Hands-On Growth Laws Theory Cookbook
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Abstract
This tutorial covers the emerging field of coarse-grained cellular growth modeling, and aims to bridge the gap between theoretical foundations and practical application. By adopting an original “cookbook” approach, it is designed to offer a hands-on guide for constructing and analyzing different key aspects of cellular growth, focusing on available results for bacteria and beyond. The tutorial is structured as a series of step-by-step “recipes,” and covers essential concepts, recent literature, and key challenges. It aims to empower a broad audience, from students to seasoned researchers, to replicate, extend, and innovate in this scientific area. Specifically, each section provides detailed, bare-bones models to start working in each area, from basic steady-state growth to variable environments and focusing on different key layers relevant to biosynthesis, transcription, translation, nutrient sensing, and protein degradation, links between cell cycle and growth, ending with ecological insights.
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Cites
mTOR Signaling in Growth Control and Disease
Laplante, M., & Sabatini, D. M. (2012) · Cell · doi:10.1016/j.cell.2012.03.017 · Cited by 8,509 · see citing works
Global quantification of mammalian gene expression control
Schwanhäusser, B., Busse, D., Li, N., Dittmar, G., Schuchhardt, J., Wolf, J., Chen, W., & Selbach, M. (2011) · Nature · doi:10.1038/nature10098 · Cited by 6,566 · see citing works
TOR signaling in growth and metabolism
Wullschleger, S., Loewith, R., & Hall, M. N. (2006) · Cell · doi:10.1016/j.cell.2006.01.016 · Cited by 5,787 · see citing works
Genomic Expression Programs in the Response of Yeast Cells to Environmental Changes
Gasch, A. P., Spellman, P. T., Kao, C. M., Carmel-Harel, O., Eisen, M. B., Storz, G., Botstein, D., & Brown, P. O. (2000) · Molecular Biology of the Cell · doi:10.1091/mbc.11.12.4241 · Cited by 4,815 · see citing works
Microbial interactions: from networks to models
Faust, K., & Raes, J. (2012) · Nature Reviews Microbiology · doi:10.1038/nrmicro2832 · Cited by 4,138 · see citing works
More Is Different: Broken symmetry and the nature of the hierarchical structure of science.
Anderson, P. W. (1972) · Science · doi:10.1126/science.177.4047.393 · Cited by 4,018 · see citing works
THE GROWTH OF BACTERIAL CULTURES
Monod, J. (1949) · Annual Review of Microbiology · doi:10.1146/annurev.mi.03.100149.002103 · Cited by 3,853 · see citing works
Protein degradation and protection against misfolded or damaged proteins.
Goldberg, A. L. (2003) · Nature · doi:10.1038/nature02263 · Cited by 2,088 · see citing works
Automated design of synthetic ribosome binding sites to control protein expression
Salis, H. M., Mirsky, E. A., & Voigt, C. A. (2009) · Nature Biotechnology · doi:10.1038/nbt.1568 · Cited by 1,844 · see citing works
Intracellular Protein Degradation in Mammalian and Bacterial Cells
Goldberg, A. L., & Dice, J. F. (1974) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.43.070174.004155 · Cited by 1,778 · see citing works
Dynamics and diversity in autophagy mechanisms: lessons from yeast
Nakatogawa, H., Suzuki, K., Kamada, Y., & Ohsumi, Y. (2009) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2708 · Cited by 1,718 · see citing works
Interdependence of Cell Growth and Gene Expression: Origins and Consequences
Scott, M., Gunderson, C. W., Mateescu, E. M., Zhang, Z., & Hwa, T. (2010) · Science · doi:10.1126/science.1192588 · Cited by 1,470 · see citing works
Schaechter, M., MaalOe, O., & Kjeldgaard, N. O. (1958) · Journal of General Microbiology · doi:10.1099/00221287-19-3-592 · Cited by 1,435 · see citing works
Phenotypic Diversity, Population Growth, and Information in Fluctuating Environments
Kussell, E. L., & Leibler, S. (2005) · Science · doi:10.1126/science.1114383 · Cited by 1,357 · see citing works
TRANSLATIONAL REGULATION OFGCN4AND THE GENERAL AMINO ACID CONTROL OF YEAST
Hinnebusch, A. G. (2005) · Annual Review of Microbiology · doi:10.1146/annurev.micro.59.031805.133833 · Cited by 1,258 · 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
The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss
Morris, J., Lenski, R. E., & Zinser, E. R. (2012) · mBio · doi:10.1128/mbio.00036-12 · Cited by 1,212 · see citing works
Potrykus, K., & Cashel, M. (2008) · Annual Review of Microbiology · doi:10.1146/annurev.micro.62.081307.162903 · Cited by 1,170 · see citing works
Species packing and competitive equilibrium for many species
MacArthur, R. H. (1970) · Theoretical Population Biology · doi:10.1016/0040-5809(70)90039-0 · Cited by 1,093 · see citing works
Edwards, J. S., Ibarra, R. U., & Palsson, B. Ø. (2001) · Nature Biotechnology · doi:10.1038/84379 · Cited by 941 · see citing works
Ubiquitin, proteasomes, and the regulation of intracellular protein degradation
Hochstrasser, M. (1995) · Current Opinion in Cell Biology · doi:10.1016/0955-0674(95)80031-x · Cited by 895 · see citing works
Kinetics of biopolymerization on nucleic acid templates
MacDonald, C. T., Gibbs, J. H., & PIPKIN, A. C. (1968) · Biopolymers · doi:10.1002/bip.1968.360060102 · Cited by 884 · see citing works
Overflow metabolism in Escherichia coli results from efficient proteome allocation
Basan, M., Hui, S., Okano, H., Zhang, Z., Shen, Y., Williamson, J. R., & Hwa, T. (2015) · Nature · doi:10.1038/nature15765 · Cited by 785 · see citing works
Two Compounds implicated in the Function of the RC Gene of Escherichia coli
