Beyond Homeostasis: A Predictive-Dynamic Framework for Understanding Cellular Behavior

Genetic regulatory mechanisms in the synthesis of proteins.

Jacob, F., & Monod, J. (1961) · Journal of Molecular Biology · doi:10.1016/s0022-2836(61)80072-7 · Cited by 5,995 · 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

Functional profiling of the Saccharomyces cerevisiae genome

Giaever, G., Chu, A. M., Ni, L., Connelly, C., Riles, L., Véronneau, S., Dow, S., Lucau-Danila, A., Anderson, K., André, B., et al. (2002) · Nature · doi:10.1038/nature00935 · Cited by 4,316 · see citing works

The Role of Chromatin during Transcription

Li, B., Carey, M., & Workman, J. L. (2007) · Cell · doi:10.1016/j.cell.2007.01.015 · Cited by 3,503 · see citing works

Network motifs: theory and experimental approaches

Alon, U. (2007) · Nature Reviews Genetics · doi:10.1038/nrg2102 · Cited by 3,279 · see citing works

Bacterial Persistence as a Phenotypic Switch

Balaban, N. Q., Merrin, J., Chait, R., Kowalik, L., & Leibler, S. (2004) · Science · doi:10.1126/science.1099390 · Cited by 2,952 · see citing works

Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences

Raj, A., & van Oudenaarden, A. (2008) · Cell · doi:10.1016/j.cell.2008.09.050 · Cited by 2,593 · see citing works

Quantifying <i>E. coli</i> Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells

Taniguchi, Y., Choi, P. J., Li, G.-W., Chen, H., Babu, M., Hearn, J., Emili, A., & Xie, X. S. (2010) · Science · doi:10.1126/science.1188308 · Cited by 1,982 · see citing works

Noise in Gene Expression: Origins, Consequences, and Control

Raser, J. M., & O’Shea, E. K. (2005) · Science · doi:10.1126/science.1105891 · Cited by 1,719 · see citing works

Comparative Metagenomics of Microbial Communities

Tringe, S. G., von Mering, C., Kobayashi, A., Salamov, A. A., Chen, K., Chang, H. W., Podar, M., Short, J. M., Mathur, E. J., Detter, J. C., et al. (2005) · Science · doi:10.1126/science.1107851 · Cited by 1,677 · 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

Transgenerational Epigenetic Inheritance: Prevalence, Mechanisms, and Implications for the Study of Heredity and Evolution

Jablonka, E., & Raz, G. (2009) · The Quarterly Review of Biology · doi:10.1086/598822 · Cited by 1,659 · see citing works

Circadian rhythms from multiple oscillators: lessons from diverse organisms

Bell‐Pedersen, D., Cassone, V. M., Earnest, D. J., Golden, S. S., Hardin, P. E., Thomas, T. L., & Zoran, M. J. (2005) · Nature Reviews Genetics · doi:10.1038/nrg1633 · Cited by 1,481 · 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

Functional roles for noise in genetic circuits

Eldar, A., & Elowitz, M. B. (2010) · Nature · doi:10.1038/nature09326 · Cited by 1,440 · see citing works

Dependency on Medium and Temperature of Cell Size and Chemical Composition during Balanced Growth of Salmonella typhimurium

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

Remodeling of Yeast Genome Expression in Response to Environmental Changes

Causton, H. C., Ren, B., Koh, S. S., Harbison, C. T., Kanin, E. I., Jennings, E. G., Lee, T. I., True, H. L., Lander, E. S., & Young, R. A. (2001) · Molecular Biology of the Cell · doi:10.1091/mbc.12.2.323 · Cited by 1,364 · 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

Self-perpetuating states in signal transduction: positive feedback, double-negative feedback and bistability

Ferrell, J. E. (2002) · Current Opinion in Cell Biology · doi:10.1016/s0955-0674(02)00314-9 · Cited by 1,121 · see citing works

Gene Regulation at the Single-Cell Level

Rosenfeld, N., Young, J. W., Alon, U., Swain, P. S., & Elowitz, M. B. (2005) · Science · doi:10.1126/science.1106914 · Cited by 1,104 · see citing works

Targeted Recruitment of Set1 Histone Methylase by Elongating Pol II Provides a Localized Mark and Memory of Recent Transcriptional Activity

Ng, H., Robert, F., Young, R. A., & Struhl, K. (2003) · Molecular Cell · doi:10.1016/s1097-2765(03)00092-3 · Cited by 1,097 · see citing works

Multistability in the lactose utilization network of Escherichia coli

Ozbudak, E. M., Thattai, M., Lim, H. N., Shraiman, B. I., & van Oudenaarden, A. (2004) · Nature · doi:10.1038/nature02298 · Cited by 1,030 · see citing works

Revealing the world of RNA interference

Mello, C. C., & Conte, D. (2004) · Nature · doi:10.1038/nature02872 · Cited by 997 · see citing works

Stochastic switching as a survival strategy in fluctuating environments

Açar, M., Mettetal, J. T., & van Oudenaarden, A. (2008) · Nature Genetics · doi:10.1038/ng.110 · Cited by 899 · see citing works

ENZYME INDUCTION AS AN ALL-OR-NONE PHENOMENON

Novick, A., & Weiner, M. (1957) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.43.7.553 · Cited by 891 · see citing works

Specialized Persister Cells and the Mechanism of Multidrug Tolerance in Escherichia coli

Keren, I., Shah, D., Spoering, A. L., Kaldalu, N., & Lewis, K. (2004) · Journal of Bacteriology · doi:10.1128/jb.186.24.8172-8180.2004 · Cited by 857 · see citing works

