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Brian P. Ingalls, Ph.D. - Publications

Affiliations: 
2001 Rutgers University, New Brunswick, New Brunswick, NJ, United States 
Area:
Mathematics, System Science Engineering
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45 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Braniff N, Pearce T, Lu Z, Astwood M, Forrest WSR, Receno C, Ingalls B. NLoed: A Python Package for Nonlinear Optimal Experimental Design in Systems Biology. Acs Synthetic Biology. PMID 36473701 DOI: 10.1021/acssynbio.2c00131  0.384
2022 Yip A, Smith-Roberge J, Khorasani SH, Aucoin MG, Ingalls BP. Calibrating spatiotemporal models of microbial communities to microscopy data: A review. Plos Computational Biology. 18: e1010533. PMID 36227846 DOI: 10.1371/journal.pcbi.1010533  0.355
2020 Chavez Rodriguez L, Ingalls B, Schwarz E, Streck T, Uksa M, Pagel H. Gene-Centric Model Approaches for Accurate Prediction of Pesticide Biodegradation in Soils. Environmental Science & Technology. 54: 13638-13650. PMID 33064475 DOI: 10.1021/acs.est.0c03315  0.314
2019 Braniff N, Richards A, Ingalls B. Optimal Experimental Design for a Bistable Gene Regulatory Network Ifac-Papersonline. 52: 255-261. DOI: 10.1016/J.Ifacol.2019.12.267  0.475
2019 Mori Y, Kuroe Y, Ingalls B. A method for design of expression tracking controllers for gene regulatory networks Ifac-Papersonline. 52: 135-142. DOI: 10.1016/J.Ifacol.2019.12.248  0.332
2018 Braniff N, Reed M, Ingalls B. Optimal experimental design for characterizing gene expression: sample scheduling Ifac-Papersonline. 51: 48-51. DOI: 10.1016/J.Ifacol.2018.09.036  0.348
2018 Smith-Roberge J, Stietz MS, Dong TG, Ingalls B. ATPase binding and consequent disassembly of the type VI secretion system in Vibrio cholerae: a dynamic model Ifac-Papersonline. 51: 82-83. DOI: 10.1016/J.Ifacol.2018.09.035  0.321
2018 Avery L, Ingalls B, Artyukhin A. Numerical Modelling of C. elegans L1 Aggregation Ifac-Papersonline. 51: 12-15. DOI: 10.1016/J.Ifacol.2018.09.012  0.418
2018 Braniff N, Ingalls B. New opportunities for optimal design of dynamic experiments in systems and synthetic biology Current Opinion in Systems Biology. 9: 42-48. DOI: 10.1016/J.Coisb.2018.02.005  0.488
2017 Morshed M, Ingalls B, Ilie S. Effective implicit finite-difference method for sensitivity analysis of stiff stochastic discrete biochemical systems Iet Systems Biology. 12: 123-130. PMID 33451187 DOI: 10.1049/Iet-Syb.2017.0048  0.626
2017 Ingalls B, Mincheva M, Roussel MR. Parametric Sensitivity Analysis of Oscillatory Delay Systems with an Application to Gene Regulation. Bulletin of Mathematical Biology. PMID 28608044 DOI: 10.1007/S11538-017-0298-X  0.486
2017 Malwade A, Nguyen A, Sadat-Mousavi P, Ingalls BP. Predictive Modeling of a Batch Filter Mating Process. Frontiers in Microbiology. 8: 461. PMID 28377756 DOI: 10.3389/Fmicb.2017.00461  0.749
2017 Morshed M, Ingalls B, Ilie S. An efficient finite-difference strategy for sensitivity analysis of stochastic models of biochemical systems. Biosystems. 151: 43-52. PMID 27914944 DOI: 10.1016/J.Biosystems.2016.11.006  0.622
2015 Ingalls BP, Bembenek E. Exploiting stoichiometric redundancies for computational efficiency and network reduction. In Silico Biology. 12: 55-67. PMID 25547516 DOI: 10.3233/Isb-140464  0.333
