the effect of cell division on expression patterns of the segment polarity genes
Gains and Optimal Design in Signaling Pathways (2009)
Madalena Chaves, Eduardo D. Sontag, Robert J. Dinerstein
Abstract — Signal amplification and other input-to-output properties of signaling cascades are characterized by the H∞ gain in the case of linear systems, or by the L 2 induced norm in the...
Shape, Size, and Robustness: Feasible Regions in the Parameter Space of Biochemical Networks (2009)
Adel Dayarian, Madalena Chaves, Eduardo D. Sontag, Anirvan M. Sengupta
The concept of robustness of regulatory networks has received much attention in the last decade. One measure of robustness has been associated with the volume of the feasible region, namely, the...
Comparison between Boolean and piecewise affine differential models for genetic networks (2009)
Chaves, Madalena, Tournier, Laurent, Gouze, Jean-Luc
Multi-level discrete models of genetic networks, or the more general piecewise affine differential models, provide qualitative information on the dynamics of the system, based on a small number of...
Comparison between Boolean and piecewise affine differential models for genetic networks (2009)
Chaves, Madalena, Tournier, Laurent, Gouze, Jean-Luc
Multi-level discrete models of genetic networks, or the more general piecewise affine differential models, provide qualitative information on the dynamics of the system, based on a small number of...
Uncovering operational interactions in genetic networks using asynchronous boolean dynamics (2008)
Tournier, Laurent, Chaves, Madalena
To analyze and gain intuition on the mechanisms of complex systems of large dimensions, one strategy is to simplify the model by identifying a reduced system, in the form of a smaller set of...
Uncovering operational interactions in genetic networks using asynchronous boolean dynamics (2008)
Tournier, Laurent, Chaves, Madalena
To analyze and gain intuition on the mechanisms of complex systems of large dimensions, one strategy is to simplify the model by identifying a reduced system, in the form of a smaller set of...
Poster Submission Title: Preservation of bistability in the reduction of an apoptosis model (2008)
Steffen Waldherr, Thomas Eissing, Madalena Chaves, S. Waldherr, T. Eissing, M. Chaves, ...
Contact
Uncovering operational interactions in genetic networks using asynchronous boolean dynamics (2008)
Tournier, Laurent, Chaves, Madalena
To analyze and gain intuition on the mechanisms of complex systems of large dimensions, one strategy is to simplify the model by identifying a reduced system, in the form of a smaller set of...
Uncovering operational interactions in genetic networks using asynchronous boolean dynamics (2008)
Tournier, Laurent, Chaves, Madalena
To analyze and gain intuition on the mechanisms of complex systems of large dimensions, one strategy is to simplify the model by identifying a reduced system, in the form of a smaller set of...
Bistability preserving model reduction in apoptosis (2007)
Waldherr, Steffen, Eissing, Thomas, Chaves, Madalena, Allgower, Frank
Biological systems are typically very complex and need to be reduced before they are amenable to a thorough analysis. Also, they often possess functionally important dynamic features like...
J. Math. Biol. DOI 10.1007/s00285-008-0230-y Mathematical Biology (2007)
Madalena Chaves, Anirvan Sengupta, Eduardo D. Sontag, M. Chaves, A. Sengupta
Geometry and topology of parameter space: investigating measures of robustness in regulatory networks
Methods of robustness analysis for Boolean models of gene control networks (2006)
Chaves, Madalena, Sontag, Eduardo D., Albert, Reka
As a discrete approach to genetic regulatory networks, Boolean models provide an essential qualitative description of the structure of interactions among genes and proteins. Boolean models generally...
Robustness and fragility of Boolean models for genetic regulatory networks (2005)
Chaves, Madalena, Albert, Reka, Sontag, Eduardo D.
Interactions between genes and gene products give rise to complex circuits that enable cells to process information and respond to external signals. Theoretical studies often describe these...
Computation of amplification for systems arising from cellular signaling pathways (2004)
Sontag, Eduardo D., Chaves, Madalena
A commonly employed measure of the signal amplification properties of an input/output system is its induced L2 norm, sometimes also known as "H infinity" gain. In general, however, it is extremely...
Optimal Length and Signal Amplification in Weakly Activated Signal Transduction Cascades (2004)
Madalena Chaves, Eduardo D. Sontag, Robert J. Dinerstein
Weakly activated signaling cascades can be modeled as linear systems. The input-to-output transfer function and the internal gain of a linear system provide natural measures for the propagation of...
Optimal length and signal amplification in weakly activated signal transduction cascades (2003)
Chaves, Madalena, Sontag, Eduardo D., Dinerstein, Robert J.
Weakly activated signaling cascades can be modeled as linear systems. The input-to-output transfer function and the internal gain of a linear system, provide natural measures for the propagation of...
A parameter-robust observer as an application of iss techniques (2002)
Systems that model chemical networks are often defined through a set of parameters (the reaction rate constants) whose values may be determined with a small margin of error. These parameters will...
Vehicle networks: Achieving regular formation (2002)
Madalena Chaves, Robert Day, Lucia Gomez-ramos, Parthasarathi Nag, Anca Williams, Wei Zhang, ...
Abstract. In this paper we will consider a network of vehicles exchanging information among themselves with the intention of achieving a specified polygonal formation. The network achieves the...
State-estimators for chemical reaction networks of Feinberg-Horn-Jackson zero-deficiency type (2001)
Madalena Chaves, Eduardo D. Sontag
This paper provides a necessary and sufficient condition for detectability, and an explicit construction of observers when this condition is satisfied, for chemical reaction networks of the...
State-estimators for chemical reaction networks of Feinberg-Horn-Jackson zero deficiency type (2000)
Chaves, Madalena, Sontag, Eduardo D.
One of the most interesting questions in control theory is that of constructing observers. Observers compute estimates of the internal states of a dynamical system, using data provided by measurement...
Shape, Size, and Robustness: Feasible Regions in the Parameter Space of Biochemical Networks
Dayarian, Adel, Chaves, Madalena, Sontag, Eduardo D., Sengupta, Anirvan M.
The concept of robustness of regulatory networks has received much attention in the last decade. One measure of robustness has been associated with the volume of the feasible region, namely, the...
State-Estimators for Chemical Reaction Networks of Feinberg-Horn-Jackson Zero Deficiency Type
Madalena Chaves, Eduardo D. Sontag
This paper provides a necessary and sufficient condition for detectability for chemical reaction networks of the Feinberg-Horn-Jackson zero deficiency type. Under this condition, an explicit...
Studying the effect of cell division on expression patterns of the segment polarity genes
Chaves, Madalena, Albert, Réka
The segment polarity gene family, and its gene regulatory network, is at the basis of Drosophila embryonic development. The network's capacity for generating and robustly maintaining a specific gene...