RNAi-mediated pathways in the nucleus

Matzke, M. A., & Birchler, J. A. (2005) · Nature Reviews Genetics · doi:10.1038/nrg1500 · Cited by 840 · see citing works

Description of the Chemostat

Novick, A., & Szilard, L. (1950) · Science · doi:10.1126/science.112.2920.715 · Cited by 766 · see citing works

Phase and Antigenic Variation in Bacteria

van der Woude, M. W., & Bäumler, A. J. (2004) · Clinical Microbiology Reviews · doi:10.1128/cmr.17.3.581-611.2004 · Cited by 766 · see citing works

Optimality and evolutionary tuning of the expression level of a protein

Dekel, E., & Alon, U. (2005) · Nature · doi:10.1038/nature03842 · Cited by 766 · see citing works

Protein molecules as computational elements in living cells

Bray, D. (1995) · Nature · doi:10.1038/376307a0 · Cited by 748 · see citing works

A positive-feedback-based bistable ‘memory module’ that governs a cell fate decision.

Xiong, W., & Ferrell, J. E. (2003) · Nature · doi:10.1038/nature02089 · Cited by 741 · see citing works

Signaling switches and bistability arising from multisite phosphorylation in protein kinase cascades

Markevich, N. I., Hoek, J. B., & Kholodenko, B. Ν. (2004) · The Journal of Cell Biology · doi:10.1083/jcb.200308060 · Cited by 708 · see citing works

Oxford Surveys in Evolutionary Biology, edited by R.Dawkins and M.Ridley. Oxford University Press; Volume 1, pp. 222; Volume 2, pp. 243; 1984, 1985. NZ$100 (approx.) each.

Flux, J. E. C. (1986) · Journal of the Royal Society of New Zealand · doi:10.1080/03036758.1986.10418172 · Cited by 682 · see citing works

A yeast prion provides a mechanism for genetic variation and phenotypic diversity

True, H. L., & Lindquist, S. L. (2000) · Nature · doi:10.1038/35035005 · Cited by 672 · see citing works

Experimental evolution of bet hedging

Beaumont, H. J. E., Gallie, J., Kost, C., Ferguson, G. C., & Rainey, P. B. (2009) · Nature · doi:10.1038/nature08504 · Cited by 665 · see citing works

Maltose/Maltodextrin System of Escherichia coli : Transport, Metabolism, and Regulation

Boos, W., & Shuman, H. A. (1998) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.62.1.204-229.1998 · Cited by 638 · see citing works

Phenotypic Consequences of Promoter-Mediated Transcriptional Noise

Blake, W. J., Balázsi, G., Kohanski, M. A., Isaacs, F. J., Murphy, K. F., Kuang, Y., Cantor, C. R., Walt, D. R., & Collins, J. J. (2006) · Molecular Cell · doi:10.1016/j.molcel.2006.11.003 · Cited by 617 · see citing works

Stress-controlled transcription factors, stress-induced genes and stress tolerance in budding yeast

Estruch, F. (2000) · FEMS Microbiology Reviews · doi:10.1111/j.1574-6976.2000.tb00551.x · Cited by 616 · see citing works

RNA meets chromatinPreprint

Bernstein, E., & Allis, C. D. (2005) · Genes & Development · doi:10.1101/gad.1324305 · Cited by 609 · see citing works

Adaptive prediction of environmental changes by microorganisms

Mitchell, A., Romano, G. H., Groisman, B., Yona, A., Dekel, E., Kupiec, M., Dahan, O., & Pilpel, Y. (2009) · Nature · doi:10.1038/nature08112 · Cited by 581 · see citing works

Stochastic Gene Expression in Fluctuating Environments

Thattai, M., & van Oudenaarden, A. (2004) · Genetics · doi:10.1534/genetics.167.1.523 · Cited by 526 · see citing works

Predictive Behavior Within Microbial Genetic Networks

Tagkopoulos, I., Liu, Y.-C., & Tavazoie, S. (2008) · Science · doi:10.1126/science.1154456 · Cited by 519 · see citing works

From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli

Thieffry, D., Huerta, A. M., Pérez‐Rueda, E., & Collado‐Vides, J. (1998) · BioEssays · doi:10.1002/(sici)1521-1878(199805)20:5 · Cited by 501 · see citing works

Enhancement of cellular memory by reducing stochastic transitions

Açar, M., Becskei, A., & van Oudenaarden, A. (2005) · Nature · doi:10.1038/nature03524 · Cited by 484 · see citing works

Diversity in Chemotaxis Mechanisms among the Bacteria and Archaea

Szurmant, H., & Ordal, G. (2004) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.68.2.301-319.2004 · Cited by 473 · see citing works

Bow ties, metabolism and disease

Csete, M., & Doyle, J. (2004) · Trends in biotechnology · doi:10.1016/j.tibtech.2004.07.007 · Cited by 468 · see citing works

Stress signaling in yeast

Ruis, H., & Schüller, C. (1995) · BioEssays · doi:10.1002/bies.950171109 · Cited by 406 · see citing works

Amoebae Anticipate Periodic Events

Saigusa, T., Tero, A., Nakagaki, T., & Kuramoto, Y. (2008) · Physical Review Letters · doi:10.1103/physrevlett.100.018101 · Cited by 403 · see citing works

H2A.Z-Mediated Localization of Genes at the Nuclear Periphery Confers Epigenetic Memory of Previous Transcriptional State

Brickner, D. G., Cajigas, I., Fondufe‐Mittendorf, Y. N., Ahmed, S. A. A., Lee, P., Widom, J., & Brickner, J. H. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050081 · Cited by 390 · see citing works

