Ingalls, B. P., Mathematical Modeling in Systems Biology: an introduction, MIT Press, Cambridge, Massachusetts, 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. 6 (2013) doi: 10.1098 rsif.2012.0935.

Jafari, M., Zargar, B., Soltani, M., Karunaratne, D. N., Ingalls, B. and Chen, P. (2012) Intelligent Drug Delivery Systems for Cancer Therapy, in Biomedical Materials and Diagnostic Devices (eds A. Tiwari, M. Ramalingam, H. Kobayashi and A. P.F. Turner), John Wiley & Sons, Inc., Hoboken, NJ, USA. doi: 10.1002/9781118523025.ch15

Gidvani, R.~D., Sudmant, P., Li, G., DaSilva, L.~F., McConkey, B.~J., Duncker, B.~P., and Ingalls, B.~P. ``A quantitative {\em in silico} mathematical model of the initiation of DNA replication in Saccharomyces cerevisiae predicts the effects of system perturbations,'' BMC Systems Biology (2012), 6:78 doi:10.1186/1752-0509-6-78.

Meshram, M., Naderi, S., McConkey, B., Budman, H. and Scharer, J., Ingalls, B. ``Population-based modeling of the progression of apoptosis in mammalian cell culture,'' Biotechnology and Bioengineering 2012 May;109(5):1193-204. doi: 10.1002 bit.24392.

Dhawan,
A., Hamadeh, A. O. and Ingalls, B. P., “Designing synchronization
protocols in networks of coupled nodes under uncertainty,” Proceedings
of the American Control Conference,
Montreal, June 2012.

A.O. Hamadeh, B.P. Ingalls, and E.D. Sontag. Fold-Change Detection As a Chemotaxis Model Discrimination Tool. Proc. IEEE Conf. Decision and Control, Maui, Dec. 2012.

Kim, D.-R., Gidvani, R. D., Ingalls, B. P., Duncker, B. P. and McConkey, B. J., ``Differential chromatin proteomics of the MMS-induced checkpoint response in yeast'', Proteome Research (2011) 9: 62.

Wei, Y.-Y., C., Naderi, S., Meshram, M., McConkey, B., Ingalls, B., Budman, H. and Scharer, J., ``Proteomics Analysis of Protein-Producing Chinese Hamster Ovary Cells during Apoptosis in Prolonged Cultivation,'' Cytotechnology (2011) 63, pp.~663-677.

A. O. Hamadeh, E. August, M. A. J. Roberts, P. Maini, J. Armitage, B. P. Ingalls, A. Papachristodoulou, ``Feedback Control Architecture of the R. sphaeroides Chemotaxis Network,'' Proceedings of the 50th IEEE Conference on Decision and Control and European Control Conference.

Rosati, B., Yan, Q., Lee, M. S., Liou, S.-R., Ingalls, B., Foell, J., Kamp, T. J., and McKinnon, D. ``Robust L-Type Calcium Current Expression following Heterozygous Knockout of the Cav1.2 Gene in Adult Mouse Heart,'' The Journal of Physiology (2011) 589 pp. 3275-3288.

Naderi, S., Meshram, M., Wei, C., McConkey, B., Ingalls, B., Budman, H. and Scharer, J., ``Development of a mathematical model for evaluating the dynamics of normal and apoptotic CHO cells in batch culture,'' Biotechnology Progress (2011) DOI: 10.1002/btpr.647.

Ang, J., Ingalls, B. and McMillen, D. ``Probing the Input-Output Behaviour of Biochemical and Genetic Systems: Systems Identification Methods from Control Theory,'' Methods in Enzymology 487 (2011) Computer Methods, Part C, Johnson, M. L. and Brand, L. eds. pp.~279-317.

Meshram, M., Naderi, S., Wei, Y.-Y., C., McConkey, B., Ingalls, B., Budman, H. and Scharer, J.,``Dynamic Modeling of Apoptosis and its Interaction with Cell Growth in Mammalian Cell Culture,''

Ang, J., Sangram, B., Ingalls, B. P. and McMillen, D. R., ``Considerations for using Integral Feedback Control to Construct a Perfectly Adapting Synthetic Gene Network,''

Song, C., Phenix, H., Abedi, V., Scott, M., Ingalls, B. P., Kaern, M. and Perkins, T. J., ``Estimating the Stochastic Bifurcation Structure of Cellular Networks,''

Meshram, M., Wei, C., Naderi, S., McConkey, B., Ingalls, B., Budman, H. and Scharer, J., ``Modeling the progression of apoptosis in Chinese Hamster Ovary cells,''

Naderi, S., Meshram, M., Wei, C., Scharer, J., Budman, H., McConkey, B. sand Ingalls, B., ``Metabolic flux and nutrient uptake modeling of normal and apoptoic CHO cells,''

