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Items: 1 to 50 of 167


Dynamical systems approaches to personalized medicine.

Davis JD, Kumbale CM, Zhang Q, Voit EO.

Curr Opin Biotechnol. 2019 Apr 9;58:168-174. doi: 10.1016/j.copbio.2019.03.005. [Epub ahead of print] Review.


Agent-based modeling of morphogenetic systems: Advantages and challenges.

Glen CM, Kemp ML, Voit EO.

PLoS Comput Biol. 2019 Mar 28;15(3):e1006577. doi: 10.1371/journal.pcbi.1006577. eCollection 2019 Mar. Review.


Metrics for regulated biochemical pathway systems.

Davis JD, Voit EO.

Bioinformatics. 2019 Jun 1;35(12):2118-2124. doi: 10.1093/bioinformatics/bty942.


Analysis of erythrocyte dynamics in Rhesus macaque monkeys during infection with Plasmodium cynomolgi.

Fonseca LL, Joyner CJ, Saney CL; MaHPIC Consortium, Moreno A, Barnwell JW, Galinski MR, Voit EO.

Malar J. 2018 Nov 6;17(1):410. doi: 10.1186/s12936-018-2560-6.


A dynamic model of lignin biosynthesis in Brachypodium distachyon.

Faraji M, Fonseca LL, Escamilla-Treviño L, Barros-Rios J, Engle NL, Yang ZK, Tschaplinski TJ, Dixon RA, Voit EO.

Biotechnol Biofuels. 2018 Sep 19;11:253. doi: 10.1186/s13068-018-1241-6. eCollection 2018.


Effect of Hf-doping on electrochemical performance of anatase TiO2 as an anode material for lithium storage.

Gnedenkov SV, Sinebryukhov SL, Zheleznov VV, Opra DP, Voit EI, Modin EB, Sokolov AA, Yu Ustinov A, Sergienko VI.

R Soc Open Sci. 2018 Jun 6;5(6):171811. doi: 10.1098/rsos.171811. eCollection 2018 Jun.


The three-legged stool of understanding metabolism: integrating metabolomics with biochemical genetics and computational modeling.

Downs DM, Bazurto JV, Gupta A, Fonseca LL, Voit EO.

AIMS Microbiol. 2018 Apr 8;4(2):289-303. doi: 10.3934/microbiol.2018.2.289. eCollection 2018.


A Mathematical Model of the Phosphoinositide Pathway.

Olivença DV, Uliyakina I, Fonseca LL, Amaral MD, Voit EO, Pinto FR.

Sci Rep. 2018 Mar 2;8(1):3904. doi: 10.1038/s41598-018-22226-8.


Mathematical models of lignin biosynthesis.

Faraji M, Fonseca LL, Escamilla-Treviño L, Barros-Rios J, Engle N, Yang ZK, Tschaplinski TJ, Dixon RA, Voit EO.

Biotechnol Biofuels. 2018 Feb 9;11:34. doi: 10.1186/s13068-018-1028-9. eCollection 2018.


Metabolic modeling helps interpret transcriptomic changes during malaria.

Tang Y, Gupta A, Garimalla S; MaHPIC Consortium. Electronic address:, Galinski MR, Styczynski MP, Fonseca LL, Voit EO.

Biochim Biophys Acta Mol Basis Dis. 2018 Jun;1864(6 Pt B):2329-2340. doi: 10.1016/j.bbadis.2017.10.023. Epub 2017 Oct 22.


A model of Plasmodium vivax concealment based on Plasmodium cynomolgi infections in Macaca mulatta.

Fonseca LL, Joyner CJ; MaHPIC Consortium, Galinski MR, Voit EO.

Malar J. 2017 Sep 18;16(1):375. doi: 10.1186/s12936-017-2008-4.


Plasmodium knowlesi: a superb in vivo nonhuman primate model of antigenic variation in malaria.

Galinski MR, Lapp SA, Peterson MS, Ay F, Joyner CJ, LE Roch KG, Fonseca LL, Voit EO; MAHPIC CONSORTIUM.

Parasitology. 2018 Jan;145(1):85-100. doi: 10.1017/S0031182017001135. Epub 2017 Jul 17. Review.


Crops In Silico: Generating Virtual Crops Using an Integrative and Multi-scale Modeling Platform.

Marshall-Colon A, Long SP, Allen DK, Allen G, Beard DA, Benes B, von Caemmerer S, Christensen AJ, Cox DJ, Hart JC, Hirst PM, Kannan K, Katz DS, Lynch JP, Millar AJ, Panneerselvam B, Price ND, Prusinkiewicz P, Raila D, Shekar RG, Shrivastava S, Shukla D, Srinivasan V, Stitt M, Turk MJ, Voit EO, Wang Y, Yin X, Zhu XG.

Front Plant Sci. 2017 May 15;8:786. doi: 10.3389/fpls.2017.00786. eCollection 2017.


The best models of metabolism.

Voit EO.

Wiley Interdiscip Rev Syst Biol Med. 2017 Nov;9(6). doi: 10.1002/wsbm.1391. Epub 2017 May 19. Review.