Circadian orchestration of gene expression in cyanobacteria.Preprint

Liu, Y., Tsinoremas, N. F., Johnson, C. H., Lebedeva, N. V., Golden, S. S., Ishiura, M., & Kondo, T. (1995) · Genes & Development · doi:10.1101/gad.9.12.1469 · Cited by 373 · see citing works

Regulation of phenotypic variability by a threshold-based mechanism underlies bacterial persistence

Rotem, E., Loinger, A., Ronin, I., Levin-Reisman, I., Gabay, C., Noam Shoresh, F., Biham, O., & Balaban, N. Q. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1004333107 · Cited by 351 · see citing works

Roles of DNA Adenine Methylation in Regulating Bacterial Gene Expression and Virulence

Low, D. A., Weyand, N. J., & Mahan, M. J. (2001) · Infection and Immunity · doi:10.1128/iai.69.12.7197-7204.2001 · Cited by 337 · see citing works

The Genome-wide Transcriptional Responses of Saccharomyces cerevisiae Grown on Glucose in Aerobic Chemostat Cultures Limited for Carbon, Nitrogen, Phosphorus, or Sulfur

Boer, V. M., de Winde, J. H., Pronk, J. T., & Piper, M. D. W. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m209759200 · Cited by 326 · see citing works

Strategies for cellular decision‐making

Perkins, T. J., & Swain, P. S. (2009) · Molecular Systems Biology · doi:10.1038/msb.2009.83 · Cited by 317 · see citing works

Escherichia coli Habitats, Cell Types, and Molecular Mechanisms of Gene Control

Savageau, M. A. (1983) · The American Naturalist · doi:10.1086/284168 · Cited by 315 · see citing works

The Seven Pillars of Life

Koshland, D. E. (2002) · Science · doi:10.1126/science.1068489 · Cited by 298 · see citing works

The role of physiological heterogeneity in microbial population behavior

Lidstrom, M. E., & Konopka, M. (2010) · Nature Chemical Biology · doi:10.1038/nchembio.436 · Cited by 295 · see citing works

Yeast Stress Response and Fermentation Efficiency: How to Survive the Making of Wine – A Review

Bauer, F. F., & Pretorius, I. S. (2000) · South African Journal of Enology and Viticulture · doi:10.21548/21-1-3557 · Cited by 284 · see citing works

Diversity in times of adversity: probabilistic strategies in microbial survival games

Wolf, D. M., Vazirani, V. V., & Arkin, A. P. (2005) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2004.11.020 · Cited by 270 · see citing works

Single-cell genomics

Tomer Kalisky, C., & Quake, S. R. (2011) · Nature Methods · doi:10.1038/nmeth0411-311 · Cited by 270 · see citing works

Prion Switching in Response to Environmental Stress

Tyedmers, J., Madariaga, M. L. L., & Lindquist, S. L. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060294 · Cited by 270 · see citing works

Flux analysis and control of the central metabolic pathways in Escherichia coli

Holms, H. (1996) · FEMS Microbiology Reviews · doi:10.1111/j.1574-6976.1996.tb00255.x · Cited by 260 · see citing works

Bayes’ theorem and its applications in animal behaviour

McNamara, J. M., Green, R. F., & Olsson, O. (2006) · Oikos · doi:10.1111/j.0030-1299.2006.14228.x · Cited by 259 · see citing works

Mechanisms for the Inheritance of Chromatin States

Moazed, D. (2011) · Cell · doi:10.1016/j.cell.2011.07.013 · Cited by 243 · see citing works

Using movies to analyse gene circuit dynamics in single cells

Locke, J. C. W., & Elowitz, M. B. (2009) · Nature Reviews Microbiology · doi:10.1038/nrmicro2056 · Cited by 238 · see citing works

Large-scale reconstruction and phylogenetic analysis of metabolic environments

Borenstein, E., Kupiec, M., Feldman, M. W., & Ruppin, E. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0806162105 · Cited by 238 · see citing works

A chance at survival: gene expression noise and phenotypic diversification strategies

Fraser, D., & Kærn, M. (2009) · Molecular Microbiology · doi:10.1111/j.1365-2958.2009.06605.x · Cited by 219 · see citing works

Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli

Liu, M., Durfee, T., Cabrera, J. E., Zhao, K., Jin, D. J., & Blattner, F. R. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m414050200 · Cited by 209 · see citing works

Environmental variability and modularity of bacterial metabolic networks

Parter, M., Kashtan, N., & Alon, U. S. (2007) · BMC Evolutionary Biology · doi:10.1186/1471-2148-7-169 · Cited by 201 · see citing works

Glucose Promotes Stress Resistance in the Fungal PathogenCandida albicans

Rodaki, A., Bohovych, I., Enjalbert, B., Young, T., Odds, F. C., Gow, N. A. R., & Brown, A. J. P. (2009) · Molecular Biology of the Cell · doi:10.1091/mbc.e09-01-0002 · Cited by 192 · see citing works

Genes Induced Late in Infection Increase Fitness of Vibrio cholerae after Release into the Environment

Schild, S., Tamayo, R., Nelson, E. J., Qadri, F., Calderwood, S. B., & Camilli, A. (2007) · Cell Host & Microbe · doi:10.1016/j.chom.2007.09.004 · Cited by 188 · see citing works

Cyanobacterial daily life with Kai-based circadian and diurnal genome-wide transcriptional control in Synechococcus elongatus

Ito, H., Mutsuda, M., Murayama, Y., Tomita, J., Hosokawa, N., Terauchi, K., Sugita, C., Sugita, M., Kondo, T., & Iwasaki, H. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0902587106 · Cited by 186 · see citing works

