Modelling and analysis of gene regulatory networks
Open accessAbstract
Gene regulatory networks have an important role in every process of life, including cell differentiation, metabolism, the cell cycle and signal transduction. By understanding the dynamics of these networks we can shed light on the mechanisms of diseases that occur when these cellular processes are dysregulated. Accurate prediction of the behaviour of regulatory networks will also speed up biotechnological projects, as such predictions are quicker and cheaper than lab experiments. Computational methods, both for supporting the development of network models and for the analysis of their functionality, have already proved to be a valuable research tool.
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The number of mRNA molecules may sometimes not correlate well with the numbers of their protein products at the same time point.
“Third, the number of mRNA molecules may sometimes not correlate well with the numbers of their protein products at the same time point180–184”
From Revealing the vectors of cellular identity with single-cell genomics (2016) · cites this paper as [180]
Cites
Golub, G. (2012) · doi:10.56021/9781421407944 · Cited by 34,505 · see citing works
Molecular Evolutionary Genetics
Nei, M. (1987) · Columbia University Press eBooks · doi:10.7312/nei-92038 · Cited by 16,583 · see citing works
(1988) · Cited by 16,582 · see citing works
Exact stochastic simulation of coupled chemical reactions
Gillespie, D. T. (1977) · The Journal of Physical Chemistry · doi:10.1021/j100540a008 · Cited by 9,969 · see citing works
EVOLUTION IN MENDELIAN POPULATIONS
Wright, S. (1931) · Genetics · doi:10.1093/genetics/16.2.97 · Cited by 9,078 · see citing works
Markov Chain Monte Carlo in Practice
Gilks, W. R., Richardson, S. T., & Spiegelhalter, D. J. (1995) · Chapman & Hall/CRC eBooks · doi:10.1201/b14835 · Cited by 7,927 · see citing works
The Origins of Order: Self-Organization and Selection in Evolution
Kauffman, S. A. (1993) · doi:10.1093/oso/9780195079517.001.0001 · Cited by 7,855 · see citing works
The origins of order; self organization and selection in evolution
Kauffman, S. A. (1994) · International Journal of Biochemistry · doi:10.1016/0020-711x(94)90119-8 · Cited by 6,753 · see citing works
Factor graphs and the sum-product algorithm
Kschischang, F. R., Frey, B. J., & Loeliger, H.-A. (2001) · IEEE Transactions on Information Theory · doi:10.1109/18.910572 · Cited by 6,486 · see citing works
Gillespie, D. T. (1976) · Journal of Computational Physics · doi:10.1016/0021-9991(76)90041-3 · Cited by 6,029 · see citing works
Spellman, P. T., Sherlock, G. J., Zhang, M. Q., Iyer, V. R., Anders, K. R., Eisen, M. B., Brown, P. O., Botstein, D., & Futcher, B. (1998) · Molecular Biology of the Cell · doi:10.1091/mbc.9.12.3273 · Cited by 4,724 · see citing works
Petri Net theory and the modeling of systems
(1982) · Mathematics and Computers in Simulation · doi:10.1016/0378-4754(82)90066-0 · Cited by 3,609 · see citing works
Using Bayesian Networks to Analyze Expression Data
Friedman, N., Michal Linial, B., Nachman, I., & Pe’er, D. (2000) · Journal of Computational Biology · doi:10.1089/106652700750050961 · Cited by 3,248 · see citing works
Transcriptional Regulatory Networks in <i>Saccharomyces cerevisiae</i>
Lee, T. I., Rinaldi, N. J., Robert, F., Odom, D. T., Bar-Joseph, Z., Gerber, G. K., Hannett, N. M., Harbison, C. T., Thompson, C. M., Simon, I., et al. (2002) · Science · doi:10.1126/science.1075090 · Cited by 2,956 · see citing works
Petri, C. A. (1962) · Cited by 2,159 · see citing works
Stochastic Simulation of Chemical Kinetics
Gillespie, D. T. (2006) · Annual Review of Physical Chemistry · doi:10.1146/annurev.physchem.58.032806.104637 · Cited by 2,072 · see citing works
MicroRNA biogenesis: coordinated cropping and dicing
Kim, V. N. (2005) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1644 · Cited by 2,019 · see citing works
Stochastic mechanisms in gene expression.
