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Daniel Zielinski - Publications

Affiliations: 
2015 Bioengineering University of California, San Diego, La Jolla, CA 
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37 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
2024 Josephs-Spaulding J, Rajput A, Hefner Y, Szubin R, Balasubramanian A, Li G, Zielinski DC, Jahn L, Sommer M, Phaneuf P, Palsson BO. Reconstructing the transcriptional regulatory network of probiotic is enabled by transcriptomics and machine learning. Msystems. e0125723. PMID 38349131 DOI: 10.1128/msystems.01257-23  0.439
2024 Qiu S, Wan X, Liang Y, Lamoureux C, Akbari A, Palsson BO, Zielinski DC. Inferred regulons are consistent with regulator binding sequences in E. coli. Plos Computational Biology. 20: e1011824. PMID 38252668 DOI: 10.1371/journal.pcbi.1011824  0.402
2023 Mattei G, Gan Z, Ramazzotti M, Palsson BO, Zielinski DC. Differential Expression Analysis Utilizing Condition-Specific Metabolic Pathways. Metabolites. 13. PMID 37999223 DOI: 10.3390/metabo13111127  0.523
2023 Lamoureux CR, Decker KT, Sastry AV, Rychel K, Gao Y, McConn JL, Zielinski DC, Palsson BO. A multi-scale expression and regulation knowledge base for Escherichia coli. Nucleic Acids Research. PMID 37713610 DOI: 10.1093/nar/gkad750  0.747
2023 Chowdhury S, Zielinski DC, Dalldorf C, Rodrigues JV, Palsson BO, Shakhnovich EI. Empowering drug off-target discovery with metabolic and structural analysis. Nature Communications. 14: 3390. PMID 37296102 DOI: 10.1038/s41467-023-38859-x  0.446
2023 Hirose Y, Poudel S, Sastry AV, Rychel K, Lamoureux CR, Szubin R, Zielinski DC, Lim HG, Menon ND, Bergsten H, Uchiyama S, Hanada T, Kawabata S, Palsson BO, Nizet V. Elucidation of independently modulated genes in reveals carbon sources that control its expression of hemolytic toxins. Msystems. e0024723. PMID 37278526 DOI: 10.1128/msystems.00247-23  0.694
2023 Dalldorf C, Rychel K, Szubin R, Hefner Y, Patel A, Zielinski D, Palsson B. The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions. Research Square. PMID 37090546 DOI: 10.21203/rs.3.rs-2729651/v1  0.387
2021 Phaneuf PV, Zielinski DC, Yurkovich JT, Johnsen J, Szubin R, Yang L, Kim SH, Schulz S, Wu M, Dalldorf C, Ozdemir E, Lennen RM, Palsson BO, Feist AM. Data-Driven Strain Design Using Aggregated Adaptive Laboratory Evolution Mutational Data. Acs Synthetic Biology. PMID 34762392 DOI: 10.1021/acssynbio.1c00337  0.739
2021 Akbari A, Yurkovich JT, Zielinski DC, Palsson BO. The quantitative metabolome is shaped by abiotic constraints. Nature Communications. 12: 3178. PMID 34039963 DOI: 10.1038/s41467-021-23214-9  0.712
2021 Haiman ZB, Zielinski DC, Koike Y, Yurkovich JT, Palsson BO. MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics. Plos Computational Biology. 17: e1008208. PMID 33507922 DOI: 10.1371/journal.pcbi.1008208  0.75
2020 Zielinski DC, Patel A, Palsson BO. The Expanding Computational Toolbox for Engineering Microbial Phenotypes at the Genome Scale. Microorganisms. 8. PMID 33371386 DOI: 10.3390/microorganisms8122050  0.482
2020 Hanna EM, Zhang X, Eide M, Fallahi S, Furmanek T, Yadetie F, Zielinski DC, Goksøyr A, Jonassen I. ReCodLiver0.9: Overcoming Challenges in Genome-Scale Metabolic Reconstruction of a Non-model Species. Frontiers in Molecular Biosciences. 7: 591406. PMID 33324679 DOI: 10.3389/fmolb.2020.591406  0.347
2018 Heckmann D, Zielinski DC, Palsson BO. Modeling genome-wide enzyme evolution predicts strong epistasis underlying catalytic turnover rates. Nature Communications. 9: 5270. PMID 30532008 DOI: 10.1038/S41467-018-07649-1  0.788
2018 Heckmann D, Lloyd CJ, Mih N, Ha Y, Zielinski DC, Haiman ZB, Desouki AA, Lercher MJ, Palsson BO. Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models. Nature Communications. 9: 5252. PMID 30531987 DOI: 10.1038/S41467-018-07652-6  0.767
2018 Du B, Zielinski DC, Palsson BO. Estimating Metabolic Equilibrium Constants: Progress and Future Challenges. Trends in Biochemical Sciences. 43: 960-969. PMID 30472988 DOI: 10.1016/J.Tibs.2018.09.009  0.552
2018 Du B, Zielinski DC, Monk JM, Palsson BO. Thermodynamic favorability and pathway yield as evolutionary tradeoffs in biosynthetic pathway choice. Proceedings of the National Academy of Sciences of the United States of America. PMID 30309961 DOI: 10.1073/Pnas.1805367115  0.722
2018 Du B, Zhang Z, Grubner S, Yurkovich JT, Palsson BO, Zielinski DC. Temperature-Dependent Estimation of Gibbs Energies Using an Updated Group-Contribution Method. Biophysical Journal. 114: 2691-2702. PMID 29874618 DOI: 10.1016/J.Bpj.2018.04.030  0.741