Methylation of H3K4 Is Required for Inheritance of Active Transcriptional States

Muramoto, T., Müller, I. I., Thomas, G., Melvin, A., & Chubb, J. R. (2010) · Current Biology · doi:10.1016/j.cub.2010.01.017 · Cited by 181 · see citing works

Adaptation in bacterial flagellar and motility systems: from regulon members to ‘foraging’-like behavior in E. coli

Zhao, K., Liu, M., & Burgess, R. R. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm456 · Cited by 179 · see citing works

Nutritional Homeostasis in Batch and Steady-State Culture of Yeast

Saldanha, A. J., Brauer, M. J., & Botstein, D. (2004) · Molecular Biology of the Cell · doi:10.1091/mbc.e04-04-0306 · Cited by 176 · see citing works

Chromatin remodeling complexes: strength in diversity, precision through specialization

Cairns, B. R. (2005) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2005.01.003 · Cited by 174 · see citing works

Analysis of Gene Expression in Escherichia coli in Response to Changes of Growth-Limiting Nutrient in Chemostat Cultures

Hua, Q., Chen, Y., Oshima, T., Mori, H., & Shimizu, K. (2004) · Applied and Environmental Microbiology · doi:10.1128/aem.70.4.2354-2366.2004 · Cited by 170 · see citing works

Dynamic nucleosomes and gene transcription

Mellor, J. (2006) · Trends in Genetics · doi:10.1016/j.tig.2006.03.008 · Cited by 168 · see citing works

Yeast cells can access distinct quiescent statesPreprint

Klosinska, M. M., Crutchfield, C. A., Bradley, P. H., Rabinowitz, J. D., & Broach, J. R. (2011) · Genes & Development · doi:10.1101/gad.2011311 · Cited by 168 · see citing works

Flagellar Phase Variation inSalmonella entericaIs Mediated by a Posttranscriptional Control Mechanism

Bonifield, H. R., & Hughes, K. T. (2003) · Journal of Bacteriology · doi:10.1128/jb.185.12.3567-3574.2003 · Cited by 166 · see citing works

Prions, protein homeostasis, and phenotypic diversity

Halfmann, R., Alberti, S., & Lindquist, S. L. (2010) · Trends in Cell Biology · doi:10.1016/j.tcb.2009.12.003 · Cited by 164 · see citing works

RNAi‐directed assembly of heterochromatin in fission yeast

Verdel, A., & Moazed, D. (2005) · FEBS Letters · doi:10.1016/j.febslet.2005.08.083 · Cited by 152 · see citing works

SWI/SNF is required for transcriptional memory at the yeast GAL gene clusterPreprint

Kundu, S., Horn, P. J., & Peterson, C. L. (2007) · Genes & Development · doi:10.1101/gad.1506607 · Cited by 152 · see citing works

A Yeast Catabolic Enzyme Controls Transcriptional Memory

Zacharioudakis, I. M., Gligoris, T. G., & Tzamarias, D. (2007) · Current Biology · doi:10.1016/j.cub.2007.10.044 · Cited by 147 · see citing works

INHIBITION BY GLUCOSE OF THE INDUCED SYNTHESIS OF THE β-GALACTOSIDE-ENZYME SYSTEM OF ESCHERICHIA COLI . ANALYSIS OF MAINTENANCE

Cohn, M., & Horibata, K. (1959) · Journal of Bacteriology · doi:10.1128/jb.78.5.601-612.1959 · Cited by 144 · see citing works

Memory in Microbes: Quantifying History-Dependent Behavior in a Bacterium

Wolf, D. M., Fontaine, L., Bischofs, I., Price, G., Keasling, J. D., & Arkin, A. P. (2008) · PLoS ONE · doi:10.1371/journal.pone.0001700 · Cited by 143 · see citing works

Control of bacterial chemotaxis

Eisenbach, M. (1996) · Molecular Microbiology · doi:10.1111/j.1365-2958.1996.tb02531.x · Cited by 134 · see citing works

Molecular circuits for associative learning in single-celled organisms

Fernando, C., Liekens, A. M. L., Bingle, L. E. H., Beck, C., Lenser, T., Stekel, D. J., & Rowe, J. E. (2008) · Journal of The Royal Society Interface · doi:10.1098/rsif.2008.0344 · Cited by 131 · see citing works

Classical conditioning in paramecia

Hennessey, T. M., Rucker, W. B., & McDiarmid, C. G. (1979) · Animal Learning & Behavior · doi:10.3758/bf03209695 · Cited by 113 · see citing works

Cyanobacterial circadian clocks — timing is everything

Golden, S. S., & Canales, S. R. (2003) · Nature Reviews Microbiology · doi:10.1038/nrmicro774 · Cited by 112 · see citing works

Promoter architecture and the evolvability of gene expression

Tirosh, I., Barkai, N., & Verstrepen, K. J. (2009) · Journal of Biology · doi:10.1186/jbiol204 · Cited by 108 · see citing works

Phenotypic heterogeneity can enhance rare‐cell survival in ‘stress‐sensitive’ yeast populations

Bishop, A. L., Rab, F. A., Sumner, E. R., & Avery, S. V. (2006) · Molecular Microbiology · doi:10.1111/j.1365-2958.2006.05504.x · Cited by 103 · see citing works

Noisy information processing through transcriptional regulation

Libby, E., Perkins, T. J., & Swain, P. S. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0608963104 · Cited by 96 · see citing works

Cost–benefit theory and optimal design of gene regulation functions

Tomer Kalisky, C., Dekel, E., & Alon, U. S. (2007) · Physical Biology · doi:10.1088/1478-3975/4/4/001 · Cited by 95 · see citing works

