Ribosome biogenesis in replicating cells: integration of experiment and theory
Open accessAbstract
Ribosomes—the primary macromolecular machines responsible for translating the genetic code into proteins—are complexes of precisely folded RNA and proteins. The ways in which their production and assembly are managed by the living cell is of deep biological importance. Here we extend a recent spatially resolved whole‐cell model of ribosome biogenesis in a fixed volume [Earnest et al., Biophys J 2015, 109, 1117–1135] to include the effects of growth, DNA replication, and cell division. All biological processes are described in terms of reaction‐diffusion master equations and solved stochastically using the Lattice Microbes simulation software. In order to determine the replication parameters, we construct and analyze a series of Escherichia coli strains with fluorescently labeled genes distributed evenly throughout their chromosomes. By measuring these cells’ lengths and number of gene copies at the single‐cell level, we could fit a statistical model of the initiation and duration of chromosome replication. We found that for our slow‐growing (120 min doubling time) E. coli cells, replication was initiated 42 min into the cell cycle and completed after an additional 42 min. While simulations of the biogenesis model produce the correct ribosome and mRNA counts over the cell cycle, the kinetic parameters for transcription and degradation are lower than anticipated from a recent analytical time dependent model of in vivo mRNA production. Describing expression in terms of a simple chemical master equation, we show that the discrepancies are due to the lack of nonribosomal genes in the extended biogenesis model which effects the competition of mRNA for ribosome binding, and suggest corrections to parameters to be used in the whole‐cell model when modeling expression of the entire transcriptome. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 735–751, 2016.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Components of a ribosome biogenesis model developed for slow-growing E. coli have on average 50% sequence identity to genetic information processing genes in JCVI-syn3A.
“As its components have on average 50% sequence identity to those genetic information processing genes in JCVI-syn3A”
From Essential metabolism for a minimal cell (2019) · cites this paper as Earnest et al., 2016
The Introduction describes a ribosome-biogenesis model for slow-growing E. coli, and Section 2.2 identifies its ribosomal components. Our copy does not report a comparison with JCVI-syn3A genes or the claimed average 50% sequence identity; searches for those terms found no supporting passage. (LLM, conf=0.84)
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Storn, R., & Price, K. (1997) · Journal of Global Optimization · doi:10.1023/a:1008202821328 · Cited by 29,569 · see citing works
One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products.
Datsenko, K., & Wanner, B. (2000) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.120163297 · Cited by 15,902 · see citing works
scikit-image: image processing in Python
(2014) · doi:10.7717/peerj.453 · Cited by 6,794 · see citing works
Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.
Woese, C. R., Kandler, O., & Wheelis, M. L. (1990) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.87.12.4576 · Cited by 6,128 · see citing works
Woese, C. R. (1987) · Microbiological Reviews · doi:10.1128/mr.51.2.221-271.1987 · Cited by 5,042 · see citing works
IPython: A System for Interactive Scientific Computing
Pérez, F., & Granger, B. (2007) · Computing in Science & Engineering · doi:10.1109/mcse.2007.53 · Cited by 3,927 · see citing works
