Modeling transcriptional control in gene networks - Methods, recent results, and future directions

Bulletin of Mathematical Biology

Volumn 62, Issue 2, 2000, Pages 247-292

  Smolen, Paul ^a   Baxter, Douglas A ^a   Byrne, John H ^a  

^a UNIVERSITY OF TEXAS MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR;

CIRCADIAN RHYTHM; COMPUTER SIMULATION; FLUORESCENCE IN SITU HYBRIDIZATION; GENETIC TRANSCRIPTION; MATHEMATICAL MODEL; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; OLIGOMERIZATION; REVIEW;

EID: 0033782304     PISSN: 00928240     EISSN: None     Source Type: Journal    
DOI: 10.1006/bulm.1999.0155     Document Type: Article

References (140)

1. Memory suppressor genes: Inhibitory constraints on the storage of long-term memory
2. Binding of disparate transcriptional activators to nucleosomal DNA is inherently cooperative
3. The jun proto-oncogene is positively autoregulated by its product, Jun-AP-1
4. Stochastic kinetic analysis of developmental pathway bifurcation in phage λ-infected E. coli cells
5. A test case of correlation metric construction of a reaction pathway from measurements
6. Counting and classifying attractors in high dimensional dynamical systems
7. Stability of cyclic gene models for systems involving expression
8. CREB1 encodes a nuclear activator, a repressor, and a cytoplasmic modulator that form a regulatory unit critical for long-term facilitation
9. Aplysia CREB2 represses long-term facilitation: Relief of repression converts a transient facilitation into long-term functional and structural change
10. Theoretical analysis of the regulation of interferon expression during priming and blocking
11. The complete genome sequence of Escherichia coli K-12
12. Role of feedback inhibition in stabilizing the classical operon
13. 2+ imaging in Aplysia sensory neurons
14. Programming the Drosophila embryo
15. Interaction of spatial diffusion and delays in models of genetic control by repression
16. Neural and molecular bases of nonassociative and associative learning in Aplysia
17. Genome sequence of the nematode C. elegans: A platform for investigating biology
18. Mechanistic modeling of prokaryotic mRNA decay
19. 2+-regulated transcriptional repressor
20. Dynamic monitoring and quantification of gene expression in single, living cells: A molecular basis for secretory cell heterogeneity
21. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence
22. Control site location and transcriptional regulation in Escherichia coli
23. New goals for the U.S. human genome project: 1998-2003
24. Characterization and phosphorylation of CREB-like proteins in Aplysia central nervous system
25. AUTO: A program for the automatic bifurcation analysis of autonomous systems
26. The cell cycle of Escherichia coli
27. DNA topology and the global control of bacterial gene expression: Implications for the regulation of virulence gene expression
28. Cell signaling and the control of gene transcription
29. Cluster analysis and display of genome-wide expression patterns
30. Visualization of single RNA transcripts in situ
31. A third component causing variability beside environment and genotype. A reason for the limited success of a 30 year long effort to standardize laboratory animals?
32. DNA chips: Promising toys have become powerful tools
33. Exact stochastic simulation of coupled chemical reactions
34. The logical analysis of continuous, non-linear biochemical control networks
35. Impaired experience-dependent plasticity in barrel cortex of mice lacking the α and δ isoforms of CREB
36. A model for circadian oscillations in the Drosophila period (PER) protein
37. Oscillatory behavior of enzymatic control processes
38. Mathematics of cellular control processes I. Negative feedback to one gene
39. Mathematics of cellular control processes II. Positive feedback to one gene
40. Antisense oligodeoxynucleotide-mediated disruption of hippocampal cAMP response element binding protein levels impairs consolidation of memory for water maze training
41. Quantitative study of the control of HIV-1 gene expression
42. A model of excitation and adaptation in bacterial chemotaxis
43. Hippocampal plasticity involves extensive gene induction and multiple cellular mechanisms
44. Altering the level and regulation of the major sigma subunit of RNA polymerase affects gene expression and development in Bacillus subtilus
45. Statistical analysis of array expression data as applied to the problem of tamoxifen resistance
46. A composite Ets/Pit-1 binding site in the prolactin gene can mediate transcriptional responses to multiple signal transduction pathways
47. Crosstalk between the thyroid hormone and peroxisome proliferator-activated receptors in regulating peroxisome proliferator-responsive genes
48. Expression of a gene cluster kaiABC as a circadian feedback process in cyanobacteria
49. Regulated expression of the neural cell adhesion molecule L1 by specific patterns of neural impulses
50. The transcriptional program in the response of human fibroblasts to serum
51. Microbial asymmetric cell division: Localization of cell fate determinants
52. On the regulation of gene activity
53. Signal transduction from the cell surface to the nucleus through the phosphorylation of transcription factors
54. Specifying epigenetic states with autoregulatory transcription factors
55. Model genetic circuits encoding autoregulatory transcription factors
56. Accurate reading of morphogen concentrations by nuclear receptors: A formal model of complex transduction pathways
57. A model for reading morphogenetic gradients: Autocatalysis and competition at the gene level
58. Properties of learning curves under varied distributions of practice
59. Molecular basis for cytoplasmic localization
60. A stochastic model for gene induction
61. Genetically structured mathematical modeling of trp attenuator mechanism
62. The role of the leucine zipper in the fos-jun interaction
63. cAMP response element-binding protein in the amygdala is required for long- but not short-term conditioned taste aversion memory
64. The Drosophila CLOCK protein undergoes daily rhythms in abundance, phosphorylation, and interactions with the PER-TIM complex
