Daniel E. Zak

Article Importance of Input Perturbations and Stochastic Gene Expression in the Reverse Engineering of Genetic Regulatory Networks: Insights From an Identifiability Analysis of an In Silico Network (2008)

Daniel E. Zak, Gregory E. Gonye, James S. Schwaber

Gene expression profiles are an increasingly common data source that can yield insights into the functions of cells at a system-wide level. The present work considers the limitations in information...

Quantifying gene network connectivity in silico: Scalability and accuracy of a modular approach (2006)

Yalamanchili, Nirupama, Zak, Daniel E., Ogunnaike, Babatunde A., Schwaber, James S., Kriete, Andres, Kholodenko, Boris N.

Large, complex data sets that are generated from microarray experiments, create a need for systematic analysis techniques to unravel the underlying connectivity of gene regulatory networks. A modular...

Systems analysis of circadian time-dependent neuronal epidermal growth factor receptor signaling (2006)

Zak, Daniel E, Hao, Haiping, Vadigepalli, Rajanikanth, Miller, Gregory M, Ogunnaike, Babatunde A, Schwaber, James S

Abstract Background Identifying the gene regulatory networks governing physiological signal integration remains an important challenge in circadian biology. Epidermal growth factor receptor (EGFR)...

Systems analysis of circadian time-dependent neuronal epidermal growth factor receptor signaling (2006)

Zak, Daniel E., Hao, Haiping, Vadigepalli, Rajanikanth, Miller, Gregory M., Ogunnaike, Babatunde A., Schwaber, James S.

Background Identifying the gene regulatory networks governing physiological signal integration remains an important challenge in circadian biology. Epidermal growth factor receptor (EGFR) has been...

Systems analysis of circadian time-dependent neuronal epidermal growth factor receptor signaling (2006)

Zak, Daniel E., Hao, Haiping, Vadigepalli, Rajanikanth, Miller, Gregory M., Ogunnaike, Babatunde A., Schwaber, James S.

Background Identifying the gene regulatory networks governing physiological signal integration remains an important challenge in circadian biology. Epidermal growth factor receptor (EGFR) has been...

Importance of Input Perturbations and Stochastic Gene Expression in the Reverse Engineering of Genetic Regulatory Networks: Insights From an Identifiability Analysis of an In Silico Network (2003)

Zak, Daniel E., Gonye, Gregory E., Schwaber, James S., Doyle, Francis J.

Gene expression profiles are an increasingly common data source that can yield insights into the functions of cells at a system-wide level. The present work considers the limitations in information...

Importance of Input Perturbations and Stochastic Gene Expression in the Reverse Engineering of Genetic Regulatory Networks: Insights From an Identifiability Analysis of an In Silico Network

Zak, Daniel E., Gonye, Gregory E., Schwaber, James S., Doyle, Francis J.

Gene expression profiles are an increasingly common data source that can yield insights into the functions of cells at a system-wide level. The present work considers the limitations in information...

Importance of Input Perturbations and Stochastic Gene Expression in the Reverse Engineering of Genetic Regulatory Networks: Insights From an Identifiability Analysis of an In Silico Network

Zak, Daniel E., Gonye, Gregory E., Schwaber, James S., Doyle, Francis J.

Gene expression profiles are an increasingly common data source that can yield insights into the functions of cells at a system-wide level. The present work considers the limitations in information...

Systems analysis of circadian time-dependent neuronal epidermal growth factor receptor signaling

Zak, Daniel E, Hao, Haiping, Vadigepalli, Rajanikanth, Miller, Gregory M, Ogunnaike, Babatunde A, Schwaber, James S

A systems level analysis of circadian time-dependent signaling via the epidermal growth factor receptor in the suprachiasmatic nucleus suggests several transcription factors that mediate the...

Modeling the VPAC2-Activated cAMP/PKA Signaling Pathway: From Receptor to Circadian Clock Gene Induction

Hao, Haiping, Zak, Daniel E., Sauter, Thomas, Schwaber, James, Ogunnaike, Babatunde A.

Increasing evidence suggests an important role for VPAC2-activated signal transduction pathways in maintaining a synchronized biological clock in the suprachiasmatic nucleus (SCN). Activation of the...

Uncovering a Macrophage Transcriptional Program by Integrating Evidence from Motif Scanning and Expression Dynamics

Ramsey, Stephen A., Klemm, Sandy L., Zak, Daniel E., Kennedy, Kathleen A., Thorsson, Vesteinn, Li, Bin, ...

Macrophages are versatile immune cells that can detect a variety of pathogen-associated molecular patterns through their Toll-like receptors (TLRs). In response to microbial challenge, the...