D. Zielinski

发表

Personalized Whole-Cell Kinetic Models of Metabolism for Discovery in Genomics and Pharmacodynamics.

Daniel C. Zielinski, B. Palsson, A. Bordbar, 2015, Cell systems.

Recon3D enables a three-dimensional view of gene variation in human metabolism

Daniel C. Zielinski, Maike K. Aurich, Anand V. Sastry, 2018 .

Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models

Daniel C. Zielinski, Abdelmoneim Amer Desouki, Zachary B. Haiman, 2018, Nature Communications.

Modeling genome-wide enzyme evolution predicts strong epistasis underlying catalytic turnover rates

Daniel C. Zielinski, B. Palsson, D. Zielinski, 2018, Nature Communications.

The Expanding Computational Toolbox for Engineering Microbial Phenotypes at the Genome Scale

Daniel C. Zielinski, B. Palsson, D. Zielinski, 2020, Microorganisms.

Temperature-dependent estimation of Gibbs energies using an updated group contribution method

Daniel C. Zielinski, James T. Yurkovich, B. Palsson, 2018, bioRxiv.

Topological and kinetic determinants of the modal matrices of dynamic models of metabolism

Daniel C. Zielinski, B. Palsson, D. Zielinski, 2017, bioRxiv.

Topological and Kinetic Determinants of the Modal Matrices of Dynamic Models of Metabolism

B. Palsson, D. Zielinski, Bin Du, 2017, bioRxiv.

The quantitative metabolome is shaped by abiotic constraints

Daniel C. Zielinski, James T. Yurkovich, B. Palsson, 2020, Nature Communications.

Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli.

Adam M. Feist, Daniel C. Zielinski, Markus J. Herrgård, 2010, Metabolic engineering.

A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism.

Daniel C. Zielinski, Zachary A. King, David E. Ruckerbauer, 2016, Cell systems.

A Systematic Evaluation of Methods for Tailoring Genome-Scale Metabolic Models.

Anne Richelle, Daniel C. Zielinski, Nathan E Lewis, 2017, Cell systems.

Recon3D: A Resource Enabling A Three-Dimensional View of Gene Variation in Human Metabolism

Avlant Nilsson, Ronan M. T. Fleming, Elizabeth Brunk, 2018, Nature Biotechnology.

Metabolic impact of an NADH-producing glucose-6-phosphate dehydrogenase in Escherichia coli.

Adam M. Feist, Daniel C. Zielinski, A. Feist, 2014, Microbiology.

Genome-Scale Metabolic Model for the Green Alga Chlorella vulgaris UTEX 395 Accurately Predicts Phenotypes under Autotrophic, Heterotrophic, and Mixotrophic Growth Conditions1

Daniel C. Zielinski, Christopher P. Long, Christopher P Long, 2016, Plant Physiology.

Temperature-dependent estimation of Gibbs energies using an updated group contribution method

B. Palsson, D. Zielinski, J. Yurkovich, 2018, bioRxiv.

ReCodLiver0.9: Overcoming Challenges in Genome-Scale Metabolic Reconstruction of a Non-model Species

E. M. Hanna, I. Jonassen, D. Zielinski, 2020, Frontiers in Molecular Biosciences.

Estimating Metabolic Equilibrium Constants: Progress and Future Challenges.

Daniel C. Zielinski, B. Palsson, D. Zielinski, 2018, Trends in biochemical sciences.

context-sensitive creation of kinetic equations in biochemical

A. Zell, D. Zielinski, Johannes Eichner, 2015 .

Elucidation of independently modulated genes in Streptococcus pyogenes reveals carbon sources that control its expression of hemolytic toxins

Daniel C. Zielinski, Anand V. Sastry, V. Nizet, 2022, bioRxiv.

Empowering systems-guided drug target discovery with metabolic and structural analysis

Daniel C. Zielinski, E. Shakhnovich, D. Zielinski, 2022, bioRxiv.

