Publications – metabolism

[2024] A mathematical model of melatonin synthesis and interactions with the circadian clock. Best J, Kim R, Reed MC, Nijhout HF. Mathematical Biosciences 377 (2024) 109280. https://doi.org/10.1016/j.mbs.2024.109280
[2024] Lower hepatic CBS and PEMT expression in advanced NAFLD: inferencing strategies to lower homocysteine with a mathematical model. Suzuki A, Henao R, Reed MC, Nijhout HF, Tripathi M, Singh BK, Yen PM, Diehl AM, Abdelmalek MF. Metab Target Organ Damage 2024;4:21. https://dx.doi.org/10.20517/mtod.2024.16
[2024] Modulation of serotonin transporter expression by escitalopram under inflammation. Mena S, Cruikshank A, Best J, Nijhout HF, Reed MC, Hashemi P. Communications Biology 7:710. doi: 10.1038/s42003-024-06240-3
[2024] Sex differences in glutathione metabolism and acetaminophen toxicity. Cruikshank A, Reed MC, Nijhout HF. Metab. Target Organ Damage 2024;4:17. doi: 10.20517/mtod.2023.44
[2024] Serotonin as a biomarker of toxin‑induced Parkinsonism. Buchanan AM, Mena S, Choukari I, Vasa A, Crawford JN, Fadel J, Maxwell, N, Reagan, L, Cruikshank A, Best J, Nijhout, HF, Reed MC, Hashemi P. Molecular Medicine (2024) 30:33. doi.org/10.1186/s10020-023-00773-9.
[2023] Serotonin is a common thread linking different classes of antidepressants. Witt CE, et al. Research Square https://doi.org/10.21203/rs.3.rs-2741902/v1
[2023] Dynamical questions in volume transmission. Cruikshank A, Nijhout HF, Best J, Reed MC. Journal of Biological Dynamics 17: 1,2269986.
[2023] Mathematical insights into the role of dopamine signaling in circadian entrainment. Kim R, Nijhout HF, Reed MC. Mathematical Biosciences 356 (2023) 108956.
[2022] A voltammetric approach for characterizing the biophysical and chemical functionality of human induced pluripotent stem cell-derived serotonin neurons. Holmes J, Lau T, Fernandez-Novel N, Hersey RS, M., Hampel, DKL., Horschitz, S, Reed, MC, Nijhout, HF, Koch P, Hashemi, P. Analytical Chemistry. [doi:10.1021/acs.analchem.1c05082]
[2022] An in vivo definition of brain histamine dynamics reveals critical neuromodulatory roles for this elusive messenger. Berger SN, Baumberger B, Samaranayake S, Hersey M, Mena S, Bain I, Duncan W, Reed MC, Nijhout HF, Best J, Hashemi P. Int. .J. Mol. Sci. 22002222,, 2233,, 1×4 F8O62R
[2022] Spiracular fluttering decouples oxygen uptake and water loss: a stochastic PDE model of respiratory water loss in insects. Lawley S, Nijhout HF, Reed MC. Journal of Mathematical Biology 84:40.
[2021] One-carbon metabolism during the menstrual cycle and pregnancy. Kim, R., Nijhout HF, and Reed MC. PLOS Computational Biology | https://doi.org/10.1371/journal.pcbi.1009708.
[2021] Inflammation-induced histamine impairs the capacity of escitalopram to increase hippocampal extracellular serotonin. Hersey M, Samaranayake S, Berger SN, Tavakoli N, Mena S, Nijhout HF, Reed MC, Best J, Blakely RD, Lawrence P, Reagan LP and Hashemi P. The Journal of Neuroscience, 41:6564–6577. (public press).
[2021] Mathematical models of serotonin, histamine, and depression. Best J, Buchanan AM, Nijhout HF, Hashemi P, Reed, MC. In: New Developments in Pharmacology and Therapeutics (B. Olivier, Ed.). Intech, UK.
[2021] A mathematical model of circadian rhythms and dopamine. Kim R, Reed MC. Theoretical Biology and Medical Modelling, 18:8.
[2020] Autoreceptor control of serotonin dynamics. Best J, Duncan W, Sadre-Marandi F, Hashemi P, Nijhout HF, Reed MC. BMC Neuroscience, 21:40.