McAdams, H., & Arkin, A. (1997) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.94.3.814 · Cited by 1,970 · see citing works
Approximate accelerated stochastic simulation of chemically reacting systems
Gillespie, D. T. (2001) · The Journal of Chemical Physics · doi:10.1063/1.1378322 · Cited by 1,890 · see citing works
Structure and function of the feed-forward loop network motif
Mangan, S., & Alon, U. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2133841100 · Cited by 1,827 · see citing works
Stochastic mRNA Synthesis in Mammalian Cells
Raj, A., Peskin, C. S., Tranchina, D., Vargas, D. Y., & Tyagi, S. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040309 · Cited by 1,737 · see citing works
Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels
Gibson, M., & Bruck, J. (2000) · The Journal of Physical Chemistry A · doi:10.1021/jp993732q · Cited by 1,724 · see citing works
Segal, E., Shapira, M., Regev, A., Pe’er, D., Botstein, D., Koller, D., & Friedman, N. (2003) · Nature Genetics · doi:10.1038/ng1165 · Cited by 1,686 · see citing works
Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks
Ilya Shmulevich, C., Dougherty, E. R., Kim, S., & Zhang, W. (2002) · Bioinformatics · doi:10.1093/bioinformatics/18.2.261 · Cited by 1,609 · see citing works
A genomic regulatory network for development
Davidson, E. H., Rast, J. P., Oliveri, P., Ransick, A., Calestani, C., Yuh, C.-H., Minokawa, T., Amore, G., Hinman, V., Arenas-Mena, C., et al. (2002) · Science · doi:10.1126/science.1069883 · Cited by 1,567 · see citing works
Regulation of noise in the expression of a single gene
Özbudak, E. M., Thattai, M., Kurtser, I., Grossman, A. D., & van Oudenaarden, A. (2002) · Nature Genetics · doi:10.1038/ng869 · Cited by 1,559 · see citing works
Arkin, A. P., Ross, J., & McAdams, H. H. (1998) · Genetics · doi:10.1093/genetics/149.4.1633 · Cited by 1,492 · see citing works
The retardation of aging and disease by dietary restriction
(1989) · Choice Reviews Online · doi:10.5860/choice.26-5101 · Cited by 1,477 · see citing works
Widespread translational inhibition by plant miRNAs and siRNAs
Brodersen, P., Sakvarelidze-Achard, L., Bruun-Rasmussen, M., Dunoyer, P., Yamamoto, Y. Y., Sieburth, L., & Voinnet, O. (2008) · Science · doi:10.1126/science.1159151 · Cited by 1,477 · see citing works
The chemical Langevin equation
Gillespie, D. T. (2000) · The Journal of Chemical Physics · doi:10.1063/1.481811 · Cited by 1,475 · see citing works
Real-Time Kinetics of Gene Activity in Individual Bacteria
Golding, I., Paulsson, J., Zawilski, S. M., & Cox, E. C. (2005) · Cell · doi:10.1016/j.cell.2005.09.031 · Cited by 1,468 · see citing works
Markov Chain Monte Carlo in Practice.
