Zak DE (speaker), Egan B, Schwaber JS, Ogunnaike BA. "Gene dynamics and transcription networks," To be presented at the: American Institute of Chemical Engineers Annual Meeting, Austin, TX, November 2004.
Miller GM (speaker), Zak DE, Schwaber JS, Ogunnaike BA. "Modeling and Identification of the Gene Regulatory Network Describing the Liver Response to Corticosteroids," To be presented at the: American Institute of Chemical Engineers Annual Meeting, Austin, TX, November 2004.
Gonye GE (speaker), Vadigepalli R, Zak DE, Chakravarthula P, Liu H, Pearson RK, Schwaber JS. "Neuropeptide-dependent Transcription Regulatory Network Analysis," 14th Annual Summer Neuropeptide Conference, Miami Beach, FL, July 2004.
Zak DE (speaker), Pearson RK, Vadigepalli R, Gonye GE, Schwaber JS, Ogunnaike BA. "Assigning Significance to the Appearance of Regulatory Elements in Experimentally Defined Collections of DNA Sequences Using Empirical Reference Distributions," American Institute of Chemical Engineers Annual Meeting, San Francisco, CA, November 2003. [Abstract-PDF]
Zak DE (speaker), Lombardo TG, Kholodenko BN, Su C, Ogunnaike BN. "Modeling the Interaction of Growth Factor and Apoptosis Subsystems in Cancer," American Institute of Chemical Engineers Annual Meeting, San Francisco, CA, November 2003. [Abstract-PDF]
Vadigepalli R (speaker), Chakravarthula P, Zak DE, Schwaber JS, Gonye GE. "From Genome to Candidate Cis-regulatory Networks: A Bioinformatics Approach," American Institute of Chemical Engineers Annual Meeting, San Francisco, CA, November 2003. [Abstract-PDF]
Zak DE, Gonye GE, Schwaber JS, Doyle FJ 3rd (speaker). "Systems identification concepts in the reverse engineering of gene networks." Third International Conference on Systems Biology, Stockholm, Sweden, December 2002. [Related-Abstract] [Related-FullText] [Related-PDF] [Supplementary Material] [Model Files]
Zak DE (speaker), Doyle FJ 3rd, Pearson RK, Schwaber JS. "Experimental Design in Genetic Regulatory Network Identification: Results From In Silico Studies," American Institute of Chemical Engineers Annual Meeting, Indianapolis, IN, November 2002. [Abstract-PDF] [Extended Abstract-PDF]
Vadigepalli R, Pearson RK, Zak DE (speaker), Schwaber JS. "Qualitative Modeling Framework for Identification of Genetic Regulatory Networks," American Institute of Chemical Engineers Annual Meeting, Indianapolis, IN, November 2002. [Abstract-PDF]
Doyle FJ 3rd (speaker), Stelling J, Zak DE, Gilles D. "Conservation of Robustness in a Gene Regulatory Network Underlying Circadian Rhythms," American Institute of Chemical Engineers Annual Meeting, Indianapolis, IN, November 2002. [Abstract-PDF]
Zak DE (speaker), Doyle FJ 3rd, Schwaber JS, Pearson RK. "Genetic Regulatory Network Simulations for Data Analysis." DIMACS Workshop on Complexity in Biosystems, Piscataway, NJ, April 2002. [Abstract-PDF]
Zak DE (speaker), Doyle FJ 3rd, Vlachos DG and, Schwaber JS. "Stochastic kinetic analysis of transcriptional feedback models for circadian rhythms." 40th IEEE Conference on Decision and Control, Orlando, FL, December 2001, paper TuP01-3. [PDF]
Bennett DL (speaker), Kovak KW, Zak DE. "Optimization of Sieve-Type Distillation Trays." American Institute of Chemical Engineers Annual Meeting, Los Angeles, CA, November 1997.
Zak DE (speaker). "Structured modeling of transcription networks: computational and experimental applications in mammalian systems biology," To be presented at the: American Institute of Chemical Engineers Annual Meeting, Austin, TX, November 2004. [Abstract-PDF]
Hao H (speaker), Zak DE, Sauter T, Schwaber JS, Ogunnaike BA. "VIP signal transduction pathway modeling in SCN 2.2 cells," To be presented at the: American Institute of Chemical Engineers Annual Meeting, Austin, TX, November 2004.
Zak DE (speaker), Vadigepalli R, Schwaber JS, Gonye GE, Ogunnaike BA. "Integrating multiple genomic data types into structured models of gene regulatory networks," Fourth International Conference on Systems Biology, St. Louis, MO, November 2003. [Abstract-PDF]
Zak DE (speaker), Pearson RK, Vadigepalli R, Gonye GE, Schwaber JS, Ogunnaike BA. "Inferring transcription factor activities using empirical reference distributions," Fourth International Conference on Systems Biology, St. Louis, MO, November 2003. [Abstract-PDF]
Zak DE (speaker), Vadigepalli R, Schwaber JS, Gonye GE, Ogunnaike BA. "Integrating multiple genomic data types into structured models of gene regulatory networks," NIH-BISTI Symposium, "Digital Biology: The Emerging Paradigm", Bethesda, MD, November 2003. [Abstract-PDF]
Vadigepalli R (speaker), Chakravarthula P, Zak DE, Schwaber JS, Gonye GE. "From Genome to Candidate Cis-regulatory Networks: A Bioinformatics Approach," NIH-BISTI Symposium, "Digital Biology: The Emerging Paradigm", Bethesda, MD, November 2003. [Abstract-PDF]
Zak DE (speaker), Vadigepalli R, Schwaber JS, Gonye GE, Ogunnaike BA. "Integrating multiple genomic data types into structured models of gene regulatory networks," Greater Philadelphia Bioinformatics Alliance Symposium, Philadelphia, PA, October 2003. [Abstract-PDF]
Hao H (speaker), Sauter T, Zak DE, Schwaber JS, Ogunnaike BA. "VIP signaling transduction pathway modeling in SCN2.2 cells," Greater Philadelphia Bioinformatics Alliance Symposium, Philadelphia, PA, October 2003.
Gonye GE (speaker), Zak DE, Vadigepalli R, Liu H, Egan B, Labhart P, Schwaber JS. "Integration of Functional and Structural Genomic Data to Derive Models of Transcriptional Regulation During Angiotensin II Neuromodulation," 13th Annual Summer Neuropeptide Conference, Montauk, NY, June 2003.
Zak DE, Doyle FJ 3rd (speaker), Schwaber JS. "Local identifiability: when can genetic networks be identified from microarray data?" Third International Conference on Systems Biology, Stockholm, Sweden, December 2002. [Abstract-PDF]
Stelling J (speaker), Doyle FJ 3rd, Zak DE. "Structurally conserved robustness and fragility in oscillatory genetic circuits." Third International Conference on Systems Biology, Stockholm, Sweden, December 2002. [Abstract-PDF]
Zak, DE (speaker), Doyle, FJ 3rd, Gonye GE, Schwaber JS. "Simulation studies for the identification of genetic networks from cDNA array and regulatory activity data." Second International Conference on Systems Biology, Pasadena, CA, November 2001, poster 063. [PDF] [Model Files]
Zak DE (speaker), Slepchenko BM, Kholodenko BN. "Control of protein phosphorylation by diffusion in cellular signaling pathways." Second International Conference on Systems Biology, Pasadena, CA, November 2001, poster 006. [Abstract-PDF]