Microscopic simulation of membrane molecule diffusion on corralled membrane surfaces (2008)
Niehaus, Anne Marie S., Vlachos, Dionisios G., Edwards, Jeremy S., Plechac, Petr, Tribe, Roger
The current understanding of how receptors diffuse and cluster in the plasma membrane is limited. Data from single-particle tracking and laser tweezer experiments have suggested that membrane...
Neema Jamshidi, Jeremy S. Edwards, Tom Fahl, George M. Church, Bernhard O. Palsson
Dynamic simulation of the human red blood cell
Designing experiments that aid in the identification of regulatory networks (2006)
Kauffman, Kenneth J., Ogunnaike, Babatunde A., Edwards, Jeremy S.
Predictive mathematical models of the interactions of a genetic network can provide insight into the mechanisms of gene regulation, the role of various genes within a network and how multiple genes...
Designing experiments that aid in the identification of regulatory networks (2006)
Kauffman, Kenneth J., Ogunnaike, Babatunde A., Edwards, Jeremy S.
Predictive mathematical models of the interactions of a genetic network can provide insight into the mechanisms of gene regulation, the role of various genes within a network and how multiple genes...
Computational modeling reveals molecular details of epidermal growth factor binding (2005)
Mayawala, Kapil, Vlachos, Dionisios G, Edwards, Jeremy S
Abstract Background The ErbB family of receptors are dysregulated in a number of cancers, and the signaling pathway of this receptor family is a critical target for several anti-cancer drugs....
[Abstract] [Full Text] [PDF] Multiscale Modeling of Cardiac Cellular Energetics (2005)
Ramprasad Ramakrishna, Jeremy S. Edwards, Andrew Mcculloch, O. Palsson, Am J Physiol, Regulatory Integrative, ...
You might find this additional information useful... This article cites 15 articles, 4 of which you can access free at:
Chatterjee, Abhijit, Mayawala, Kapil, Edwards, Jeremy S., Vlachos, Dionisios G.
Summary: Developing a quantitative understanding of intracellular networks requires simulations and computational analyses. However, traditional differential equation modeling tools are often...
Chatterjee, Abhijit, Mayawala, Kapil, Edwards, Jeremy S., Vlachos, Dionisios G.
Summary: Developing a quantitative understanding of intracellular networks requires simulations and computational analyses. However, traditional differential equation modeling tools are often...
Detection of allelic variations of human gene expression by polymerase colonies (2004)
Butz, James A, Yan, Hai, Mikkilineni, Venugopal, Edwards, Jeremy S
Abstract Background Quantification of variations of human gene expression is complicated by the small differences between different alleles. Recent work has shown that variations do exist in the...
Digital Quantitative Measurements of Gene Expression (2003)
Venugopal Mikkilineni, Robi D. Mitra, Joshua Merritt, Jason R. Ditonno, George M. Church, Babatunde Ogunnaike, ...
Abstract: One of the primary goals of functional genomics is to provide a quantitative understanding of gene function. However, the success of this enterprise is dependent on the accuracy and...
Dynamic flux balance analysis of diauxic growth in escherichia coli (2002)
Radhakrishnan Mahadevan, Jeremy S. Edwards, Francis J. Doyle
ABSTRACT Flux Balance Analysis (FBA) has been used in the past to analyze microbial metabolic networks. Typically, FBA is used to study the metabolic flux at a particular steady state of the system....
Genome-Scale Metabolic Model of Helicobacter pylori 26695 (2002)
Christophe H. Schilling, Markus W. Covert, Iman Famili, George M. Church, Jeremy S. Edwards, ...
this article cannot proceed without the signature of the person who read and corrected the proof on behalf of all the authors: signature date Fn* AQ: A can be learned from the genome of...
Dynamic simulation of the human red blood cell metabolic network (2001)
Jamshidi, Neema, Edwards, Jeremy S., Fahland, Tom, Church, George M., Palsson, Bernhard O.
Summary: We have developed a Mathematica®application package to perform dynamic simulations of the red blood cell (RBC) metabolic network. The package relies on, and integrates, many years of...
Edwards, Jeremy S, Palsson, Bernhard O
Abstract Background Genome sequencing and bioinformatics are producing detailed lists of the molecular components contained in many prokaryotic organisms. From this 'parts catalogue' of a microbial...
Genome-Scale Metabolic Model of Helicobacter pylori 26695
Schilling, Christophe H., Covert, Markus W., Famili, Iman, Church, George M., Edwards, Jeremy S., Palsson, Bernhard O.