Responding to attraction: chemotaxis and chemotropism in Dictyostelium and yeast

Arkowitz, R. A. (1999) · Trends in Cell Biology · doi:10.1016/s0962-8924(98)01412-3 · Cited by 92 · see citing works

Circadian Rhythms in Microorganisms: New Complexities

Lakin‐Thomas, P. L., & Brody, S. (2004) · Annual Review of Microbiology · doi:10.1146/annurev.micro.58.030603.123744 · Cited by 90 · see citing works

DNA methylation regulates phenotype-dependent transcriptional activity in <i>Candida albicans</i>

Mishra, P. K., Baum, M., & Carbon, J. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1109631108 · Cited by 84 · see citing works

Epigenetic learning in non-neural organisms

Ginsburg, S., & Jablonka, E. (2009) · Journal of Biosciences · doi:10.1007/s12038-009-0081-8 · Cited by 83 · see citing works

Analysis of Expressed Sequence Tags From Two Starvation, Time-of-Day-Specific Libraries of Neurospora crassa Reveals Novel Clock-Controlled Genes

Zhu, H., Nowrousian, M., Kupfer, D. M., Colot, H. V., Berrocal-Tito, G. M., Lai, H., Bell‐Pedersen, D., Roe, B. A., Loros, J., & Dunlap, J. (2001) · Genetics · doi:10.1093/genetics/157.3.1057 · Cited by 82 · see citing works

Topological Signatures of Species Interactions in Metabolic Networks

Borenstein, E., & Feldman, M. W. (2009) · Journal of Computational Biology · doi:10.1089/cmb.2008.06tt · Cited by 79 · see citing works

Transcriptome Analysis of the Progressive Adaptation of Lactococcus lactis to Carbon Starvation

Redon, E., Loubière, P., & Cocaign‐Bousquet, M. (2005) · Journal of Bacteriology · doi:10.1128/jb.187.10.3589-3592.2005 · Cited by 74 · see citing works

Food quality and the risk of light exposure affect patch‐choice decisions in the slime mold Physarum polycephalum

Latty, T. M., & Beekman, M. (2010) · Ecology · doi:10.1890/09-0358.1 · Cited by 72 · see citing works

Implementation of Dynamic Bayesian Decision Making by Intracellular Kinetics

Kobayashi, T. J. (2010) · Physical Review Letters · doi:10.1103/physrevlett.104.228104 · Cited by 68 · see citing works

A mathematical model for adaptive prediction of environmental changes by microorganisms

Mitchell, A., & Pilpel, Y. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1019754108 · Cited by 67 · see citing works

Regulatory Control and the Costs and Benefits of Biochemical Noise

Tănase‐Nicola, S., & ten Wolde, P. R. (2008) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000125 · Cited by 63 · see citing works

Dominant Role for Signal Transduction in the Transcriptional Memory of Yeast GAL Genes

Kundu, S., & Peterson, C. L. (2010) · Molecular and Cellular Biology · doi:10.1128/mcb.01675-09 · Cited by 60 · see citing works

Demand Theory of Gene Regulation. II. Quantitative Application to the Lactose and Maltose Operons of Escherichia coli

Savageau, M. A. (1998) · Genetics · doi:10.1093/genetics/149.4.1677 · Cited by 53 · see citing works

Predictive Behavior within Microbial Genetic Networks

Tagkopoulos, I., Liu, Y.-C., & Tavazoie, S. (2009) · Topologica · doi:10.3731/topologica.2.018 · Cited by 53 · see citing works

Protoplasmic movement in slime mold plasmodia: The diffusion drag force hypothesis

Stewart, P. A., & Stewart, B. T. (1959) · Experimental Cell Research · doi:10.1016/0014-4827(59)90151-x · Cited by 48 · see citing works

Decomposition of complex microbial behaviors into resource-based stress responses

Carlson, R. P. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn589 · Cited by 46 · see citing works

Discrimination Learning and Extinction in Paramecia ( P. Caudatum )

Armus, H. L., Montgomery, A. R., & Gurney, R. L. (2006) · Psychological Reports · doi:10.2466/pr0.98.3.705-711 · Cited by 44 · see citing works

Associative learning in biochemical networks.

Gandhi, N., Ashkenasy, G., & Tannenbaum, E. (2007) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2007.07.004 · Cited by 43 · see citing works

Recent Transcription-induced Histone H3 Lysine 4 (H3K4) Methylation Inhibits Gene Reactivation

Zhou, B. O., Zhou, J., & Zhou, J. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.273128 · Cited by 35 · see citing works

Global discovery of adaptive mutations

Goodarzi, H., Hottes, A. K., & Tavazoie, S. (2009) · Nature Methods · doi:10.1038/nmeth.1352 · Cited by 31 · see citing works

Time at the end of the millennium: the Neurospora clock

Loros, J. (1998) · Current Opinion in Microbiology · doi:10.1016/s1369-5274(98)80118-5 · Cited by 23 · see citing works

Dynamics of intracellular information decoding

Kobayashi, T. J., & Kamimura, A. (2011) · Physical Biology · doi:10.1088/1478-3975/8/5/055007 · Cited by 21 · see citing works

Association analysis of the general environmental conditions and prokaryotes’ gene distributions in various functional groups

Wu, H., & Moore, E. (2010) · Genomics · doi:10.1016/j.ygeno.2010.03.007 · Cited by 15 · see citing works

A comparison of high frequency switching in the yeast Candida albicans and the slime mold Dictyostelium discoideum

Soll, D. R., & Kraft, B. (1988) · Developmental Genetics · doi:10.1002/dvg.1020090438 · Cited by 15 · see citing works

The theory of constructed emotion: an active inference account of interoception and categorization