Kass, R. E., Gilks, W. R., Richardson, S. T., & Spiegelhalter, D. J. (1997) · Journal of the American Statistical Association · doi:10.2307/2965438 · Cited by 1,380 · see citing works
Feist, A. M., Henry, C. S., Reed, J. L., Krummenacker, M., Joyce, A. R., Karp, P. D., Broadbelt, L. J., Vassily Hatzimanikatis, A., & Palsson, B. Ø. (2007) · Molecular Systems Biology · doi:10.1038/msb4100155 · Cited by 1,367 · see citing works
Theoretical Ecology: Principles and Applications
Elliott, J. M., & May, R. M. (1982) · Journal of Animal Ecology · doi:10.2307/3996 · Cited by 1,268 · see citing works
Inferring Cellular Networks Using Probabilistic Graphical Models
Friedman, N. (2004) · Science · doi:10.1126/science.1094068 · Cited by 1,208 · see citing works
Stochastic protein expression in individual cells at the single molecule level
Cai, L., Friedman, N., & Xie, X. S. (2006) · Nature · doi:10.1038/nature04599 · Cited by 1,145 · see citing works
The yeast cell-cycle network is robustly designed
Li, F., Long, T., Lu, Y., Ouyang, Q., & Tang, C. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0305937101 · Cited by 1,110 · see citing works
Boolean formalization of genetic control circuits
Thomas, R. (1973) · Journal of Theoretical Biology · doi:10.1016/0022-5193(73)90247-6 · Cited by 989 · see citing works
The logical analysis of continuous, non-linear biochemical control networks
Glass, L., & Kauffman, S. A. (1973) · Journal of Theoretical Biology · doi:10.1016/0022-5193(73)90208-7 · Cited by 940 · see citing works
Probing Gene Expression in Live Cells, One Protein Molecule at a Time
Yu, J., Xiao, J., Ren, X., Lao, K., & Xie, X. S. (2006) · Science · doi:10.1126/science.1119623 · Cited by 918 · see citing works
How do site-specific DNA-binding proteins find their targets?
Halford, S. E. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh624 · Cited by 891 · see citing works
Bernstein, J. A., Khodursky, A. B., Lin, P., Lin‐Chao, S., & Cohen, S. N. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.112318199 · Cited by 859 · see citing works
It’s a noisy business! Genetic regulation at the nanomolar scale
McAdams, H. H., & Arkin, A. P. (1999) · Trends in Genetics · doi:10.1016/s0168-9525(98)01659-x · Cited by 848 · see citing works
Noise in protein expression scales with natural protein abundance
Bar-Even, A., Paulsson, J., Maheshri, N., Carmi, M., O'Shea, E., Pilpel, Y., & Barkai, N. (2006) · Nature Genetics · doi:10.1038/ng1807 · Cited by 807 · see citing works
Integrating high-throughput and computational data elucidates bacterial networks
Covert, M. W., Knight, E. M., Reed, J. L., Herrgard, M. J., & Palsson, B. O. (2004) · Nature · doi:10.1038/nature02456 · Cited by 792 · see citing works
E-CELL: software environment for whole-cell simulation
Tomita, M., Hashimoto, K., Takahashi, K., Shimizu, T. S., Matsuzaki, Y., Miyoshi, F., Saito, K., Tanida, S., Yugi, K., Venter, J. C., et al. (1999) · Bioinformatics · doi:10.1093/bioinformatics/15.1.72 · Cited by 764 · see citing works
Advances in flux balance analysis
Kauffman, K. J., Prakash, P., & Edwards, J. S. (2003) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2003.08.001 · Cited by 744 · see citing works
Multiplexed protein measurement: technologies and applications of protein and antibody arrays
Kingsmore, S. F. (2006) · Nature Reviews Drug Discovery · doi:10.1038/nrd2006 · Cited by 717 · see citing works
Akutsu, T., Miyano, S., & Kuhara, S. (1998) · Pacific Symposium on Biocomputing (PSB) · doi:10.1142/9789814447300_0003 · Cited by 694 · see citing works
Rao, C. V., & Arkin, A. P. (2003) · The Journal of Chemical Physics · doi:10.1063/1.1545446 · Cited by 687 · see citing works
Systems biology properties of reconstructed networks
Palsson, B. Ø. (2006) · Cited by 684 · see citing works
Reverse engineering gene networks using singular value decomposition and robust regression
