From molecular to modular cell biology.

A quantitative description of membrane current and its application to conduction and excitation in nerve

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Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA Microarray

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Escherichia coli and Salmonella :cellular and molecular biology

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More Is Different: Broken symmetry and the nature of the hierarchical structure of science.

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Evolution and Tinkering

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Exploring the new world of the genome with DNA microarrays

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From Levinthal to pathways to funnels

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CYCLIN-DEPENDENT KINASES: Engines, Clocks, and Microprocessors

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More Is Different: Broken symmetry and the nature of the hierarchical structure of science.

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Parallel Networks that Learn to Pronounce English Text

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Robustness in simple biochemical networks

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Evolvability

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MAP kinase pathways in yeast: For mating and more

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Self-organization of microtubules into bipolar spindles around artificial chromosomes in Xenopus egg extracts

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Protein molecules as computational elements in living cells

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Controlling Cell Chemistry with Caged Compounds

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Circuit Simulation of Genetic Networks

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Construction of artificial chromosomes in yeast

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How the λ repressor and cro work

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Real-time visualization of cell cycle-dependent changes in microtubule dynamics in cytoplasmic extracts

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LYSOGENY

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THE LYSIS-LYSOGENY DECISION OF PHAGE λ: EXPLICIT PROGRAMMING AND RESPONSIVENESS

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The coming Kuhnian revolution in biology

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Specific Binding of the λ Phage Repressor to λ DNA

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Sensory transduction in Escherichia coli : Role of a protein methylation reaction in sensory adaptation

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The C-terminus of the S. cerevisiae α-pheromone receptor mediates an adaptive response to pheromone

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Signal transduction by MAP kinase cascades in budding yeast

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Pleiotropy and the Preservation of Perfection

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Okadaic acid induces interphase to mitotic-like microtubule dynamic instability by inactivating rescue.

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Unscrambling the puzzle of biological machines: The importance of the details

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The Limits of Reductionism in Biology

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Physics, Computation, and Why Biology Looks so Different

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Genome System Architecture and Natural Genetic Engineering in Evolution

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A Physicist Looks at Bacterial ChemotaxisPreprint

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Slow and incomplete inactivations of voltage-gated channels dominate encoding in synthetic neurons

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Network biology: understanding the cell's functional organization

Barabási, A.-L., & Oltvai, Z. N. (2004) · Nature Reviews Genetics · doi:10.1038/nrg1272 · Cited by 7,903 · see citing works

Error and attack tolerance of complex networks

Albert, R., Jeong, H., & Barabási, A.-L. (2000) · Nature · doi:10.1038/35019019 · Cited by 7,534 · see citing works

A General Framework for Weighted Gene Co-Expression Network Analysis

Zhang, B., & Horvath, S. (2005) · Statistical Applications in Genetics and Molecular Biology · doi:10.2202/1544-6115.1128 · Cited by 5,684 · see citing works

Network medicine: a network-based approach to human disease

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Hierarchical Organization of Modularity in Metabolic Networks

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The Large-Scale Organization of Metabolic Networks

Jeong, H., Tombor, B., Albert, R., Oltvai, Z. N., & Barabási, A.-L. (2000) · Nature · doi:10.1038/35036627 · Cited by 4,972 · see citing works

Functional cartography of complex metabolic networks

Guimerà, R., & Nunes Amaral, L. A. (2005) · Nature · doi:10.1038/nature03288 · Cited by 3,983 · see citing works

BioGRID: a general repository for interaction datasets

Stark, C. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkj109 · Cited by 3,960 · see citing works

Resolution limit in community detection

Fortunato, S., & Barthélemy, M. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0605965104 · Cited by 3,024 · see citing works

Biological robustness

Kitano, H. (2004) · Nature Reviews Genetics · doi:10.1038/nrg1471 · Cited by 2,278 · 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

Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell

Tyson, J. J., Chen, K. C., & Novak, B. (2003) · Current Opinion in Cell Biology · doi:10.1016/s0955-0674(03)00017-6 · Cited by 1,583 · see citing works

Reverse engineering of biological complexity

Csete, M. E., & Doyle, J. C. (2002) · Science · doi:10.1126/science.1069981 · Cited by 1,215 · see citing works