[2020] Spiracular fluttering increases oxygen uptake. Lawley SD, Reed MC, Nijhout HF. PLoS ONE 15(5): e0232450
[2019] In vivo Hippocampal Serotonin Dynamics in Male and Female Mice: Determining Effects of Acute Escitalopram Using Fast Scan Cyclic Voltammetry. Saylor RA, Hersey M, West A, Buchanan AM, Berger SN, Nijhout HF, Reed MC, Best J, Hashemi, P. Frontiers Neurosci., 23;13:362. doi: 10.3389
[2019] Fast serotonin voltammetry as a versatile tool for mapping dynamic tissue architecture: I. Responses at carbon fibers describe local tissue physiology. Abdalla A, West A, Jin Y, Saylor RA, Qiang B, Peña E, Linden DJ, Nijhout HF, Reed MC, Best J, Hashemi P., J. Neurochem. doi: 10.1111/jnc.14854
[2019] Voltammetric evidence for discrete serotonin circuits, linked to specific reuptake domains, in the mouse medial prefrontal cortex. A. West, J. Best, A. Abdalla, H. F. Nijhout, M. Reed, P. Hashemi, Neurochem. Inter. 123:50-58.
[2018] Systems biology of robustness and homeostatic mechanisms. H. F. Nijhout, J. A. Best, M. C. Reed, WIREs Syst. Biol. Med. 2018;e1440.
[2018] Sex differences in hepatic one-carbon metabolism. F. Sadre-Marandi, T. Dahdoul, M. C. Reed, H. F. Nijhout. BMC Systems Biology, 12:89.
[2018] Homeostasis despite instability. W. Duncan, J. Best, M. Golubitsky, H. F. Nijhout, M. Reed. Mathematical Biosciences, 300:130-137.
[2017] A mathematical model for histamine synthesis, release, and control in varicosities. J. Best, H. F. Nijhout, S. Samaranayake, P. Hashemi, M. Reed, Theoretical Biology and Medical Modelling, 14:24.
[2017] Analysis of Homeostatic Mechanisms in Biochemical Networks. M. Reed, J. Best, M. Golubitsky, I. Stewart, H. F. Nijhout. Bulletin of Mathematical Biology, 79:2534-2557.
[2017] Systems Biology of Phenotypic Robustness and Plasticity. H. F. Nijhout, F. Sadre-Marandi, J. Best, M. Reed. Integrative and Comparative Biology, 57: 171-184.
[2017] Mathematical models of neuromodulation and implications for neurology and psychiatry. J. A. Best, H. F. Nijhout, M. C. Reed. In: Computational Neurology and Psychiatry (Editors: Érdi, Péter, Sen Bhattacharya, Basabdatta, Cochran, Amy L.), Springer, NY.
[2016] A volta metric and mathematical analysis of histaminergic modulation of serotonin in the mouse hypothalamus. S. Samaranayake, A. Abdalla, R. Robke, H. F.Nijhout, M. Reed, J. Best, P. Hashemi J. Neurochem. 138, 374-383.
[2016] Neurotransmitter concentrations in the presence of neural switching in one dimension. S. D. Lawley, J. A. Best, M. C. Reed, AIMS J. Disc. and Cont. Dyn. Sys. B, 21, 2255-2274.
[2016] Mathematical modelling of the effect of a high dose acetylcysteine regimen based on the SNAP trial on hepatic glutathione regeneration and hepatocyte death. Thanacoody HKR, Nijhout FH, Reed MC, Thomas SHL.Clinical Toxicology 54(4):494-494.
[2016] Mathematical modeling of perifusion cell culture experiments on GnRH signaling. Temamogullari NE, Nijhout HF, Reed MC. Math. Biosci. 276, 121-132.
[2015] Mathematical biology is good for mathematics. Reed MC. Notices of the AMS 62: 1172-1176.
[2015] Using mathematical models to understand metabolism, genes and disease. Nijhout HF, Best JA, Reed MC. BMC Biology 13:79.
[2015] Mathematical analysis of the regulation of competing methyltransferases. Reed MC, Gamble MV, Hall MN Nijhout HF. BMC Systems Biology 9:69. (Supplementary materials).
[2015] The role of skeletal muscle in liver glutathione metabolism during acetaminophen overdose. Bilinsky L, Reed MC, Nijhout HF. J. Theoret. Biol. 376: 118-133.
[2014] Targeted metabolomics and mathematical modeling demonstrate that vitamin B-6 restriction alters one-carbon metabolism in cultured HepG2 cells. da Silva VR, Ralat MA, Quinlivan EP, Garrett, TJ, Chi Y-Y, Nijhout HF, Reed MC, Gregory JF. Amer. J. Physiol. – Endocrinol. and Metab. 307 , E93-E101.
[2014] Escape from homeostasis. Nijhout HF, Best J, Reed, MC. Mathematical Biosciences 257, 104-110.
[2014] Mathematical modeling of the effects of glutathione on arsenic methylation. Lawley SD, Yun J, Gamble MV, Hall MH, Reed MC, Nijhout HF. Theoretical Biology and Medical Modelling 11,20.