Cashel, M., & Gallant, J. (1969) · Nature · doi:10.1038/221838a0 · Cited by 769 · see citing works
Novick, A., & Szilard, L. (1950) · Science · doi:10.1126/science.112.2920.715 · Cited by 766 · see citing works
Kraft, C., Deplazes, A., Sohrmann, M., & Peter, M. (2008) · Nature Cell Biology · doi:10.1038/ncb1723 · Cited by 733 · see citing works
PROTEASES AND THEIR TARGETS IN ESCHERICHIA COLI
Gottesman, S. (1996) · Annual Review of Genetics · doi:10.1146/annurev.genet.30.1.465 · Cited by 729 · 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
Growth Rate-Dependent Global Effects on Gene Expression in Bacteria
Klumpp, S., Zhang, Z., & Hwa, T. (2009) · Cell · doi:10.1016/j.cell.2009.12.001 · Cited by 703 · see citing works
Relationship between Cell Size and Time of Initiation of DNA Replication
Donachie, W. D. (1968) · Nature · doi:10.1038/2191077a0 · Cited by 688 · see citing works
Nutrient sensing and TOR signaling in yeast and mammals
González, A., & Hall, M. (2017) · EMBO Journal · doi:10.15252/embj.201696010 · Cited by 684 · see citing works
Regulation of Cell Volume by Active Cation Transport in High and Low Potassium Sheep Red Cells
Tosteson, D. C., & Hoffman, J. F. (1960) · The Journal of General Physiology · doi:10.1085/jgp.44.1.169 · Cited by 673 · see citing works
ppGpp: a global regulator in Escherichia coli
Magnusson, L. U., Farewell, A., & Nyström, T. (2005) · Trends in Microbiology · doi:10.1016/j.tim.2005.03.008 · Cited by 644 · see citing works
Coordination of microbial metabolism
Chubukov, V., Gerosa, L., Kochanowski, K., & Sauer, U. (2014) · Nature Reviews Microbiology · doi:10.1038/nrmicro3238 · Cited by 606 · see citing works
Optimization of lag time underlies antibiotic tolerance in evolved bacterial populations
Fridman, O., Goldberg, A., Ronin, I., Shoresh, N., & Balaban, N. Q. (2014) · Nature · doi:10.1038/nature13469 · Cited by 603 · see citing works
Coordination of Growth Rate, Cell Cycle, Stress Response, and Metabolic Activity in Yeast
Brauer, M. J., Huttenhower, C., Airoldi, E. M., Rosenstein, R., Matese, J. C., Gresham, D., Boer, V. M., Troyanskaya, O. G., & Botstein, D. (2008) · Molecular Biology of the Cell · doi:10.1091/mbc.e07-08-0779 · Cited by 558 · see citing works
Ecology and evolution of metabolic cross-feeding interactions in bacteria
D’Souza, G. G., Shitut, S., Preußger, D., Yousif, G., Waschina, S., & Kost, C. (2018) · Natural Product Reports · doi:10.1039/c8np00009c · Cited by 556 · see citing works
Bremer, H., & Dennis, P. P. (2008) · EcoSal Plus · doi:10.1128/ecosal.5.2.3 · Cited by 539 · see citing works
mTORC1 Controls Phase Separation and the Biophysical Properties of the Cytoplasm by Tuning Crowding
Delarue, M., Brittingham, G. P., Pfeffer, S., Surovtsev, I. V., Pinglay, S., Kennedy, K. J., Schaffer, M., Gutierrez, J. I., Sang, D., Poterewicz, G., et al. (2018) · Cell · doi:10.1016/j.cell.2018.05.042 · Cited by 526 · see citing works
Excessive Cell Growth Causes Cytoplasm Dilution And Contributes to Senescence
Neurohr, G. E., Terry, R. L., Lengefeld, J., Bonney, M., Brittingham, G. P., Moretto, F., Miettinen, T. P., Vaites, L. P., Soares, L. M., Paulo, J. A., et al. (2019) · Cell · doi:10.1016/j.cell.2019.01.018 · Cited by 518 · see citing works
Mayer, C., Zhao, J., Yuan, X., & Grummt, I. (2004) · Genes & Development · doi:10.1101/gad.285504 · Cited by 506 · see citing works
Non-equilibrium statistical mechanics: from a paradigmatic model to biological transport
Chou, T., Mallick, K., & Zia, R. K. P. (2011) · Reports on Progress in Physics · doi:10.1088/0034-4885/74/11/116601 · Cited by 505 · see citing works
SURVEY AND SUMMARY Transcription by RNA polymerases I and III
Paule, M. R. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.6.1283 · Cited by 503 · see citing works
TOR Regulates Ribosomal Protein Gene Expression via PKA and the Forkhead Transcription Factor FHL1
Martin, D. E., Soulard, A., & Hall, M. N. (2004) · Cell · doi:10.1016/j.cell.2004.11.047 · Cited by 481 · see citing works
Regulation by proteolysis: energy-dependent proteases and their targets
Gottesman, S., & Maurizi, M. R. (1992) · Microbiological Reviews · doi:10.1128/mr.56.4.592-621.1992 · Cited by 465 · see citing works
Atkinson, G. C., Tenson, T., & Hauryliuk, V. (2011) · PLoS ONE · doi:10.1371/journal.pone.0023479 · Cited by 447 · see citing works
Emergence of robust growth laws from optimal regulation of ribosome synthesis
Scott, M., Klumpp, S., Mateescu, E. M., & Hwa, T. (2014) · Molecular Systems Biology · doi:10.15252/msb.20145379 · Cited by 443 · see citing works
Onodera, J., & Ohsumi, Y. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m506736200 · Cited by 441 · see citing works
Coordination of bacterial proteome with metabolism by cyclic AMP signalling
You, C., Okano, H., Hui, S., Zhang, Z., Kim, M., Gunderson, C. W., Wang, Y.-P., Lenz, P., Yan, D., & Hwa, T. (2013) · Nature · doi:10.1038/nature12446 · Cited by 432 · see citing works
Stochasticity of metabolism and growth at the single-cell level
Kiviet, D. J., Nghe, P., Walker, N., Boulineau, S., Šunderlíková, V., & Tans, S. J. (2014) · Nature · doi:10.1038/nature13582 · Cited by 419 · see citing works
Proteases and protein degradation inEscherichia coli
Maurizi, M. R. (1992) · Cellular and Molecular Life Sciences · doi:10.1007/bf01923511 · Cited by 406 · see citing works
On being the right (cell) size
Ginzberg, M., Kafri, R., & Kirschner, M. (2015) · Science · doi:10.1126/science.1245075 · Cited by 390 · see citing works
Mechanistic links between cellular trade-offs, gene expression, and growth