Effects of Storage Time on Glycolysis in Donated Human Blood Units.

Qi Z, Roback JD, Voit EO.

Metabolites. 2017 Mar 29;7(2). pii: E12. doi: 10.3390/metabo7020012.


Stepwise inference of likely dynamic flux distributions from metabolic time series data.

Faraji M, Voit EO.

Bioinformatics. 2017 Jul 15;33(14):2165-2172. doi: 10.1093/bioinformatics/btx126.


Inference of cancer mechanisms through computational systems analysis.

Qi Z, Voit EO.

Mol Biosyst. 2017 Feb 28;13(3):489-497. doi: 10.1039/c6mb00672h.


It happened fifty years ago….

Bertram R, Voit EO.

Math Biosci. 2017 May;287:1-2. doi: 10.1016/j.mbs.2017.01.001. Epub 2017 Jan 4. No abstract available.


Nonparametric dynamic modeling.

Faraji M, Voit EO.

Math Biosci. 2017 May;287:130-146. doi: 10.1016/j.mbs.2016.08.004. Epub 2016 Aug 30.


Quantifying the removal of red blood cells in Macaca mulatta during a Plasmodium coatneyi infection.

Fonseca LL, Alezi HS, Moreno A, Barnwell JW, Galinski MR, Voit EO.

Malar J. 2016 Aug 12;15(1):410. doi: 10.1186/s12936-016-1465-5.


Strategies for Comparing Metabolic Profiles: Implications for the Inference of Biochemical Mechanisms from Metabolomics Data.

Qi Z, Voit EO.

IEEE/ACM Trans Comput Biol Bioinform. 2017 Nov-Dec;14(6):1434-1445. doi: 10.1109/TCBB.2016.2586065. Epub 2016 Jul 7.


A heuristic model for working memory deficit in schizophrenia.

Qi Z, Yu GP, Tretter F, Pogarell O, Grace AA, Voit EO.

Biochim Biophys Acta. 2016 Nov;1860(11 Pt B):2696-705. doi: 10.1016/j.bbagen.2016.04.031. Epub 2016 May 10.


Dynamic models of the complex microbial metapopulation of lake mendota.

Dam P, Fonseca LL, Konstantinidis KT, Voit EO.

NPJ Syst Biol Appl. 2016 Mar 24;2:16007. doi: 10.1038/npjsba.2016.7. eCollection 2016.


Identification of Metabolic Pathway Systems.

Dolatshahi S, Voit EO.

Front Genet. 2016 Feb 10;7:6. doi: 10.3389/fgene.2016.00006. eCollection 2016.


Analysis of the Involvement of Different Ceramide Variants in the Response to Hydroxyurea Stress in Baker's Yeast.

Chen PW, Fonseca LL, Hannun YA, Voit EO.

PLoS One. 2016 Jan 19;11(1):e0146839. doi: 10.1371/journal.pone.0146839. eCollection 2016.


New insights into the complex regulation of the glycolytic pathway in Lactococcus lactis. I. Construction and diagnosis of a comprehensive dynamic model.

Dolatshahi S, Fonseca LL, Voit EO.

Mol Biosyst. 2016 Jan;12(1):23-36. doi: 10.1039/c5mb00331h. Epub 2015 Nov 26.


From within host dynamics to the epidemiology of infectious disease: Scientific overview and challenges.

Gutierrez JB, Galinski MR, Cantrell S, Voit EO.

Math Biosci. 2015 Dec;270(Pt B):143-55. doi: 10.1016/j.mbs.2015.10.002. Epub 2015 Oct 16. Review.


Computational inference of the structure and regulation of the lignin pathway in Panicum virgatum.

Faraji M, Fonseca LL, Escamilla-Treviño L, Dixon RA, Voit EO.

Biotechnol Biofuels. 2015 Sep 17;8:151. doi: 10.1186/s13068-015-0334-8. eCollection 2015.


Comparison of mathematical frameworks for modeling erythropoiesis in the context of malaria infection.

Fonseca LL, Voit EO.

Math Biosci. 2015 Dec;270(Pt B):224-36. doi: 10.1016/j.mbs.2015.08.020. Epub 2015 Sep 8.


An Efficient and Very Accurate Method for Calculating Steady-State Sensitivities in Metabolic Reaction Systems.

Shiraishi F, Yoshida E, Voit EO.

IEEE/ACM Trans Comput Biol Bioinform. 2014 Nov-Dec;11(6):1077-86. doi: 10.1109/TCBB.2014.2338311.


Dynamics of the Heat Stress Response of Ceramides with Different Fatty-Acyl Chain Lengths in Baker's Yeast.

Chen PW, Fonseca LL, Hannun YA, Voit EO.

PLoS Comput Biol. 2015 Aug 4;11(8):e1004373. doi: 10.1371/journal.pcbi.1004373. eCollection 2015 Aug.


WITHDRAWN: From within host dynamics to the epidemiology of infectious disease: Scientific overview and challenges.