Intrinsic and extrinsic contributions to stochasticity in gene expression
Swain, P. S., Elowitz, M. B., & Siggia, E. D. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.162041399 · Cited by 1,661 · see citing works
Cython: The Best of Both Worlds
Behnel, S., Bradshaw, R., Citro, C., Dalcín, L., Seljebotn, D. S., & Smith, K. (2010) · Computing in Science & Engineering · doi:10.1109/mcse.2010.118 · Cited by 1,233 · see citing works
Li, G., Burkhardt, D. H., Gross, C. A., & Weissman, J. S. (2014) · Cell · doi:10.1016/j.cell.2014.02.033 · Cited by 1,218 · see citing works
Robust Growth of Escherichia coli
Wang, P., Robert, L., Pelletier, J., Dang, W. L., Taddei, F., Wright, A., & Jun, S. (2010) · Current Biology · doi:10.1016/j.cub.2010.04.045 · Cited by 1,014 · see citing works
Analytical distributions for stochastic gene expression
Shahrezaei, V., & Swain, P. S. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0803850105 · Cited by 829 · see citing works
Littlewood, D. T. J., Rohde, K., & Clough, K. A. (1999) · Biological Journal of the Linnean Society · doi:10.1111/j.1095-8312.1999.tb01918.x · Cited by 745 · see citing works
Cell-Size Control and Homeostasis in Bacteria
Taheri-Araghi, S., Bradde, S., Sauls, J. T., Hill, N. S., Levin, P. A., Paulsson, J., Vergassola, M., & Jun, S. (2014) · Current Biology · doi:10.1016/j.cub.2014.12.009 · Cited by 715 · see citing works
Linking Stochastic Dynamics to Population Distribution: An Analytical Framework of Gene Expression
Friedman, N., Cai, L., & Xie, X. S. (2006) · Physical Review Letters · doi:10.1103/physrevlett.97.168302 · Cited by 700 · see citing works
Genome-wide expression profiling in Escherichia coli K-12
Richmond, C. S. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.19.3821 · Cited by 580 · see citing works
A Constant Size Extension Drives Bacterial Cell Size Homeostasis
Campos, M., Surovtsev, I. V., Kato, S., Paintdakhi, A., Beltran, B. G., Ebmeier, S., & Jacobs, C. (2014) · Cell · doi:10.1016/j.cell.2014.11.022 · Cited by 472 · see citing works
Superresolution imaging of ribosomes and RNA polymerase in live <i>Escherichia coli</i> cells
Bakshi, S., Siryaporn, A., Goulian, M., & Weisshaar, J. C. (2012) · Molecular Microbiology · doi:10.1111/j.1365-2958.2012.08081.x · Cited by 456 · see citing works
Growth Rate and Generation Time of Bacteria, with Special Reference to Continuous Culture
Powell, E. O. (1956) · Journal of General Microbiology · doi:10.1099/00221287-15-3-492 · Cited by 429 · see citing works
Optical measurement of cycle-dependent cell growth
Mir, M., Wang, Z., Shen, Z. Z., Bednarz, M., Bashir, R., Golding, I., Prasanth, S. G., & Popescu, G. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1100506108 · Cited by 411 · see citing works
Using buoyant mass to measure the growth of single cells
Godin, M., Delgado, F. F., Son, S., Grover, W. H., Bryan, A. K., Tzur, A., Jorgensen, P., Payer, K., Grossman, A. D., Kirschner, M. W., et al. (2010) · Nature Methods · doi:10.1038/nmeth.1452 · Cited by 394 · see citing works
Chromosome Organization by a Nucleoid-Associated Protein in Live Bacteria
Wang, W., Li, G., Chen, C., Xie, X. S., & Zhuang, X. (2011) · Science · doi:10.1126/science.1204697 · Cited by 380 · see citing works
Bates, D. B., & Kleckner, N. E. (2005) · Cell · doi:10.1016/j.cell.2005.04.013 · Cited by 323 · see citing works
Cell Size Regulation in Bacteria
Amir, A. (2014) · Physical Review Letters · doi:10.1103/physrevlett.112.208102 · Cited by 319 · see citing works
Site-specific chromosomal integration of large synthetic constructs
Kuhlman, T. E., & Cox, E. C. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkp1193 · Cited by 259 · see citing works
Self-citationA Model for Statistics of the Cell Division Process
