Computational studies of gene regulatory networks: in numero molecular biology

By Jeff Hasty, David R. McMillen, Farren J. Isaacs, James J. Collins. Nature reviews genetics, 2001

643 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/c4fe1fc9730bb5601803f1805072040429898be3

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

In Molecular Biology

Citations in the corpus

Thirteen Years of Building Constraint-Based In Silico Models of Escherichia coli (2003, methodology): “Many of these methodologies have been reviewed else-where (5, 20, 25, 40, 46, 52, 62).”
Regulation of noise in the expression of a single gene (2002, methodology): “The technique of translational noise control can be applied in the fast-growing field of artificial genetic network”
Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks (2002, background): “…Hartemink et al., 2001; Moler et al., 2000), neural networks (Weaver et al., 1999), differential equations (Mestl et al., 1995), and models including stochastic components on the molecular level (Arkin et al., 1998; see Smolen et al., 2000 and Hasty et al., 2001 for reviews of general models).”
Stochasticity in transcriptional regulation: origins, consequences, and mathematical representations. (2001, methodology): “We derive and solve equations for the mean waiting times for spontaneous transitions between quasistable states in these switches.”
Modeling and Simulation of Genetic Regulatory Systems: A Literature Review (2002, neutral): “While it was being prepared, several other reviews on the modeling and simulation of genetic regulatory systems appeared (Endy and Brent, 2001; Hasty et al., 2001; McAdams and Arkin, 1998; Smolen et al., 2000) [see Glass (1977), Rosen (1968), Thomas (1979) for earlier reviews].”
Transcriptional Regulation by the Numbers 2: Applications (2004, background): “Often, even qualitative features of a gene circuit (e.g., whether a circuit can be bistable or can spontaneously oscillate) cannot be determined without quantitative knowledge of the transcription regulation of key genes in the circuit [3].”
Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. (2003, background): “Excellent reviews from other perspectives can be found elsewhere [17,18 ,19–22,23 ,24 ,25], and also book-length treatments [26–29].”
Boolean Network Model Predicts Cell Cycle Sequence of Fission Yeast (2007, background): “[2] Hasty J, McMillen D, Isaacs F, Collins JJ (2001) Computational studies of gene regulatory networks: in numero molecular biology.”
Experimental Determination and System Level Analysis of Essential Genes in Escherichia coli MG1655 (2003, background): “It is widely recognized that the thousands of components of a living cell are dynamically interconnected, so that cellular functional properties are a result of the complex intracellular web of molecular interactions within the cell (14, 22, 23).”