Causal Concepts Guiding Model Specification in Systems Biology

Albert, Réka. 2007. Network inference, analysis, and modeling in systems biology. The Plant Cell 19: 3327–38.10.1105/tpc.107.054700Open DOISearch in Google Scholar

Bansal, Mukesh; Belcastro, Vincenzo; Ambesi-Impiombato, Alberto; and di Bernardo, Diego. 2007. How to infer gene networks from expression profiles. Molecular Systems Biology 3: 1–10.10.1038/msb4100158Open DOISearch in Google Scholar

Braillard, Pierre-Alain. 2010. Systems biology and the mechanistic framework. History and Philosophy of Life Sciences 32: 43–62.Search in Google Scholar

Cartwright, Nancy. 1993. Mark and probabilities: two ways to find causal structure. In Scientific Philosophy: Origins and Development, ed. by F. Stadler.Dordrecht: Kluwer.10.1007/978-94-017-2964-2_7Open DOISearch in Google Scholar

Cartwright, Nancy. 2002. Against modularity, the causal markov condition and any link between the two: comments on hausman and woodward. British Journal for the Philosophy of Science 53: 411–53.Search in Google Scholar

Cartwright, Nancy. 2007. Hunting Causes and Using Them: Approaches in Philosophy and Economics. New York: Cambridge University Press.10.1017/CBO9780511618758Search in Google Scholar

Cartwright, Nancy; Shomar, T.; and Suárez, M. 1995. The tool box of science. In Theories and models in scientific processes. Amsterdam: Rodopi.Search in Google Scholar

Chickering, David Maxwell. 1996. Learning bayesian networks is NP-complete. In Learning from Data: Artificial Intelligence and Statistics V. New York: Springer-Verlag.10.1007/978-1-4612-2404-4_12Search in Google Scholar

Chickering, David Maxwell; Heckerman, David; and Meek, Christopher. 2004. Large-sample learning of bayesian networks is NP-Hard. Journal of Machine Learning 5: 1287–330.Search in Google Scholar

Craver, Carl. 2007. Explaining the Brain: Mechanisms and the Mosaic Unity of Neuroscience. Oxford: Oxford University Press.10.1093/acprof:oso/9780199299317.003.0007Search in Google Scholar

De Backer, Phillipe; De Waele, Danny; and Van Speybroeck, Linda. 2010. Ins and outs of systems biology vis-à-vis molecular biology: continuation or clear cut? Acta Biotheoretic 58: 15–49.10.1007/s10441-009-9089-6Search in Google Scholar

Douglas, Heather. 2000. Inductive risk and values in science. Philosophy of Science 67: 559–79.10.1086/392855Search in Google Scholar

Friedman, Nir; Linial, Michal; Nachman, Iftach; and Pe’er, De’er. 2000. Using bayesian networks to analyze expression data. Journal of Computational Biology 7: 601–20.10.1089/106652700750050961Open DOISearch in Google Scholar

Hartemink, Alexander J.; Gifford, David K.; Jaakola, Tommi S.; and Young, Richard A. 2002. Combining location and expression data for principled discovery of genetic regulatory network models. In Pacific Symposium on Biocomputing 2002: Kauai, Hawaii, 3-7 January 2002: 437–49.Search in Google Scholar

Hausman, Daniel W.; and Woodward, James. 1999. Independence, invariance and the causal markov condition. British Journal for the Philosophy of Science 50: 521–83.Search in Google Scholar

Hausman, Daniel W.; and Woodward, James. 2004. Modularity and the causal markov condition: a restatement. British Journal for the Philosophy of Science 55: 147–61.10.1093/bjps/55.1.147Open DOISearch in Google Scholar

He, Feng; Balling, Rudi; Zeng, An-Ping. 2009. Reverse engineering and verification of gene networks: principles, assumptions and limitations of present methods and future perspectives. Journal of Biotechnology 144: 190–203.Search in Google Scholar

Le Novère, Nicolas. 2015. Quantitative and logic modelling of molecular and gene networks. Nature Reviews: Genetics 16: 146–58.10.1038/nrg3885Search in Google Scholar

Levins, Richard. 1966. The strategy of model building in population biology. American Scientist 54: 421–31.Search in Google Scholar

Levy, Arnon; and Bechtel, William. 2013. Abstraction and the organization of mechanisms. Philosophy of Science 80: 241–61.10.1086/670300Open DOISearch in Google Scholar

MacKay, David J. C. 1992. Bayesian interpolation. Neural Computation 4: 415–47.10.1162/neco.1992.4.3.415Open DOISearch in Google Scholar

