Computational systems biology.

Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings 1PII of original article: S0169-409X(96)00423-1. The article was originally published in Advanced Drug Delivery Reviews 23 (1997) 3–25. 1

Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (2001) · Advanced Drug Delivery Reviews · doi:10.1016/s0169-409x(00)00129-0 · Cited by 18,139 · 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

Surfing the p53 network

Vogelstein, B., Lane, D., & Levine, A. J. (2000) · Nature · doi:10.1038/35042675 · Cited by 6,607 · see citing works

Cybernetics. Or Control and Communication in the Animal and the Machine

N., E., & Wiener, N. (1949) · The Journal of Philosophy · doi:10.2307/2020260 · Cited by 3,590 · see citing works

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

Biological robustness

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

Universally Sloppy Parameter Sensitivities in Systems Biology Models

Gutenkunst, R. N., Waterfall, J. J., Casey, F. P., Brown, K. S., Myers, C. R., & Sethna, J. P. (2007) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0030189 · Cited by 1,261 · see citing works

A Comprehensive Survey of Recent Advancements in Molecular Communication

Farsad, N., Yilmaz, H. B., Eckford, A., Chae, C.-B., & Guo, W. (2016) · IEEE Communications Surveys & Tutorials · doi:10.1109/comst.2016.2527741 · Cited by 968 · see citing works

Minimum information requested in the annotation of biochemical models (MIRIAM)

Novère, N. L., Finney, A., Hucka, M., Bhalla, U. S., Campagne, F., Collado-Vides, J., Crampin, E. J., Halstead, M., Klipp, E., Mendes, P., et al. (2005) · Nature Biotechnology · doi:10.1038/nbt1156 · Cited by 622 · see citing works

Bifurcation dynamics in lineage-commitment in bipotent progenitor cells

Huang, S., Guo, Y.-P., May, G., & Enver, T. (2007) · Developmental Biology · doi:10.1016/j.ydbio.2007.02.036 · Cited by 560 · see citing works

Here is the evidence, now what is the hypothesis? The complementary roles of inductive and hypothesis‐driven science in the post‐genomic era

Kell, D. B., & Oliver, S. G. (2004) · BioEssays · doi:10.1002/bies.10385 · Cited by 535 · see citing works

Metabolomics and systems biology: making sense of the soup

KELL, D. (2004) · Current Opinion in Microbiology · doi:10.1016/j.mib.2004.04.012 · Cited by 529 · see citing works

Sobol Sensitivity Analysis: A Tool to Guide the Development and Evaluation of Systems Pharmacology Models

Zhang, X., Trame, M., Lesko, L., & Schmidt, S. (2015) · CPT: Pharmacometrics & Systems Pharmacology · doi:10.1002/psp4.6 · Cited by 467 · see citing works

Cancer as a robust system: implications for anticancer therapy

Kitano, H. (2004) · Nature reviews. Cancer · doi:10.1038/nrc1300 · Cited by 456 · see citing works

Exercise benefits on Alzheimer’s disease: State-of-the-science

Valenzuela, P. L., Castillo-García, A., Morales, J. S., de la Villa, P., Hampel, H., Emanuele, E., Lista, S., & Lucia, A. (2020) · Ageing Research Reviews · doi:10.1016/j.arr.2020.101108 · Cited by 337 · see citing works

A Logical Model Provides Insights into T Cell Receptor Signaling

Saez-Rodriguez, J., Simeoni, L., Lindquist, J. A., Hemenway, R., Bommhardt, U., Arndt, B., Haus, U.-U., Weismantel, R., Gilles, E. D., Klamt, S., et al. (2007) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0030163 · Cited by 352 · see citing works

Function of C/EBPδ in a regulatory circuit that discriminates between transient and persistent TLR4-induced signals

Litvak, V., Ramsey, S. A., Rust, A. G., Zak, D. E., Kennedy, K. A., Lampano, A. E., Nykter, M., Shmulevich, I., & Aderem, A. (2009) · Nature Immunology · doi:10.1038/ni.1721 · Cited by 295 · see citing works

Bayesian parameter inference for stochastic biochemical network models using particle Markov chain Monte Carlo

Golightly, A., & Wilkinson, D. J. (2011) · Interface Focus · doi:10.1098/rsfs.2011.0047 · Cited by 282 · see citing works

Bacterial adaptation through distributed sensing of metabolic fluxes

Kotte, O., Zaugg, J. B., & Heinemann, M. (2010) · Molecular Systems Biology · doi:10.1038/msb.2010.10 · Cited by 260 · see citing works

Systems Biology of Metabolism

Nielsen, J. (2017) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-061516-044757 · Cited by 252 · see citing works

Bayesian methods in bioinformatics and computational systems biology

Wilkinson, D. J. (2006) · Briefings in Bioinformatics · doi:10.1093/bib/bbm007 · Cited by 230 · see citing works

Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria

Farasat, I., Kushwaha, M., Collens, J., Easterbrook, M., Guido, M., & Salis, H. M. (2014) · Molecular Systems Biology · doi:10.15252/msb.20134955 · Cited by 235 · see citing works

A complex systems approach to aging biology

Cohen, A. A., Ferrucci, L., Fülöp, T., Gravel, D., Hao, N., Kriete, A., Levine, M. E., Lipsitz, L. A., Olde Rikkert, M. G. M., Rutenberg, A., et al. (2022) · Nature Aging · doi:10.1038/s43587-022-00252-6 · Cited by 221 · see citing works