Weiße, A. Y., Oyarzún, D. A., Vincent Danos, A., & Swain, P. S. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1416533112 · Cited by 390 · see citing works
Burden-driven feedback control of gene expression
Ceroni, F., Boo, A., Furini, S., Gorochowski, T. E., Borkowski, O., Ladak, Y., Awan, A. R., Gilbert, C., Stan, G.-B. V., & Ellis, T. (2018) · Nature Methods · doi:10.1038/nmeth.4635 · Cited by 375 · see citing works
Quantitative proteomic analysis reveals a simple strategy of global resource allocation in bacteria
Hui, S., Silverman, J. M., Chen, S. S., Erickson, D. W., Basan, M., Wang, J., Hwa, T., & Williamson, J. R. (2015) · Molecular Systems Biology · doi:10.15252/msb.20145697 · Cited by 369 · see citing works
Studies on the role of ribonucleic acid in the growth of bacteria
Neidhardt, F. C., & Magasanik, B. (1960) · Biochimica et Biophysica Acta · doi:10.1016/0006-3002(60)90757-5 · Cited by 359 · see citing works
The Cost of Protein Production
Kafri, M., Metzl-Raz, E., Jona, G., & Barkai, N. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.12.015 · Cited by 348 · see citing works
Totally asymmetric exclusion process with extended objects: A model for protein synthesis
Shaw, L. B., Zia, R. K. P., & Lee, K. H. (2003) · Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics · doi:10.1103/physreve.68.021910 · Cited by 348 · see citing works
MacArthur's consumer-resource model
Chesson, P. (1990) · Theoretical Population Biology · doi:10.1016/0040-5809(90)90025-q · Cited by 341 · see citing works
Protein Synthesis upon Acute Nutrient Restriction Relies on Proteasome Function
Vabulas, R. M., & Hartl, F. U. (2005) · Science · doi:10.1126/science.1121925 · Cited by 339 · see citing works
Protein oxidation in response to increased transcriptional or translational errors
Dukan, S., Farewell, A., Ballesteros, M., Taddéi, F., Radman, M., & Nyström, T. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.100422497 · Cited by 334 · see citing works
The Synchronization of Replication and Division Cycles in Individual E. coli Cells
Wallden, M., Fange, D., Lundius, E. G., Baltekin, Ö., & Elf, J. (2016) · Cell · doi:10.1016/j.cell.2016.06.052 · Cited by 331 · see citing works
Dai, X., Zhu, M., Warren, M., Balakrishnan, R., Patsalo, V., Okano, H., Williamson, J. R., Fredrick, K. L., Wang, Y., & Terence Hwa, B. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.231 · Cited by 320 · 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
Bacterial growth laws and their applications
Scott, M., & Hwa, T. (2011) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2011.04.014 · Cited by 309 · see citing works
Dissection of the Mechanism for the Stringent Factor RelA
Wendrich, T. M., Blaha, G. M., Wilson, D. N., Marahiel, M. A., & Nierhaus, K. H. (2002) · Molecular Cell · doi:10.1016/s1097-2765(02)00656-1 · Cited by 300 · see citing works
Degradation of Abnormal Proteins in Escherichia coli
Goldberg, A. L. (1972) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.69.2.422 · Cited by 298 · see citing works
Physical limits of cells and proteomes
Dill, K. A., Ghosh, K., & Schmit, J. D. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1114477108 · Cited by 298 · see citing works
Concerning the kinetics of polypeptide synthesis on polyribosomes
MacDonald, C. T., & Gibbs, J. H. (1969) · Biopolymers · doi:10.1002/bip.1969.360070508 · Cited by 294 · see citing works
Molecular crowding limits translation and cell growth
Klumpp, S., Scott, M., Pedersen, S., & Hwa, T. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1310377110 · Cited by 293 · see citing works
Short-range interactions govern the dynamics and functions of microbial communities
Co, A. D., van Vliet, S., Kiviet, D. J., Schlegel, S., & Ackermann, M. (2020) · Nature Ecology & Evolution · doi:10.1038/s41559-019-1080-2 · Cited by 289 · see citing works
Metabolic exchanges are ubiquitous in natural microbial communities
Kost, C., Patil, K. R., Friedman, J., Garcia, S. L., & Ralser, M. (2023) · Nature Microbiology · doi:10.1038/s41564-023-01511-x · Cited by 281 · see citing works
Global Proteome Turnover Analyses of the Yeasts S. cerevisiae and S. pombe
Christiano, R., Nagaraj, N., Fröhlich, F., & Walther, T. C. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.10.065 · Cited by 268 · see citing works
A universal trade-off between growth and lag in fluctuating environments
Basan, M., Honda, T., Christodoulou, D., Hörl, M., Chang, Y., Leoncini, E., Mukherjee, A., Okano, H., Taylor, B. R., Silverman, J. M., et al. (2020) · Nature · doi:10.1038/s41586-020-2505-4 · Cited by 257 · see citing works
Ecological modelling approaches for predicting emergent properties in microbial communities
van den Berg, N. I., Machado, D., Santos, S., Rocha, I., Chacón, J. M., Harcombe, W. R., Mitri, S., & Patil, K. R. (2022) · Nature Ecology & Evolution · doi:10.1038/s41559-022-01746-7 · Cited by 253 · see citing works
Mechanistic Origin of Cell-Size Control and Homeostasis in Bacteria
Si, F., Treut, G. L., Sauls, J. T., Vadia, S., Levin, P. A., & Jun, S. (2019) · Current Biology · doi:10.1016/j.cub.2019.04.062 · Cited by 250 · see citing works
Invariance of Initiation Mass and Predictability of Cell Size in Escherichia coli
Si, F., Li, D., Cox, S. E., Sauls, J. T., Azizi, O., Sou, C., Schwartz, A. B., Erickstad, M. J., Jun, Y., Li, X., et al. (2017) · Current Biology · doi:10.1016/j.cub.2017.03.022 · Cited by 240 · see citing works
A global resource allocation strategy governs growth transition kinetics of Escherichia coli