Flexible nets: The roles of intrinsic disorder in protein interaction networks

Dunker, A. K., Cortese, M. S., Romero, P., Iakoucheva, L. M., & Uversky, V. N. (2005) · The FEBS Journal · doi:10.1111/j.1742-4658.2005.04948.x · Cited by 1,122 · see citing works

Robustness of cellular functions

Stelling, J., Sauer, U., Szallasi, Z., Doyle, F. J., & Doyle, J. (2004) · Cell · doi:10.1016/j.cell.2004.09.008 · Cited by 1,049 · see citing works

Initial impact of the sequencing of the human genome

Lander, E. S. (2011) · Nature · doi:10.1038/nature09792 · Cited by 1,044 · see citing works

Control, exploitation and tolerance of intracellular noise

Rao, C. V., Wolf, D. M., & Arkin, A. P. (2002) · Nature · doi:10.1038/nature01258 · Cited by 1,006 · see citing works

Performance of modularity maximization in practical contexts

Good, B. H., de Montjoye, Y.-A., & Clauset, A. (2010) · Physical Review E · doi:10.1103/physreve.81.046106 · Cited by 937 · see citing works

Eigengene networks for studying the relationships between co-expression modules

Langfelder, P., & Horvath, S. (2007) · BMC Systems Biology · doi:10.1186/1752-0509-1-54 · Cited by 867 · see citing works

Modularity from fluctuations in random graphs and complex networks

Guimerà, R., Sales-Pardo, M., & Amaral, L. A. N. (2004) · Physical Review E · doi:10.1103/physreve.70.025101 · Cited by 894 · see citing works

Variations in DNA elucidate molecular networks that cause disease

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The origin and evolution of cell types

Arendt, D., Musser, J. M., Baker, C. V. H., Bergman, A., Cepko, C., Erwin, D. H., Pavlicev, M., Schlosser, G., Widder, S., Laubichler, M. D., et al. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.127 · Cited by 764 · see citing works

Showing your ID: intrinsic disorder as an ID for recognition, regulation and cell signaling

Uversky, V. N., Oldfield, C. J., & Dunker, A. K. (2005) · Journal of Molecular Recognition · doi:10.1002/jmr.747 · Cited by 847 · see citing works

Protein networks in disease

Ideker, T., & Sharan, R. (2008) · Genome Research · doi:10.1101/gr.071852.107 · Cited by 817 · 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

Biological networks: the tinkerer as an engineer

Alon, U. (2003) · Science · doi:10.1126/science.1089072 · Cited by 706 · see citing works

Conservation and evolution of gene coexpression networks in human and chimpanzee brains

Oldham, M. C., Horvath, S., & Geschwind, D. H. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0605938103 · Cited by 566 · see citing works

Modular epistasis in yeast metabolism

Segrè, D., DeLuna, A., Church, G. M., & Kishony, R. (2005) · Nature Genetics · doi:10.1038/ng1489 · Cited by 575 · see citing works

Modular cell biology: retroactivity and insulation

Del Vecchio, D., Ninfa, A. J., & Sontag, E. D. (2008) · Molecular Systems Biology · doi:10.1038/msb4100204 · Cited by 519 · see citing works

Integrative approaches for finding modular structure in biological networks

Mitra, K., Carvunis, A.-R., Ramesh, S. K., & Ideker, T. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3552 · Cited by 535 · see citing works

Nova regulates brain-specific splicing to shape the synapse

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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

Integrating Genetic and Network Analysis to Characterize Genes Related to Mouse Weight

Ghazalpour, A., Doss, S., Zhang, B., Wang, S., Plaisier, C., Castellanos, R., Brozell, A., Schadt, E. E., Drake, T. A., Lusis, A. J., et al. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020130 · Cited by 462 · see citing works

Transcriptional Architecture of Synaptic Communication Delineates GABAergic Neuron Identity

Paul, A., Crow, M., Raudales, R., He, M., Gillis, J., & Huang, Z. J. (2017) · Cell · doi:10.1016/j.cell.2017.08.032 · Cited by 421 · see citing works

Revealing modular architecture of human brain structural networks by using cortical thickness from MRI

Chen, Z. J., He, Y., Rosa-Neto, P., Germann, J., & Evans, A. C. (2008) · Cerebral Cortex · doi:10.1093/cercor/bhn003 · Cited by 484 · see citing works