Gutierrez JB, Galinski MR, Cantrell S, Voit EO.

Math Biosci. 2015 Apr 15. pii: S0025-5564(15)00085-1. doi: 10.1016/j.mbs.2015.04.004. [Epub ahead of print]


150 years of the mass action law.

Voit EO, Martens HA, Omholt SW.

PLoS Comput Biol. 2015 Jan 8;11(1):e1004012. doi: 10.1371/journal.pcbi.1004012. eCollection 2015 Jan.


A U-system approach for predicting metabolic behaviors and responses based on an alleged metabolic reaction network.

Sriyudthsak K, Sawada Y, Chiba Y, Yamashita Y, Kanaya S, Onouchi H, Fujiwara T, Naito S, Voit EO, Shiraishi F, Hirai MY.

BMC Syst Biol. 2014;8 Suppl 5:S4. doi: 10.1186/1752-0509-8-S5-S4. Epub 2014 Dec 12.


Identification of cancer mechanisms through computational systems modeling.

Qi Z, Voit EO.

Transl Cancer Res. 2014 Jun 1;3(3):233-242.


A heuristic model of alcohol dependence.

Qi Z, Tretter F, Voit EO.

PLoS One. 2014 Mar 21;9(3):e92221. doi: 10.1371/journal.pone.0092221. eCollection 2014.


Rotenone and paraquat perturb dopamine metabolism: A computational analysis of pesticide toxicity.

Qi Z, Miller GW, Voit EO.

Toxicology. 2014 Jan 6;315:92-101. doi: 10.1016/j.tox.2013.11.003. Epub 2013 Nov 20.


Metabolic and transcriptional analysis of acid stress in Lactococcus lactis, with a focus on the kinetics of lactic acid pools.

Carvalho AL, Turner DL, Fonseca LL, Solopova A, Catarino T, Kuipers OP, Voit EO, Neves AR, Santos H.

PLoS One. 2013 Jul 3;8(7):e68470. doi: 10.1371/journal.pone.0068470. Print 2013.


Coordination of rapid sphingolipid responses to heat stress in yeast.

Chen PW, Fonseca LL, Hannun YA, Voit EO.

PLoS Comput Biol. 2013;9(5):e1003078. doi: 10.1371/journal.pcbi.1003078. Epub 2013 May 30.


The neurochemical mobile with non-linear interaction matrix: an exploratory computational model.

Qi Z, Fieni D, Tretter F, Voit EO.

Pharmacopsychiatry. 2013 May;46 Suppl 1:S53-63. doi: 10.1055/s-0033-1337920. Epub 2013 Apr 18. Review.


Mesoscopic modeling as a starting point for computational analyses of cystic fibrosis as a systemic disease.

Voit EO.

Biochim Biophys Acta. 2014 Jan;1844(1 Pt B):258-70. doi: 10.1016/j.bbapap.2013.03.023. Epub 2013 Apr 6.


Function and design of the Nox1 system in vascular smooth muscle cells.

Yin W, Voit EO.

BMC Syst Biol. 2013 Mar 11;7:20. doi: 10.1186/1752-0509-7-20.


Characterizability of metabolic pathway systems from time series data.

Voit EO.

Math Biosci. 2013 Dec;246(2):315-25. doi: 10.1016/j.mbs.2013.01.008. Epub 2013 Feb 5.


Functional analysis of metabolic channeling and regulation in lignin biosynthesis: a computational approach.

Lee Y, Escamilla-Treviño L, Dixon RA, Voit EO.

PLoS Comput Biol. 2012;8(11):e1002769. doi: 10.1371/journal.pcbi.1002769. Epub 2012 Nov 8.


A feel for systems.

Voit EO, Newstetter WC, Kemp ML.

Mol Syst Biol. 2012;8:609. doi: 10.1038/msb.2012.41. No abstract available.


Estimation of dynamic flux profiles from metabolic time series data.

Chou IC, Voit EO.

BMC Syst Biol. 2012 Jul 9;6:84. doi: 10.1186/1752-0509-6-84.


Mesoscopic models of neurotransmission as intermediates between disease simulators and tools for discovering design principles.

Voit EO, Qi Z, Kikuchi S.

Pharmacopsychiatry. 2012 May;45 Suppl 1:S22-30. doi: 10.1055/s-0032-1304653. Epub 2012 May 7. Review. Erratum in: Pharmacopsychiatry. 2012 May;45 Suppl 1:e1. Qui, Z [corrected to Qi, Z].


Canonical modeling of the multi-scale regulation of the heat stress response in yeast.

Fonseca LL, Chen PW, Voit EO.

Metabolites. 2012 Feb 27;2(1):221-41. doi: 10.3390/metabo2010221.


Mathematical modeling and validation of the ergosterol pathway in Saccharomyces cerevisiae.

Alvarez-Vasquez F, Riezman H, Hannun YA, Voit EO.

PLoS One. 2011;6(12):e28344. doi: 10.1371/journal.pone.0028344. Epub 2011 Dec 14.

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