This bibliography gathers publications over many years from a variety of researchers exploring topics of agency, directionality, and function (among others) with a special emphasis on CASP members. It began with work from teams within the initial Agency, Directionality and Function project and continues to be populated with papers and articles from diverse researchers looking to further develop and expand ways of working interdisciplinarily on the complex theme of teleology.
Included in the bibliography are entries for publications and books that many scholars involved in the Agency, Directionality and Function project recommended as foundational texts in their field of study. We welcome suggestions for additions to the bibliography from CASP members.
Methods
Allen, B. (2023). Symmetry in models of natural selection. Journal of The Royal Society Interface, 20(208), 20230306.
Allen, B., & McAvoy, A. (2022). The coalescent with arbitrary spatial and genetic structure (arXiv:2207.02880). arXiv.
Álvarez-Carretero, S., Kapli, P., & Yang, Z. (2023). Beginner’s Guide on the Use of PAML to Detect Positive Selection. Molecular Biology and Evolution, 40(4), msad041.
Álvarez-Carretero, S., Kapli, P., & Yang, Z. (2023). Beginner’s Guide on the Use of PAML to Detect Positive Selection. Molecular Biology and Evolution, 40(4), msad041.
Au, E. H., Fauci, C., Luo, Y., Mangan, R. J., Snellings, D. A., Shoben, C. R., Weaver, S., Simpson, S. K., & Lowe, C. B. (2023). Gonomics: uniting high performance and readability for genomics with Go. Bioinformatics, 39(8), btad516.
Barbier, M. (2023). Perturbation. In B. M. Haddad & B. D. Solomon (Eds.), Dictionary of Ecological Economics (pp. 405–406). Edward Elgar Publishing.
Davín, A. A., Schrempf, D., Williams, T. A., Hugenholtz, P., & Szöllősi, G. J. (2022). Relative Time Inference Using Lateral Gene Transfers. In H. Luo (Ed.), Environmental Microbial Evolution (Vol. 2569, pp. 75–94). Springer US. https://doi.org/10.1007/978-1-0716-2691-7_4
Foster, P. G., Schrempf, D., Szöllősi, G. J., Williams, T. A., Cox, C. J., & Embley, T. M. (2023). Recoding Amino Acids to a Reduced Alphabet may Increase or Decrease Phylogenetic Accuracy. Systematic Biology, 72(3), 723–737.
Gomes, T., Ribeiro, P. S., Carvalho, N. B., El-Hani, C. N., Figueira, C. P., & Ristow, P. (2023). Impact of Extracellular DNA on Architectural Parameters of Leptospira biflexa Biofilm. Indian Journal of Microbiology.
Goswami, S., Ramachandran, R. V., Bhat, R., Dasgupta, D., Barman, A., Saini, D. K., & Ghosh, A. (2022). Evidence for the Successful Manipulation of a Magnetic Nanorobot Inside the Hard Tumor of a Live Animal. 2022 IEEE International Conference on Emerging Electronics (ICEE), 1–4.
Holland, I., Shu, W., & Davies, J. A. (2023). Stratified tissue biofabrication by rotational internal flow layer engineering. Biofabrication, 15(4), 045003.
Holm, S. (2023). Egalitarianism and Algorithmic Fairness. Philosophy & Technology, 36(1), 6.
Holm, S. (2023). On the Justified Use of AI Decision Support in Evidence-Based Medicine: Validity, Explainability, and Responsibility. Cambridge Quarterly of Healthcare Ethics, 1–7.
Holm, S. (2023). Statistical evidence and algorithmic decision-making. Synthese, 202(1), 28.
Holm, S. (2023). The Fairness in Algorithmic Fairness. Res Publica, 29(2), 265–281.
Holm, S., Petersen, E., Ganz, M., & Feragen, A. (2023). Bias in context: What to do when complete bias removal is not an option. Proceedings of the National Academy of Sciences, 120(23), e2304710120.
Linquist, S., Fullerton, B., & Grewal, A. (2023). Epigenetic this, epigenetic that: comparing two digital humanities methods for analyzing a slippery scientific term. Synthese, 202(3), 68.
Liu, S., Ramadge, P. J., & Adams, R. P. (2023). Generative Marginalization Models (arXiv:2310.12920). arXiv.
Mirramezani, M., Oktay, D., & Adams, R. P. (2023). A rapid and automated computational approach to the design of multistable soft actuators (arXiv:2309.04970). arXiv.
Morel, B., Williams, T. A., & Stamatakis, A. (2023). Asteroid: a new algorithm to infer species trees from gene trees under high proportions of missing data. Bioinformatics, 39(1), btac832.
Nieves Delgado, A., Ludwig, D., & El-Hani, C. (2023). Pluralist Ethnobiology: Between Philosophical Reflection and Transdisciplinary Action. Journal of Ethnobiology, 43(3), 191–197.
Petersen, E., Ganz, M., Holm, S. H., & Feragen, A. (2023). On (assessing) the fairness of risk score models (arXiv:2302.08851). arXiv.
Petersen, E., Holm, S., Ganz, M., & Feragen, A. (2023). The path toward equal performance in medical machine learning. Patterns, 4(7), 100790.
Sarkar S. GWASs and polygenic scores inherit all the old problems of heritability estimates. Behavioral and Brain Sciences. 2023;46:e227.