NJ Treloar, N Braniff, B Ingalls, CP Barnes (2022) Deep Reinforcement Learning for Optimal Experimental Design in Biology, PLOS Computational Biology

N Braniff, T Pearce, Z Lu, M Astwood, WSR Forrest, C Receno, and B Ingalls, (2022) NLoed: A Python Package for Nonlinear Optimal Experimental Design in Systems Biology ACS Synthetic Biology, https://pubs.acs.org/doi/10.1021/acssynbio.2c00131

A Yip, J Smith-Roberge, S Haghayegh Khorasani, MG Aucoin, BP Ingalls, (2022), Calibrating spatiotemporal models of microbial communities to microscopy data: A review. PLoS Computational Biology, https://doi.org/10.1371/journal.pcbi.1010533

L Chavez Rodriguez, A González‐Nicolás, B Ingalls, T Streck, W Nowak, S Xiao and H Pagel, (2022). Optimal design of experiments to improve the characterisation of atrazine degradation pathways in soil. European Journal of Soil Science, 73(1), p.e13211.

P Diep, A Boucinha, B Kell, BRA Yeung, X Chen, D Tsyplenkov, A Escobar, A Gnanapragasam, CA Emond, VA Sajtovich, R Mahadevan, DM Kilkenny, G Gini-Newman, M Kaern  and B Ingalls (2021). Advancing undergraduate synthetic biology education: insights from a Canadian iGEM student perspective. Canadian Journal of Microbiology, 67(10), 749-770.

L Chavez Rodriguez, B Ingalls, J Meierdierks, K Kundu, T Streck and H Pagel, (2021). Modeling bioavailability limitations of atrazine degradation in soils. Frontiers in Environmental Science, 361.

L Avery, B Ingalls, C Dumur and A Artyukhin. "A Keller-Segel model for C elegans L1 aggregation." PLoS Computational Biology 17, no. 7 (2021): e1009231.

L Chavez Rodriguez, B Ingalls, E Schwarz, T Streck, M Uksa, and H Pagel, (2020) Gene-Centric Model Approaches for Accurate Prediction of Pesticide Biodegradation in Soils, Environmental Science & Technology, DOI: 10.1021/acs.est.0c03315

Treloar, N. J., Fedorec, A. J., Ingalls, B., & Barnes, C. P. (2020). Deep reinforcement learning for the control of microbial co-cultures in bioreactors. PLOS Computational Biology, 16(4), e1007783.

Braniff, N., Richards, A., & Ingalls, B. (2019). Optimal Experimental Design for a Bistable Gene Regulatory Network. IFAC-PapersOnLine, 52(26), 255-261.

Y Mori, Y Kuroe, BP Ingalls, A method for design of expression tracking controllers for gene regulatory networks, Proceedings of the 8th IFAC Conference on Foundations of Systems Biology in Engineering, Valencia, Spain, 2019

J Venkiteswaran, S Schiff, B Ingalls, Quantifying the Fate of Wastewater Nitrogen Discharged to a Canadian River,  FACETS 4:1, pp. 315-335
(2019) doi 10.1139/facets-2018-0028.

Braniff, Nathan, Matthew Scott, and Brian Ingalls. "Component Characterization in a Growth-Dependent Physiological Context: Optimal Experimental Design." Processes 7.1 (2019): 52.

N. Braniff, P. M. M. Reed and B. P. Ingalls, Optimal experimental design for characterizing gene expression: sample scheduling, Proceedings of the 7th IFAC Conference on Foundations of Systems Biology in Engineering, Chicago, USA, Aug. 5-8, 2018, IFAC-PapersOnLine 51.19 (2018): 48-51.

L. Avery, B. P. Ingalls, A. Artyukhin, Numerical Modelling of C elegans L1 Aggregation,Proceedings of the 7th IFAC Conference on Foundations of Systems Biology in Engineering, Chicago, USA, Aug. 5-8, 2018,IFAC-PapersOnLine 51.19 (2018): 12-15.

J. Kazemi, S. Ozgoli, B. P. Ingalls, Comparator-based gene regulatory network designs for control of expression,Proceedings of the 7th IFAC Conference on Foundations of Systems Biology in Engineering, Chicago, USA, Aug. 5-8, 2018,;IFAC-PapersOnLine 51.19 (2018): 38-41.