Barrett, L. F. (2016) · Social Cognitive and Affective Neuroscience · doi:10.1093/scan/nsw154 · Cited by 1,426 · see citing works

The theory of constructed emotion: an active inference account of interoception and categorization

Barrett, L. F. (2017) · Social Cognitive and Affective Neuroscience · doi:10.1093/scan/nsx060 · Cited by 950 · see citing works

The cognitive cell: bacterial behavior reconsidered

Lyon, P. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.00264 · Cited by 411 · see citing works

On Having No Head: Cognition throughout Biological Systems

Baluška, F., & Levin, M. G. (2016) · Frontiers in Psychology · doi:10.3389/fpsyg.2016.00902 · Cited by 383 · see citing works

Bacterial Adaptation through Loss of Function

Hottes, A. K., Freddolino, L., Khare, A., Donnell, Z. N., Liu, J. C., & Tavazoie, S. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003617 · Cited by 270 · see citing works

The power of predictions: An emerging paradigm for psychological research

Hutchinson, J. B., & Barrett, L. F. (2019) · Current Directions in Psychological Science · doi:10.1177/0963721419831992 · Cited by 216 · see citing works

From allostatic agents to counterfactual cognisers: active inference, biological regulation, and the origins of cognition

Corcoran, A. W., Pezzulo, G., & Hohwy, J. (2020) · Biology &amp; Philosophy · doi:10.1007/s10539-020-09746-2 · Cited by 161 · see citing works

Learning action-oriented models through active inference

Tschantz, A., Seth, A. K., & Buckley, C. L. (2020) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1007805 · Cited by 121 · see citing works

Control mechanisms: Explaining the integration and versatility of biological organisms

Bich, L., & Bechtel, W. (2022) · Adaptive Behavior · doi:10.1177/10597123221074429 · Cited by 108 · see citing works

Biological information systems: Evolution as cognition-based information management

Miller, W. B. (2017) · Progress in Biophysics and Molecular Biology · doi:10.1016/j.pbiomolbio.2017.11.005 · Cited by 101 · see citing works

Affective Value in the Predictive Mind

Van De Cruys, S. (2017) · Theoretical Philosophy/MIND Group – JGU Mainz · doi:10.15502/9783958573253 · Cited by 100 · see citing works

Cognition, Information Fields and Hologenomic Entanglement: Evolution in Light and Shadow

Miller, W. B. (2016) · Biology · doi:10.3390/biology5020021 · Cited by 97 · see citing works

Biological evolution as defense of 'self'

Miller, W. B., Torday, J. S., & Baluška, F. (2018) · Progress in Biophysics and Molecular Biology · doi:10.1016/j.pbiomolbio.2018.10.002 · Cited by 81 · see citing works

There’s Plenty of Room Right Here: Biological Systems as Evolved, Overloaded, Multi-Scale Machines

Bongard, J., & Levin, M. G. (2023) · Biomimetics · doi:10.3390/biomimetics8010110 · Cited by 66 · see citing works

The origins of mutational robustness

Fares, M. A. (2015) · Trends in Genetics · doi:10.1016/j.tig.2015.04.008 · Cited by 60 · see citing works

Cellular signaling pathways as plastic, proto-cognitive systems: Implications for biomedicine

Mathews, J., Chang, A. (., Devlin, L., & Levin, M. G. (2023) · Patterns · doi:10.1016/j.patter.2023.100737 · Cited by 59 · see citing works

The Theory of Constructed Emotion: More Than a Feeling

Barrett, L. F., Atzil, S., Bliss‐Moreau, E., Chanes, L., Gendron, M., Hoemann, K., Katsumi, Y., Kleckner, I. R., Lindquist, K. A., Quigley, K. S., et al. (2025) · Perspectives on Psychological Science · doi:10.1177/17456916251319045 · Cited by 55 · see citing works

Near-Real-Time Analysis of the Phenotypic Responses of Escherichia coli to 1-Butanol Exposure Using Raman Spectroscopy

Zu, T. N. K., Athamneh, A. I. M., Wallace, R. S., Collakova, E., & Senger, R. S. (2014) · Journal of Bacteriology · doi:10.1128/jb.01590-14 · Cited by 40 · see citing works

Regenerative Adaptation to Electrochemical Perturbation in Planaria: A Molecular Analysis of Physiological Plasticity

Emmons‐Bell, M., Durant, F., Tung, A., Pietak, A. M., Miller, K. A., Kane, A., Martyniuk, C. J., Davidian, D. C. C., Morokuma, J., & Levin, M. G. (2019) · iScience · doi:10.1016/j.isci.2019.11.014 · Cited by 35 · see citing works

Balanced Trade-Offs between Alternative Strategies Shape the Response of C. elegans Reproduction to Chronic Heat Stress

Zucker-Aprison, E., & Ruvinsky, I. (2014) · PLoS ONE · doi:10.1371/journal.pone.0105513 · Cited by 37 · see citing works

A systematic approach to cancer: evolution beyond selection

Miller, W. B., & Torday, J. S. (2017) · Clinical and Translational Medicine · doi:10.1186/s40169-016-0131-4 · Cited by 35 · see citing works

The multiscale wisdom of the body: collective intelligence as a tractable interface for next-generation biomedicine

Levin, M. (2025) · BioEssays · doi:10.1002/bies.202400196 · Cited by 34 · see citing works

Craving for the future: the brain as a nutritional prediction system

Walker, S. J., Goldschmidt, D., & Ribeiro, C. (2017) · Current Opinion in Insect Science · doi:10.1016/j.cois.2017.07.013 · Cited by 31 · see citing works

Allostatic Changes in the cAMP System Drive Opioid-Induced Adaptation in Striatal Dopamine Signaling