[2014] Voltametric and mathematical evidence for dual transport mediation of serotonin clearance in vivo. Wood KM, Zequja A, Nijhout HF, Reed MC, Best J, Hashemi P. J. Neurochemistry 130 ,351-359.

[2014] Homeostasis and dynamic stability of the phenotype link robustness and stability. Nijhout HF, Reed, MC. Integrative and Comparative Biology 54 , 264-275.
[2014] Projecting biochemistry over long distances. Reed MC, Nijhout HF, Best J. Math. Model. Nat. Phenom. 9 , 133-138.
[2013] The biochemistry of acetaminophen hepatotoxicity and rescue: a mathematical model. Ben-Shachar R, Chen Y, Luo S, Hartman C, Reed MC, Nijhout HF. Theoretical Biology and Medical Modelling 9,55.
[2013] A mathematical model of tryptophan metabolism via the kynurenine pathway provides insights into the effects of vitamin B-6 deficiency, tryptophan loading, and induction of tryptophan 2,3-dioxygenase. Rios-Avila L, Nijhout HF, Reed MC, Sitren HS, Gregory JF. J. Nutriution (doi: 10.3945/jn.113.174599). 143, 1508-1519.
[2013] A population model of folate-mediated one-carbon metabolism. Duncan TM, Reed MC, Nijhout HF. Nutrients. 5 , 2457-2574.
[2013] Computational studies of the role of serotonin in the basal ganglia. Reed MC, Nijhout HF, Best J. Frontiers in Integrative Neuroscience. 7 , 1-8.
[2013] The relationship between intracellular and plasma levels of folate and metabolites in the methionine cycle: A model. Duncan TM, Reed MC, Nijhout HF. Mol. Nutr. Food Res. 57 , 626-636.
[2012] The impact of host immune status on the within-host and population dynamics of antigenic immune escape. Luo S, Reed MC, Mattingly J, Koelle K. J. R. Soc. Interface (2012) 9, 2603–2613.
[2012] Mathematical insights into the effects of levodopa. Reed MC, Nijhout HF, and Best J. Frontiers in Integrative Neuroscience 6, 1-24.
[2011] Bursts and the efficacy of selective reuptake inhibitors. Best J, Nijhout HF, and Reed MC. Pharmacopsychiatry 44 (supp. 1),S76-S83.
[2011] Mathematical modeling of cell metabolism. Reed MC, Kurtz T and Nijhout HF. In: Encyclopedia of Applied and Computational Mathematics. (Ed. Engquist, B). Springer, New York. (in press)
[2011] A mathematical modelling approach to assessing the reliability of biomarkers of glutathione metabolism. Geenen S, du Preez FB, Reed MC, Nijhout HF, Kenna JG, Wilson ID, Westerhoff HV and Snoep JL. European Journal of Pharmaceutical Sciences (doi:10.1016/j.ejps.2011.08.017).
[2011] Mathematical models: Interactions between serotonin and dopamine in Parkinson’s Disease. Best J, Oakley G, Reed MC and Nijhout HF. In: Etiology and Pathophysiology of Parkinson’s Disease. Chapter 18, pp 405-420. (Ed. Abdul Qayyum Rana). InTech Publ.
[2011] Mathematical modeling predicts the effect of folate deficiency and excess on cancer-related biomarkers. Neuhouser ML, Nijhout HF, Gregory JF, Reed MC, James SJ, Liu A, Shane B and Ulrich CM. Cancer Epidemiology Biomarkers & Prevention 20, 1912-1917.
[2011] Mathematical model insights into arsenic methylation. Lawley S, Cinderella M, Hall M, Gamble M, Nijhout HF and Reed MC. Theoretical Biology and Medical Modelling 8, 1.
[2010] The biological significance of substrate inhibition: A mechanism with many functions. Reed MC, Lieb, A., Nijhout HF. BioEssays 32, 422-429.
[2010] Serotonin synthesis, release, and reuptake in terminals: a mathematical model. Best J, Nijhout HF, Reed MC. Theoretical Biology and Medical Modelling 7, 34.
[2010] Models of dopaminergic and serotonergic signaling. Best J, Reed MC, Nijhout HF. Pharmacopsychiatry 43 (supp. 1),S61-S66.
[2009] Use of pathway information in molecular epidemiology. Thomas DC, Conti DV, Baurley, J, Nijhout HF, Reed MC, Ulrich CM. Human Genomics 4,21-42.
[2009] Singularity in polarization: rewiring yeast cells to make two buds. Howell AS, Savage NS, Johnson SA, Bose I, Wagner AW, Zyla TR, Nijhout HF, Reed MC, Goryachev AB, Lew DJ. Cell 139, 731-43. (supplementary materials)
[2009] Homeostatic mechanisms in dopamine synthesis and release: a mathematical model. Best J, Nijhout HF, Reed MC, Theoretical Biology and Medical Modelling 6, 21.
