Orr, S. Itzkovitz, N. Kashtan, D. Chklovskii and U. Alon (2002) Network motifs: Simple building blocks of complex networks. Scienc 298 824-827.
-
(2002)
Scienc
, vol.298
, pp. 824-827
-
-
Milo, R.1
Shen-Orr, S.2
Itzkovitz, S.3
Kashtan, N.4
Chklovskii, D.5
Alon, U.6
-
81
-
-
73049167504
-
Teleonomic mechanisms in cellular metabolism, growth, and differentiation
-
J. Monod and F. Jacob (1961) Teleonomic mechanisms in cellular metabolism, growth, and differentiation. Cold Spring Harb. Symp. Quant. Biol. 26 389-401.
-
(1961)
Cold Spring Harb. Symp. Quant. Biol.
, vol.26
, pp. 389-401
-
-
Monod, J.1
Jacob, F.2
-
82
-
-
0030088078
-
Chromatin diminution in nematodes
-
F. Muller, V. Bernard and H. Tobler (1996) Chromatin diminution in nematodes. Bioessays 18 133-138.
-
(1996)
Bioessays
, vol.18
, pp. 133-138
-
-
Muller, F.1
Bernard, V.2
Tobler, H.3
-
83
-
-
85147616647
-
-
Personal Coummonication
-
Myer, J. (2001). Personal Coummonication.
-
(2001)
-
-
Myer, J.1
-
84
-
-
0034656393
-
GATA-1 interacts with the myeloid PU.1 transcription factor and represses PU.1-dependent transcription
-
C. Nerlov, E. Querfurth, H. Kulessa and T. Graf (2000) GATA-1 interacts with the myeloid PU.1 transcription factor and represses PU.1-dependent transcription. Blood 95 2543-2551.
-
(2000)
Blood
, vol.95
, pp. 2543-2551
-
-
Nerlov, C.1
Querfurth, E.2
Kulessa, H.3
Graf, T.4
-
85
-
-
0001389945
-
Enzyme induction as an all-or-none phenomenon
-
A. Novick and M. Weiner (1957) Enzyme induction as an all-or-none phenomenon. Proc. Natl. Acad. Sci. USA 43 553-566.
-
(1957)
Proc. Natl. Acad. Sci. USA
, vol.43
, pp. 553-566
-
-
Novick, A.1
Weiner, M.2
-
86
-
-
10744227070
-
Control of pancreas and liver gene expression by HNF transcription factors
-
D.T. Odom, N. Zizlsperger, D.B. Gordon, G.W. Bell, N.J. Rinaldi, H.L. Murray, T.L. Volkert, J. Schreiber, P.A. Rolfe, D.K. Gifford, 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
-
87
-
-
0036435483
-
Roles of hematopoietic transcription factors GATA-1 and GATA-2 in the development of red blood cell lineage
-
K. Ohneda and M. Yamamoto (2002) Roles of hematopoietic transcription factors GATA-1 and GATA-2 in the development of red blood cell lineage. Acta Haematol. 108 237-245.
-
(2002)
Acta Haematol.
, vol.108
, pp. 237-245
-
-
Ohneda, K.1
Yamamoto, M.2
-
88
-
-
1442354192
-
Multistability in the lactose utilization network of Escherichia coli
-
E.M. Ozbudak, M. Thattai, H.N. Lim, B.I. Shraiman and A. Van Oudenaarden (2004) Multistability in the lactose utilization network of Escherichia coli. Nature 427 737-740.
-
(2004)
Nature
, vol.427
, pp. 737-740
-
-
Ozbudak, E.M.1
Thattai, M.2
Lim, H.N.3
Shraiman, B.I.4
Van Oudenaarden, A.5
-
89
-
-
0842285841
-
Summing up the noise in gene networks
-
J. Paulsson (2004) Summing up the noise in gene networks. Nature 427 415-418.
-
(2004)
Nature
, vol.427
, pp. 415-418
-
-
Paulsson, J.1
-
90
-
-
0034691214
-
Stochastic focusing: Fluctuationenhanced sensitivity of intracellular regulation
-
J. Paulsson, O.G. Berg and M. Ehrenberg (2000) Stochastic focusing: Fluctuationenhanced sensitivity of intracellular regulation. Proc. Natl. Acad. Sci. USA 97 7148-7153.
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 7148-7153
-
-
Paulsson, J.1
Berg, O.G.2
Ehrenberg, M.3
-
91
-
-
0034680102
-
Molecular portraits of human breast tumours
-
C.M. Perou, T. Sorlie, M.B. Eisen, M. van de Rijn, S.S. Jeffrey, C.A. Rees, J.R. Pollack, D.T. Ross, H. Johnsen, L.A. Akslen, et al. (2000) Molecular portraits of human breast tumours. Nature 406 747-752.