Systematic reviews of animal models: methodology versus epistemology

Greek, R., & Menache, A. (2013) · International Journal of Medical Sciences · doi:10.7150/ijms.5529 · Cited by 207 · see citing works

Sensitivity analysis methods in the biomedical sciences

Qian, G., & Mahdi, A. (2020) · Mathematical Biosciences · doi:10.1016/j.mbs.2020.108306 · Cited by 169 · 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

Optimal Experimental Design for Parameter Estimation of a Cell Signaling Model

Bandara, S., Schlöder, J. P., Eils, R., Bock, H. G., & Meyer, T. (2009) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000558 · Cited by 135 · see citing works

Systems biology: model based evaluation and comparison of potential explanations for given biological data

Cedersund, G., & Roll, J. (2009) · The FEBS Journal · doi:10.1111/j.1742-4658.2008.06845.x · Cited by 127 · see citing works

PEtab—Interoperable specification of parameter estimation problems in systems biology

Schmiester, L., Schälte, Y., Bergmann, F. T., Camba, T., Dudkin, E., Egert, J., Fröhlich, F., Fuhrmann, L., Hauber, A. L., Kemmer, S., et al. (2021) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1008646 · Cited by 96 · see citing works

Conclusions via unique predictions obtained despite unidentifiability—new definitions and a general method

Cedersund, G. (2012) · The FEBS Journal · doi:10.1111/j.1742-4658.2012.08725.x · Cited by 81 · see citing works

Dissecting the energy metabolism in Mycoplasma pneumoniae through genome-scale metabolic modeling

Wodke, J. A. H., Puchałka, J., Lluch‐Senar, M., Marcos, J., Yus, E., Godinho, M., Gutiérrez‐Gallego, R., dos Santos, V. A. P. M., Serrano, L., Klipp, E., et al. (2013) · Molecular Systems Biology · doi:10.1038/msb.2013.6 · Cited by 89 · see citing works

Connecting a Connectome to Behavior: An Ensemble of Neuroanatomical Models of C. elegans Klinotaxis

Izquierdo, E. J., & Beer, R. D. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002890 · Cited by 84 · see citing works

Inference of complex biological networks: distinguishability issues and optimization-based solutions

Szederkényi, G., Banga, J. R., & Alonso, A. A. (2011) · BMC Systems Biology · doi:10.1186/1752-0509-5-177 · Cited by 78 · 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

Primer on Medical Genomics Part XIV: Introduction to Systems Biology—A New Approach to Understanding Disease and Treatment

Morel, N. M., Holland, J. M., van der Greef, J., Marple, E. W., Clish, C., Loscalzo, J., & Naylor, S. (2004) · Mayo Clinic Proceedings · doi:10.4065/79.5.651 · Cited by 71 · see citing works

Applicability Analysis of Validation Evidence for Biomedical Computational Models

Pathmanathan, P., Gray, R. A., Romero, V. J., & Morrison, T. M. (2017) · Journal of Verification Validation and Uncertainty Quantification · doi:10.1115/1.4037671 · Cited by 68 · see citing works

Parameter identifiability of power-law biochemical system models

Srinath, S., & Gunawan, R. (2010) · Journal of Biotechnology · doi:10.1016/j.jbiotec.2010.02.019 · Cited by 68 · see citing works

Systems interface biology

Doyle, F. J., & Stelling, J. (2006) · Journal of The Royal Society Interface · doi:10.1098/rsif.2006.0143 · Cited by 60 · see citing works

Extend mixed models to multilayer neural networks for genomic prediction including intermediate omics data

Zhao, T., Zeng, J., & Cheng, H. (2022) · Genetics · doi:10.1093/genetics/iyac034 · Cited by 52 · see citing works

When the Optimal Is Not the Best: Parameter Estimation in Complex Biological Models

Fernández Slezak, D., Suárez, C., Cecchi, G. A., Marshall, G., & Stolovitzky, G. (2010) · PLoS ONE · doi:10.1371/journal.pone.0013283 · Cited by 57 · see citing works

Systems biology in neuroscience: bridging genes to cognition

Grant, S. G. (2003) · Current Opinion in Neurobiology · doi:10.1016/j.conb.2003.09.016 · Cited by 53 · see citing works

Systems analysis of cellular networks under uncertainty

Kaltenbach, H.-M., Dimopoulos, S., & Stelling, J. (2009) · FEBS Letters · doi:10.1016/j.febslet.2009.10.074 · Cited by 40 · see citing works

How difficult is inference of mammalian causal gene regulatory networks?

Djordjevic, D., Yang, A., Zadoorian, A., Rungrugeecharoen, K., & Ho, J. W. K. (2014) · PLoS ONE · doi:10.1371/journal.pone.0111661 · Cited by 29 · see citing works

Parameter adaptations during phenotype transitions in progressive diseases

Tiemann, C. A., Vanlier, J., Hilbers, P. A., & van Riel, N. A. (2011) · BMC Systems Biology · doi:10.1186/1752-0509-5-174 · Cited by 22 · see citing works

A Network Approach to Wound Healing

Arodz, T., Bonchev, D., & Diegelmann, R. F. (2013) · Advances in Wound Care · doi:10.1089/wound.2012.0386 · Cited by 22 · see citing works

Inferring catalysis in biological systems

Kondofersky, I., Theis, F. J., & Fuchs, C. (2016) · IET Systems Biology · doi:10.1049/iet-syb.2015.0087 · Cited by 1 · see citing works