MacLeod, Miles; and Nersessian, Nancy. J. 2013. Building simulations from the ground up: modeling and theory in systems biology. Philosophy of Science 80: 533–56.10.1086/673209Open DOISearch in Google Scholar

MacLeod, Miles; and Nersessian, Nancy J. 2015. Modeling systems-level dynamics: understanding without mechanistic explanation in integrative systems biology. Studies in History and Philosophy of Science Part C—Biological and Biomedical Science 49: 1–11.10.1016/j.shpsc.2014.10.004Search in Google Scholar

Markowetz, Florian; and Spang, Rainer. 2007. Inferring cellular networks—a review. BMC Bioinformatics 8 (Suppl 6) S5. <www.biomedcentral.com/1471-2105/8/S6/S5>10.1186/1471-2105-8-S6-S5Search in Google Scholar

Matthiessen, Dana. 2015. Mechanistic explanation in systems biology: cellular networks. British Journal for the Philosophy of Science. <http://bjps.oxfordjournals.org/content/early/2015/04/09/bjps.axv011.full.pdf+html>Search in Google Scholar

McMullin, Ernan. 1985. Galilean idealization. Studies in the History and Philosophy of Science 16: 247–73.10.1016/0039-3681(85)90003-2Open DOISearch in Google Scholar

Mitchell, Sandra. 2008. Exporting causal knowledge in evolutionary and developmental biology. Philosophy of Science 75: 697–706.10.1086/594515Open DOISearch in Google Scholar

Morgan, Mary; and Morrison, Margaret. 1999. Models as Mediators: Perspectives on Natural and Social Science. Cambridge: Cambridge University Press.10.1017/CBO9780511660108Search in Google Scholar

Opgen-Rhein, Rainer; and Strimmer, Korbinian. 2007. From correlation to causation networks: a simple approximate learning algorithm and its application to high-dimensional plant gene expression data. BMC Systems Biology 1. <www.biomedcentral.com/1752-0509/1/37>.10.1186/1752-0509-1-37Search in Google Scholar

Pearl, Judea. 2000. Causality: Models, Reasoning, and Inference. New York: Cambridge University Press.Search in Google Scholar

Peter, Isabelle S.; and Davidson, Eric H. 2015. Genomic Control Process: Development and Evolution. New York: Elsevier.Search in Google Scholar

Sachs, Karen; Perez, Omar; Pe’er, Dana; Lauffenburger, Douglas A.; Nolan, Garry P. 2005. Causal protein-signaling networks derived from multiparameter single-cell data. Science 308: 523–9.10.1126/science.1105809Search in Google Scholar

Spirtes, Peter; Glymour, Clark; and Scheines, Richard. 1993. Causation, Prediction, and Search. New York: Springer-Verlag.10.1007/978-1-4612-2748-9Search in Google Scholar

Woodward, James. 2003. Making Things Happen: A Theory of Causal Explanation. New York: Oxford University Press.10.1093/0195155270.001.0001Search in Google Scholar

Woodward, James. 2010. Causation in biology: stability, specificity, and the choice of levels of explanation. Biology and Philosophy 25: 287–318.Search in Google Scholar

Woodward, James. 2013. Mechanistic explanation: its scopes and limits. Proceedings of the Aristotelian Society S87: 39–65.10.1111/j.1467-8349.2013.00219.xSearch in Google Scholar

Weisberg, Michael. 2013. Simulation and Similarity: Using Models to Understand the World. New York: Oxford University Press.10.1093/acprof:oso/9780199933662.001.0001Search in Google Scholar

Westerhoff, Hans V.; and Kell, Douglas B. 2007. The methodologies of systems biology. In Systems Biology: Philosophical Foundations. New York: Elsevier.10.1016/B978-044452085-2/50004-8Search in Google Scholar

Winsberg, Eric. 2010. Science in the Age of Computer Simulation. Chicago: University of Chicago Press.10.7208/chicago/9780226902050.001.0001Search in Google Scholar

Wouters, Arno G. 2007. Design explanation: determining the constraints on what can be alive. Erkenntnis 67: 65–80.10.1007/s10670-007-9045-2Open DOISearch in Google Scholar

Yu, Jing; Smith, V. Anne; Wang, Paul P.; Hartemink, Alexander J.; and Jarvis, Erich D. 2004. Advances to Bayesian network inference for generating causal networks from observational biological data. Bioinformatics 20: 3594–603.10.1093/bioinformatics/bth448Open DOISearch in Google Scholar