International alliances for quantitative modeling in systems biology

Toxicity Testing in the 21st Century: A Vision and a Strategy

Krewski, D. R., Acosta, D., Andersen, M. E., Anderson, H. A., Bailar, J. C., Boekelheide, K., Brent, R., Charnley, G., Cheung, V. G., Green, S., et al. (2010) · Journal of Toxicology and Environmental Health Part B · doi:10.1080/10937404.2010.483176 · Cited by 1,696 · see citing works

Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood

Raue, A., Kreutz, C., Maiwald, T., Bachmann, J., Schilling, M., Klingmüller, U., & Timmer, J. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp358 · Cited by 1,442 · see citing works

Biomodels database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems

Le Novere, N. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkj092 · Cited by 762 · see citing works

Unveiling the role of network and systems biology in drug discovery

Pujol, A., Mosca, R., Farrés, J., & Aloy, P. (2010) · Trends in Pharmacological Sciences · doi:10.1016/j.tips.2009.11.006 · Cited by 343 · see citing works

Reverse engineering and identification in systems biology: strategies, perspectives and challenges

Villaverde, A. F., & Banga, J. R. (2014) · Journal of The Royal Society Interface · doi:10.1098/rsif.2013.0505 · Cited by 229 · see citing works

Measuring enzyme activities under standardized in vivo ‐like conditions for systems biology

van Eunen, K., Bouwman, J., Daran-Lapujade, P. A. S., Postmus, J., Canelas, A. B., Mensonides, F. I. C., Orij, R., Tüzün, I., van den Brink, J., Smits, G. J., et al. (2010) · FEBS Journal · doi:10.1111/j.1742-4658.2009.07524.x · Cited by 178 · see citing works

RIP1-dependent linear and nonlinear recruitments of caspase-8 and RIP3 respectively to necrosome specify distinct cell death outcomes

Li, X., Zhong, C., Wu, R., Xu, X., Yang, Z., Cai, S., Wu, X., Chen, X., Yin, Z., He, Q., et al. (2021) · Protein & Cell · doi:10.1007/s13238-020-00810-x · Cited by 116 · see citing works

Kinetic modelling of plant metabolic pathways

Rohwer, J. M. (2012) · Journal of Experimental Botany · doi:10.1093/jxb/ers080 · Cited by 106 · see citing works

Computational approaches to the topology, stability and dynamics of metabolic networks

Steuer, R. (2007) · Phytochemistry · doi:10.1016/j.phytochem.2007.04.041 · Cited by 88 · see citing works

Computational Models of Metabolism: Stability and Regulation in Metabolic Networks

Steuer, R., & Junker, B. H. (2008) · Advances in chemical physics · doi:10.1002/9780470475935.ch3 · Cited by 76 · see citing works

Auxin transport and gravitational research: perspectives

Palme, K. J., Dovzhenko, A., & Ditengou, F. A. (2006) · PROTOPLASMA · doi:10.1007/s00709-006-0216-9 · Cited by 51 · see citing works

From genomes to systems: the path with yeast

Oliver, S. G. (2006) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2005.1805 · Cited by 46 · see citing works

Circular permutation of ligand‐binding module improves dynamic range of genetically encoded FRET‐based nanosensor

Okada, S., Ota, K., & Ito, T. (2009) · Protein Science · doi:10.1002/pro.266 · Cited by 43 · see citing works

Metabolite channeling and compartmentation in the human cell line AGE1.HN determined by 13C labeling experiments and 13C metabolic flux analysis

Niklas, J., Sandig, V., & Heinzle, E. (2011) · Journal of Bioscience and Bioengineering · doi:10.1016/j.jbiosc.2011.07.021 · Cited by 40 · see citing works

Modeling and simulation in signal transduction pathways: a systems biology approach

SURESHBABU, C., JOOSONG, E., & YOO, Y. (2005) · Biochimie · doi:10.1016/j.biochi.2005.08.006 · Cited by 33 · see citing works

Computational modeling with forward and reverse engineering links signaling network and genomic regulatory responses: NF-κB signaling-induced gene expression responses in inflammation

Peng, S. C., Wong, D. S., Tung, K.-C., Chen, Y. Y., Chao, C., Peng, C.-H., Chuang, Y., & Tang, C. Y. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-308 · Cited by 29 · see citing works

Identifying and characterising regulatory metabolites with generalised supply–demand analysis

Rohwer, J. M., & Hofmeyr, J. S. (2007) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2007.10.032 · Cited by 28 · see citing works

Long-term prediction of fish growth under varying ambient temperature using a multiscale dynamic model

Bar, N., & Radde, N. E. (2009) · BMC Systems Biology · doi:10.1186/1752-0509-3-107 · Cited by 24 · see citing works

Ins and Outs of Systems Biology vis-à-vis Molecular Biology: Continuation or Clear Cut?