Yeung, M. K. S., Tegnér, J., & Collins, J. J. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.092576199 · Cited by 667 · see citing works
Duarte, N. C., Herrgård, M. J., & Palsson, B. Ø. (2004) · Genome Research · doi:10.1101/gr.2250904 · Cited by 639 · see citing works
Integrative Analysis of Cell Cycle Control in Budding Yeast
Chen, K. C., Calzone, L., Csikász‐Nagy, A., Cross, F. R., Novák, B., & Tyson, J. J. (2004) · Molecular Biology of the Cell · doi:10.1091/mbc.e03-11-0794 · Cited by 625 · see citing works
Systems Biology: Properties of Reconstructed Networks
Palsson, B. Ø. (2006) · doi:10.1017/cbo9780511790515 · Cited by 617 · see citing works
Weinberger, L. S., Burnett, J., Toettcher, J. E., Arkin, A. P., & Schaffer, D. V. (2005) · Cell · doi:10.1016/j.cell.2005.06.006 · Cited by 616 · see citing works
Petri net theory and the modeling of systems
(1982) · Mathematics and Computers in Simulation · doi:10.1016/0378-4754(82)90087-8 · Cited by 615 · see citing works
Introduction to Monte Carlo Methods
Mackay, D. (1998) · Springer eBooks · doi:10.1007/978-94-011-5014-9_7 · Cited by 581 · see citing works
PROTEIN TRANSPORT ACROSS THE EUKARYOTIC ENDOPLASMIC RETICULUM AND BACTERIAL INNER MEMBRANES
Rapoport, T. A., Jungnickel, B., & Kutay, U. (1996) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.65.070196.001415 · Cited by 559 · see citing works
Global Analysis of the Genetic Network Controlling a Bacterial Cell Cycle
Laub, M. T., McAdams, H. H., Feldblyum, T. V., Fraser, C. M., & Shapiro, L. (2000) · Science · doi:10.1126/science.290.5499.2144 · Cited by 557 · see citing works
Random Boolean network models and the yeast transcriptional network
Kauffman, S. A., Peterson, C., Samuelsson, B., & Troein, C. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2036429100 · Cited by 552 · see citing works
Crossing the Nuclear Envelope: Hierarchical Regulation of Nucleocytoplasmic Transport
Terry, L. J., Shows, E. B., & Wente, S. R. (2007) · Science · doi:10.1126/science.1142204 · Cited by 543 · see citing works
The OR control system of bacteriophage lambda
Shea, M. A., & Ackers, G. K. (1985) · Journal of Molecular Biology · doi:10.1016/0022-2836(85)90086-5 · Cited by 528 · see citing works
Theoretical Ecology: Principles and Applications
Elliott, J. M., & May, R. M. (1977) · Journal of Animal Ecology · doi:10.2307/3843 · Cited by 525 · see citing works
Circuit Simulation of Genetic Networks
McAdams, H. H., & Shapiro, L. (1995) · Science · doi:10.1126/science.7624793 · Cited by 519 · see citing works
Temporal organization in cells
Rosén, R. (1965) · Bulletin of Mathematical Biology · doi:10.1007/bf02476853 · Cited by 476 · see citing works
Predicting expression patterns from regulatory sequence in Drosophila segmentation
Segal, E., Raveh-Sadka, T., Schroeder, M., Unnerstall, U., & Gaul, U. (2008) · Nature · doi:10.1038/nature06496 · Cited by 466 · see citing works
Integrative model of the response of yeast to osmotic shock
Klipp, E., Nordlander, B., Krüger, R., Gennemark, P., & Hohmann, S. (2005) · Nature Biotechnology · doi:10.1038/nbt1114 · Cited by 447 · see citing works
Regulation of Gene Expression in Flux Balance Models of Metabolism
Covert, M. W., Schilling, C. H., & Palsson, B. Ø. (2001) · Journal of Theoretical Biology · doi:10.1006/jtbi.2001.2405 · Cited by 431 · see citing works
MODELING REGULATORY NETWORKS WITH WEIGHT MATRICES
Weaver, D. C., Workman, C. T., & Stormo, G. D. (1998) · Pacific Symposium on Biocomputing (PSB) · doi:10.1142/9789814447300_0011 · Cited by 403 · see citing works
Fisher, R. A. (1990) · Bulletin of Mathematical Biology · doi:10.1016/s0092-8240(05)80012-6 · Cited by 393 · see citing works
Klipp, E., Herwig, R., Kowald, A., Wierling, C., & Lehrach, H. R. (2005) · Wiley eBooks · doi:10.1002/3527603603 · Cited by 392 · see citing works
