Daniel Zielinski

Title(s)Associate Project Scientist, Bioengineering
SchoolVc-academic Affairs
Address9500 Gilman Drive #
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. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. PanKB: An interactive microbial pangenome knowledgebase for research, biotechnological innovation, and knowledge mining. Nucleic Acids Res. 2024 Nov 22. Sun B, Pashkova L, Pieters PA, Harke AS, Mohite OS, Santos A, Zielinski DC, Palsson BO, Phaneuf PV. PMID: 39574409.
      View in: PubMed   Mentions:    Fields:    
    2. Diversity of transcriptional regulatory adaptation in E. coli. Mol Biol Evol. 2024 Nov 12. Dalldorf C, Hefner Y, Szubin R, Johnsen J, Mohamed E, Li G, Krishnan J, Feist AM, Palsson BO, Zielinski DC. PMID: 39531644.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    3. iModulonDB 2.0: dynamic tools to facilitate knowledge-mining and user-enabled analyses of curated transcriptomic datasets. Nucleic Acids Res. 2024 Nov 04. Catoiu EA, Krishnan J, Li G, Lou XA, Rychel K, Yuan Y, Bajpe H, Patel A, Choe D, Shin J, Burrows J, Phaneuf PV, Zielinski DC, Palsson BO. PMID: 39494532.
      View in: PubMed   Mentions:    Fields:    
    4. iModulonMiner and PyModulon: Software for unsupervised mining of gene expression compendia. PLoS Comput Biol. 2024 Oct 23; 20(10):e1012546. Sastry AV, Yuan Y, Poudel S, Rychel K, Yoo R, Lamoureux CR, Li G, Burrows JT, Chauhan S, Haiman ZB, Al Bulushi T, Seif Y, Palsson BO, Zielinski DC. PMID: 39441835.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    5. Modulating bacterial function utilizing A knowledge base of transcriptional regulatory modules. Nucleic Acids Res. 2024 Oct 14; 52(18):11362-11377. Shin J, Zielinski DC, Palsson BO. PMID: 39193902; PMCID: PMC11472167.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    6. A genome-scale metabolic model of a globally disseminated hyperinvasive M1 strain of Streptococcus pyogenes. mSystems. 2024 Sep 17; 9(9):e0073624. Hirose Y, Zielinski DC, Poudel S, Rychel K, Baker JL, Toya Y, Yamaguchi M, Heinken A, Thiele I, Kawabata S, Palsson BO, Nizet V. PMID: 39158303; PMCID: PMC11406949.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    7. The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions. mSystems. 2024 Jul 23; 9(7):e0030524. Dalldorf C, Rychel K, Szubin R, Hefner Y, Patel A, Zielinski DC, Palsson BO. PMID: 38829048; PMCID: PMC11264592.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    8. Deciphering nutritional stress responses via knowledge-enriched transcriptomics for microbial engineering. Metab Eng. 2024 Jul; 84:34-47. Shin J, Zielinski DC, Palsson BO. PMID: 38825177.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    9. Escherichia coli non-coding regulatory regions are highly conserved. NAR Genom Bioinform. 2024 Jun; 6(2):lqae041. Lamoureux CR, Phaneuf PV, Palsson BO, Zielinski DC. PMID: 38774514; PMCID: PMC11106028.
      View in: PubMed   Mentions:
    10. Bottom-up parameterization of enzyme rate constants: Reconciling inconsistent data. Metab Eng Commun. 2024 Jun; 18:e00234. Zielinski DC, Matos MRA, de Bree JE, Glass K, Sonnenschein N, Palsson BO. PMID: 38711578; PMCID: PMC11070925.
      View in: PubMed   Mentions:
    11. Reconstructing the transcriptional regulatory network of probiotic L. reuteri is enabled by transcriptomics and machine learning. mSystems. 2024 Mar 19; 9(3):e0125723. Josephs-Spaulding J, Rajput A, Hefner Y, Szubin R, Balasubramanian A, Li G, Zielinski DC, Jahn L, Sommer M, Phaneuf P, Palsson BO. PMID: 38349131; PMCID: PMC10949432.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    12. Inferred regulons are consistent with regulator binding sequences in E. coli. PLoS Comput Biol. 2024 Jan; 20(1):e1011824. Qiu S, Wan X, Liang Y, Lamoureux CR, Akbari A, Palsson BO, Zielinski DC. PMID: 38252668; PMCID: PMC10833566.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    13. Differential Expression Analysis Utilizing Condition-Specific Metabolic Pathways. Metabolites. 2023 Nov 03; 13(11). Mattei G, Gan Z, Ramazzotti M, Palsson BO, Zielinski DC. PMID: 37999223; PMCID: PMC10672963.