-
(2000)
Nature
, vol.406
, pp. 747-752
-
-
Perou, C.M.1
Sorlie, T.2
Eisen, M.B.3
van de Rijn, M.4
Jeffrey, S.S.5
Rees, C.A.6
Pollack, J.R.7
Ross, D.T.8
Johnsen, H.9
Akslen, L.A.10
-
93
-
-
0026504147
-
Social controls on cell survival and cell death
-
M.C. Raff (1992) Social controls on cell survival and cell death. Nature 356 397-400.
-
(1992)
Nature
, vol.356
, pp. 397-400
-
-
Raff, M.C.1
-
94
-
-
0037199968
-
Hierarchical organization of modularity in metabolic networks
-
E. Ravasz, A.L. Somera, D.A. Mongru, Z.N. Oltvai and A.L. Barabasi (2002) Hierarchical organization of modularity in metabolic networks. Science 297 1551-1555.
-
(2002)
Science
, vol.297
, pp. 1551-1555
-
-
Ravasz, E.1
Somera, A.L.2
Mongru, D.A.3
Oltvai, Z.N.4
Barabasi, A.L.5
-
95
-
-
0025237515
-
On the nature of enduring modifications induced in cells and organisms
-
H. Rubin (1990) On the nature of enduring modifications induced in cells and organisms. Am. J. Physiol. 258 L19-L24.
-
(1990)
Am. J. Physiol.
, vol.258
, pp. L19-L24
-
-
Rubin, H.1
-
96
-
-
0035162782
-
RegulonDB (version 3.2): Transcriptional regulation and operon organization in Escherichia coli K-12
-
H. Salgado, A. Santos-Zavaleta, S. Gama-Castro, D. Millan-Zarate, E. Diaz-Peredo, F. Sanchez-Solano, E. Perez-Rueda, C. Bonavides-Martinez and J. Collado-Vides (2001) RegulonDB (version 3.2): Transcriptional regulation and operon organization in Escherichia coli K-12. Nucleic Acids Res. 29 72-74.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 72-74
-
-
Salgado, H.1
Santos-Zavaleta, A.2
Gama-Castro, S.3
Millan-Zarate, D.4
Diaz-Peredo, E.5
Sanchez-Solano, F.6
Perez-Rueda, E.7
Bonavides-Martinez, C.8
Collado-Vides, J.9
-
97
-
-
0029134903
-
Michaelis-Menten mechanism reconsidered: Implications of fractal kinetics
-
M.A. Savageau (1995) Michaelis-Menten mechanism reconsidered: Implications of fractal kinetics. J. Theo. Biol. 176 115-124.
-
(1995)
J. Theo. Biol.
, vol.176
, pp. 115-124
-
-
Savageau, M.A.1
-
98
-
-
0032720438
-
GM-CSF stimulates proliferation of clonal leukemic bone marrow cells in acute myeloid leukemia (AML) in vitro
-
H.M. Schmetzer, H.H. Gerhartz and W. Wilmanns (1999) GM-CSF stimulates proliferation of clonal leukemic bone marrow cells in acute myeloid leukemia (AML) in vitro. Ann. Hematol. 78 449-455.
-
(1999)
Ann. Hematol.
, vol.78
, pp. 449-455
-
-
Schmetzer, H.M.1
Gerhartz, H.H.2
Wilmanns, W.3
-
99
-
-
0037417803
-
Hysteresis drives cell-cycle transitions in Xenopus laevis egg extracts
-
W. Sha, J. Moore, K. Chen, A.D. Lassaletta, C.S. Yi, J.J. Tyson and J.C. Sible (2003) Hysteresis drives cell-cycle transitions in Xenopus laevis egg extracts. Proc. Natl. Acad. Sci. USA 100 975-980.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 975-980
-
-
Sha, W.1
Moore, J.2
Chen, K.3
Lassaletta, A.D.4
Yi, C.S.5
Tyson, J.J.6
Sible, J.C.7
-
100
-
-
0036578795
-
Network motifs in the transcriptional regulation network of Escherichia coli
-
S.S. Shen-Orr, R. Milo, S. Mangan and U. Alon (2002) Network motifs in the transcriptional regulation network of Escherichia coli. Nat. Genet. 31 64-68.
-
(2002)
Nat. Genet.
, vol.31
, pp. 64-68
-
-
Shen-Orr, S.S.1
Milo, R.2
Mangan, S.3
Alon, U.4
-
101
-
-
85088493259
-
Activities and sensitivities in Boolean network models
-
I. Shmulevich and S.A. Kauffman (2004) Activities and sensitivities in Boolean network models. Phys. Rev. Lett. (in press)
-
(2004)
Phys. Rev. Lett.
-
-
Shmulevich, I.1
Kauffman, S.A.2
-
102
-
-
2942617034
-
Has the yo-yo stopped? An assessment of human protein-coding gene number
-
C. Southan (2004) Has the yo-yo stopped? An assessment of human protein-coding gene number. Proteomics 4 1712-1726.
-
(2004)
Proteomics
, vol.4
, pp. 1712-1726
-
-
Southan, C.1
-
103
-
-
0035826155
-
Exploring complex networks
-
S.H. Strogatz (2001) Exploring complex networks. Nature 410 268-276.
