Stochastic kinetic analysis of transcriptional feedback models for circadian rhythms. - Daniel E. Zak; Francis J. Doyle III; Dionisios G. Vlachos; James S. Schwaber (CDC, 2001)

Sensitivity analysis of oscillatory (bio)chemical systems. - Daniel E. Zak; Jörg Stelling; Francis J. Doyle III (Comput. Chem. Eng., 2005)

Unconventional systems analysis problems in molecular biology: a case study in gene regulatory network modeling. - Daniel E. Zak; Rajanikanth Vadigepalli; Gregory E. Gonye; Francis J. Doyle III; James S. Schwaber; Babatunde A. Ogunnaike (Comput. Chem. Eng., 2005)

Uncovering a Macrophage Transcriptional Program by Integrating Evidence from Motif Scanning and Expression Dynamics. - Stephen A. Ramsey; Sandy L. Klemm; Daniel E. Zak; Kathleen A. Kennedy; Vesteinn Thorsson; Bin Li; Mark Gilchrist; Elizabeth S. Gold; Carrie D. Johnson; Vladimir Litvak; Garnet Navarro; Jared C. Roach; et al. (PLoS Comput. Biol., 2008)

Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites. - Stephen A. Ramsey; Theo A. Knijnenburg; Kathleen A. Kennedy; Daniel E. Zak; Mark Gilchrist; Elizabeth S. Gold; Carrie D. Johnson; Aaron E. Lampano; Vladimir Litvak; Garnet Navarro; Tetyana Stolyar; Alan Aderem; et al. (Bioinform., 2010)