      View in: PubMed   Mentions:
    14. A multi-scale expression and regulation knowledge base for Escherichia coli. Nucleic Acids Res. 2023 10 27; 51(19):10176-10193. Lamoureux CR, Decker KT, Sastry AV, Rychel K, Gao Y, McConn JL, Zielinski DC, Palsson BO. PMID: 37713610; PMCID: PMC10602906.
      View in: PubMed   Mentions: 16     Fields:    Translation:Cells
    15. Empowering drug off-target discovery with metabolic and structural analysis. Nat Commun. 2023 06 09; 14(1):3390. Chowdhury S, Zielinski DC, Dalldorf C, Rodrigues JV, Palsson BO, Shakhnovich EI. PMID: 37296102; PMCID: PMC10256842.
      View in: PubMed   Mentions: 2     Fields:    
    16. Elucidation of independently modulated genes in Streptococcus pyogenes reveals carbon sources that control its expression of hemolytic toxins. mSystems. 2023 Jun 29; 8(3):e0024723. 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. PMID: 37278526; PMCID: PMC10308926.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    17. The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions. Res Sq. 2023 Apr 12. Dalldorf C, Rychel K, Szubin R, Hefner Y, Patel A, Zielinski DC, Palsson BO. PMID: 37090546; PMCID: PMC10120744.
      View in: PubMed   Mentions:
    18. Escherichia coli Data-Driven Strain Design Using Aggregated Adaptive Laboratory Evolution Mutational Data. ACS Synth Biol. 2021 12 17; 10(12):3379-3395. 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. PMID: 34762392; PMCID: PMC8870144.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    19. The quantitative metabolome is shaped by abiotic constraints. Nat Commun. 2021 05 26; 12(1):3178. Akbari A, Yurkovich JT, Zielinski DC, Palsson BO. PMID: 34039963; PMCID: PMC8155068.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    20. MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics. PLoS Comput Biol. 2021 01; 17(1):e1008208. Haiman ZB, Zielinski DC, Koike Y, Yurkovich JT, Palsson BO. PMID: 33507922; PMCID: PMC7872247.
      View in: PubMed   Mentions: 16     Fields:    
    21. The Expanding Computational Toolbox for Engineering Microbial Phenotypes at the Genome Scale. Microorganisms. 2020 Dec 21; 8(12). Zielinski DC, Patel A, Palsson BO. PMID: 33371386; PMCID: PMC7767376.
      View in: PubMed   Mentions: 8  
    22. Modeling genome-wide enzyme evolution predicts strong epistasis underlying catalytic turnover rates. Nat Commun. 2018 12 10; 9(1):5270. Heckmann D, Zielinski DC, Palsson BO. PMID: 30532008; PMCID: PMC6288127.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    23. Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models. Nat Commun. 2018 12 07; 9(1):5252. Heckmann D, Lloyd CJ, Mih N, Ha Y, Zielinski DC, Haiman ZB, Desouki AA, Lercher MJ, Palsson BO. PMID: 30531987; PMCID: PMC6286351.
      View in: PubMed   Mentions: 62     Fields:    Translation:Cells
    24. Estimating Metabolic Equilibrium Constants: Progress and Future Challenges. Trends Biochem Sci. 2018 12; 43(12):960-969. Du B, Zielinski DC, Palsson BO. PMID: 30472988.
      View in: PubMed   Mentions: 7     Fields:    
    25. Thermodynamic favorability and pathway yield as evolutionary tradeoffs in biosynthetic pathway choice. Proc Natl Acad Sci U S A. 2018 10 30; 115(44):11339-11344. Du B, Zielinski DC, Monk JM, Palsson BO. PMID: 30309961; PMCID: PMC6217407.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    26. Temperature-Dependent Estimation of Gibbs Energies Using an Updated Group-Contribution Method. Biophys J. 2018 06 05; 114(11):2691-2702. Du B, Zhang Z, Grubner S, Yurkovich JT, Palsson BO, Zielinski DC. PMID: 29874618; PMCID: PMC6129446.
      View in: PubMed   Mentions: 15     Fields:    
    27. Recon3D enables a three-dimensional view of gene variation in human metabolism. Nat Biotechnol. 2018 03; 36(3):272-281. Brunk E, Sahoo S, Zielinski DC, 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. PMID: 29457794; PMCID: PMC5840010.
      View in: PubMed   Mentions: 295     Fields:    Translation:Humans
    28. Topological and kinetic determinants of the modal matrices of dynamic models of metabolism. PLoS One. 2017; 12(12):e0189880. Du B, Zielinski DC, Palsson BO. PMID: 29267329; PMCID: PMC5739448.