Erickson, D. W., Schink, S. J., Patsalo, V., Williamson, J. R., Gerland, U., & Terence Hwa, B. (2017) · Nature · doi:10.1038/nature24299 · Cited by 239 · see citing works
Microorganisms maintain crowding homeostasis
van den Berg, J., Boersma, A. J., & Poolman, B. (2017) · Nature Reviews Microbiology · doi:10.1038/nrmicro.2017.17 · Cited by 237 · see citing works
Cooperation Between RNA Polymerase Molecules in Transcription Elongation
Epshtein, V., & Nudler, E. (2003) · Science · doi:10.1126/science.1083219 · Cited by 234 · see citing works
LESS IS MORE: SELECTIVE ADVANTAGES CAN EXPLAIN THE PREVALENT LOSS OF BIOSYNTHETIC GENES IN BACTERIA
D’Souza, G. G., Waschina, S., Pande, S., Bohl, K., Kaleta, C., & Kost, C. (2014) · Evolution · doi:10.1111/evo.12468 · Cited by 232 · see citing works
Bosdriesz, E., Douwe Molenaar, B., Teusink, B., & Bruggeman, F. J. (2015) · FEBS Journal · doi:10.1111/febs.13258 · Cited by 229 · see citing works
The TOR signalling network from yeast to man
VIRGILIO, C. D., & Loewith, R. (2006) · The International Journal of Biochemistry & Cell Biology · doi:10.1016/j.biocel.2006.02.013 · Cited by 227 · see citing works
Bello, M. D., Lee, H., Goyal, A., & Gore, J. (2021) · Nature Ecology & Evolution · doi:10.1038/s41559-021-01535-8 · Cited by 225 · see citing works
Bacterial growth: global effects on gene expression, growth feedback and proteome partition
Klumpp, S., & Terence Hwa, B. (2014) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2014.01.001 · Cited by 224 · see citing works
Relative Rates of Surface and Volume Synthesis Set Bacterial Cell Size
Harris, L. K., & Theriot, J. A. (2016) · Cell · doi:10.1016/j.cell.2016.05.045 · Cited by 222 · see citing works
Principles of cellular resource allocation revealed by condition-dependent proteome profiling
Metzl-Raz, E., Kafri, M., Yaakov, G., Soifer, I., Gurvich, Y., & Barkai, N. (2017) · eLife · doi:10.7554/elife.28034 · Cited by 221 · see citing works
Cost of Unneeded Proteins in E. coli Is Reduced after Several Generations in Exponential Growth
Shachrai, I., Zaslaver, A., Alon, U. S., & Dekel, E. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.04.015 · Cited by 208 · see citing works
Inflating bacterial cells by increased protein synthesis
Basan, M., Zhu, M., Dai, X., Warren, M., Sévin, D. C., Wang, Y., & Terence Hwa, B. (2015) · Molecular Systems Biology · doi:10.15252/msb.20156178 · Cited by 208 · see citing works
Genome‐wide study of mRNA degradation and transcript elongation in Escherichia coli
Chen, H., Shiroguchi, K., Ge, H., & Xie, X. S. (2015) · Molecular Systems Biology · doi:10.15252/msb.20145794 · Cited by 207 · see citing works
The regulation of cell size and the control of mitosis
Fantes, P. A., Grant, W. D., Pritchard, R. H., Sudbery, P. E., & Wheals, A. E. (1975) · Journal of Theoretical Biology · doi:10.1016/0022-5193(75)90034-x · Cited by 203 · see citing works
Growth rate of Escherichia coli
Marr, A. G. (1991) · Microbiological Reviews · doi:10.1128/mr.55.2.316-333.1991 · Cited by 197 · see citing works
Macromolecular Composition During Steady-State Growth of <i>Escherichia coli</i> B/r
Dennis, P. P., & Bremer, H. (1974) · Journal of Bacteriology · doi:10.1128/jb.119.1.270-281.1974 · Cited by 196 · see citing works
The Innate Growth Bistability and Fitness Landscapes of Antibiotic-Resistant Bacteria
Deris, J. B., Kim, M., Zhang, Z., Okano, H., Hermsen, R., Groisman, A., & Terence Hwa, B. (2013) · Science · doi:10.1126/science.1237435 · Cited by 193 · see citing works
Complexity of the TOR signaling network
Inoki, K., & Guan, K. (2006) · Trends in Cell Biology · doi:10.1016/j.tcb.2006.02.002 · Cited by 191 · 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
SYNCHRONIZATION OF CELL DIVISION
Campbell, A. (1957) · Bacteriological Reviews · doi:10.1128/br.21.4.263-272.1957 · Cited by 186 · see citing works
Jun, S., Si, F., Pugatch, R., & Scott, M. (2018) · Reports on Progress in Physics · doi:10.1088/1361-6633/aaa628 · Cited by 186 · see citing works
Systematic analysis of ribophagy in human cells reveals bystander flux during selective autophagy
An, H., & Harper, J. W. (2018) · Nature Cell Biology · doi:10.1038/s41556-017-0007-x · Cited by 181 · 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
Self-citationRegulation of microbial growth by turgor pressure
Rojas, E., & Huang, K. C. (2017) · Current Opinion in Microbiology · doi:10.1016/j.mib.2017.10.015 · Cited by 180 · see citing works
Homeostasis of protein and mRNA concentrations in growing cells
Lin, J., & Amir, A. (2018) · Nature Communications · doi:10.1038/s41467-018-06714-z · Cited by 180 · see citing works
Moehle, C. M., & Hinnebusch, A. G. (1991) · Molecular and Cellular Biology · doi:10.1128/mcb.11.5.2723 · Cited by 178 · see citing works
The Classification and Evolution of Bacterial Cross-Feeding
Smith, N. W., Shorten, P. R., Altermann, E., Roy, N. C., & McNabb, W. C. (2019) · Frontiers in Ecology and Evolution · doi:10.3389/fevo.2019.00153 · Cited by 178 · see citing works
Control of production of ribosomal protein
Schleif, R. F. (1967) · Journal of Molecular Biology · doi:10.1016/0022-2836(67)90350-6 · Cited by 168 · see citing works
Relevance and Regulation of Cell Density
Neurohr, G. E., & Amon, A. (2020) · Trends in Cell Biology · doi:10.1016/j.tcb.2019.12.006 · Cited by 166 · see citing works
Cell growth dilutes the cell cycle inhibitor Rb to trigger cell division
Zatulovskiy, E. A., Zhang, S., Berenson, D. F., Topacio, B. R., & Skotheim, J. M. (2020) · Science · doi:10.1126/science.aaz6213 · Cited by 164 · see citing works