Brain reward circuitry beyond the mesolimbic dopamine system: a neurobiological theory

Ikemoto, S. (2010) · Neuroscience & Biobehavioral Reviews · doi:10.1016/j.neubiorev.2010.02.001 · Cited by 454 · see citing works

Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks

Wolfe, C. J., Kohane, I. S., & Butte, A. J. (2005) · BMC Bioinformatics · doi:10.1186/1471-2105-6-227 · Cited by 422 · see citing works

Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system

Collins, B. C., Gillet, L. C., Rosenberger, G., Röst, H. L., Vichalkovski, A., Gstaiger, M., & Aebersold, R. (2013) · Nature Methods · doi:10.1038/nmeth.2703 · Cited by 314 · see citing works

Motifs, modules and games in bacteria

Wolf, D. M., & Arkin, A. P. (2003) · Current Opinion in Microbiology · doi:10.1016/s1369-5274(03)00033-x · Cited by 303 · see citing works

EpiFactors: a comprehensive database of human epigenetic factors and complexes

Medvedeva, Y. A., Lennartsson, A., Ehsani, R., Kulakovskiy, I. V., Vorontsov, I. E., Panahandeh, P., Khimulya, G., Kasukawa, T., The FANTOM Consortium, & Drabløs, F. (2015) · Database · doi:10.1093/database/bav067 · Cited by 298 · see citing works

Programmable on-chip DNA compartments as artificial cells

Karzbrun, E., Tayar, A. M., Noireaux, V., & Bar-Ziv, R. H. (2014) · Science · doi:10.1126/science.1255550 · Cited by 264 · see citing works

More than the sum of their parts: On the evolution of proteins from peptides

Söding, J., & Lupas, A. N. (2003) · BioEssays · doi:10.1002/bies.10321 · Cited by 252 · see citing works

The diversity of GABAergic neurons and neural communication elements

Huang, Z. J., & Paul, A. (2019) · Nature Reviews Neuroscience · doi:10.1038/s41583-019-0195-4 · Cited by 201 · see citing works

Phenotypic convergence: distinct transcription factors regulate common terminal features

Konstantinides, N., Kapuralin, K., Fadil, C., Barboza, L., Satija, R., & Desplan, C. (2018) · Cell · doi:10.1016/j.cell.2018.05.021 · Cited by 226 · see citing works

A genome-wide atlas of co-essential modules assigns function to uncharacterized genes

Wainberg, M., Kamber, R. A., Balsubramani, A., Meyers, R. M., Sinnott-Armstrong, N., Hornburg, D., Jiang, L., Chan, J., Jian, R., Gu, M., et al. (2021) · Nature Genetics · doi:10.1038/s41588-021-00840-z · Cited by 204 · see citing works

Modeling formalisms in Systems Biology

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

Protein Homeostasis and the Phenotypic Manifestation of Genetic Diversity: Principles and Mechanisms

Jarosz, D. F., Taipale, M., & Lindquist, S. (2010) · Annual Review of Genetics · doi:10.1146/annurev.genet.40.110405.090412 · Cited by 179 · see citing works

Some new directions in control theory inspired by systems biology

Sontag, E. D. (2004) · Systems Biology · doi:10.1049/sb:20045006 · Cited by 171 · see citing works

Mathematical models in microbial systems biology

Stelling, J. (2004) · Current Opinion in Microbiology · doi:10.1016/j.mib.2004.08.004 · Cited by 164 · see citing works

Response Delays and the Structure of Transcription Networks

Rosenfeld, N., & Alon, U. (2003) · Journal of Molecular Biology · doi:10.1016/s0022-2836(03)00506-0 · Cited by 148 · see citing works

Complex‐centric proteome profiling by SEC‐SWATH‐MS

Heusel, M., Bludau, I., Rosenberger, G., Hafen, R., Frank, M., Banaei‐Esfahani, A., van Drogen, A., Collins, B. C., Gstaiger, M., & Aebersold, R. (2019) · Molecular Systems Biology · doi:10.15252/msb.20188438 · Cited by 141 · see citing works

Hierarchical modularity of nested bow-ties in metabolic networks

Zhao, J., Yu, H., Luo, J.-H., Cao, Z.-W., & Li, Y.-X. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-386 · Cited by 128 · see citing works

