Academic lineage
- Bernhard Ø Palsson - Ph.D. student
Escherichia coli Data-Driven Strain Design Using Aggregated Adaptive Laboratory Evolution Mutational Data
- Patrick V Phaneuf, Daniel C Zielinski, James T Yurkovich, …, Rebecca M Lennen, Bernhard O Palsson, Adam M Feist
- ACS Synth Biol, 10.1021/acssynbio.1c00337
The quantitative metabolome is shaped by abiotic constraints
- Amir Akbari, James T Yurkovich, Daniel C Zielinski, …, James T Yurkovich, Daniel C Zielinski, Bernhard O Palsson
- Nat Commun, 10.1038/s41467-021-23214-9
MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics
- Zachary B Haiman, Daniel C Zielinski, Yuko Koike, James T Yurkovich, Bernhard O Palsson
- PLoS Comput Biol, 10.1371/journal.pcbi.1008208
The Expanding Computational Toolbox for Engineering Microbial Phenotypes at the Genome Scale
- Daniel Craig Zielinski, Arjun Patel, Bernhard O Palsson
- None, 10.3390/microorganisms8122050
ReCodLiver0.9: Overcoming Challenges in Genome-Scale Metabolic Reconstruction of a Non-model Species
- Eileen Marie Hanna, Xiaokang Zhang, Marta Eide, …, Daniel Craig Zielinski, Anders Goksøyr, Inge Jonassen
- None, 10.3389/fmolb.2020.591406
Modeling genome-wide enzyme evolution predicts strong epistasis underlying catalytic turnover rates
- David Heckmann, Daniel C Zielinski, Bernhard O Palsson
- Nat Commun, 10.1038/s41467-018-07649-1
Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models
- David Heckmann, Colton J Lloyd, Nathan Mih, …, Abdelmoneim Amer Desouki, Martin J Lercher, Bernhard O Palsson
- Nat Commun, 10.1038/s41467-018-07652-6
Estimating Metabolic Equilibrium Constants: Progress and Future Challenges
- Bin Du, Daniel C Zielinski, Bernhard O Palsson
- Trends Biochem Sci, 10.1016/j.tibs.2018.09.009
Thermodynamic favorability and pathway yield as evolutionary tradeoffs in biosynthetic pathway choice
- Bin Du, Daniel C Zielinski, Jonathan M Monk, Bernhard O Palsson
- Proc Natl Acad Sci U S A, 10.1073/pnas.1805367115
Temperature-Dependent Estimation of Gibbs Energies Using an Updated Group-Contribution Method
- Bin Du, Zhen Zhang, Sharon Grubner, James T Yurkovich, Bernhard O Palsson, Daniel C Zielinski
- Biophys J, 10.1016/j.bpj.2018.04.030
Recon3D enables a three-dimensional view of gene variation in human metabolism
- Elizabeth Brunk, Swagatika Sahoo, Daniel C Zielinski, …, Jens Nielsen, Ines Thiele, Bernhard O Palsson
- Nat Biotechnol, 10.1038/nbt.4072