2018 Brunk E, Sahoo S, Zielinski DC, Altunkaya A, Dräger A, Mih N, Gatto F, Nilsson A, Preciat Gonzalez GA, Aurich MK, Prlić A, Sastry A, Danielsdottir AD, Heinken A, Noronha A, et al. Recon3D enables a three-dimensional view of gene variation in human metabolism. Nature Biotechnology. PMID 29457794 DOI: 10.1038/Nbt.4072  0.785
2017 Du B, Zielinski DC, Palsson BO. Topological and kinetic determinants of the modal matrices of dynamic models of metabolism. Plos One. 12: e0189880. PMID 29267329 DOI: 10.1371/Journal.Pone.0189880  0.593
2017 Yurkovich JT, Zielinski DC, 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. The Journal of Biological Chemistry. PMID 29030425 DOI: 10.1074/Jbc.M117.804914  0.784
2017 Opdam S, Richelle A, Kellman B, Li S, Zielinski DC, Lewis NE. A Systematic Evaluation of Methods for Tailoring Genome-Scale Metabolic Models. Cell Systems. PMID 28215528 DOI: 10.1016/J.Cels.2017.01.010  0.605
2017 Zielinski DC, Jamshidi N, Corbett AJ, Bordbar A, Thomas A, Palsson BO. Systems biology analysis of drivers underlying hallmarks of cancer cell metabolism. Scientific Reports. 7: 41241. PMID 28120890 DOI: 10.1038/Srep41241  0.765
2016 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 DC, Quek LE, et al. A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism. Cell Systems. 3: 434-443.e8. PMID 27883890 DOI: 10.1016/J.Cels.2016.10.020  0.801
2016 Zuñiga C, Li CT, Huelsman T, Levering J, Zielinski DC, 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 Physiology. PMID 27372244 DOI: 10.1104/Pp.16.00593  0.422
2016 Swainston N, Smallbone K, Hefzi H, Dobson PD, Brewer J, Hanscho M, Zielinski DC, Ang KS, Gardiner NJ, Gutierrez JM, Kyriakopoulos S, Lakshmanan M, Li S, Liu JK, Martínez VS, et al. Recon 2.2: from reconstruction to model of human metabolism. Metabolomics : Official Journal of the Metabolomic Society. 12: 109. PMID 27358602 DOI: 10.1007/S11306-016-1051-4  0.587
2016 Du B, Zielinski DC, 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 Systems Biology. 10: 40. PMID 27266508 DOI: 10.1186/S12918-016-0283-2  0.729
2015 Bordbar A, McCloskey D, Zielinski DC, Sonnenschein N, Jamshidi N, Palsson BO. Personalized Whole-Cell Kinetic Models of Metabolism for Discovery in Genomics and Pharmacodynamics. Cell Systems. 1: 283-292. PMID 27136057 DOI: 10.1016/J.Cels.2015.10.003  0.777
2015 Dräger A, Zielinski DC, Keller R, Rall M, Eichner J, Palsson BO, Zell A. SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks. Bmc Systems Biology. 9: 68. PMID 26452770 DOI: 10.1186/S12918-015-0212-9  0.438
2015 Zielinski DC, 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. Nature Communications. 6: 7101. PMID 26055627 DOI: 10.1038/Ncomms8101  0.775
2015 Bordbar A, McCloskey D, Zielinski DC, Sonnenschein N, Jamshidi N, Palsson BO. Personalized Whole-Cell Kinetic Models of Metabolism for Discovery in Genomics and Pharmacodynamics Cell Systems. 1: 283-292. DOI: 10.1016/j.cels.2015.10.003  0.799
2014 Olavarria K, De Ingeniis J, Zielinski DC, Fuentealba M, Muñoz R, McCloskey D, Feist AM, Cabrera R. Metabolic impact of an NADH-producing glucose-6-phosphate dehydrogenase in Escherichia coli. Microbiology (Reading, England). 160: 2780-93. PMID 25246670 DOI: 10.1099/Mic.0.082180-0  0.629
2014 Nam H, Campodonico M, Bordbar A, Hyduke DR, Kim S, Zielinski DC, Palsson BO. A systems approach to predict oncometabolites via context-specific genome-scale metabolic networks. Plos Computational Biology. 10: e1003837. PMID 25232952 DOI: 10.1371/Journal.Pcbi.1003837  0.674
2013 Zielinski DC, Palsson BO. Kinetic modeling of metabolic networks Systems Metabolic Engineering. 25-55. DOI: 10.1007/978-94-007-4534-6_2  0.513
2012 Schellenberger J, Zielinski DC, 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 Systems Biology. 6: 9. PMID 22289253 DOI: 10.1186/1752-0509-6-9  0.76
2011 Schellenberger J, Que R, Fleming RM, Thiele I, Orth JD, Feist AM, Zielinski DC, 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. Nature Protocols. 6: 1290-307. PMID 21886097 DOI: 10.1038/Nprot.2011.308  0.77
2011 Hyduke D, Schellenberger J, Que R, Fleming R, Thiele I, Orth J, Feist A, Zielinski D, Bordbar A, Lewis N, Rahmanian S, Kang J, Palsson B. COBRA Toolbox 2.0 Protocol Exchange. DOI: 10.1038/Protex.2011.234  0.708
2010 Feist AM, Zielinski DC, Orth JD, Schellenberger J, Herrgard MJ, Palsson BO. Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli Metabolic Engineering. 12: 173-186. PMID 19840862 DOI: 10.1016/J.Ymben.2009.10.003  0.749
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