Bacterial growth laws reflect the evolutionary importance of energy efficiency
Maitra, A., & Dill, K. A. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1421138111 · Cited by 162 · see citing works
Stein, K. C., & Frydman, J. (2018) · Journal of Biological Chemistry · doi:10.1074/jbc.rev118.002814 · Cited by 160 · see citing works
Li, H., Li, Z., Park, J. O., King, C. G., Rabinowitz, J. D., Wingreen, N. S., & Gitai, Z. (2018) · Nature Microbiology · doi:10.1038/s41564-018-0199-2 · Cited by 157 · see citing works
Drivers of Bacterial Maintenance and Minimal Energy Requirements
Kempes, C. P., van Bodegom, P. M., Wolpert, D. H., Libby, E., Amend, J. P., & Hoehler, T. M. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.00031 · Cited by 157 · see citing works
Growth‐dependent bacterial susceptibility to ribosome‐targeting antibiotics
Greulich, P., Scott, M., Evans, M. R., & Allen, R. J. (2015) · Molecular Systems Biology · doi:10.15252/msb.20145949 · Cited by 152 · see citing works
Protein Degradation in Escherichia coli
Nath, K., & Koch, A. L. (1970) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)63072-8 · Cited by 150 · see citing works
The Stringent Response and Cell Cycle Arrest in Escherichia coli
Ferullo, D. J., & Lovett, S. T. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000300 · Cited by 150 · see citing works
Obligate cross-feeding expands the metabolic niche of bacteria
Oña, L., Giri, S., Avermann, N., Kreienbaum, M., Thormann, K. M., & Kost, C. (2021) · Nature Ecology & Evolution · doi:10.1038/s41559-021-01505-0 · Cited by 150 · see citing works
Experimental Evolution of Metabolic Dependency in Bacteria
D’Souza, G. G., & Kost, C. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1006364 · Cited by 146 · see citing works
The physics of cell-size regulation across timescales
Cadart, C., Venkova, L. S., Recho, P., Lagomarsino, M. C., & Piel, M. (2019) · Nature Physics · doi:10.1038/s41567-019-0629-y · Cited by 146 · see citing works
Self-citationMake and break the alarmone: regulation of (p)ppGpp synthetase/hydrolase enzymes in bacteria
Ronneau, S., & Hallez, R. (2019) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuz009 · Cited by 144 · see citing works
From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions
Mori, M., Zhang, Z., Banaei‐Esfahani, A., Lalanne, J., Okano, H., Collins, B. C., Schmidt, A., Schubert, O. T., Lee, D., Li, G., et al. (2021) · Molecular Systems Biology · doi:10.15252/msb.20209536 · Cited by 143 · see citing works
Bacterial growth: a statistical physicist’s guide
Allen, R. J., & Waclaw, B. (2018) · Reports on Progress in Physics · doi:10.1088/1361-6633/aae546 · Cited by 142 · see citing works
Interrogating the Escherichia coli cell cycle by cell dimension perturbations
Zheng, H., Ho, P.-Y., Jiang, M., Tang, B. H., Liu, W., Li, D., Yu, X., Kleckner, N. E., Amir, A., & Liu, C. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1617932114 · Cited by 141 · see citing works
The international system of units (SI):
Newell, D. B., & Tiesinga, E. (2019) · doi:10.6028/nist.sp.330-2019 · Cited by 140 · see citing works
Principles of gene regulation quantitatively connect DNA to RNA and proteins in bacteria
Balakrishnan, R., Mori, M., Šegota, I., Zhang, Z., Aebersold, R. H., Ludwig, C., & Hwa, T. (2022) · Science · doi:10.1126/science.abk2066 · Cited by 137 · see citing works
Quantifying the benefit of a proteome reserve in fluctuating environments
Mori, M., Schink, S. J., Erickson, D. W., Gerland, U., & Terence Hwa, B. (2017) · Nature Communications · doi:10.1038/s41467-017-01242-8 · Cited by 136 · see citing works
Shaping of microbial phenotypes by trade-offs
Zhu, M., & Dai, X. (2024) · Nature Communications · doi:10.1038/s41467-024-48591-9 · Cited by 132 · see citing works
Shaping bacterial gene expression by physiological and proteome allocation constraints
Scott, M., & Terence Hwa, B. (2022) · Nature Reviews Microbiology · doi:10.1038/s41579-022-00818-6 · Cited by 128 · see citing works
Karpinets, T. V., Greenwood, D. J., Sams, C. E., & Ammons, J. T. (2006) · BMC Biology · doi:10.1186/1741-7007-4-30 · Cited by 126 · see citing works
Biselli, E., Schink, S. J., & Gerland, U. (2020) · Molecular Systems Biology · doi:10.15252/msb.20209478 · Cited by 118 · see citing works
Bakshi, S., Leoncini, E., Baker, C. J., Cañas-Duarte, S. J., Okumuş, B., & Paulsson, J. (2021) · Nature Microbiology · doi:10.1038/s41564-021-00900-4 · Cited by 117 · see citing works
General quantitative relations linking cell growth and the cell cycle in Escherichia coli
Zheng, H., Bai, Y., Jiang, M., Tokuyasu, T. A., Huang, X., Zhong, F., Wu, Y., Fu, X., Kleckner, N. E., Terence Hwa, B., et al. (2020) · Nature Microbiology · doi:10.1038/s41564-020-0717-x · Cited by 115 · see citing works
Giordano, N., Mairet, F., Gouzé, J., Geiselmann, J., & de Jong, H. (2016) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004802 · Cited by 113 · see citing works
Coupling the initiation of chromosome replication to cell size in Escherichia coli
Donachie, W. D., & Blakely, G. W. (2003) · Current Opinion in Microbiology · doi:10.1016/s1369-5274(03)00026-2 · Cited by 112 · see citing works
Fundamental limits on the rate of bacterial growth and their influence on proteomic composition
Belliveau, N. M., Chure, G., Hueschen, C. L., García, H. G., Kondev, J., Fisher, D. S., Theriot, J. A., & Phillips, R. (2021) · Cell Systems · doi:10.1016/j.cels.2021.06.002 · Cited by 111 · see citing works