N. Braniff and B. Ingalls "New Opportunities for Optimal Design of Dynamic Experiments in Systems and Synthetic Biology." Current Opinion in Systems Biology(2018). doi. 10.1016/j.coisb.2018.02.005

A. Ahmedzadegan, A. Hamadeh, M. K. Sukumaran and B. Ingalls, 'Bioaugmentation approaches for suppression of antibiotic resistance: model-based design', in Emerging Applications of Systems and Control Theory, R. Tempo, S. Yurkovich, and P. Misra, eds. Springer, 2018, pp. 193-204.

M. Morshed, B. Ingalls, and S. Ilie, "An effective implicit finite-difference method for sensitivity analysis of stiff stochastic discrete biochemical systems", IET Systems Biology. (2017) doi. 10.1049/iet-syb.2017.0048

B. Ingalls, M. Mincheva and M. Roussel, "Parametric sensitivity analysis of oscillatory delay systems with an application to gene regulation" Bulletin of Mathematical Biology (2017) 79(7), 1539-1563 doi. 10.1007/s11538-017-0298-x

A. Malwade, A. Nguyen, P. Sadat-Mousavi, and B. Ingalls, "Predictive modelling of a batch filter mating process", Frontiers in Microbiology (2017) vol. 8, pg. 461, doi. 10.3389/fmicb.2017.00461

M. Morshed, B. Ingalls, and S. Ilie, "An efficient finite-difference strategy for sensitivity analysis of stochastic models of biochemical systems", Biosystems (2017) vol 151, pg. 43-52.

M. Wong, X.Liang, M. Smart, L. Tang, R. Moore, B. Ingalls, and T. Dong "Microbial herd protection mediated by antagonistic interaction in polymicrobial communities ", Applied and Environmental Microbiology (2016) vol 82. pg. 6881-6888.

R. Gooding-Townsend, S. ten Holder and B. P. Ingalls. Displacement of bacterial plasmids by engineered unilateral incompatibility, IEEE Life Sciences Letters, vol. 1, no. 1, pp. 19-21, June 2015.

B. Ingalls and E. Bembenek. Exploiting stoichiometric redundancies for computational efficiency and network reduction, In Silico Biology vol. 12, no. 1,2, pp. 55-67, 2015.

P. Greer, W. Sangrar, C. Shi, D. LeBrun, B. Ingalls, and G. Mullins. Amplied Ras-MAPK signal states correlate with accelerated EGFR internalization, cytostasis and delayed HER2 tumor onset in Fer-decient model systems, Oncogene (2015) 34, 4109-4117; doi:10.1038/onc.2014.34.

Saeideh Naderi, Ali Nikdel, Mukesh Meshram, Brendan McConkey, Brian Ingalls, Hector Budman, Jeno Scharer, "Modeling of cell culture damage and recovery leads to increased antibody and biomass productivity in CHO cell cultures" Biotechnology Journal (2014) DOI:10.1002/biot.201300287

Antti Häkkinen, Huy Tran, Olli Yli-Harja, Brian Ingalls, Andre S Ribeiro, "Effects of multimerization on the temporal variability of protein complex abundance"BMC Systems Biology 2013, 7(Suppl 1): S3 doi:10.1186/1752-0509-7-S1-S3

Meshram, M., Naderi, S., McConkey, B., Ingalls, B., Scharer, J., and Budman, H. Modeling the coupled extracellular and intracellular environments in mammalian cell culture. Metabolic Engineering (2013), 19, pp 57-68.

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 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,'' Proceedings of the 18th IFAC World Congress, Milano, Italy 2011,

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,'' Journal of Theoretical Biology 266 (2010), pp. 723-738.

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,'' PLoS Compututational Biology 6(3) 2010: e1000699. doi:10.1371.

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,'' Proceedings of the 11th Computer Applications in Biotechnology (CAB) Conference, Leuven, Belgium, 2009.

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,'' Proceedings of the 11th Computer Applications in Biotechnology (CAB) Conference, Leuven, Belgium, 2009.