A genome-scale metabolic model of Helicobacter pylori 26695 was constructed from genome sequence annotation, biochemical, and physiological data. This represents an in silico model largely derived...
Merritt, Joshua, DiTonno, Jason R., Mitra, Robi D., Church, George M., Edwards, Jeremy S.
We describe a strategy to analyze the impact of single nucleotide mutations on protein function. Our method utilizes a combination of yeast functional complementation, growth competition of mutant...
Detection of allelic variations of human gene expression by polymerase colonies
Butz, James A, Yan, Hai, Mikkilineni, Venugopal, Edwards, Jeremy S
Description and analysis of metabolic connectivity and dynamics in the human red blood cell.
Kauffman, Kenneth J, Pajerowski, John David, Jamshidi, Neema, Palsson, Bernhard O, Edwards, Jeremy S
The human red blood cell (hRBC) metabolic network is relatively simple compared with other whole cell metabolic networks, yet too complicated to study without the aid of a computer model. Systems...
Dynamic flux balance analysis of diauxic growth in Escherichia coli.
Mahadevan, Radhakrishnan, Edwards, Jeremy S, Doyle, Francis J
Flux Balance Analysis (FBA) has been used in the past to analyze microbial metabolic networks. Typically, FBA is used to study the metabolic flux at a particular steady state of the system. However,...
MAPK Cascade Possesses Decoupled Controllability of Signal Amplification and Duration
Mayawala, Kapil, Gelmi, Claudio A., Edwards, Jeremy S.
The three important characteristics of the output signal of mitogen activated protein kinase (MAPK) cascade are time delay between stimulus and response, amplitude gain, and duration of the output...
Genome-Scale Metabolic Model of Helicobacter pylori 26695
Schilling, Christophe H., Covert, Markus W., Famili, Iman, Church, George M., Edwards, Jeremy S., Palsson, Bernhard O.
A genome-scale metabolic model of Helicobacter pylori 26695 was constructed from genome sequence annotation, biochemical, and physiological data. This represents an in silico model largely derived...
Merritt, Joshua, DiTonno, Jason R., Mitra, Robi D., Church, George M., Edwards, Jeremy S.
We describe a strategy to analyze the impact of single nucleotide mutations on protein function. Our method utilizes a combination of yeast functional complementation, growth competition of mutant...
Detection of allelic variations of human gene expression by polymerase colonies
Butz, James A, Yan, Hai, Mikkilineni, Venugopal, Edwards, Jeremy S
Description and analysis of metabolic connectivity and dynamics in the human red blood cell.
Kauffman, Kenneth J, Pajerowski, John David, Jamshidi, Neema, Palsson, Bernhard O, Edwards, Jeremy S
The human red blood cell (hRBC) metabolic network is relatively simple compared with other whole cell metabolic networks, yet too complicated to study without the aid of a computer model. Systems...
Dynamic flux balance analysis of diauxic growth in Escherichia coli.
Mahadevan, Radhakrishnan, Edwards, Jeremy S, Doyle, Francis J
Flux Balance Analysis (FBA) has been used in the past to analyze microbial metabolic networks. Typically, FBA is used to study the metabolic flux at a particular steady state of the system. However,...
MAPK Cascade Possesses Decoupled Controllability of Signal Amplification and Duration
Mayawala, Kapil, Gelmi, Claudio A., Edwards, Jeremy S.
The three important characteristics of the output signal of mitogen activated protein kinase (MAPK) cascade are time delay between stimulus and response, amplitude gain, and duration of the output...
q-bio 2007: a watershed moment in modern biology
Edwards, Jeremy S, Faeder, James R, Hlavacek, William S, Jiang, Yi, Nemenman, Ilya, Wall, Michael E
Parallel analysis of tetramerization domain mutants of the human p53 protein using PCR colonies
Merritt, Joshua, Roberts, Kim G., Butz, James A., Edwards, Jeremy S.
A highly-parallel yeast functional assay, capable of screening approximately 100–1,000 mutants in parallel and designed to screen the activity of transcription activator proteins, was utilized to...
Microscopic Simulation of Membrane Molecule Diffusion on Corralled Membrane Surfaces
Niehaus, Anne Marie S., Vlachos, Dionisios G., Edwards, Jeremy S., Plechac, Petr, Tribe, Roger
The current understanding of how receptors diffuse and cluster in the plasma membrane is limited. Data from single-particle tracking and laser tweezer experiments have suggested that membrane...