[2009]Passive and active stabilization of dopamine in the striatum. Reed MC, Best J, Nijhout HF, Bioscience Hypotheses, 2, 240-244
[2009] A mathematical model gives insights into the effects of B6 deficiency on one-carbon and glutathione metabolism. Journal of Nutrition, Nijhout HF, Gregory JF, Fitzpatrick C, Cho E, Ulrich CM, Reed MC, J. Nutrition, 139, 784-791.
[2008] Mathematical models of one-carbon metabolism. Nijhout HF, Reed M, Ulrich C, Vitamins and Hormones, Volume 79 (G. Litwack, ed.), Elsevier, pp.42-85.

[2008] Mathematical modeling of folate metabolism: Predicted effects of genetic polymorphisms on mechanisms and biomarkers relevant to carcinogenesis. Ulrich CM, Neuhouser M, Liu A, Boynton A, Gregory JF, Shane B, James SJ, Reed MC, Nijhout HF, Cancer Epidemiol. Biomark. Prevent. 17, 1822-1831.
[2008] Modeling folate, one-carbon metabolism, and DNA methylation. Ulrich CM, Reed MC, Nijhout HF Nutrition Reviews, 66 Suppl 1, S27-S30.
[2008] Mathematical Biology. Reed, MC. In: The Princeton Companion for Mathematics, (Ed. T. Gowers), Princeton U. Press, Princeton.
[2008] A mathematical model of glutathione metabolism; Reed MC, Thomas R, Pavisic J, Nijhout HF, James SJ, Ulrich CM. , Theoretical Biology and Medical Modelling 5:doi:10.1186/1742-4682-5-8.
[2008] A mathematical model for juvenile hormone titers; Nijhout HF, Reed MC, J. Insect Physiol, 54, 255-264.
[2007] Flavin-dependent thymidylate synthase ThyX activity: Implications for the folate cycle in Bacteria; Leduc D, Escartin F, Nijhout HF, Reed MC, Liebl U, Skouloubris S, Myllykallio H, Journal of Bacteriology, 189, 8537-8545.
[2007] A day in the life of cell metabolism; Nijhout HF, Reed MC, Ulrich CM, Journal of Biological Theory, 2,124-127.
[2007] Folate and cancer–Timing is everything; Ulrich CM, Potter JD, Journal of the American Medical Association, 297, 2408-2409
[2007] Propagation of fluctuations in biochemical systems, II: Nonlinear chains; DAnderson D, Mattingly J, IET-Systems Biology, 1, 313-325.
[2007] Propagation of fluctuations in biochemical systems, I: Linear SSC networks; DAnderson D, JMattingly J, Nijhout HF, Reed MC, Bulletin of Mathematical Biology. 69, 1791-1813
[2006] Mathematical modeling: Epidemiology meets systems biology; Ulrich CM, Nijhout HF, and Reed MC, Cancer Epidemiology, Biomarkers and Prevention, 15, 827-829.
[2006] Long-Range Allosteric Interactions between the Folate and Methionine Cycles Stabilize DNA Methylation Reaction Rate; Nijhout HF, Reed MC, Anderson DF, Mattingly JC, James SJ, Ulrich CM, Epigenetics, 1, 81-87.
[2006] A mathematical model gives insights into nutritional and genetic aspects of folate-mediated one-carbon metabolism; Reed MC, Nijhout HF, Neuhouser ML, Gregory JF-III, Shane B, James SJ, Boynton A, Ulrich CM, The Journal of Nutrition, 136, 2653-2661. Supplementary Materials/Model Details
[2006] Neural tube defects and folate pathway genes: Family-based association tests of gene-gene and gene-environment interactions; Boyles AL, Billups AV, Deak KL, Siegel DG, Mehltretter L, Slifer SH, Bassuk AG, Kessler JA, Reed MC, Nijhout HF, George TM, Enterline DS, Gilbert JR, Speer MC, Environmental Health Perspectives, 114, 1547-1551
[2006] In silico experimentation with a model of hepatic mitochondrial folate metabolism; Nijhout HF, Reed MC, Lam S-L, Gregory JF-III, Ulrich CM; Theoretical Biology and Medical Modeling, 3:40. Supplementary Materials/Model Details
[2004] Why is mathematical biology so hard? Reed MC. Notices of the AMS 51: 338-342.
[2004] A mathematical model of the folate cycle: New insights into folate homeostasis; Nijhout HF, Reed MC, Budu P, Ulrich CM, Journal of Biological Chemistry, 279, 55008-55016.
[2004] A mathematical model of the methionine cycle; Reed MC, Nijhout HF, Sparks R and Ulrich CM, Journal of Theoretical Biology, 226, 33-43.