-
(2001)
Nature
, vol.410
, pp. 268-276
-
-
Strogatz, S.H.1
-
104
-
-
0242285692
-
TGF-beta switches from tumor suppressor to prometastatic factor in a model of breast cancer progression
-
B. Tang, M. Vu, T. Booker, S.J. Santner, F.R. Miller, M.R. Anver and L.M. Wakefield (2003) TGF-beta switches from tumor suppressor to prometastatic factor in a model of breast cancer progression. J. Clin. Invest. 112 1116-1124.
-
(2003)
J. Clin. Invest.
, vol.112
, pp. 1116-1124
-
-
Tang, B.1
Vu, M.2
Booker, T.3
Santner, S.J.4
Miller, F.R.5
Anver, M.R.6
Wakefield, L.M.7
-
105
-
-
10944230777
-
Duplication and divergence: The evolution of new genes and old ideas
-
J.S. Taylor and J. Raes (2004) Duplication and divergence: The evolution of new genes and old ideas. Ann. Rev. Genet. 38 615-643.
-
(2004)
Ann. Rev. Genet.
, vol.38
, pp. 615-643
-
-
Taylor, J.S.1
Raes, J.2
-
106
-
-
0018080896
-
Logical analysis of systems comprising feedback loops
-
R. Thomas (1978) Logical analysis of systems comprising feedback loops. J. Theo. Biol. 73 631-656.
-
(1978)
J. Theo. Biol.
, vol.73
, pp. 631-656
-
-
Thomas, R.1
-
107
-
-
0037376655
-
Sniffers, buzzers, toggles and blinkers: Dynamics of regulatory and signaling pathways in the cell
-
J.J. Tyson, K.C. Chen and B. Novak (2003) Sniffers, buzzers, toggles and blinkers: Dynamics of regulatory and signaling pathways in the cell. Curr. Opin. Cell Biol. 15 221-231.
-
(2003)
Curr. Opin. Cell Biol.
, vol.15
, pp. 221-231
-
-
Tyson, J.J.1
Chen, K.C.2
Novak, B.3
-
109
-
-
0032482432
-
Collective dynamics of “small-world” networks
-
D.J. Watts and S.H. Strogatz (1998) Collective dynamics of “small-world” networks. Nature 393 440-442.
-
(1998)
Nature
, vol.393
, pp. 440-442
-
-
Watts, D.J.1
Strogatz, S.H.2
-
110
-
-
0031630211
-
Genomic regulation modeled as a network with basins of attraction
-
A. Wuensche (1998) Genomic regulation modeled as a network with basins of attraction. Pac. Symp. Biocomput. 89-102.
-
(1998)
Pac. Symp. Biocomput.
, pp. 89-102
-
-
Wuensche, A.1
-
111
-
-
0345359924
-
A positive-feedback-based bistable “memory module’ that governs a cell fate decision
-
W. Xiong and J.E. Ferrell Jr. (2003) A positive-feedback-based bistable “memory module’ that governs a cell fate decision. Nature 426 460-465.
-
(2003)
Nature
, vol.426
, pp. 460-465
-
-
Xiong, W.1
Ferrell, J.E.2
-
112
-
-
0037197936
-
Reverse engineering gene networks using singular value decomposition and robust regression
-
M.K. Yeung, J. Tegner and J.J. Collins (2002) Reverse engineering gene networks using singular value decomposition and robust regression. Proc. Natl. Acad. Sci. USA 99 6163-6168.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 6163-6168
-
-
Yeung, M.K.1
Tegner, J.2
Collins, J.J.3
-
113
-
-
0034667672
-
PU.1 inhibits GATA-1 function and erythroid differentiation by blocking GATA-1 DNA binding
-
P. Zhang, X. Zhang, A. Iwama, C. Yu, K.A. Smith, B.U. Mueller, S. Narravula, B.E. Torbett, S.H. Orkin and D.G. Tenen (2000) PU.1 inhibits GATA-1 function and erythroid differentiation by blocking GATA-1 DNA binding. Blood 96 2641-2648.
-
(2000)
Blood
, vol.96
, pp. 2641-2648
-
-
Zhang, P.1
Zhang, X.2
Iwama, A.3
Yu, C.4
Smith, K.A.5
Mueller, B.U.6
Narravula, S.7
Torbett, B.E.8
Orkin, S.H.9
Tenen, D.G.10
-
114
-
-
0028364906
-
MyoD1 promoter autoregulation is mediated by two proximal E-boxes
-
J.M. Zingg, G. Pedraza-Alva and J.P. Jost (1994) MyoD1 promoter autoregulation is mediated by two proximal E-boxes. Nucleic Acids Res. 22 2234-2241.
-
(1994)
Nucleic Acids Res.
, vol.22
, pp. 2234-2241
-
-
Zingg, J.M.1
Pedraza-Alva, G.2
Jost, J.P.3
|