Backer, P. D., Waele, D. D., & Speybroeck, L. V. (2009) · Acta Biotheoretica · doi:10.1007/s10441-009-9089-6 · Cited by 23 · see citing works

Systems pharmacology of the nerve growth factor pathway: use of a systems biology model for the identification of key drug targets using sensitivity analysis and the integration of physiology and pharmacology

Benson, N., Matsuura, T., Smirnov, S., Demin, O., Jones, H. M., Dua, P., & van der Graaf, P. H. (2013) · Interface Focus · doi:10.1098/rsfs.2012.0071 · Cited by 20 · see citing works

Computational Tools for Modeling Protein Networks

Bergmann, F., Vallabhajosyula, R. R., & Sauro, H. M. (2006) · Current Proteomics · doi:10.2174/157016406779475380 · Cited by 19 · see citing works

Introducing Computational Systems Biology

Kriete, A., & Eils, R. (2006) · Elsevier eBooks · doi:10.1016/b978-012088786-6/50020-4 · Cited by 15 · see citing works

A new regulatory principle for in vivo biochemistry: Pleiotropic low affinity regulation by the adenine nucleotides – Illustrated for the glycolytic enzymes of Saccharomyces cerevisiae

Mensonides, F. I. C., Bakker, B. M., Crémazy, F. G. E., Messiha, H. L., Mendes, P., Boogerd, F. C., & Westerhoff, H. V. (2013) · FEBS Letters · doi:10.1016/j.febslet.2013.07.013 · Cited by 14 · see citing works

Workflow for Data Analysis in Experimental and Computational Systems Biology: Using Python as ‘Glue’

Badenhorst, M., Barry, C. J., Swanepoel, C. J., van Staden, C. T., Wissing, J., & Rohwer, J. M. (2019) · Processes · doi:10.3390/pr7070460 · Cited by 13 · see citing works

A Mechanistic Site-Of-Action Model: A Tool for Informing Right Target, Right Compound, And Right Dose for Therapeutic Antagonistic Antibody Programs

Kapitanov, G., Chabot, J., Narula, J., Roy, M., Neubert, H., Palandra, J., Farrokhi, V., Johnson, J. S., Webster, R., & Jones, H. M. (2021) · Frontiers in Bioinformatics · doi:10.3389/fbinf.2021.731340 · Cited by 8 · see citing works

Systems Biology of the Endoplasmic Reticulum Stress Response

Caruso, M.-E., & Chevet, É. (2007) · Springer eBooks · doi:10.1007/978-1-4020-5943-8_13 · Cited by 8 · see citing works

Understanding Complex Regulatory Systems: Integrating Molecular Biology and Systems Analysis

Bocharov, G. A. (2005) · Transfusion Medicine and Hemotherapy · doi:10.1159/000089117 · Cited by 8 · see citing works

Algorithmic algebraic model checking: hybrid automata and systems biology

Mishra, B., & Mysore, V. (2006) · Cited by 7 · see citing works

System and Control Theory Furthers the Understanding of Biological Signal Transduction

Bullinger, E., Findeisen, R., Kalamatianos, D., & Wellstead, P. E. (2007) · Springer eBooks · doi:10.1007/978-3-540-71988-5_6 · Cited by 6 · see citing works

A new growth curve model for giant freshwater prawn Macrobrachium rosenbergii in a prawn–plant symbiotic system

Chen, T., Lv, M., Wu, Y., He, J., Huang, G., Wang, D., & Ma, H. (2019) · Ecological Modelling · doi:10.1016/j.ecolmodel.2019.108801 · Cited by 6 · see citing works

Network-based metabolite ratios for an improved functional characterization of genome-wide association study resultsPreprint

Krumsiek, J., Stückler, F., Suhre, K., Gieger, C., Spector, T. D., Soranzo, N., Kastenmüller, G., & Theis, F. J. (2016) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/048512 · Cited by 5 · see citing works

Towards a Full Quantitative Description of Yeast Metabolism

Messiha, H. L., Malys, N., & Carroll, K. M. (2011) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/b978-0-12-385118-5.00012-8 · Cited by 4 · see citing works

Estimating chain length for time delays in dynamical systems using profile likelihood

Hauber, A. L., Engesser, R., Vanlier, J., & Timmer, J. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz838 · Cited by 2 · see citing works

Athena: Modular CAM/CAD Software for Synthetic BiologyPreprint

Chandran, D., Bergmann, F., & Sauro, H. M. (2009) · arXiv (Cornell University) · doi:10.48550/arxiv.0902.2598 · Cited by 2 · see citing works

Systems Biology and Metabolic Modeling

Rohwer, J. M., & Uys, L. (2013) · doi:10.1002/9781118771280.ch22 · Cited by 2 · see citing works

Cellular Metabolism at the Systems Level

Güell, O. (2017) · Springer theses · doi:10.1007/978-3-319-64000-6_1 · Cited by 1 · see citing works

UNRAVELLING THE INTERCONNECTIONS OF CELLULAR REGULATION

Rohwer, J. M. (2012) · SUNScholar (Stellenbosch University)

strategies, perspectives and challenges Reverse engineering and identification in systems biology:

Villaverde, A. F., & Banga, J. R. (2014)

Moving from Genetics to Systems Biology

Hohmann, S. (2016) · History, philosophy and theory of the life sciences · doi:10.1007/978-3-319-47000-9_12 · Cited by 1 · see citing works

Genome Scale Modeling in Systems Biology: Algorithms and Resources

Najafi, A., Bidkhori, G., Bozorgmehr, J. H., Koch, I., & Masoudi‐Nejad, A. (2014) · Current Genomics · doi:10.2174/1389202915666140319002221 · Cited by 34 · see citing works

Understanding diseases by mouse click: the promise and potential of computational approaches in Systems Biology

Klauschen, F., Angermann, B. R., & Meier‐Schellersheim, M. (2007) · Clinical & Experimental Immunology · doi:10.1111/j.1365-2249.2007.03472.x · Cited by 16 · see citing works

Charting a New Frontier Integrating Mathematical Modeling in Complex Biological Systems from Molecules to Ecosystems

White, K. A., McEntire, K. D., Buan, N. R., Robinson, L., & Barbar, E. J. (2021) · Integrative and Comparative Biology · doi:10.1093/icb/icab165 · Cited by 4 · see citing works

Systems biology: will it work?

Williamson, M. P. (2005) · Biochemical Society Transactions · doi:10.1042/bst0330503 · Cited by 12 · see citing works