Muntean, B. S., Dao, M. T., & Martemyanov, K. A. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.09.034 · Cited by 26 · see citing works

Learning action-oriented models through active inferencePreprint

Tschantz, A., Seth, A. K., & Buckley, C. L. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/764969 · Cited by 28 · see citing works

Modeling autopoiesis and cognition with reaction networks

Heylighen, F., & Busseniers, E. (2023) · Biosystems · doi:10.1016/j.biosystems.2023.104937 · Cited by 27 · see citing works

Distinct heterochromatin‐like domains promote transcriptional memory and silence parasitic genetic elements in bacteria

Amemiya, H. M., Goss, T. J., Nye, T. M., Hurto, R. L., Simmons, L. A., & Freddolino, P. L. (2021) · The EMBO Journal · doi:10.15252/embj.2021108708 · Cited by 27 · see citing works

Naturalising Agent Causation

Potter, H. D., & Mitchell, K. J. (2022) · Entropy · doi:10.3390/e24040472 · Cited by 27 · see citing works

Anticipation: Beyond synthetic biology and cognitive robotics

Nasuto, S. J., & Hayashi, Y. (2016) · Biosystems · doi:10.1016/j.biosystems.2016.07.011 · Cited by 26 · see citing works

Predicting microbial response to anthropogenic environmental disturbances using artificial neural network and multiple linear regression

Sharma, S., Gupta, R., Bhatia, R., Toor, A. P., & Setia, H. (2021) · International Journal of Cognitive Computing in Engineering · doi:10.1016/j.ijcce.2021.03.001 · Cited by 19 · see citing works

Dual role of starvation signaling in promoting growth and recovery

Gurvich, Y., Leshkowitz, D., & Barkai, N. (2017) · PLoS Biology · doi:10.1371/journal.pbio.2002039 · Cited by 16 · see citing works

Biological Prescience: The Role of Anticipation in Organismal Processes

Deans, C. (2021) · Frontiers in Physiology · doi:10.3389/fphys.2021.672457 · Cited by 18 · see citing works

Emerging cancer therapies: targeting physiological networks and cellular bioelectrical differences with non-thermal systemic electromagnetic fields in the human body – a comprehensive review

Costa, F. P., Wiedenmann, B. J., Schöll, E., & Tuszyński, J. A. (2024) · Frontiers in Network Physiology · doi:10.3389/fnetp.2024.1483401 · Cited by 17 · see citing works

A self‐propagating, barcoded transposon system for the dynamic rewiring of genomic networks

English, M. A., Alcantar, M. A., & Collins, J. J. (2023) · Molecular Systems Biology · doi:10.15252/msb.202211398 · Cited by 15 · see citing works

Preferences need inferences: Learning, valuation, and curiosity in aesthetic experiencePreprint

de Cruys, S. V., Bervoets, J., & Moors, A. (2021) · doi:10.31234/osf.io/zh6nt · Cited by 17 · see citing works

Adaptation of bacterial communities and plant strategies for amelioration and eco-restoration of an organometallic industrial waste polluted site

Tripathi, S., Singh, K. K., & Chandra, R. (2021) · Elsevier eBooks · doi:10.1016/b978-0-12-824448-7.00005-x · Cited by 14 · see citing works

Stress sharing as cognitive glue for collective intelligences: A computational model of stress as a coordinator for morphogenesis

Shreesha, L., & Levin, M. G. (2024) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2024.150396 · Cited by 13 · see citing works

A bacterial signaling system regulates noise to enable bet hedging

Carey, J. N., & Goulian, M. (2018) · Current Genetics · doi:10.1007/s00294-018-0856-2 · Cited by 13 · see citing works

A cAMP/CRP-controlled mechanism for the incorporation of extracellular ADP-glucose in Escherichia coli involving NupC and NupG nucleoside transporters

Almagro, G., Viale, A. M., Montero, M., Muñoz, F. J., Baroja‐Fernández, E., Mori, H., & Pozueta‐Romero, J. (2018) · Scientific Reports · doi:10.1038/s41598-018-33647-w · Cited by 11 · see citing works

Categorization is ‘baked’ into the brain

Barrett, L. F., & Miller, E. K. (2026) · Nature reviews. Neuroscience · doi:10.1038/s41583-026-01036-2 · Cited by 15 · see citing works

Living cognition and the nature of organisms

Just, B. B., & de Farías, S. T. (2024) · Biosystems · doi:10.1016/j.biosystems.2024.105356 · Cited by 10 · see citing works

Exploiting Information and Control Theory for Directing Gene Expression in Cell Populations

Henrion, L., Delvenne, M., Kakahi, F. B., Moreno, F., & Delvigne, F. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.869509 · Cited by 8 · see citing works

Many Paths to Anticipatory Behavior: Anticipatory Model Acquisition Across Phylogenetic and Ontogenetic Timescales

Sims, M. (2023) · Biological Theory · doi:10.1007/s13752-022-00426-w · Cited by 8 · see citing works

From Russia with Love / Russian experimental and empirical contributions informed by an anticipatory perspective

Nadin, M., & Kurismaa, A. (2015) · International Journal of General Systems · doi:10.1080/03081079.2015.1032074 · Cited by 6 · see citing works

Cough-Anal Reflex May Be the Expression of a Pre-Programmed Postural Action

Cavallari, P., Bolzoni, F., Esposti, R., & Bruttini, C. (2017) · Frontiers in Human Neuroscience · doi:10.3389/fnhum.2017.00475 · Cited by 6 · see citing works

Genes and knowledge: Response to Baverstock, K. the gene an appraisal. https://doi.org/10.1016/j.pbiomolbio.2021.04.005