      View in: PubMed   Mentions:    Fields:    
    29. 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. 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. PMID: 29030425; PMCID: PMC5712598.
      View in: PubMed   Mentions: 29     Fields:    Translation:HumansCells
    30. A Systematic Evaluation of Methods for Tailoring Genome-Scale Metabolic Models. Cell Syst. 2017 03 22; 4(3):318-329.e6. Opdam S, Richelle A, Kellman B, Li S, Zielinski DC, Lewis NE. PMID: 28215528; PMCID: PMC5526624.
      View in: PubMed   Mentions: 102     Fields:    Translation:HumansAnimals
    31. Systems biology analysis of drivers underlying hallmarks of cancer cell metabolism. Sci Rep. 2017 01 25; 7:41241. Zielinski DC, Jamshidi N, Corbett AJ, Bordbar A, Thomas A, Palsson BO. PMID: 28120890; PMCID: PMC5264163.
      View in: PubMed   Mentions: 55     Fields:    Translation:HumansCells
    32. A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism. Cell Syst. 2016 11 23; 3(5):434-443.e8. 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, 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. PMID: 27883890; PMCID: PMC5132346.
      View in: PubMed   Mentions: 63     Fields:    Translation:HumansAnimalsCells
    33. 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 09; 172(1):589-602. Zuñiga C, Li CT, Huelsman T, Levering J, Zielinski DC, McConnell BO, Long CP, Knoshaug EP, Guarnieri MT, Antoniewicz MR, Betenbaugh MJ, Zengler K. PMID: 27372244; PMCID: PMC5074608.
      View in: PubMed   Mentions: 31     Fields:    Translation:AnimalsCells
    34. Evaluation of rate law approximations in bottom-up kinetic models of metabolism. BMC Syst Biol. 2016 06 06; 10(1):40. Du B, Zielinski DC, Kavvas ES, Dräger A, Tan J, Zhang Z, Ruggiero KE, Arzumanyan GA, Palsson BO. PMID: 27266508; PMCID: PMC4895898.
      View in: PubMed   Mentions: 14     Fields:    
    35. Personalized Whole-Cell Kinetic Models of Metabolism for Discovery in Genomics and Pharmacodynamics. Cell Syst. 2015 Oct 28; 1(4):283-92. Bordbar A, McCloskey D, Zielinski DC, Sonnenschein N, Jamshidi N, Palsson BO. PMID: 27136057.
      View in: PubMed   Mentions: 49     Fields:    
    36. SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks. BMC Syst Biol. 2015 Oct 09; 9:68. Dräger A, Zielinski DC, Keller R, Rall M, Eichner J, Palsson BO, Zell A. PMID: 26452770; PMCID: PMC4600286.
      View in: PubMed   Mentions: 9     Fields:    
    37. Pharmacogenomic and clinical data link non-pharmacokinetic metabolic dysregulation to drug side effect pathogenesis. Nat Commun. 2015 Jun 09; 6:7101. Zielinski DC, Filipp FV, Bordbar A, Jensen K, Smith JW, Herrgard MJ, Mo ML, Palsson BO. PMID: 26055627; PMCID: PMC4468904.
      View in: PubMed   Mentions: 20     Fields:    Translation:Humans
    38. A systems approach to predict oncometabolites via context-specific genome-scale metabolic networks. PLoS Comput Biol. 2014 Sep; 10(9):e1003837. Nam H, Campodonico M, Bordbar A, Hyduke DR, Kim S, Zielinski DC, Palsson BO. PMID: 25232952; PMCID: PMC4168981.
      View in: PubMed   Mentions: 35     Fields:    Translation:HumansCells
    39. Predicting outcomes of steady-state ¹³C isotope tracing experiments using Monte Carlo sampling. BMC Syst Biol. 2012 Jan 30; 6:9. Schellenberger J, Zielinski DC, Choi W, Madireddi S, Portnoy V, Scott DA, Reed JL, Osterman AL, Palsson B. PMID: 22289253; PMCID: PMC3323462.
      View in: PubMed   Mentions: 17     Fields:    Translation:Cells
    40. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nat Protoc. 2011 Aug 04; 6(9):1290-307. 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. PMID: 21886097; PMCID: PMC3319681.
      View in: PubMed   Mentions: 593     Fields:    
    41. Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli. Metab Eng. 2010 May; 12(3):173-86. Feist AM, Zielinski DC, Orth JD, Schellenberger J, Herrgard MJ, Palsson BØ. PMID: 19840862; PMCID: PMC3125152.
      View in: PubMed   Mentions: 87     Fields:    Translation:Cells
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