Bansal, M., Gatta, G. D., & di Bernardo, D. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl003 · Cited by 384 · see citing works
Extension of a genetic network model by iterative experimentation and mathematical analysis
Locke, J. C. W., Southern, M. M., Kozma‐Bognár, L., Hibberd, V., Brown, P. E., Turner, M. S., & Millar, A. J. (2005) · Molecular Systems Biology · doi:10.1038/msb4100018 · Cited by 381 · see citing works
Beg, Q. K., Vazquez, A., Ernst, J., de Menezes, M. A., Bar-Joseph, Z., Barabási, A.-L., & Oltvai, Z. N. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0609845104 · Cited by 368 · see citing works
Metabolic modelling of microbes: the flux‐balance approach
Edwards, J. S., Covert, M., & Palsson, B. (2002) · Environmental Microbiology · doi:10.1046/j.1462-2920.2002.00282.x · Cited by 365 · see citing works
Systems biology in practice: concepts, implementation and application
(2005) · Choice Reviews Online · doi:10.5860/choice.43-2192 · Cited by 356 · see citing works
Transcriptional Regulation in Constraints-based Metabolic Models of Escherichia coli
Covert, M. W., & Palsson, B. Ø. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m201691200 · Cited by 341 · see citing works
Transcribing RNA Polymerase II Is Phosphorylated at CTD Residue Serine-7
Chapman, R. D., Heidemann, M., Albert, T., Mailhammer, R., Flatley, A., Meisterernst, M., Kremmer, E., & Eick, D. (2007) · Science · doi:10.1126/science.1145977 · Cited by 323 · see citing works
Müller‐Hill, B. (1996) · De Gruyter eBooks · doi:10.1515/9783110879476 · Cited by 320 · see citing works
Regulation of the bacterial cell cycle by an integrated genetic circuit
Biondi, E. G., Reisinger, S. J., Skerker, J. M., et al. (2006) · Nature · doi:10.1038/nature05321 · Cited by 318 · see citing works
Inferring gene networks from time series microarray data using dynamic Bayesian networks
Kim, S. Y. (2003) · Briefings in Bioinformatics · doi:10.1093/bib/4.3.228 · Cited by 308 · see citing works
On Learning Gene Regulatory Networks Under the Boolean Network Model
Lähdesmäki, H. J., Shmulevich, I., & Yli-Harja, O. P. (2003) · Machine Learning · doi:10.1023/a:1023905711304 · Cited by 301 · see citing works
DISCOVERY OF REGULATORY INTERACTIONS THROUGH PERTURBATION: INFERENCE AND EXPERIMENTAL DESIGN
Ideker, T., THORSSONt, V., & Karp, R. M. (1999) · Pacific Symposium on Biocomputing (PSB) · doi:10.1142/9789814447331_0029 · Cited by 275 · see citing works
Network motifs: Structure does not determine function.
Ingram, P. J., Stumpf, M. P., & Stark, J. (2006) · BMC Genomics · doi:10.1186/1471-2164-7-108 · Cited by 267 · see citing works
Shlomi, T., Eisenberg, Y., Sharan, R., & Ruppin, E. (2007) · Molecular Systems Biology · doi:10.1038/msb4100141 · Cited by 254 · see citing works
Dynamic Analysis of Integrated Signaling, Metabolic, and Regulatory Networks
Lee, J. M., Gianchandani, E. P., Eddy, J. A., & Papin, J. A. (2008) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000086 · Cited by 225 · see citing works
Herrgård, M. J., Lee, B.-S., Portnoy, V. A., & Palsson, B. Ø. (2006) · Genome Research · doi:10.1101/gr.4083206 · Cited by 224 · see citing works
Oscillating Global Regulators Control the Genetic Circuit Driving a Bacterial Cell Cycle
Holtzendorff, J., Hung, D. Y., Brende, P., et al. (2004) · Science · doi:10.1126/science.1095191 · Cited by 217 · see citing works
Temporal organization in cells; a dynamic theory of cellular control processes
GOODWIN, B. C. (1963) · Academic Press eBooks · doi:10.5962/bhl.title.6268 · Cited by 196 · see citing works
Inferring quantitative models of regulatory networks from expression data
Nachman, I., Regev, A., & Friedman, N. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth941 · Cited by 193 · see citing works
Graphic requirements for multistability and attractive cycles in a Boolean dynamical framework
Rémy, É., Ruet, P., & Thieffry, D. (2008) · Advances in Applied Mathematics · doi:10.1016/j.aam.2007.11.003 · Cited by 191 · see citing works