65. A model for circadian rhythms in Drosophila incorporating the formation of a complex between the PER and TIM proteins
66. A comprehensive dynamical model of pulsatile secretion of the hypothalamo-pituitary-gonadal axis in man
67. Nuclear localization is required for function of the essential clock protein FRQ
68. A possible role in chemical carcinogenesis for epigenetic, heritable changes in gene expression
69. Cellular control models with linked positive and negative feedback and delays. I: The models
70. Oscillations in a model of repression with external control
71. Models of genetic control by repression with time delays and spatial effects
72. MAP kinase translocates into the nucleus of the presynaptic cell and is required for long-term facilitation in Aplysia
73. Stochastic mechanisms in gene expression
74. Simulation of prokaryotic genetic circuits
75. Circuit simulation of genetic networks
76. Dissection of a circadian oscillation into discrete domains
77. Chaos in high-dimensional neural and gene networks
78. A mathematical framework for describing and analyzing gene regulatory networks
79. Periodic solutions in systems of piecewise linear differential equations
80. The promoter of the gene encoding cAMP response element binding protein contains cAMP response elements: Evidence for positive autoregulation of gene transcription
81. Knowledge-based simulation of genetic regulation in bacteriophage λ
82. Inducibility and negative autoregulation of CREM: An alternative promoter directs the expression of ICER, and early response repressor
83. Mathematical model of the fission yeast cell cycle with checkpoint controls at the G1/S, G2/M, and metaphase/anaphase transitions
84. Model scenarios for evolution of the eukaryotic cell cycle
85. Cell cycle control in fission yeast and mammals: Identification of new regulatory mechanisms
86. Long-term structural remodeling in Aplysia sensory neurons requires de novo protein synthesis during a critical time period
87. Description and analysis of switchlike regulatory networks exemplified by a model of cellular iron homeostasis
88. Global analysis of steady points for systems of differential equations with sigmoid interactions
89. A methodological basis for description and analysis of systems with complex switch-like interactions
90. A model for the cooperative binding of eukaryotic regulatory proteins to nucleosomal target sites
91. A clockwork explosion!
92. Analysis of the structural properties of cAMP-responsive element binding protein (CREB) and phosphorylated CREB
93. Developmental programs in bacteria
94. Genetic variation in pathogenic bacteria
95. Recent developments in the theory of control and regulation of cellular processes
96. Of fin and fur: Mutational analysis of vertebrate embryonic development
97. Axonal transport of tubulin in Ti1 Pioneer neurons in situ
98. Transcription factors responsive to cAMP
99. Transcriptional autoregulation of the proto-oncogene fos
100. A mathematical model for the intracellular circadian rhythm generator
101. Kinesin hydrolyses one ATP per 8-nm step
102. Multiple protein factors interact with the cis-regulatory elements of the proximal promoter in a cell-specific manner and regulate transcription of the dopamine β-hydroxylase gene
103. Autoregulation - A common property of eukaryotic transcription factors?
104. Protein localization and cell fate in bacteria
105. Specific regulation of immediate-early genes by patterned neuronal activity
106. Oscillations and multiple steady states in a cyclic gene model with repression
107. Monotone semiflows generated by functional differential equations
108. Frequency selectivity, multistability, and oscillations emerge from models of genetic regulatory systems
109. Effects of macromolecular transport and stochastic fluctuations on the dynamics of genetic regulatory systems
110. Modeling clarifies the role of delays and feedback in circadian oscillators
111. Logical identification of all steady states: The concept of feedback loop characteristic states
112. Modeling the complexty of genetic networks: Understanding multigenic and pleiotropic regulation
113. The gene expression matrix: Towards the extraction of genetic network architectures
114. A model of excitation and inhibition in bacterial chemotaxis
115. Adrenergic signals direct rhythmic expression of transcriptional repressor CREM in the pineal gland
116. Positive autoregulation of the myogenic determination gene MyoD1
117. The role of feedback circuits: Positive feedback circuits are a necessary condition for positive real eigenvalues of the Jacobian matrix
118. Dynamical behaviour of biological regulatory networks - I. Biological role of feedback loops and practical use of the concept of the loop-characteristic state
119. E-CELL: A software environment for whole-cell simulation
120. Genetic dissection of consolidated memory in Drosophila melanogaster
121. The dynamics of feedback control circuits in biochemical pathways
122. A dynamic model of the E. coli phosphate-starvation response
123. Theoretical modeling of protein synthesis
124. Expression of the gene encoding transcription factor CREB: Regulation by follicle-stimulating hormone-induced cAMP signaling in primary rat sertoli cells
125. Large-scale temporal gene expression mapping of central nervous system development
126. Direct allelic variation scanning of the entire yeast genome
127. On the relationship between genomic regulatory element organization and gene regulatory dynamics
128. A mathematical model of the lac operon-inducer exclusion, catabolite repression, and diauxic growth on glucose and lactose
129. On the relation between effector concentration and the rate of induced enzyme synthesis
130. CREB as a memory modulator: Induced expression of a dCREB2 activator isoform enhances long-term memory in Drosophila
131. CREB and the formation of long-term memory
132. A two-step model for the localization of maternal mRNA in Xenopus oocytes: Involvement of microtubules and microfilaments in the translocation and anchoring of Vg1 mRNA
133. Genomic cis-regulatory logic, experimental and computational analysis of a sea urchin gene
134. Macromolecular crowding: Biochemical, biophysical, and physiological consequences