Zargar, B., Chen, P., and Ingalls, B. P. A synthetic biology approach to bacteria mediated tumor targeting,'' Proceedings of the Conference on Foundations of Systems Biology in Engineering (FOSBE), Denver, Colorado, August 2009.

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,'' Proceedings of the Conference on Foundations of Systems Biology in Engineering (FOSBE), Denver, Colorado, August 2009.

Ingalls, B. P., Stoichiometric redundancy: computational efficiencies and steady-state-consistent network reductions'' Proceedings of the Conference on Foundations of Systems Biology in Engineering (FOSBE), Denver, Colorado, August 2009.

Iglesias, P. A. and Ingalls, B. P., editors, Control-Theoretic Approaches in Systems Biology, MIT Press, Cambridge, Massachusetts, 2009.

Ingalls, B. P. and Iglesias, P. A., A Primer on Control Engineering,'' in Control-Theoretic Approaches in Systems Biology, Iglesias, P. A. and Ingalls, B. P., editors, MIT Press, Cambridge, Massachusetts, 2009.

Ingalls, B. P., A Control-Theoretic Interpretation of Metabolic Control Analysis,'' in Control-Theoretic Approaches in Systems Biology, Iglesias, P. A. and Ingalls, B. P., editors, MIT Press, Cambridge, Massachusetts, 2009.

Oyarzun, D. O., Ingalls, B. P., Middleton, R and Kalamatianos, D., Sequential activation of metabolic pathways: a dynamic optimization approach,'' Bulletin of Mathematical Biology 71 (2009), pp. 1851-1872.

Oyarzun, D. O., Ingalls, B. P., Middleton, R and Kalamatianos, D., Optimal metabolic pathway activation,'' Proceedings of the 17th International Federation of Automatic Control (IFAC) World Congress, Seoul, Korea, July 2008.

Ingalls, B. P., Sensitivity analysis: detecting key variables in networks,'' Essays in Biochemistry 45 (2008), pp. 177-193.

Alwan M., Liu, X.-Z., and Ingalls, B. Exponential stability of singularly perturbed switched systems with time delay,'' Nonlinear Analysis: Hybrid Systems 2 (2008), pp. 913-921.

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., The 'Cell-See-Us' cellular thermometer, IET Synthetic Biology 1 (2007) 79-82.

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, Proceedings of the National Academy of Sciences USA, 104 (2007) 7402-7407.

Ingalls, B. P., Review of Mathematical Systems Theory I by D. Hinrichsen and A. J. Pritchard, IEEE Control Systems Magazine 26 (2006), pp. 95-97.

Ingalls, B. P., Iglesias, P. I. and Yi, T.-M., Using Control Theory to Study Biology,'' in System Modeling in Cellular Biology, Szallasi, Z., Stelling, J., Periwal, V., eds. MIT Press, Cambridge, 2006, pp. 243-267.

Scott, M., Ingalls, B. P. and Kaern, M., Estimations of intrinsic and extrinsic noise in models of nonlinear genetic networks, Chaos 16 (2006), 026107.

Ingalls, B. P., "Metabolic Control Analysis" from a control-theoretic perspective," Proceedings of the 45th IEEE Conference on Decision and Control, San Diego, December, 2006. 

Ingalls, B. P. and Rao, C. V., Metabolic Control Analysis and Local Controllability of Biochemical Networks, Proceedings of the AIChE Conference on Foundations of Systems Biology in Engineering (FOSBE) 2005, Santa Barbara, California, August 2005.

Scott, M. and Ingalls, B. P., Using the Linear Noise Approximation to Characterize Molecular Noise in Reaction Pathways, Proceedings of the AIChE Conference on Foundations of Systems Biology in Engineering (FOSBE) 2005, Santa Barbara, California, August 2005.

Vu, L. and Ingalls, B. P., Detectability of nonlinear systems under singular perturbations. Proceedings of the DCDIS 4th International Conference on Engineering Applications and Computational Algorithms, Guelph, Canada, July 2005.

Ingalls, B. P. and Sontag, E. D., Smooth Lyapunov characterization of measurement to error stability, in "Unsolved Problems in Mathematical Control Theory", Blondel, V. D. and Megretski, A. eds., Princeton University Press, Princeton, 2004.

