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Eduardo D. Sontag, PhD

Selected Publications

M. Margaliot, E.D. Sontag, and T. Tuller. Entrainment to periodic initiation and transition rates in a computational model for gene translation. PLoS ONE, 9(5):e96039, 2014.

S. Prabakaran, J. Gunawardena, and E.D. Sontag. Paradoxical results in perturbation-based signaling network reconstruction. Biophysical Journal, 106:2720-2728, 2014.

M. Skataric, E.V. Nikolaev, and E.D. Sontag. A fundamental limitation to fold-change detection by biological systems with multiple time scales. IET Systems Biology, To appear, 2014.

T.H. Segall-Shapiro, A.J. Meyer, E.D. Sontag, A.D. Ellington, and C.A. Voigt. A 'resource allocator' for transcription based on a highly fragmented T7 RNA polymerase. Nature Molecular Systems Biology, To appear, 2014.

J. Barton and E.D. Sontag. The energy costs of insulators in biochemical networks. Biophysical Journal, 104:1390-1380, 2013.

A.O. Hamadeh, B.P. Ingalls, and E.D. Sontag. Transient dynamic phenotypes as criteria for model discrimination: fold-change detection in Rhodobacter sphaeroides chemotaxis. Proc. Royal Society Interface, 10:20120935, 2013.

T. Kang, J.T. White, Z. Xie, Y. Benenson, E.D. Sontag, and L. Bleris. Reverse engineering validation using a benchmark synthetic gene circuit in human cells. ACS Synthetic Biology, 2:255-262, 2013.

L. Liu, G. Duclos, B. Sun, J. Lee, A. Wu, Y. Kam, E.D. Sontag, H.A. Stone, J.C. Sturm, R.A. Gatenby, and R.H. Austin. Minimization of thermodynamic costs in cancer cell invasion. Proc Natl Acad Sci USA, 110:1686-1691, 2013.

V. Shimoga, J.T. White, Y. Li, E.D. Sontag, and L. Bleris. Synthetic mammalian transgene negative autoregulation. Nature Molecular Systems Biology, 9:670-, 2013.

M. Miller, M. Hafner, E.D. Sontag, N. Davidsohn, S. Subramanian, P. E. M. Purnick, D. Lauffenburger, and R. Weiss. Modular design of artificial tissue homeostasis: robust control through synthetic cellular heterogeneity. PLoS Computational Biology, 8:e1002579-, 2012.

K. Wood, S. Nishida, E.D. Sontag, and P. Cluzel. Mechanism-independent method for predicting response to multiple drug exposure in bacteria. Proc Natl Acad Sci USA, 109:12254-12259, 2012.

O. Shoval, L. Goentoro, Y. Hart, A. Mayo, E.D. Sontag, and U. Alon. Fold change detection and scalar symmetry of sensory input fields. Proc Natl Acad Sci USA, 107:15995-16000, 2010.

G. Russo, M. di Bernardo, and E.D. Sontag. Global entrainment of transcriptional systems to periodic inputs. PLoS Computational Biology, 6:e1000739, 2010.

A.M. Weinstein and E.D. Sontag. Modeling proximal tubule cell homeostasis: Tracking changes in luminal flow. Bulletin of Mathematical Biology, 71:1285-1322, 2009.

T. Riley, X. Yu, E.D. Sontag, and A. Levine. The P53HMM algorithm: using novel profile Hidden Markov Models to detect p53-responsive genes. BMC Bioinformatics, 10:111, 2009.

T. Riley, E.D. Sontag, P. Chen, and A. Levine. The transcriptional regulation of human p53-regulated genes. Nature Reviews Molecular Cell Biology, 9:402-412, 2008.

D. Angeli, J. E. Ferrell, and E.D. Sontag. Detection of multistability, bifurcations, and hysteresis in a large class of biological positive-feedback systems. Proc Natl Acad Sci USA, 101(7):1822-1827, 2004.

E.D. Sontag, A. Kiyatkin, and B.N. Kholodenko. Inferring dynamic architecture of cellular networks using time series of gene expression, protein and metabolite data. Bioinformatics, 20(12):1877-1886, 2004.

M. Chaves, R.J. Dinerstein, and E.D. Sontag. Optimal length and signal amplification in weakly activated signal transduction cascades. J. Physical Chemistry, 108:15311-15320, 2004.

J. R. Pomerening, E.D. Sontag, and J. E. Ferrell. Building a cell cycle oscillator: hysteresis and bistability in the activation of cdc2. Nature Cell Biology, 5(4):346-351, 2003.

E.D. Sontag. Structure and stability of certain chemical networks and applications to the kinetic proofreading model of T-cell receptor signal transduction. IEEE Trans. Automat. Control, 46(7):1028-1047, 2001.