Author

D. C. Zielinski

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Microbiology· 2 Bioengineering· 1 Evolutionary Biology· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 3 Assay:bulk RNA-seq· 2 Organism:E. coli· 2 Organism:bacteria (other)· 1 Research Focus:cell type annotation· 1 Research Focus:drug response / drug discovery· 1 Research Focus:gene regulatory network inference· 1 Approach:machine learning (classical)· 1

Frequent Co-Authors

B. O. Palsson· 4 shared L. Yang· 2 shared R. Szubin· 2 shared S. H. Kim· 2 shared A. Feist· 1 shared A. Patel· 1 shared A. V. Sastry· 1 shared C. Dalldorf· 1 shared

Activity by Year

2018-2024 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 25 mutual co-author links

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4 shared papersMicrobiology

B. O. Palsson

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Author profile →

4 papers

Recent·Most cited

Trade-off Between Resistance and Persistence in High Cell Density Escherichia Coli Cultures

F. Beulig, J. Bafna-Ruehrer, P. E. Jensen, S. H. Kim, A. Patel, V. Kandasamy, C. Steffen, K. Decker, D. C. Zielinski, L. Yang, E. Oezdemir, S. Sudarsan, B. O. Palsson

The paper investigates high cell density physiology in Escherichia coli, revealing a trade-off between resistance and persistence through transcriptional analysis and machine learning.

bioRxiv · Jan 29, 2024 · PreprintMicrobiology

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

Y. Hirose, S. Poudel, A. V. Sastry, R. Szubin, D. C. Zielinski, H. G. Lim, N. D. Menon, H. Bergsten, S. Uchiyama, T. Hanada, S. Kawabata, B. O. Palsson, V. Nizet

The paper identifies carbon sources that regulate hemolytic toxin expression in Streptococcus pyogenes using transcriptome-wide independent component analysis.

bioRxiv · Aug 4, 2022Microbiology

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

P. V. Phaneuf, D. C. Zielinski, J. T. Yurkovich, J. Johnsen, R. Szubin, L. Yang, S. H. Kim, S. Schulz, M. Wu, C. Dalldorf, E. Ozdemir, B. O. Palsson, A. Feist

This paper presents a data-driven workflow to design microbial strains using aggregated ALE mutational data, revealing gene-centric mutations that significantly alter cellular states.

bioRxiv · Jul 19, 2021Bioengineering

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

D. Heckmann, D. C. Zielinski, B. O. Palsson

The paper models the evolution of enzyme turnover rates using genome-scale metabolic and population genetics models, finding strong epistasis shapes kcat evolution and limits adaptation.

bioRxiv · May 10, 2018Evolutionary Biology