2015 Sangrar W, Shi C, Mullins G, LeBrun D, Ingalls B, Greer PA. Amplified Ras-MAPK signal states correlate with accelerated EGFR internalization, cytostasis and delayed HER2 tumor onset in Fer-deficient model systems Oncogene. 34: 4109-4117. DOI: 10.1038/Onc.2014.340  0.315
2014 Naderi S, Nikdel A, Meshram M, McConkey B, Ingalls B, Budman H, Scharer J. Modeling of cell culture damage and recovery leads to increased antibody and biomass productivity in CHO cell cultures. Biotechnology Journal. 9: 1152-63. PMID 24852214 DOI: 10.1002/Biot.201300287  0.385
2013 Meshram M, Naderi S, McConkey B, Ingalls B, Scharer J, Budman H. Modeling the coupled extracellular and intracellular environments in mammalian cell culture. Metabolic Engineering. 19: 57-68. PMID 23810769 DOI: 10.1016/J.Ymben.2013.06.002  0.389
2013 Hamadeh A, Ingalls B, Sontag E. Transient dynamic phenotypes as criteria for model discrimination: fold-change detection in Rhodobacter sphaeroides chemotaxis. Journal of the Royal Society, Interface. 10: 20120935. PMID 23293140 DOI: 10.1098/Rsif.2012.0935  0.623
2012 Gidvani RD, Sudmant P, Li G, DaSilva LF, McConkey BJ, Duncker BP, Ingalls BP. A quantitative model of the initiation of DNA replication in Saccharomyces cerevisiae predicts the effects of system perturbations. Bmc Systems Biology. 6: 78. PMID 22738223 DOI: 10.1186/1752-0509-6-78  0.437
2012 Meshram M, Naderi S, McConkey B, Budman H, Scharer J, Ingalls B. Population-based modeling of the progression of apoptosis in mammalian cell culture. Biotechnology and Bioengineering. 109: 1193-204. PMID 22125113 DOI: 10.1002/Bit.24392  0.347
2011 Naderi S, Meshram M, Wei C, McConkey B, Ingalls B, Budman H, Scharer J. Development of a mathematical model for evaluating the dynamics of normal and apoptotic Chinese hamster ovary cells. Biotechnology Progress. 27: 1197-205. PMID 21618458 DOI: 10.1002/Btpr.647  0.521
2011 Ang J, Ingalls B, McMillen D. Probing the input-output behavior of biochemical and genetic systems system identification methods from control theory. Methods in Enzymology. 487: 279-317. PMID 21187229 DOI: 10.1016/B978-0-12-381270-4.00010-X  0.407
2011 Meshram M, Naderi S, Wei Y, McConkey B, Ingalls B, Budman H, Scharer J. Dynamic Modeling of Apoptosis and its Interaction with Cell Growth in Mammalian Cell Culture Ifac Proceedings Volumes. 44: 9691-9696. DOI: 10.3182/20110828-6-It-1002.02462  0.43
2010 Ang J, Bagh S, Ingalls BP, McMillen DR. Considerations for using integral feedback control to construct a perfectly adapting synthetic gene network. Journal of Theoretical Biology. 266: 723-38. PMID 20688080 DOI: 10.1016/J.Jtbi.2010.07.034  0.33
2010 Song C, Phenix H, Abedi V, Scott M, Ingalls BP, Kaern M, Perkins TJ. Estimating the stochastic bifurcation structure of cellular networks. Plos Computational Biology. 6: e1000699. PMID 20221261 DOI: 10.1371/Journal.Pcbi.1000699  0.484
2010 Meshram M, Wei Y, Naderi S, McConkey B, Ingalls B, Budman H, Scharer J. Modeling the progression of apoptosis in Chinese Hamster Ovary cells Ifac Proceedings Volumes. 43: 467-472. DOI: 10.3182/20100707-3-Be-2012.0026  0.42
2010 Naderi S, Meshram M, Wei C, McConkey B, Ingalls B, Budman H, Scharer J. Metabolic flux and nutrient uptake modeling of normal and apoptotic CHO cells Ifac Proceedings Volumes. 43: 395-400. DOI: 10.3182/20100707-3-Be-2012.0005  0.368
2009 Oyarzún DA, Ingalls BP, Middleton RH, Kalamatianos D. Sequential activation of metabolic pathways: a dynamic optimization approach. Bulletin of Mathematical Biology. 71: 1851-72. PMID 19412635 DOI: 10.1007/S11538-009-9427-5  0.322
