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Daniel Zielinski

TitleAssistant Project Scientist
InstitutionUniversity of California San Diego
DepartmentBioengineering
Address9500 Gilman Drive #0419
La Jolla CA 92093
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Du B, Zhang Z, Grubner S, Yurkovich JT, Palsson BO, Zielinski D. Temperature-Dependent Estimation of Gibbs Energies Using an Updated Group-Contribution Method. Biophys J. 2018 Jun 05; 114(11):2691-2702. PMID: 29874618.
      View in: PubMed
    2. Brunk E, Sahoo S, Zielinski D, Altunkaya A, Dräger A, Mih N, Gatto F, Nilsson A, Preciat Gonzalez GA, Aurich MK, Prlic A, Sastry A, Danielsdottir AD, Heinken A, Noronha A, Rose PW, Burley SK, Fleming RMT, Nielsen J, Thiele I, Palsson BO. Recon3D enables a three-dimensional view of gene variation in human metabolism. Nat Biotechnol. 2018 Mar; 36(3):272-281. PMID: 29457794.
      View in: PubMed
    3. Du B, Zielinski D, Palsson BO. Topological and kinetic determinants of the modal matrices of dynamic models of metabolism. PLoS One. 2017; 12(12):e0189880. PMID: 29267329.
      View in: PubMed
    4. Yurkovich JT, Zielinski D, Yang L, Paglia G, Rolfsson O, Sigurjónsson ÓE, Broddrick JT, Bordbar A, Wichuk K, Brynjólfsson S, Palsson S, Gudmundsson S, Palsson BO. Quantitative time-course metabolomics in human red blood cells reveal the temperature dependence of human metabolic networks. J Biol Chem. 2017 12 01; 292(48):19556-19564. PMID: 29030425.
      View in: PubMed
    5. Opdam S, Richelle A, Kellman B, Li S, Zielinski D, Lewis NE. A Systematic Evaluation of Methods for Tailoring Genome-Scale Metabolic Models. Cell Syst. 2017 Mar 22; 4(3):318-329.e6. PMID: 28215528.
      View in: PubMed
    6. Zielinski D, Jamshidi N, Corbett AJ, Bordbar A, Thomas A, Palsson BO. Systems biology analysis of drivers underlying hallmarks of cancer cell metabolism. Sci Rep. 2017 Jan 25; 7:41241. PMID: 28120890.
      View in: PubMed
    7. Hefzi H, Ang KS, Hanscho M, Bordbar A, Ruckerbauer D, Lakshmanan M, Orellana CA, Baycin-Hizal D, Huang Y, Ley D, Martinez VS, Kyriakopoulos S, Jiménez NE, Zielinski D, Quek LE, Wulff T, Arnsdorf J, Li S, Lee JS, Paglia G, Loira N, Spahn PN, Pedersen LE, Gutierrez JM, King ZA, Lund AM, Nagarajan H, Thomas A, Abdel-Haleem AM, Zanghellini J, Kildegaard HF, Voldborg BG, Gerdtzen ZP, Betenbaugh MJ, Palsson BO, Andersen MR, Nielsen LK, Borth N, Lee DY, Lewis NE. A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism. Cell Syst. 2016 Nov 23; 3(5):434-443.e8. PMID: 27883890.
      View in: PubMed
    8. Zuñiga C, Li CT, Huelsman T, Levering J, Zielinski D, McConnell BO, Long CP, Knoshaug EP, Guarnieri MT, Antoniewicz MR, Betenbaugh MJ, Zengler K. Genome-Scale Metabolic Model for the Green Alga Chlorella vulgaris UTEX 395 Accurately Predicts Phenotypes under Autotrophic, Heterotrophic, and Mixotrophic Growth Conditions. Plant Physiol. 2016 Sep; 172(1):589-602. PMID: 27372244.
      View in: PubMed
    9. Swainston N, Smallbone K, Hefzi H, Dobson PD, Brewer J, Hanscho M, Zielinski D, Ang KS, Gardiner NJ, Gutierrez JM, Kyriakopoulos S, Lakshmanan M, Li S, Liu JK, Martínez VS, Orellana CA, Quek LE, Thomas A, Zanghellini J, Borth N, Lee DY, Nielsen LK, Kell DB, Lewis NE, Mendes P. Recon 2.2: from reconstruction to model of human metabolism. Metabolomics. 2016; 12:109. PMID: 27358602.
      View in: PubMed
    10. Du B, Zielinski D, Kavvas ES, Dräger A, Tan J, Zhang Z, Ruggiero KE, Arzumanyan GA, Palsson BO. Evaluation of rate law approximations in bottom-up kinetic models of metabolism. BMC Syst Biol. 2016 06 06; 10(1):40. PMID: 27266508; PMCID: PMC4895898.
    11. Bordbar A, McCloskey D, Zielinski D, Sonnenschein N, Jamshidi N, Palsson BO. Personalized Whole-Cell Kinetic Models of Metabolism for Discovery in Genomics and Pharmacodynamics. Cell Syst. 2015 Oct 28; 1(4):283-92. PMID: 27136057.
      View in: PubMed
    12. Dräger A, Zielinski D, Keller R, Rall M, Eichner J, Palsson BO, Zell A. SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks. BMC Syst Biol. 2015 Oct 09; 9:68. PMID: 26452770; PMCID: PMC4600286.
    13. Zielinski D, Filipp FV, Bordbar A, Jensen K, Smith JW, Herrgard MJ, Mo ML, Palsson BO. Pharmacogenomic and clinical data link non-pharmacokinetic metabolic dysregulation to drug side effect pathogenesis. Nat Commun. 2015 Jun 09; 6:7101. PMID: 26055627; PMCID: PMC4468904.
    14. Nam H, Campodonico M, Bordbar A, Hyduke DR, Kim S, Zielinski D, Palsson BO. A systems approach to predict oncometabolites via context-specific genome-scale metabolic networks. PLoS Comput Biol. 2014 Sep; 10(9):e1003837. PMID: 25232952; PMCID: PMC4168981.
    15. Schellenberger J, Zielinski D, Choi W, Madireddi S, Portnoy V, Scott DA, Reed JL, Osterman AL, Palsson B. Predicting outcomes of steady-state ¹³C isotope tracing experiments using Monte Carlo sampling. BMC Syst Biol. 2012 Jan 30; 6:9. PMID: 22289253; PMCID: PMC3323462.
    16. Schellenberger J, Que R, Fleming RM, Thiele I, Orth JD, Feist AM, Zielinski D, Bordbar A, Lewis NE, Rahmanian S, Kang J, Hyduke DR, Palsson BØ. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nat Protoc. 2011 Aug 04; 6(9):1290-307. PMID: 21886097; PMCID: PMC3319681.
    17. Feist AM, Zielinski D, Orth JD, Schellenberger J, Herrgard MJ, Palsson BØ. Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli. Metab Eng. 2010 May; 12(3):173-86. PMID: 19840862; PMCID: PMC3125152.