Coupling of Ribosome Synthesis and Translational Capacity with Cell Growth
Dai, X., & Zhu, M. (2020) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2020.04.010 · Cited by 110 · see citing works
Multiple micro-predators controlling bacterial communities in the environment
Johnke, J., Cohen, Y., de Leeuw, M., Kushmaro, A., Jurkevitch, É., & Chatzinotas, A. (2014) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2014.02.003 · Cited by 109 · see citing works
Yeast has a true stringent response
Warner, J. R., & Gorenstein, C. (1978) · Nature · doi:10.1038/275338a0 · Cited by 109 · see citing works
Searching for principles of microbial physiology
Bruggeman, F. J., Planqué, R., Douwe Molenaar, B., & Teusink, B. (2020) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuaa034 · Cited by 104 · see citing works
A growth‐rate composition formula for the growth of E. coli on co‐utilized carbon substrates
Hermsen, R., Okano, H., You, C., Werner, N., & Terence Hwa, B. (2015) · Molecular Systems Biology · doi:10.15252/msb.20145537 · Cited by 103 · see citing works
Co, A. D., van Vliet, S., & Ackermann, M. (2019) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2019.0080 · Cited by 103 · see citing works
A mechano-osmotic feedback couples cell volume to the rate of cell deformation
Venkova, L. S., Vishen, A. S., Lembo, S., Srivastava, N., Duchamp, B., Ruppel, A., Williart, A., Vassilopoulos, S., Deslys, A., ARCOS, J. M. G., et al. (2022) · eLife · doi:10.7554/elife.72381 · Cited by 102 · see citing works
Surface-to-volume scaling and aspect ratio preservation in rod-shaped bacteria
Ojkic, N., Serbanescu, D., & Banerjee, S. (2019) · eLife · doi:10.7554/elife.47033 · Cited by 100 · see citing works
Differential rate of ribosomal protein synthesis in Escherichia coli B/r
Dennis, P. P., & Bremer, H. J. (1974) · Journal of Molecular Biology · doi:10.1016/0022-2836(74)90449-5 · Cited by 99 · see citing works
Determinants and Regulation of Protein Turnover in Yeast
Martin-Perez, M., & Villén, J. (2017) · Cell Systems · doi:10.1016/j.cels.2017.08.008 · Cited by 99 · see citing works
The last generation of bacterial growth in limiting nutrient
Bren, A., Hart, Y., Dekel, E., Koster, D. A., & Alon, U. S. (2013) · BMC Systems Biology · doi:10.1186/1752-0509-7-27 · Cited by 98 · see citing works
Death Rate of E. coli during Starvation Is Set by Maintenance Cost and Biomass Recycling
Schink, S. J., Biselli, E., Ammar, C., & Gerland, U. (2019) · Cell Systems · doi:10.1016/j.cels.2019.06.003 · Cited by 98 · see citing works
Zhu, M., & Dai, X. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz211 · Cited by 96 · see citing works
Cellular perception of growth rate and the mechanistic origin of bacterial growth law
Wu, C., Balakrishnan, R., Braniff, N., Mori, M., Manzanarez, G., Zhang, Z., & Terence Hwa, B. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2201585119 · Cited by 95 · see citing works
Transcriptional response of steady-state yeast cultures to transient perturbations in carbon source
Ronen, M., & Botstein, D. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0509978103 · Cited by 94 · see citing works
How Cells Can Control Their Size by Pumping Ions
Kay, A. R. (2017) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2017.00041 · Cited by 94 · see citing works
Taggart, J., & Li, G. (2018) · Cell Systems · doi:10.1016/j.cels.2018.11.003 · Cited by 94 · see citing works
A Bacterial Growth Law out of Steady State
Kohanim, Y. K., Levi, D., Jona, G., Towbin, B. D., Bren, A., & Alon, U. S. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.05.007 · Cited by 91 · see citing works
Xia, J., Sánchez, B. J., Chen, Y., Campbell, K., Kasvandik, S., & Nielsen, J. (2022) · Nature Communications · doi:10.1038/s41467-022-30513-2 · Cited by 91 · see citing works
Eukaryotic Cell Size Control and Its Relation to Biosynthesis and Senescence
Xie, S., Swaffer, M. P., & Skotheim, J. M. (2022) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-120219-040142 · Cited by 89 · see citing works
Macromolecular crowding limits growth under pressure
Alric, B., Formosa‐Dague, C., Dague, É., Holt, L. J., & Delarue, M. (2022) · Nature Physics · doi:10.1038/s41567-022-01506-1 · Cited by 87 · see citing works
Evolutionary tradeoffs in cellular composition across diverse bacteria
Kempes, C. P., Wang, L., Amend, J. P., Doyle, J., & Hoehler, T. (2016) · The ISME Journal · doi:10.1038/ismej.2016.21 · Cited by 87 · see citing works
Physical basis of the cell size scaling laws
Rollin, R., Joanny, J., & Sens, P. (2023) · eLife · doi:10.7554/elife.82490 · Cited by 86 · see citing works
On microbial states of growth †
Fishov, I., Zaritsky, A., & Grover, N. B. (1995) · Molecular Microbiology · doi:10.1111/j.1365-2958.1995.tb02349.x · Cited by 86 · see citing works
Protein degradation on the global scale
Rusilowicz-Jones, E. V., Urbé, S., & Clague, M. J. (2022) · Molecular Cell · doi:10.1016/j.molcel.2022.02.027 · Cited by 85 · see citing works
A brief history of bacterial growth physiology
Schaechter, M. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.00289 · Cited by 84 · see citing works
Bacterial ageing in the absence of external stressors
Łapińska, U., Glover, G., Capilla‐Lasheras, P., Young, A. J., & Pagliara, S. (2019) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2018.0442 · Cited by 84 · see citing works
RNA Polymerase III Transcription
White, R. J. (1998) · Springer eBooks · doi:10.1007/978-3-662-03518-4 · Cited by 84 · see citing works
Metabolism of individual proteins in exponentially growing Escherichia coli.