Koch, A. L., & Schaechter, M. (1962) · Journal of General Microbiology · doi:10.1099/00221287-29-3-435 · Cited by 257 · see citing works
Promoter architecture dictates cell-to-cell variability in gene expression
Jones, D., Brewster, R. C., & Phillips, R. (2014) · Science · doi:10.1126/science.1255301 · Cited by 223 · see citing works
Sundararaj, S. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh108 · Cited by 211 · see citing works
Visualizing Ribosome Biogenesis: Parallel Assembly Pathways for the 30 S Subunit
Mulder, A. M., Yoshioka, C., Beck, A. H., Bunner, A. E., Milligan, R. A., Potter, C. S., Carragher, B. O., & Williamson, J. R. (2010) · Science · doi:10.1126/science.1193220 · Cited by 196 · see citing works
Soifer, I., Robert, L., & Amir, A. (2016) · Current Biology · doi:10.1016/j.cub.2015.11.067 · Cited by 187 · see citing works
Concerted control of Escherichia coli cell division
Osella, M., Nugent, E., & Lagomarsino, M. C. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1313715111 · Cited by 181 · see citing works
Sanamrad, A., Persson, F., Lundius, E. G., Fange, D., Gynnå, A. H., & Elf, J. (2014) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.1411558111 · Cited by 177 · see citing works
Intermediates and time kinetics of the in vivo assembly of Escherichia coli ribosomes
Lindahl, L. (1975) · Journal of Molecular Biology · doi:10.1016/0022-2836(75)90089-3 · Cited by 170 · see citing works
Common angiotensin receptor blockers may directly modulate the immune system via VDR, PPAR and CCR2b
Marshall, T. G., Lee, R. E., & Marshall, F. E. (2006) · Theoretical Biology and Medical Modelling · doi:10.1186/1742-4682-3-1 · Cited by 169 · see citing works
Protein-guided RNA dynamics during early ribosome assembly
Kim, H., Abeysirigunawarden, S. C., Chen, K., Mayerle, M., Ragunathan, K., Luthey-Schulten, Z. A., Ha, T., & Woodson, S. A. (2014) · Nature · doi:10.1038/nature13039 · Cited by 148 · see citing works
Self-citationCell cycle parameters of slowly growing Escherichia coli B/r studied by flow cytometry
Skarstad, K., Steen, H. B., & Boye, E. (1983) · Journal of Bacteriology · doi:10.1128/jb.154.2.656-662.1983 · Cited by 146 · see citing works
Valgepea, K., Adamberg, K., Seiman, A., & Vilu, R. (2013) · Molecular BioSystems · doi:10.1039/c3mb70119k · Cited by 145 · see citing works
Gene location and DNA density determine transcription factor distributions in Escherichia coli
Kuhlman, T. E., & Cox, E. C. (2012) · Molecular Systems Biology · doi:10.1038/msb.2012.42 · Cited by 129 · see citing works
Self-citationRoberts, E., Stone, J. E., & Luthey‐Schulten, Z. (2013) · Journal of Computational Chemistry · doi:10.1002/jcc.23130 · Cited by 117 · see citing works
Self-citationPrecise determinations of C and D periods by flow cytometry in Escherichia coli K-12 and B/r
Michelsen, O., de Mattos, M. J. T., Jensen, P. R., & Hansen, F. G. (2003) · Microbiology · doi:10.1099/mic.0.26058-0 · Cited by 114 · see citing works
Joshi, M. C., Bourniquel, A., Fisher, J. K., Ho, B. T., Magnan, D. R., Kleckner, N. E., & Bates, D. B. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1019593108 · Cited by 112 · see citing works
Organization of Ribosomes and Nucleoids in Escherichia coli Cells during Growth and in Quiescence
Chai, Q., Singh, B., Peisker, K., Metzendorf, N. G., Ge, X., Dasgupta, S., & Sanyal, S. (2014) · Journal of Biological Chemistry · doi:10.1074/jbc.m114.557348 · Cited by 111 · see citing works
Molecular signatures of ribosomal evolution
Roberts, E., Sethi, A., Montoya, J. A., Woese, C. R., & Luthey-Schulten, Z. A. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0804861105 · Cited by 107 · see citing works
Self-citationReconstitution of functionally active ribosomes from inactive subparticles and proteins.