Zargar, B., Chen, P., and Ingalls, B. P. ``A synthetic biology approach to bacteria mediated tumor targeting,''

Meshram, M., Naderi, S., Wei, C., Scharer, J., Budman, H., McConkey, B. and Ingalls, B.``Toward an understanding of the role of apoptosis in industrial Chinese Hamster Ovary (CHO) cell culture,''

Ingalls, B. P., ``Stoichiometric redundancy: computational efficiencies and steady-state-consistent network reductions''

Iglesias, P. A. and Ingalls, B. P., editors,

Ingalls, B. P. and Iglesias, P. A., ``A Primer on Control Engineering,'' in

Ingalls, B. P., ``A Control-Theoretic Interpretation of Metabolic Control Analysis,'' in

Oyarzun, D. O., Ingalls, B. P., Middleton, R and Kalamatianos, D., ``Sequential activation of metabolic pathways: a dynamic optimization approach,''

Oyarzun, D. O., Ingalls, B. P., Middleton, R and Kalamatianos, D., ``Optimal metabolic pathway activation,''

Ingalls, B. P., ``Sensitivity analysis: detecting key variables in networks,''

Alwan M., Liu, X.-Z., and Ingalls, B. ``Exponential stability of singularly perturbed switched systems with time delay,''

Ingalls, B. P., ````Metabolic Control Analysis'' from a control-theoretic perspective,''

Sauro, H. M. and Ingalls, B. P. (2007) MAPK cascades as feedback amplifiers, Technical report http://arxiv.org/abs/0710.5195

Ingalls, B. P., Duncker, B. P., Kim, D. R. and McConkey, B. J., Systems level modeling of the cell cycle using budding yeast, Cancer Informatics 2007:3 367-380.

Hung, A.; Yoon, C.; Yeung, N.; Leung, S.; Mirrahimi, F.; Xu, N.; Nagaraj, S.; Khiabani,T.; Ngai, N.; De Andrade, E.S.; Zhu, T.; Lochovsky, C.; Lukovich, J.; Yang, J.; Herriot, C.; Tran, A.; Chen, L.; Kim, H.; Ye, G.; Cheung, W.Y.; Yeung, M.; Lam, K.; Savitsky, K.; Puri, R.; Mirrahimi, A.; Sikder, H.; Najmi, A.; Qu, C.C.; Ingalls,B.; Davies, S.,

Oyarzun, D. O., Ingalls, B. and Kalamatianos, D., Optimal metabolic regulation by temporal variation of enzyme activities: A control theoretic approach, to appear in Proceedings of Conference on Foundations of Systems Biology in Engineering (FOSBE), Stuttgart, Germany, September 2007.

Scott, M, Hwa, T. and Ingalls, B., Deterministic characterization of stochastic genetic circuits,

Ingalls, B. P., Review of

Ingalls, B. P., Iglesias, P. I. and Yi, T.-M., ``Using Control Theory to Study Biology,'' in

Scott, M., Ingalls, B. P. and Kaern, M., Estimations of intrinsic and extrinsic noise in models of nonlinear genetic networks,

Ingalls, B. P.,

Ingalls, B. P. and Rao, C. V.,

Scott, M. and Ingalls, B. P.,

Vu, L. and Ingalls, B. P.,

Ingalls, B. P. and Sontag, E. D.,

Ingalls, B. P.,

Ingalls, B. P.,

Ingalls, B. P.,

Angeli, D., Ingalls, B., Sontag, E. D. and Wang, Y.,

Ingalls, B. P.,

Sauro, H. M. and Ingalls, B. P.,

Angeli, D., Ingalls, B., Sontag, E. D. and Wang, Y.,

Ingalls, B. P. and Sauro, H.M.,

Ingalls, B., Sontag, E. D. and Wang, Y.,

Erratum: For Lemma 3.3 we cited Aubin & Cellina's book. However, that text states the result under more stringent continuity assumptions than needed in our paper. We should have cited another reference, such as A.F. Filippov's "Differential Equations with Discontinuous Righthand Sides", Kluwer, Dordrecht, 1988 (Theorem 7 in Section 2.7). (Note also that our definition of locally Lipschitz inclusion should have explicitly said that F is assumed measurable in t.)

Ingalls, B., Sontag, E. D. and Wang, Y.,

Ingalls, B., Sontag, E. D.,

Ingalls, B.,

Ingalls, B., Sontag, E. D. and Wang, Y.,

Angeli, D., Ingalls, B., Sontag, E. D., and Wang, Y.,

Ingalls, B. and Wang, Y.,

Ingalls, B., Sontag, E. D. and Wang, Y.,

Ingalls, B., Sontag, E. D. and Wang, Y.,

Clements, J.C. and Ingalls, B.,

Rauch, K. P. and Ingalls, B.,

Ingalls, B.,