Simultaneous cross-evaluation of heterogeneous E. coli datasets via mechanistic simulation
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enabled us to integrate and cross-evaluate a massive, heterogeneous dataset based on measurements reported by various groups over decades. We identified inconsistencies with functional consequences across the data, including that the total output of the ribosomes and RNA polymerases described by data are not sufficient for a cell to reproduce measured doubling times, that measured metabolic parameters are neither fully compatible with each other nor with overall growth, and that essential proteins are absent during the cell cycle-and the cell is robust to this absence. Finally, considering these data as a whole leads to successful predictions of new experimental outcomes, in this case protein half-lives.
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No one organism has a complete set of experimentally determined kinetic parameters, chemical composition, and physical characteristics, so the model presented here, as well as other whole-cell models, has depended on the transferability of quantities among related organisms.
“Unfortunately, no one organism has a complete set of experimentally determined kinetic parameters, chemical composition, and physical characteristics, so the model we present here, as well as other whole-cell models, has depended on the transferability of quantities among related organisms.1”
From Bringing the genetically minimal cell to life on a computer in 4D (2026) · cites this paper as [4]
Split into 2 atoms — 0 confirmed, 2 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
Experimental — accuracy not yet measuredThe liponucleotide synthase cdsA/0304 catalyzing reaction DASYN was identified as a choke point in phospholipid biosynthesis, in agreement with a recent whole-cell model of E. coli.
“The liponucleotide synthase cdsA/0304 catalyzing reaction DASYN (Figure S2) that adds CDP to a phospholipid precursor (phosphatidic acid, PA) was identified as a “choke point” in the phoshpolipid biosynthesis, in agreement with a recent whole-cell model of E. coli (Macklin et al., 2020).”
From Fundamental behaviors emerge from simulations of a living minimal cell (2022) · cites this paper as Macklin et al., 2020
Well-stirred simulations can take as little as a few hours per cell cycle and can simulate multiple cells in parallel.
“Well-stirred simulations can take as little as a few hours per cell cycle and can simulate multiple cells in parallel.1”
From Bringing the genetically minimal cell to life on a computer in 4D (2026) · cites this paper as [4]
The paper describes simulations of E. coli cell cycles, but our copy does not state that well-stirred simulations take a few hours of computing time per cycle or that multiple cells can be simulated in parallel. The reported 125-minute doubling time is a simulated biological outcome, not simulation runtime. Searches for “well-stirred,” “parallel,” “hours,” and computational runtime did not establish the claim. (LLM, conf=0.78)
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Dynamics of chromosome organization in a minimal bacterial cell
Gilbert, B. R., Thornburg, Z. R., Brier, T. A., Stevens, J. A., Grünewald, F., Stone, J. E., Marrink, S. J., & Luthey-Schulten, Z. (2023) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2023.1214962 · Cited by 19 · see citing works
“…where the propagation is governed by the chemical and physical interactions within the cell and between the cell and its environment (Karr et al., 2012; Goldberg et al., 2018; Macklin et al., 2020; Marucci et al., 2020; Luthey-Schulten et al., 2022; Maritan et al., 2022; Thornburg et al., 2022).”
- Authors
- Macklin, D. N., Ahn-Horst, T. A., Choi, H., Ruggero, N. A., Carrera, J., Mason, J. C., Sun, G., Agmon, E., DeFelice, M. M., Maayan, I., Lane, K., Spangler, R. K., Gillies, T. E., Paull, M. L., Akhter, S., Bray, S. R., Weaver, D. S., Keseler, I. M., Karp, P. D., Morrison, J. H., & Covert, M. W.
- Affiliations
- Stanford University (US)
- SRI International (US)
- Corresponding author
- Covert, Markus W.
- ORCID
- Macklin, Derek N.
- Ahn-Horst, Travis A.
- Choi, Heejo
- Ruggero, Nicholas A.
- Mason, John C.
- Sun, Gwanggyu
- Agmon, Eran
- DeFelice, Mialy M.
- Maayan, Inbal
- Lane, Keara
- Spangler, Ryan K.
- Gillies, Taryn E.
- Paull, Morgan L.
- Akhter, Sajia
- Bray, Samuel R.
- Weaver, Daniel S.
- Keseler, Ingrid M.
- Karp, Peter D.
- Morrison, Jerry H.
- Covert, Markus W.
- Venue
- Science
- Published
- 2020-07-24
- Volume
- 369
- Issue
- 6502
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC7990026
- OpenAlex
- W3044339796
- Cited by
- 151
- References
- 84
- Citations by year
- 2026: 18 · 2025: 22 · 2024: 18 · 2023: 25 · 2022: 23 · 2021: 30 · 2020: 14 · 2019: 1
- FWCI
- 7.46
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- Funders
- National Science Foundation (Graduate Research Fellowship)
- National Institutes of Health (P50GM10715, 5DP1LM01150, GM077678)
- National Institute of Standards and Technology (70NANB15H192 (JIMB Training Grant Graduate Fellowship))
- Agilent Foundation (Graduate Student Fellowship)
- Paul G. Allen Family Foundation (Allen Discovery Center, Allen Distinguished Investigator)
- U.S. Department of Energy (DE-FG02-97ER25308)
- Stanford University (Benchmark Stanford Graduate Fellowship, Dean's Postdoctoral Fellowship, Stanford Graduate Fellowship)
- Thomas and Stacey Siebel Foundation (Graduate Scholarship)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Keywords
- Escherichia coli, mechanistic simulation, cell doubling time, metabolic parameters, essential proteins, cell cycle, data integration
- MeSH terms
- Data Analysis, Computer Simulation, Escherichia coli, Escherichia coli Proteins, Datasets as Topic
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