Hosokawa, K., Fujimura, R. K., & Nomura, M. (1966) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.55.1.198 · Cited by 104 · see citing works
Cooper, S. (2006) · Theoretical Biology and Medical Modelling · doi:10.1186/1742-4682-3-10 · Cited by 100 · see citing works
Noise Contributions in an Inducible Genetic Switch: A Whole-Cell Simulation Study
Roberts, E., Magis, A. T., Ortiz, J. O., Baumeister, W. P., & Luthey-Schulten, Z. A. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002010 · Cited by 99 · see citing works
Self-citationKoch, A. (1966) · Journal of General Microbiology · doi:10.1099/00221287-45-3-409 · Cited by 71 · see citing works
Bates, D. B., Epstein, J., Boye, E., Fahrner, K. A., Berg, H. C., & Kleckner, N. E. (2005) · Molecular Microbiology · doi:10.1111/j.1365-2958.2005.04693.x · Cited by 68 · see citing works
Sashital, D. G., Greeman, C. A., Lyumkis, D., Potter, C. S., Carragher, B. O., & Williamson, J. R. (2014) · eLife · doi:10.7554/elife.04491 · Cited by 67 · see citing works
Stochasticity and homeostasis in the E. coli replication and division cycle
Adiciptaningrum, A. M., Osella, M., Moolman, M. C., Lagomarsino, M. C., & Tans, S. J. (2015) · Scientific Reports · doi:10.1038/srep18261 · Cited by 65 · see citing works
Bunner, A. E., Beck, A. H., & Williamson, J. R. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0912007107 · Cited by 51 · see citing works
Hallock, M. J., Stone, J. E., Roberts, E., Fry, C., & Luthey-Schulten, Z. (2014) · Parallel Computing · doi:10.1016/j.parco.2014.03.009 · Cited by 50 · see citing works
Self-citationEffects of DNA replication on mRNA noise
Peterson, J. R., Cole, J. A., Fei, J., Ha, T., & Luthey-Schulten, Z. A. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1516246112 · Cited by 46 · see citing works
Self-citationAn Integrated System for Precise Genome Modification in Escherichia coli
Taş, H., Nguyen, C. T., Patel, R., Kim, N. H., & Kuhlman, T. E. (2015) · PLoS ONE · doi:10.1371/journal.pone.0136963 · Cited by 36 · see citing works
Self-citationStone, J. E., Hallock, M. J., Phillips, J. C., Peterson, J. R., Luthey-Schulten, Z. A., & Schulten, K. J. (2016) · IEEE International Symposium on Parallel & Distributed Processing, Workshops and Phd Forum · doi:10.1109/ipdpsw.2016.130 · Cited by 31 · see citing works
Self-citationToward a Whole-Cell model of ribosome biogenesis: kinetic modeling of SSU assembly
Earnest, E. E., Lai, J., Chen, K., Hallock, M. J., Williamson, J. R., & Luthey-Schulten, Z. (2015) · Biophysical Journal · doi:10.1016/j.bpj.2015.07.030 · Cited by 30 · see citing works
Self-citationKuhlman, T. E., & Cox, E. C. (2010) · Bioengineered Bugs · doi:10.4161/bbug.1.4.12386 · Cited by 28 · see citing works
Self-citationAssembly of the Five-Way Junction in the Ribosomal Small Subunit Using Hybrid MD-Go Simulations
Chen, K., Eargle, J., Lai, J., Kim, H., Abeysirigunawardena, S. C., Mayerle, M., Woodson, S. A., Ha, T., & Luthey-Schulten, Z. A. (2012) · The Journal of Physical Chemistry B · doi:10.1021/jp212614b · Cited by 23 · see citing works
Self-citationDNA-binding-protein inhomogeneity in E. colimodeled as biphasic facilitated diffusion
Kuhlman, T. E., & Cox, E. C. (2013) · Physical Review E · doi:10.1103/physreve.88.022701 · Cited by 19 · see citing works
Self-citationFunctional Role of Ribosomal Signatures
Chen, K., Eargle, J., Sarkar, K., Gruebele, M., & Luthey-Schulten, Z. A. (2010) · Biophysical Journal · doi:10.1016/j.bpj.2010.09.062 · Cited by 18 · see citing works
Self-citationStructural Intermediates and Folding Events in the Early Assembly of the Ribosomal Small Subunit
Lai, J., Chen, K., & Luthey-Schulten, Z. A. (2013) · The Journal of Physical Chemistry B · doi:10.1021/jp404106r · Cited by 10 · see citing works
Self-citationHallock, M. J., & Luthey-Schulten, Z. A. (2016) · IEEE International Symposium on Parallel & Distributed Processing, Workshops and Phd Forum · doi:10.1109/ipdpsw.2016.118 · Cited by 9 · see citing works
Self-citation
Flagged first, then by citations
1 of the 62 references couldn’t be matched to a known paper.