2009 Ingalls BP, Sontag ED. Smooth Lyapunov characterization of measurement to error stability Unsolved Problems in Mathematical Systems and Control Theory. 239-243.  0.401
2008 Ingalls B. Sensitivity analysis: from model parameters to system behaviour. Essays in Biochemistry. 45: 177-194. PMID 18793132 DOI: 10.1042/Bse0450177  0.556
2008 Oyarzún DA, Ingalls BP, Middleton R, Kalamatianos D. Optimal metabolic pathway activation Ifac Proceedings Volumes (Ifac-Papersonline). 17. DOI: 10.3182/20080706-5-Kr-1001.02130  0.325
2008 Alwan M, Liu X, Ingalls B. Exponential stability of singularly perturbed switched systems with time delay Nonlinear Analysis: Hybrid Systems. 2: 913-921. DOI: 10.1016/J.Nahs.2008.03.003  0.329
2007 Scott M, Hwa T, Ingalls B. Deterministic characterization of stochastic genetic circuits. Proceedings of the National Academy of Sciences of the United States of America. 104: 7402-7. PMID 17446275 DOI: 10.1073/Pnas.0610468104  0.441
2007 Ingalls BP, Duncker BP, Kim DR, McConkey BJ. Systems level modeling of the cell cycle using budding yeast Cancer Informatics. 3: 367-380. DOI: 10.4137/Cin.S0  0.427
2006 Scott M, Ingalls B, Kaern M. Estimations of intrinsic and extrinsic noise in models of nonlinear genetic networks. Chaos (Woodbury, N.Y.). 16: 026107. PMID 16822039 DOI: 10.1063/1.2211787  0.423
2004 Ingalls BP. Autonomously oscillating biochemical systems: parametric sensitivity of extrema and period Systems Biology. 1: 62-70. PMID 17052116 DOI: 10.1049/sb:20045005  0.352
2004 Ingalls B. Discussion on: “The Non-Uniform in Time Small-Gain Theorem for a Wide Class of Control Systems with Outputs” European Journal of Control. 10: 324-325. DOI: 10.3166/Ejc.10.324-325  0.311
2004 Angeli D, Ingalls B, Sontag ED, Wang Y. Separation Principles for Input-Output and Integral-Input-to-State Stability Siam Journal On Control and Optimization. 43: 256-276. DOI: 10.1137/S0363012902419047  0.505
2004 Angeli D, Ingalls B, Sontag ED, Wang Y. Uniform Global Asymptotic Stability of Differential Inclusions Journal of Dynamical and Control Systems. 10: 391-412. DOI: 10.1023/B:Jods.0000034437.54937.7F  0.524
2004 Ingalls BP. A frequency domain approach to sensitivity analysis of biochemical networks Journal of Physical Chemistry B. 108: 1143-1152. DOI: 10.1021/Jp036567U  0.401
2003 Ingalls BP, Sauro HM. Sensitivity analysis of stoichiometric networks: an extension of metabolic control analysis to non-steady state trajectories. Journal of Theoretical Biology. 222: 23-36. PMID 12699732 DOI: 10.1016/S0022-5193(03)00011-0  0.422
2002 Sontag ED, Ingalls B. A small-gain theorem with applications to input/output systems, incremental stability, detectability, and interconnections Journal of the Franklin Institute. 339: 211-229. DOI: 10.1016/S0016-0032(02)00022-4  0.542
2002 Ingalls BP, Sontag ED, Wang Y. Measurement to error stability: A notion of partial detectability for nonlinear systems Proceedings of the Ieee Conference On Decision and Control. 4: 3946-3951.  0.486
2001 Ingalls B, Wang Y. On Input-to-Output Stability for Systems not Uniformly Bounded Ifac Proceedings Volumes. 34: 909-914. DOI: 10.1016/S1474-6670(17)35296-5  0.335
1999 Clements JC, Ingalls B. Extended model for pairwise conflict resolution in air traffic management Optimal Control Applications and Methods. 20: 183-197. DOI: 10.1002/(Sici)1099-1514(199907/08)20:4<183::Aid-Oca655>3.0.Co;2-Z  0.344
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