Ingalls, B. P., Discussion on: "The Non-Uniform in Time Small-Gain Theorem for a Wide Class of Control Systems with Outputs" , European Journal of Control, 10 (2004) pp. 324-325.

Ingalls, B. P., Autonomously Oscillating Biochemical Systems: Parametric Sensitivity of Extrema and Period , IEE Systems Biology, 1 (2004) pp. 62--70.

Ingalls, B. P., Sensitivity Analysis of Autonomous Oscillations: application to biochemical systems , Proceedings of the Sixteenth International Symposium on Mathematical Theory of Networks and Systems (MTNS), July 2004 .

Angeli, D., Ingalls, B., Sontag, E. D. and Wang, Y., Uniform Global Asymptotic Stability of Differential Inclusions, Journal of Dynamical and Control Systems, 10 (2004) pp. 391-412.

Ingalls, B. P., A Frequency Domain Approach to Sensitivity Analysis of Biochemical Systems , Journal of Physical Chemistry B, 108 (2004) pp. 1143-1152.

Sauro, H. M. and Ingalls, B. P., Conservation Analysis in Biochemical Networks: Computational Issues for Software Writers , Biophysical Chemistry, 109 (2004) pp.1-15.

Angeli, D., Ingalls, B., Sontag, E. D. and Wang, Y., Separation Principles for Input-Output and Integral-Input to State Stability, SIAM Journal on Control and Optimization, 10 (2004) pp.256-276.

Ingalls, B. P. and Sauro, H.M., Sensitivity Analysis of Stoichiometric Networks: An Extension of Metabolic Control Analysis to Non-equilibrium Trajectories , Journal of Theoretical Biology, 222 (2003) pp. 23-36.

Ingalls, B., Sontag, E. D. and Wang, Y., A Relaxation Theorem for Differential Inclusions with Applications to Stability Properties, Proceedings of the Fifteenth International Symposium on Mathematical Theory of Networks and Systems (MTNS), University of Notre Dame, August 2002.
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., Measurement to error stability: a notion of partial detectability for nonlinear systems, Proceedings of the 41st IEEE Conference on Decision and Control, Las Vegas, Nevada, December 2002, pp. 3946-3951.

Ingalls, B., Sontag, E. D., A small-gain theorem with applications to input/output systems, incremental stability, detectability, and interconnections, Journal of the Franklin Institute 339 (2002), pp. 211-229.

Ingalls, B., Comparisons of notions of stability for nonlinear control systems with outputs, Ph.D. Thesis, Rutgers University, New Brunswick, New Jersey, USA, 2001.

Ingalls, B., Sontag, E. D. and Wang, Y., An infinite-time relaxation theorem for differential inclusions, Proceedings of the American Mathematical Society 131 (2003), pp. 487-499.

Angeli, D., Ingalls, B., Sontag, E. D., and Wang, Y., Asymptotic characterizations of IOSS, Proceedings of the IEEE Conference on Decision and Control, Orlando, Florida, December 2001, pp. 881-886.

Ingalls, B. and Wang, Y., On input-to-output stability for systems not uniformly bounded, Proceedings of the IFAC Symposium on Nonlinear Control Systems (NOLCOS), St. Petersburg, Russia, 2001, pp. 720-725.

Ingalls, B., Sontag, E. D. and Wang, Y., Generalizations of asymptotic gain characterizations of ISS to input-to-output stability, Proceedings of the AACC American Control Conference, Arlington, Virginia, 2001, pp. 2279-2284.

Ingalls, B., Sontag, E. D. and Wang, Y., Remarks on input to output stability, Proceedings of the IEEE Conference on Decision and Control, Phoenix, Arizona, December 1999, IEEE Publications, 1999, pp. 1226-1231.

Clements, J.C. and Ingalls, B., An extended model for pairwise conflict resolution in air traffic management, Optimal Control Applications & Methods, 20 (1999) pp. 183-197.

Rauch, K. P. and Ingalls, B., Resonant tidal disruption in galactic nuclei, Monthly Notices of the Royal Astronomical Society, 299 (1998) pp. 1231-1241.

Ingalls, B., Conflict resolution in air traffic management using the methods of optimal control, M.Sc. Thesis, Dalhousie University, Halifax, Nova Scotia, Canada, 1997.