Research works printed but not linked: 1
- [59]Hallock MJ Luthey-Schulten Z Parallel and Distributed Processing Symposium Workshop (IPDPSW) 2016 IEEE International accepted PMC4978513 27516922
Cited by
Sorted by citations
Essential metabolism for a minimal cell
Breuer, M., Earnest, E. E., Merryman, C., Wise, K. S., Sun, L., Lynott, M. R., Hutchison, C. A., Smith, H. O., Lapek, J. D., Gonzalez, D. J., et al. (2019) · eLife · doi:10.7554/elife.36842 · Cited by 190 · see citing works
Self-citationFundamental behaviors emerge from simulations of a living minimal cell
Thornburg, Z. R., Bianchi, D. M., Brier, T. A., Gilbert, B. R., Earnest, E. E., Melo, M. C. R., Safronova, N., Sáenz, J. P., Cook, A. T., Wise, K. S., et al. (2022) · Cell · doi:10.1016/j.cell.2021.12.025 · Cited by 165 · see citing works
“coli used a lattice with dimensions of 32 × 32× 192 sites (196,608 total sites) and a lattice size of 32 nm, with timesteps of 25 μs (Earnest et al., 2016).”
Self-citationThe correlation between cell and nucleus size is explained by an eukaryotic cell growth model
Wu, Y., Pegoraro, A. F., Weitz, D. A., Janmey, P., & Sun, S. X. (2022) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1009400 · Cited by 72 · see citing works
Bringing the genetically minimal cell to life on a computer in 4D
Thornburg, Z. R., Maytin, A., Kwon, J., Brier, T. A., Gilbert, B. R., Fu, E., Gao, Y.-L., Quenneville, J., Wu, T., Li, H., et al. (2026) · Cell · doi:10.1016/j.cell.2026.02.009 · Cited by 44 · see citing works
Self-citationSimulating biological processes: stochastic physics from whole cells to colonies
Earnest, T. M., Cole, J. A., & Luthey-Schulten, Z. A. (2018) · Reports on Progress in Physics · doi:10.1088/1361-6633/aaae2c · Cited by 29 · see citing works
Self-citationKinetic modeling of the genetic information processes in a minimal cell
Thornburg, Z. R., Melo, M. C. R., Bianchi, D., Brier, T. A., Crotty, C., Breuer, M., Smith, H. O., Hutchison, C. A., Glass, J. I., & Luthey-Schulten, Z. (2019) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2019.00130 · Cited by 22 · see citing works
Self-citationChallenges of Integrating Stochastic Dynamics and Cryo-Electron Tomograms in Whole-Cell Simulations
Earnest, T. M., Watanabe, R., Stone, J. E., Mahamid, J., Baumeister, W. P., Villa, E., & Luthey-Schulten, Z. A. (2017) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.7b00672 · Cited by 21 · see citing works
Self-citationCareful accounting of extrinsic noise in protein expression reveals correlations among its sources
Cole, J. A., & Luthey-Schulten, Z. A. (2017) · Physical review. E · doi:10.1103/physreve.95.062418 · Cited by 18 · see citing works
Self-citationBridging intracellular scales by mechanistic computational models
Widmer, L. A., & Stelling, J. (2018) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2018.02.005 · Cited by 14 · see citing works
Kang, H.-W., & Radek Erban, A. (2019) · Bulletin of Mathematical Biology · doi:10.1007/s11538-019-00613-0 · Cited by 13 · see citing works