Physiology and metabolic fluxes of wild-type and riboflavin-producing Bacillus subtilis
Sauer, U., Hatzimanikatis, V., Hohmann, H., et al. (1996) · Applied and Environmental Microbiology · doi:10.1128/aem.62.10.3687-3696.1996 · Cited by 184 · see citing works
A Bacterial Cell-Cycle Regulatory Network Operating in Time and Space
McAdams, H. H., & Shapiro, L. (2003) · Science · doi:10.1126/science.1087694 · Cited by 177 · see citing works
Qualitative analysis of biochemical reaction systems
Reddy, V. N., Liebman, M., & Mavrovouniotis, M. L. (1996) · Computers in Biology and Medicine · doi:10.1016/0010-4825(95)00042-9 · Cited by 169 · see citing works
Yeang, C., Ideker, T. E., & Jaakkola, T. (2004) · Journal of Computational Biology · doi:10.1089/1066527041410382 · Cited by 167 · see citing works
A multi-algorithm, multi-timescale method for cell simulation
Takahashi, K., Kaizu, K., Hu, B., & Tomita, M. (2004) · Bioinformatics · doi:10.1093/bioinformatics/btg442 · Cited by 164 · see citing works
Algorithms and Software for Stochastic Simulation of Biochemical Reacting Systems
Li, H., Cao, Y., Petzold, L. R., & Gillespie, D. T. (2007) · Biotechnology Progress · doi:10.1021/bp070255h · Cited by 158 · see citing works
Guptasarma, P. (1995) · BioEssays · doi:10.1002/bies.950171112 · Cited by 153 · see citing works
Steady‐state analysis of genetic regulatory networks modelled by probabilistic Boolean networks
Shmulevich, I., Gluhovsky, I., Hashimoto, R. F., et al. (2003) · Comparative and Functional Genomics · doi:10.1002/cfg.342 · Cited by 152 · see citing works
Transcription of individual genes in eukaryotic cells occurs randomly and infrequently
Ross, I. L., Browne, C. M., & Hume, D. (1994) · Immunology and Cell Biology · doi:10.1038/icb.1994.26 · Cited by 145 · see citing works
STOCKS: STOChastic Kinetic Simulations of biochemical systems with Gillespie algorithm
Kierzek, A. M. (2002) · Bioinformatics · doi:10.1093/bioinformatics/18.3.470 · Cited by 145 · see citing works
Pathway analysis in metabolic databases via differential metabolic display (DMD)
Küffner, R., Zimmer, R., & Lengauer, T. (2000) · Bioinformatics · doi:10.1093/bioinformatics/16.9.825 · Cited by 140 · see citing works
Bae, K., Lee, C., Hardin, P. E., et al. (2000) · Journal of Neuroscience · doi:10.1523/jneurosci.20-05-01746.2000 · Cited by 137 · see citing works
Qualitatively modelling and analysing genetic regulatory networks: a Petri net approach
Steggles, L. J., Banks, R., Shaw, O., et al. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl596 · Cited by 137 · see citing works
Genome‐wide transcriptional plasticity underlies cellular adaptation to novel challenge
Stern, S., Dror, T. W., Stolovicki, E., Brenner, N., & Braun, E. (2007) · Molecular Systems Biology · doi:10.1038/msb4100147 · Cited by 136 · see citing works
A Gene Regulatory Network Subcircuit Drives a Dynamic Pattern of Gene Expression
Smith, J., Theodoris, C. V., & Davidson, E. H. (2007) · Science · doi:10.1126/science.1146524 · Cited by 127 · see citing works
A General Modeling Strategy for Gene Regulatory Networks with Stochastic Dynamics
Ribeiro, A. S., Zhu, R., & Kauffman, S. A. (2006) · Journal of Computational Biology · doi:10.1089/cmb.2006.13.1630 · Cited by 127 · see citing works
Qualitative simulation of the carbon starvation response in Escherichia coli
Ropers, D., de Jong, H., Page, M., Schneider, D., & Geiselmann, J. (2005) · Biosystems · doi:10.1016/j.biosystems.2005.10.005 · Cited by 125 · see citing works
Papin, J. A., Price, N. D., Edwards, J. S., et al. (2002) · Journal of Theoretical Biology · doi:10.1006/jtbi.2001.2499 · Cited by 125 · see citing works
Studying genetic regulatory networks at the molecular level: Delayed reaction stochastic models