Richardson, K. (2021) · Progress in Biophysics and Molecular Biology · doi:10.1016/j.pbiomolbio.2021.10.003 · Cited by 6 · see citing works

A case for aneural cognition: E. coli and its cognitive repertoire

Just, B. B., & de Farías, S. T. (2025) · Biosystems · doi:10.1016/j.biosystems.2025.105645 · Cited by 5 · see citing works

On the origins of anticipation as an evolutionary framework: functional systems perspective

Kurismaa, A. (2015) · International Journal of General Systems · doi:10.1080/03081079.2015.1032530 · Cited by 5 · see citing works

The multiscale wisdom of the body: collective intelligence as a tractable interface for next-generation biomedicinePreprint

Levin, M. G. (2024) · doi:10.31219/osf.io/yq9xe · Cited by 5 · see citing works

Spatio-temporal organization of the E. coli chromosome from base to cellular length scales

Royzenblat, S. K., & Freddolino, L. (2024) · EcoSal Plus · doi:10.1128/ecosalplus.esp-0001-2022 · Cited by 5 · see citing works

Major transitions in the physiological machinery of cognition

Just, B. B., & de Farías, S. T. (2025) · Biosystems · doi:10.1016/j.biosystems.2025.105517 · Cited by 6 · see citing works

Escherichia coli YigI is a Conserved Gammaproteobacterial Acyl-CoA Thioesterase Permitting Metabolism of Unusual Fatty Acid Substrates

Schmidt, M., Proctor, T., Diao, R., & Freddolino, L. (2022) · Journal of Bacteriology · doi:10.1128/jb.00014-22 · Cited by 4 · see citing works

Synapses in Digital Medium: Computational Investigations of Neural Basis of Anticipation

Nasuto, S. J., & Hayashi, Y. (2015) · Cognitive systems monographs · doi:10.1007/978-3-319-22599-9_12 · Cited by 3 · see citing works

Assimiliating an Associative Trait: from Eco-Physiology to Epigenetics

Kurismaa, A. (2018) · Biosemiotics · doi:10.1007/s12304-018-9324-0 · Cited by 3 · see citing works

Adaptation by stochastic tuning of gene expression in mammalian cellsPreprint

Momen-Roknabadi, A., Oikonomou, P., & Tavazoie, S. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.05.07.651953 · Cited by 3 · see citing works

Cognition as a global biological process

Just, B. B., & de Farías, S. T. (2026) · Biosystems · doi:10.1016/j.biosystems.2026.105851 · Cited by 3 · see citing works

Multiscale regulation of nutrient stress responses in Escherichia coli from chromatin structure to small regulatory RNAs

Ekdahl, A. M., Julien, T., Suraj, S., Kribelbauer-Swietek, J. F., Tavazoie, S., Freddolino, L., & Contreras, L. M. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf647 · Cited by 2 · see citing works

The Control Cycle Cognitive Model in Biology, Film and Culture

Deaca, M. V. (2018) · Ekphrasis · doi:10.24193/ekphrasis.20.4 · Cited by 2 · see citing works

From integrative biology to the nerve impulse: Rethinking neural information and semiotics in functional systems perspective

Kurismaa, A. (2022) · Adaptive Behavior · doi:10.1177/10597123221089557 · Cited by 2 · see citing works

Cognition without brains? Learning and memory in microorganisms

Messer, A., Oña, L., & Kost, C. (2026) · Trends in Microbiology · doi:10.1016/j.tim.2026.03.015 · Cited by 1 · see citing works

Cognition and the Living Condition

Torday, J. S., & Miller, W. B. (2020) · Springer eBooks · doi:10.1007/978-3-030-38133-2_3

Theoretical, and epistemological challenges in scientific investigations of complex emotional states in animals

Lages, Y., Mograbi, D. C., Krahe, T. E., & Landeira-Fernández, J. (2020) · Consciousness and Cognition · doi:10.1016/j.concog.2020.103003

Escherichia coli YigI is a conserved ɣ-proteobacterial acyl-CoA thioesterase permitting metabolism of unusual fatty acid substratesPreprint

Schmidt, M., Proctor, T., Diao, R., & Freddolino, P. L. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.01.10.475765

Biological Prescience: The Role of Anticipation in Organismal DesignPreprint

Deans, C. (2024) · doi:10.22541/au.170664603.30714038/v1

Embedding ultrasensitivity via cooperation in biomolecular circuit design: a framework for robust adaptation

Procopio, A., Montefusco, F., Dragone, D., Cortese, N., Fera, N., Merola, A., Ariola, M., Amato, F., & Cosentino, C. (2025) · Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC) · doi:10.1109/embc58623.2025.11252876

Optical multi-physical field imaging within single cells

Xu, Y., Ji, C., Tan, J., & Feng, J. (2026) · Chemical Society Reviews · doi:10.1039/d6cs00641h

A mathematical model for adaptive prediction of environmental changes by microorganisms

Mitchell, A., & Pilpel, Y. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1019754108 · Cited by 67 · see citing works

Predictive Behavior within Microbial Genetic Networks

Tagkopoulos, I., Liu, Y.-C., & Tavazoie, S. (2009) · Topologica · doi:10.3731/topologica.2.018 · Cited by 53 · see citing works

Pearls Adaptive Prediction As a Strategy in Microbial Infections

Brunke, S., & Hube, B. (2016)

Adaptive Prediction As a Strategy in Microbial Infections

Brunke, S., & Hube, B. (2014) · PLoS Pathogens · doi:10.1371/journal.ppat.1004356 · Cited by 57 · see citing works

Predicting the future

Jermy, A. J. (2009) · Nature Reviews Microbiology · doi:10.1038/nrmicro2195