Mosteller, R. D., Goldstein, R. V., & Nishimoto, K. R. (1980) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)85924-0 · Cited by 83 · see citing works
Dynamics of Escherichia coli ’s passive response to a sudden decrease in external osmolarity
Buđa, R., Liu, Y., Yang, J., Hegde, S., Stevenson, K., Bai, F., & Piližota, T. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1522185113 · Cited by 83 · see citing works
Differential Scaling of Gene Expression with Cell Size May Explain Size Control in Budding Yeast
Chen, Y., Zhao, G., Zahumenský, J., Honey, S. A., & Futcher, B. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.03.012 · Cited by 82 · see citing works
Robust surface-to-mass coupling and turgor-dependent cell width determine bacterial dry-mass density
Oldewurtel, E. R., Kitahara, Y., & van Teeffelen, S. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2021416118 · Cited by 82 · see citing works
RNA polymerase II dynamics and mRNA stability feedback scale mRNA amounts with cell size
Swaffer, M. P., Marinov, G. K., Zheng, H., Valenzuela, L. F., Tsui, C. Y., Jones, A. W., Greenwood, J., Kundaje, A. B., Greenleaf, W. J., Reyes‐Lamothe, R., et al. (2023) · Cell · doi:10.1016/j.cell.2023.10.012 · Cited by 79 · see citing works
Greulich, P., Ciandrini, L., Allen, R. J., & Romano, M. C. (2012) · Physical Review E · doi:10.1103/physreve.85.011142 · Cited by 79 · see citing works
Self-citationA G1 Sizer Coordinates Growth and Division in the Mouse Epidermis
Xie, S., & Skotheim, J. M. (2020) · Current Biology · doi:10.1016/j.cub.2019.12.062 · Cited by 78 · see citing works
Effects of Environment on the Composition of Bacterial Cells
Neidhardt, F. C. (1963) · Annual Review of Microbiology · doi:10.1146/annurev.mi.17.100163.000425 · Cited by 78 · see citing works
Cherkasov, V., Groušl, T., Theer, P., Vainshtein, Y., Gläßer, C., Mongis, C., Krämer, G., Stoecklin, G., Knop, M., Mogk, A., et al. (2015) · FEBS Letters · doi:10.1016/j.febslet.2015.10.010 · Cited by 77 · see citing works
Protein charge distribution in proteomes and its impact on translation
Requião, R. D., Fernandes, L., de Souza, H. J. A., Rossetto, S., Domitrovic, T., & Palhano, F. L. (2017) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1005549 · Cited by 76 · see citing works
Suboptimal resource allocation in changing environments constrains response and growth in bacteria
Balakrishnan, R., de Silva, R. T., Terence Hwa, B., & Cremer, J. (2021) · Molecular Systems Biology · doi:10.15252/msb.202110597 · Cited by 75 · see citing works
Knight, J. (2002) · Nature · doi:10.1038/419244a · Cited by 75 · see citing works
Witz, G., van Nimwegen, E., & Julou, T. (2019) · eLife · doi:10.7554/elife.48063 · Cited by 74 · see citing works
Kraemer, J. A., Sanderlin, A. G., & Laub, M. T. (2019) · mBio · doi:10.1128/mbio.01330-19 · Cited by 72 · see citing works
Independence of buoyant cell density and growth rate in Escherichia coli
KUBITSCHEK, H. E., Baldwin, W. W., Schroeter, S., & Graetzer, R. (1984) · Journal of Bacteriology · doi:10.1128/jb.158.1.296-299.1984 · Cited by 71 · see citing works
van Vliet, S., Co, A. D., Winkler, A. R., Spriewald, S., Stecher, B., & Ackermann, M. (2018) · Cell Systems · doi:10.1016/j.cels.2018.03.009 · Cited by 71 · see citing works
Starke, S., Harris, D. M. M., Zimmermann, J., Schuchardt, S., Oumari, M., Frank, D., Bang, C., Rosenstiel, P. C., Schreiber, S., Frey, N., et al. (2023) · The ISME Journal · doi:10.1038/s41396-023-01537-3 · Cited by 70 · see citing works
Bacterial proteostasis balances energy and chaperone utilization efficiently
Santra, M., Farrell, D. W., & Dill, K. A. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1620646114 · Cited by 69 · see citing works
Slowdown of Translational Elongation in Escherichia coli under Hyperosmotic Stress
Dai, X., Zhu, M., Warren, M. R., Balakrishnan, R., Okano, H., Williamson, J. R., Fredrick, K. L., & Terence Hwa, B. (2018) · mBio · doi:10.1128/mbio.02375-17 · Cited by 69 · see citing works
Borkowski, O., Goelzer, A., Schaffer, M., Calabre, M., Mäder, U., Aymerich, S., Jules, M., & Fromion, V. (2016) · Molecular Systems Biology · doi:10.15252/msb.20156608 · Cited by 66 · see citing works
IonoBiology: The functional dynamics of the intracellular metallome, with lessons from bacteria
Galera-Laporta, L., Comerci, C. J., García‐Ojalvo, J., & Süel, G. M. (2021) · Cell Systems · doi:10.1016/j.cels.2021.04.011 · Cited by 65 · see citing works
Adachi, A., Koizumi, M., & Ohsumi, Y. (2017) · Journal of Biological Chemistry · doi:10.1074/jbc.m117.817510 · Cited by 64 · see citing works
Biphasic Cell-Size and Growth-Rate Homeostasis by Single Bacillus subtilis Cells
Nordholt, N., van Heerden, J. H., & Bruggeman, F. J. (2020) · Current Biology · doi:10.1016/j.cub.2020.04.030 · Cited by 64 · see citing works
Ribosome content and the rate of growth of Salmonella typhimurium