Zhu, R., Ribeiro, A. S., Salahub, D. R., & Kauffman, S. A. (2007) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2007.01.021 · Cited by 123 · see citing works
Hybrid simulation of cellular behavior
Kiehl, T. R., Mattheyses, R. M., & Simmons, M. K. (2004) · Bioinformatics · doi:10.1093/bioinformatics/btg409 · Cited by 122 · see citing works
Necessary conditions for multistationarity in discrete dynamical systems
Richard, A., & Comet, J. (2007) · Discrete Applied Mathematics · doi:10.1016/j.dam.2007.04.019 · Cited by 111 · see citing works
Circadian rhythms and molecular noise
Gonze, D., & Goldbeter, A. (2006) · Chaos An Interdisciplinary Journal of Nonlinear Science · doi:10.1063/1.2211767 · Cited by 109 · see citing works
Hellerstein, M. K. (2003) · Annual Review of Nutrition · doi:10.1146/annurev.nutr.23.011702.073045 · Cited by 108 · see citing works
Modeling gene regulatory networks with piecewise linear differential equations
Gebert, J., Radde, N. E., & Weber, G. (2006) · European Journal of Operational Research · doi:10.1016/j.ejor.2005.11.044 · Cited by 106 · see citing works
Bhattacharya, R. N., & Majumdar, M. (2007) · Cambridge University Press eBooks · doi:10.1017/cbo9780511618628 · Cited by 105 · see citing works
Matrix Formalism to Describe Functional States of Transcriptional Regulatory Systems
Gianchandani, E. P., Papin, J. A., Price, N. D., Joyce, A. R., & Palsson, B. Ø. (2006) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0020101 · Cited by 102 · see citing works
Metabolic Reconstruction and Modeling of Nitrogen Fixation in Rhizobium etli
Reséndis-Antonio, O., Reed, J. L., Encarnación‐Guevara, S., Collado‐Vides, J., & Palsson, B. Ø. (2007) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0030192 · Cited by 95 · see citing works
Inactivation of prophage λ repressor in Vivo
Bailone, A., Lévine, A., & Devoret, R. (1979) · Journal of Molecular Biology · doi:10.1016/0022-2836(79)90007-x · Cited by 92 · see citing works
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Simão, E., Rémy, É., Thieffry, D., et al. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti1130 · Cited by 87 · see citing works
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Yeang, C., Mak, H. C., McCuine, S., Workman, C. T., Jaakkola, T., & Ideker, T. E. (2005) · Genome biology · doi:10.1186/gb-2005-6-7-r62 · Cited by 83 · see citing works
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Barrett, C. L., & Palsson, B. Ø. (2006) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0020052 · Cited by 53 · see citing works
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VANDRIEL, R., & Fransz, P. F. (2004) · Experimental Cell Research · doi:10.1016/j.yexcr.2004.03.009 · Cited by 51 · see citing works
Dasika, M. S., GUPTA, A., & Maranas, C. D. (2003) · Pacific Symposium on Biocomputing (PSB) · doi:10.1142/9789812704856_0045 · Cited by 50 · see citing works
Tetko, I. V., Haberer, G., Rudd, S., et al. (2006) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0020021 · Cited by 50 · see citing works
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Li, Z., Shaw, S. M., Yedwabnick, M. J., et al. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btk034 · Cited by 44 · see citing works
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Ogden, S. K., Lee, K. C., Wernke-Dollries, K., Stratton, S. A., Aronow, B. J., & Barton, M. C. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.c100381200 · Cited by 42 · see citing works
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Yeang, C., & Vingron, M. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-332 · Cited by 41 · see citing works
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Gat‐Viks, I., Tanay, A., & Shamir, R. (2004) · Journal of Computational Biology · doi:10.1089/cmb.2004.11.1034 · Cited by 36 · see citing works
Self-citationIdentification of Primary Transcriptional Regulation of Cell Cycle-Regulated Genes upon DNA Damage