Hot-spot analysis for drug discovery targeting protein-protein interactions

Rosell, M., & Fernández-Recio, J. (2018) · Expert Opinion on Drug Discovery · doi:10.1080/17460441.2018.1430763 · Cited by 105 · see citing works

Spontaneous emergence of modularity in cellular networks

Solé, R. V., & Valverde, S. (2008) · Journal of The Royal Society Interface · doi:10.1098/rsif.2007.1108 · Cited by 102 · see citing works

Network-based characterization of drug-regulated genes, drug targets, and toxicity

Kotlyar, M., Fortney, K., & Jurisica, I. (2012) · Methods · doi:10.1016/j.ymeth.2012.06.003 · Cited by 92 · see citing works

The Origin of Prebiotic Information System in the Peptide/RNA World: A Simulation Model of the Evolution of Translation and the Genetic Code

Chatterjee, S., & Yadav, S. (2019) · Life · doi:10.3390/life9010025 · Cited by 80 · see citing works

Systems biology—an engineering perspective

Kremling, A., & Saez-Rodriguez, J. (2007) · Journal of Biotechnology · doi:10.1016/j.jbiotec.2007.02.009 · Cited by 76 · see citing works

Tissue Biology: In Search of a New Paradigm

Adler, M., Chavan, A. R., & Medzhitov, R. (2023) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-120420-113830 · Cited by 40 · see citing works

Systems biology: from physiology to gene regulation

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Networks of Networks: An Essay on Multi-Level Biological Organization

Uversky, V. N., & Giuliani, A. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.706260 · Cited by 28 · see citing works

D-SPIN constructs gene regulatory network models from multiplexed scRNA-seq data revealing organizing principles of cellular perturbation response

Jiang, J., Chen, S., Tsou, T., McGinnis, C. S., Khazaei, T., Zhu, Q., Park, J. H., Strazhnik, I.-M., Vielmetter, J., Gong, Y., et al. (2023) · doi:10.1101/2023.04.19.537364 · Cited by 21 · see citing works

Convergent Evolutionary Paths in Biological and Technological Networks

Solé, R. V., Valverde, S., & Rodriguez-Caso, C. (2011) · Evolution: Education and Outreach · doi:10.1007/s12052-011-0346-1 · Cited by 20 · see citing works

Thoroughly Calibrated Modular Agent-Based Model of the Human Cardiovascular and Renal Systems for Blood Pressure Regulation in Health and Disease

Kutumova, E., Kiselev, I., Sharipov, R., Lifshits, G., & Kolpakov, F. (2021) · Frontiers in Physiology · doi:10.3389/fphys.2021.746300 · Cited by 16 · see citing works

Network spectra for drug-target identification in complex diseases: new guns against old foes

Rai, A., Shinde, P., & Jalan, S. (2018) · Applied Network Science · doi:10.1007/s41109-018-0107-y · Cited by 12 · see citing works

Modular modeling of biological systems.

Kiselev, I., & Kolpakov, F. (2013) · Virtual Biology · doi:10.12704/vb/e11 · Cited by 4 · see citing works

A Synthetic Post-transcriptional Controller To Explore the Modular Design of Gene Circuits

Ceroni, F., Furini, S., Stefan, A., et al. (2012) · ACS Synthetic Biology · doi:10.1021/sb200021s · Cited by 18 · see citing works

Systems Biology as an Integrated Platform for Bioinformatics, Systems Synthetic Biology, and Systems Metabolic Engineering

Chen, B., & Wu, C. (2013) · Cells · doi:10.3390/cells2040635 · Cited by 53 · see citing works

Synthetic biology and regulatory networks: where metabolic systems biology meets control engineering

He, F., Murabito, E., & Westerhoff, H. V. (2016) · Journal of The Royal Society Interface · doi:10.1098/rsif.2015.1046 · Cited by 67 · see citing works

Industrial systems biology and its impact on synthetic biology of yeast cell factories

Fletcher, E., Krivoruchko, A., & Nielsen, J. (2015) · Biotechnology and Bioengineering · doi:10.1002/bit.25870 · Cited by 46 · see citing works

Systems biology, synthetic biology, and metabolic engineering

Xu, X., Liu, Y., Du, G., & Liu, L. (2020) · Elsevier eBooks · doi:10.1016/b978-0-12-821753-5.00001-0 · Cited by 4 · see citing works