Ecker, R. E., & Schaechter, M. (1963) · Biochimica et Biophysica Acta · doi:10.1016/0006-3002(63)90040-4 · Cited by 64 · see citing works
Warmer temperatures favor slower-growing bacteria in natural marine communities
Abreu, C. I., Bello, M. D., Bunse, C., Pinhassi, J., & Gore, J. (2023) · Science Advances · doi:10.1126/sciadv.ade8352 · Cited by 63 · see citing works
Odermatt, P. D., Miettinen, T. P., Lemiere, J. P. C., Kang, J. H., Bostan, E., Manalis, S. R., Huang, K. C., & Chang, F. (2021) · eLife · doi:10.7554/elife.64901 · Cited by 62 · see citing works
Macromolecular composition of bacteria
Churchward, G. G., Bremer, H. J., & Young, R. (1982) · Journal of Theoretical Biology · doi:10.1016/0022-5193(82)90305-8 · Cited by 61 · see citing works
Mechanisms of drug interactions between translation-inhibiting antibiotics
Kavčič, B., Tkačik, G., & Bollenbach, T. (2020) · Nature Communications · doi:10.1038/s41467-020-17734-z · Cited by 61 · see citing works
Serbanescu, D., Ojkic, N., & Banerjee, S. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.108183 · Cited by 61 · see citing works
Individuality and slow dynamics in bacterial growth homeostasis
Susman, L., Kohram, M., Vashistha, H., Nechleba, J. T., Salman, H., & Brenner, N. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1615526115 · Cited by 60 · see citing works
Global coordination of metabolic pathways in Escherichia coli by active and passive regulation
Kochanowski, K., Okano, H., Patsalo, V., Williamson, J. R., Sauer, U., & Terence Hwa, B. (2021) · Molecular Systems Biology · doi:10.15252/msb.202010064 · Cited by 57 · see citing works
Derivations of the Young-Laplace equation
Siqveland, L. M., & Skjaeveland, S. M. (2021) · Capillarity · doi:10.46690/capi.2021.02.01 · Cited by 57 · see citing works
Transcriptional regulation in eukaryotic ribosomal protein genes
Hu, H., & Li, X. (2007) · Genomics · doi:10.1016/j.ygeno.2007.07.003 · Cited by 57 · see citing works
An optimal regulation of fluxes dictates microbial growth in and out of steady state
Chure, G., & Cremer, J. (2023) · eLife · doi:10.7554/elife.84878 · Cited by 56 · see citing works
Physiology of the Bacterial Cell. A Molecular Approach
Smith, C. A. (1992) · Biochemical Education · doi:10.1016/0307-4412(92)90139-d · Cited by 55 · see citing works
Gcn4p‐mediated transcriptional repression of ribosomal protein genes under amino‐acid starvation
Joo, Y. J., Kim, J.-H., Kang, U., Yu, M., & Kim, J. (2010) · The EMBO Journal · doi:10.1038/emboj.2010.332 · Cited by 55 · see citing works
Achieving Optimal Growth through Product Feedback Inhibition in Metabolism
Goyal, S., Yuan, J., Chen, T., Rabinowitz, J. D., & Wingreen, N. S. (2010) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000802 · Cited by 55 · see citing works
Perspectives on theory at the interface of physics and biology
Bialek, W. (2017) · Reports on Progress in Physics · doi:10.1088/1361-6633/aa995b · Cited by 51 · see citing works
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Garoña, A., Lemos, M., Giometto, A., & Fumasoni, M. (2026) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2531280123 · Cited by 1 · see citing works
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From cells to populations: Multi-scale quantitative approaches to antimicrobial resistance
Yubero-Fernández, L., Molina-Hernández, J., García, M. D. L. F., Catalán, P., & Ares, S. (2026) · Current Opinion in Systems Biology · doi:10.1016/j.coisb.2026.100607
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- Authors
- Droghetti, R., Corigliano, M., Calabrese, L., Fuchs, P., Vaidyanathan, A., Keisers, J., Micali, G., Lagomarsino, M. C., & Ciandrini, L.
- Affiliations
- IFOM (IT)
- SIB Swiss Institute of Bioinformatics (CH)
- Centre National de la Recherche Scientifique (FR)
- Humanitas University (IT)
- IRCCS Humanitas Research Hospital (IT)
- University of Milan (IT)
- ORCID
- Venue
- PRX Life
- Publisher
- American Physical Society (APS)
- Published
- 2026-03-25
- Volume
- 4
- Issue
- 1
- ISSN
- 2835-8279 (ISSN-L)
- OpenAlex
- W4417264490
- Cited by
- 5
- References
- 287
- Citations by year
- 2026: 4 · 2025: 1
- FWCI
- 8.37
- Type
- journal article
- Language
- en
- Open access
- diamond
- doi.org
- Licence
- Locations
- PRX Life (publishedVersion, cc-by)
- arXiv (Cornell University) (submittedVersion)
- Archivio Istituzionale della Ricerca (Universita Degli Studi Di Milano) (submittedVersion, cc-by)
- arXiv (Cornell University)
- Funders
- Artificial Intelligence Research Center (782, 23258, 28176, 28177)
- Agence Nationale de la Recherche (ANR-21-CE45-0009)
- Topics
- 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
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
- Keywords
- coarse-grained models, bacterial growth, steady-state growth, variable environments, biosynthesis, transcription, translation (biology), nutrient sensing, protein degradation, cell cycle, ecological dynamics
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