Zhou, T., Chou, J.-H., Mullen, T. E., Elkon, R., Zhou, Y., Simpson, D. A., Bushel, P. R., Paules, R. S., Lobenhofer, E. K., Hurban, P., et al. (2007) · Cell Cycle · doi:10.4161/cc.6.8.4106 · Cited by 25 · see citing works
Ness, S. A. (2006) · Humana Press eBooks · doi:10.1385/1-59259-964-8:13 · Cited by 20 · see citing works
Koch, I., Schueler, M., & Heiner, M. (2005) · PubMed · Cited by 17 · see citing works
Niemitalo, O., Neubauer, A., Liebal, U. W., et al. (2005) · Journal of Biotechnology · doi:10.1016/j.jbiotec.2005.05.028 · Cited by 14 · see citing works
Connecting quantitative regulatory-network models to the genome
Pan, Y., Durfee, T., Bockhorst, J. P., & Craven, M. W. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm228 · Cited by 14 · see citing works
A Topographical Map of Spatiotemporal Patterns of Gene Expression
Furlong, E. E. M. (2008) · Developmental Cell · doi:10.1016/j.devcel.2008.04.007 · Cited by 2 · see citing works
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Revealing the vectors of cellular identity with single-cell genomics
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Fiers, M. W. E. J., Minnoye, L., Aibar, S., Bravo González-Blas, C., Kalender Atak, Z., & Aerts, S. (2018) · Briefings in Functional Genomics · doi:10.1093/bfgp/elx046 · Cited by 235 · see citing works
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Machado, D., Costa, R. S., Rocha, M., Ferreira, E. C., Tidor, B., & Rocha, I. (2011) · AMB Express · doi:10.1186/2191-0855-1-45 · Cited by 189 · see citing works
Palma, A., Jarrah, A. S., Tieri, P., Cesareni, G., & Castiglione, F. (2018) · Frontiers in Physiology · doi:10.3389/fphys.2018.01659 · Cited by 122 · see citing works
The evolutionary origins of hierarchy
Mengistu, H., Huizinga, J., Mouret, J.-B., & Clune, J. (2016) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1004829 · Cited by 115 · see citing works
Efficient reverse-engineering of a developmental gene regulatory network
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Network modeling of single-cell omics data: challenges, opportunities, and progresses
Blencowe, M., Arneson, D., Ding, J., Chen, Y.-W., Saleem, Z., & Yang, X. (2019) · Emerging Topics in Life Sciences · doi:10.1042/etls20180176 · Cited by 73 · see citing works
A blueprint for human whole-cell modeling
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Statistical physics of liquid brains
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- Authors
- Karlebach, G., & Shamir, R.
- Affiliations
- Tel Aviv University (IL)
- ORCID
- Karlebach, Guy
- Venue
- Nature Reviews Molecular Cell Biology
- Published
- 2008-09-17
- Volume
- 9
- Issue
- 10
- Pages
- 770-780
- ISSN
- 1471-0072 (ISSN-L)
- 1471-0080
- OpenAlex
- W2062029454
- Cited by
- 1,296
- References
- 144
- Citations by year
- 2026: 64 · 2025: 94 · 2024: 99 · 2023: 82 · 2022: 84 · 2021: 78 · 2020: 68 · 2019: 68 · 2018: 76 · 2017: 95 · 2016: 77 · 2015: 93 · 2014: 64 · 2013: 70 · 2012: 56
- FWCI
- 3.30
- Type
- journal article
- Language
- en
- Open access
- green
- zenodo.org
- Licence
- other-oa
- www.springer.com/tdm (tdm)
- Locations
- Nature Reviews Molecular Cell Biology (publishedVersion)
- PubMed (publishedVersion)
- Zenodo (CERN European Organization for Nuclear Research) (submittedVersion, other-oa)
- Funders
- Tel Aviv University
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- gene regulatory networks, network modeling, network dynamics, cell differentiation, cell cycle, signal transduction, metabolism, disease mechanisms
- MeSH terms
- Algorithms, Animals, Humans, Mathematics, Models, Biological, Models, Genetic, Bacteriophage lambda, Stochastic Processes, Transcription Factors, Models, Statistical, Linear Models, Gene Regulatory Networks
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 ›
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