A computational spatial whole-Cell model for hepatitis B viral infection and drug interactions
Ghaemi, Z., Nafiu, O., Tajkhorshid, E., Gruebele, M., & Hu, J. (2023) · Scientific Reports · doi:10.1038/s41598-023-45998-0 · Cited by 6 · see citing works
Estrogen upregulates nucleophosmin 1 expression in mouse uterus through MYC induction
Lee, G., Suh, Y., Kim, B., Kim, J., Lee, J.-M., Park, S., Lee, O., Hong, K., Lee, M. R., & Choi, Y. (2025) · Molecular and Cellular Endocrinology · doi:10.1016/j.mce.2025.112612 · Cited by 3 · see citing works
Assembly of Macromolecular Complexes in the Whole-Cell Model of a Minimal Cell
Fu, E., Thornburg, Z. R., Brier, T. A., Wei, R., Yuan, B., Gilbert, B. R., Wang, S., & Luthey-Schulten, Z. A. (2025) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.5c04532 · Cited by 2 · see citing works
Self-citationCellular Organization of the Gastrointestinal Tract
Welcome, M. (2018) · Springer eBooks · doi:10.1007/978-3-319-91056-7_3 · Cited by 1 · see citing works
A Spatial Whole-Cell Model for Hepatitis B Viral Infection and Drug InteractionsPreprint
Ghaemi, Z., Nafiu, O., Tajkhorshid, E., Gruebele, M., & Hu, J. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.06.01.494377
Yang, Q., Chen, X., Tian, F., Xing, Z., Gan, X., & Chen, J. (2026) · Physiological and Molecular Plant Pathology · doi:10.1016/j.pmpp.2026.103621
- Authors
- Earnest, E. E., Cole, J. A., Peterson, J. R., Hallock, M. J., Kuhlman, T. E., & Luthey‐Schulten, Z.
- Affiliations
- Center for the Physics of Living Cells, University of Illinois Urbana IL
- University of Illinois Urbana-Champaign (US)
- Venue
- Biopolymers
- Publisher
- Wiley
- Published
- 2016-07-22
- Volume
- 105
- Issue
- 10
- Pages
- 735-751
- ISSN
- 0006-3525 (ISSN-L)
- 1097-0282
- PMC
- PMC4958520
- OpenAlex
- W2422442815
- Cited by
- 16
- References
- 62
- Citations by year
- 2026: 2 · 2025: 2 · 2023: 1 · 2022: 3 · 2019: 3 · 2018: 3 · 2017: 2
- FWCI
- 1.39
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Biopolymers (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- National Science Foundation (NSF) (MCB-1244570)
- NSF Center for the Physics of Living Cells (PHY-1430124)
- NSF Graduate Research Fellowship (DGE-1144245)
- U.S. Department of Energy, Office of Science, Biological and Environmental Research, Adaptive Biosystems Imaging Scientific Focus Area
- Alfred P. Sloan Foundation Research Fellowship in Physics (FG-2015-65532)
- National Science Foundation (OCI-0725070, ACI-1238993)
- National Institutes of Health (9 P41 GM104601-23, GM112659)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Keywords
- ribosome biogenesis, DNA replication, cell division, whole-cell model, chemical master equation, reaction-diffusion, Escherichia coli, DNA replication timing, transcription kinetics, mRNA degradation
- MeSH terms
- Cell Division, DNA Replication, DNA, Bacterial, Escherichia coli, Models, Biological, Ribosomes
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