A multi-scale transcriptional regulatory network knowledge base for Escherichia coli

Daniel C. Zielinski, Anand V. Sastry, B. Palsson, 2021, bioRxiv.

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

Ronan M. T. Fleming, Aarash Bordbar, Adam M. Feist, 2007, Nature Protocols.

Systems biology analysis of drivers underlying hallmarks of cancer cell metabolism

Aarash Bordbar, Bernhard O. Palsson, Daniel C. Zielinski, 2017, Scientific Reports.

Recon 2.2: from reconstruction to model of human metabolism

Neil Swainston, Douglas B. Kell, Nathan E. Lewis, 2016, Metabolomics.

A Systems Approach to Predict Oncometabolites via Context-Specific Genome-Scale Metabolic Networks

Aarash Bordbar, Bernhard O. Palsson, Hojung Nam, 2014, PLoS Comput. Biol..

On-pathway multivalency of a broadly neutralizing evolution drug candidate

Daniel C. Zielinski, E. Shakhnovich, D. Zielinski, 2021 .

Kinetic Modeling of Metabolic Networks

Bernhard O. Palsson, Daniel C. Zielinski, B. Palsson, 2012 .

Modeling genome-wide evolution of catalytic turnover rates: Strong epistasis shaped modern enzyme kinetics

Daniel C. Zielinski, B. Palsson, D. Zielinski, 2018, bioRxiv.

ReCodLiver0.9: Overcoming Challenges in Genome-Scale Metabolic Reconstruction of a Non-model Species

Daniel C. Zielinski, Inge Jonassen, Anders Goksøyr, 2020, bioRxiv.

Pharmacogenomic and clinical data link non-pharmacokinetic metabolic dysregulation to drug side effect pathogenesis

Aarash Bordbar, Daniel C. Zielinski, Bernhard O Palsson, 2015, Nature Communications.

Escherichia coli Data-Driven Strain Design Using Aggregated Adaptive Laboratory Evolution Mutational Data

Adam M. Feist, Daniel C. Zielinski, James T. Yurkovich, 2021, ACS synthetic biology.

Evaluation of rate law approximations in bottom-up kinetic models of metabolism

Zhen Zhang, Bin Du, Bernhard O. Palsson, 2016, BMC Systems Biology.

SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks

Andreas Zell, Bernhard O. Palsson, Andreas Dräger, 2015, BMC Systems Biology.

A systems-guided approach to discover the intracellular target of a novel evolution-drug lead

Daniel C. Zielinski, B. Palsson, E. Shakhnovich, 2021 .

Quantitative time-course metabolomics in human red blood cells reveal the temperature dependence of human metabolic networks

Aarash Bordbar, Daniel C. Zielinski, Bernhard O Palsson, 2017, The Journal of Biological Chemistry.

MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics

Bernhard O. Palsson, Daniel C. Zielinski, James T. Yurkovich, 2020, bioRxiv.

The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions

Daniel C. Zielinski, D. Zielinski, R. Szubin, 2023, Research square.

Quantitative sequence basis for the E. coli transcriptional regulatory network

Daniel C. Zielinski, D. Zielinski, Cameron R. Lamoureux, 2022, bioRxiv.

Predicting outcomes of steady-state 13C isotope tracing experiments using Monte Carlo sampling

Bernhard O. Palsson, Daniel C. Zielinski, Andrei Osterman, 2012, BMC Systems Biology.

Thermodynamic favorability and pathway yield as evolutionary tradeoffs in biosynthetic pathway choice

Bernhard O. Palsson, Daniel C. Zielinski, Jonathan M. Monk, 2018, Proceedings of the National Academy of Sciences.

Reconstructing the Transcriptional Regulatory Network of Probiotic L. reuteri is Enabled by Transcriptomics and Machine Learning

Daniel C. Zielinski, M. Sommer, D. Zielinski, 2023, bioRxiv.