Publications

Reker, D. “Chapter 14: Active Learning for Drug Discovery and Automated Data Curation.” In Rsc Drug Discovery Series, 2021-January:301–26, 2021. https://doi.org/10.1039/9781788016841-00301.

Reker, D., E. A. Hoyt, G. J. L. Bernardes, and T. Rodrigues. “Adaptive Optimization of Chemical Reactions with Minimal Experimental Information.” Cell Reports Physical Science 1, no. 11 (November 18, 2020). https://doi.org/10.1016/j.xcrp.2020.100247.

Reker, Daniel, Steven M. Blum, Peter Wade, Christoph Steiger, and Giovanni Traverso. “Historical Evolution and Provider Awareness of Inactive Ingredients in Oral Medications.” Pharmaceutical Research 37, no. 12 (October 2020): 234. https://doi.org/10.1007/s11095-020-02953-2.

Brown, Nathan, Peter Ertl, Richard Lewis, Torsten Luksch, Daniel Reker, and Nadine Schneider. “Artificial intelligence in chemistry and drug design.” Journal of Computer-Aided Molecular Design 34, no. 7 (July 2020): 709–15. https://doi.org/10.1007/s10822-020-00317-x.

Erlach, Thomas von, Sarah Saxton, Yunhua Shi, Daniel Minahan, Daniel Reker, Farhad Javid, Young-Ah Lucy Lee, et al. “Robotically handled whole-tissue culture system for the screening of oral drug formulations.” Nature Biomedical Engineering 4, no. 5 (May 2020): 544–59. https://doi.org/10.1038/s41551-020-0545-6.

Reker, Daniel, Yunhua Shi, Ameya R. Kirtane, Kaitlyn Hess, Grace J. Zhong, Evan Crane, Chih-Hsin Lin, Robert Langer, and Giovanni Traverso. “Machine Learning Uncovers Food- and Excipient-Drug Interactions.” Cell Reports 30, no. 11 (March 2020): 3710-3716.e4. https://doi.org/10.1016/j.celrep.2020.02.094.

Reker, Daniel. “Practical considerations for active machine learning in drug discovery.” Drug Discovery Today. Technologies 32–33 (December 2019): 73–79. https://doi.org/10.1016/j.ddtec.2020.06.001.

Reker, Daniel, and Richard A. Lewis. “Advanced Editorial to announce a JCAMD Special Issue on Artificial Intelligence and Machine Learning.” Journal of Computer-Aided Molecular Design 33, no. 11 (November 2019): 941. https://doi.org/10.1007/s10822-019-00264-2.

Li, Li, Ching Chiek Koh, Daniel Reker, J. B. Brown, Haishuai Wang, Nicholas Keone Lee, Hien-Haw Liow, et al. “Predicting protein-ligand interactions based on bow-pharmacological space and Bayesian additive regression trees.” Scientific Reports 9, no. 1 (May 2019): 7703. https://doi.org/10.1038/s41598-019-43125-6.

Reker, Daniel, Steven M. Blum, Christoph Steiger, Kevin E. Anger, Jamie M. Sommer, John Fanikos, and Giovanni Traverso. “"Inactive" ingredients in oral medications.” Science Translational Medicine 11, no. 483 (March 2019): eaau6753. https://doi.org/10.1126/scitranslmed.aau6753.

Reker, Daniel, Yulia Rybakova, Ameya Kirtane, Ruonan Cao, Jee Won Yang, Natsuda Navamajiti, Apolonia Gardner, et al. “Computationally guided high-throughput design of self-assembling drug nanoparticles,” 2019. https://doi.org/10.1101/786251.

Reker, Daniel. “Cheminformatic Analysis of Natural Product Fragments.,” 110:143–75, 2019. https://doi.org/10.1007/978-3-030-14632-0_5.

Reker, Daniel, and J. B. Brown. “Selection of Informative Examples in Chemogenomic Datasets.,” 1825:369–410, 2018. https://doi.org/10.1007/978-1-4939-8639-2_13.

Reker, Daniel, Petra Schneider, Gisbert Schneider, and J. B. Brown. “Active learning for computational chemogenomics.” Future Medicinal Chemistry 9, no. 4 (March 2017): 381–402. https://doi.org/10.4155/fmc-2016-0197.

Grisoni, Francesca, Daniel Reker, Petra Schneider, Lukas Friedrich, Viviana Consonni, Roberto Todeschini, Andreas Koeberle, Oliver Werz, and Gisbert Schneider. “Matrix-based Molecular Descriptors for Prospective Virtual Compound Screening.” Molecular Informatics 36, no. 1–2 (January 2017). https://doi.org/10.1002/minf.201600091.

Cui, Jihong, Maija Hollmén, Lina Li, Yong Chen, Steven T. Proulx, Daniel Reker, Gisbert Schneider, and Michael Detmar. “New use of an old drug: inhibition of breast cancer stem cells by benztropine mesylate.” Oncotarget 8, no. 1 (January 2017): 1007–22. https://doi.org/10.18632/oncotarget.13537.

Schneider, Gisbert, Daniel Reker, Tao Chen, Kurt Hauenstein, Petra Schneider, and Karl-Heinz Altmann. “Deorphaning the Macromolecular Targets of the Natural Anticancer Compound Doliculide.” Angewandte Chemie (International Ed. in English) 55, no. 40 (September 2016): 12408–11. https://doi.org/10.1002/anie.201605707.

Rodrigues, Tiago, Daniel Reker, Petra Schneider, and Gisbert Schneider. “Counting on natural products for drug design.” Nature Chemistry 8, no. 6 (June 2016): 531–41. https://doi.org/10.1038/nchem.2479.

Reker, D., P. Schneider, and G. Schneider. “Multi-objective active machine learning rapidly improves structure-activity models and reveals new protein-protein interaction inhibitors.” Chemical Science 7, no. 6 (June 2016): 3919–27. https://doi.org/10.1039/c5sc04272k.

Schneider, P., M. Röthlisberger, D. Reker, and G. Schneider. “Spotting and designing promiscuous ligands for drug discovery.” Chemical Communications (Cambridge, England) 52, no. 6 (January 2016): 1135–38. https://doi.org/10.1039/c5cc07506h.

Rodrigues, Tiago, Daniel Reker, Martin Welin, Michael Caldera, Cyrill Brunner, Gisela Gabernet, Petra Schneider, Björn Walse, and Gisbert Schneider. “De Novo Fragment Design for Drug Discovery and Chemical Biology.” Angewandte Chemie (International Ed. in English) 54, no. 50 (December 2015): 15079–83. https://doi.org/10.1002/anie.201508055.

Rodrigues, Tiago, Daniel Reker, Jens Kunze, Petra Schneider, and Gisbert Schneider. “Revealing the Macromolecular Targets of Fragment-Like Natural Products.” Angewandte Chemie (International Ed. in English) 54, no. 36 (September 2015): 10516–20. https://doi.org/10.1002/anie.201504241.

Perna, Anna M., Tiago Rodrigues, Thomas P. Schmidt, Manja Böhm, Katharina Stutz, Daniel Reker, Bernhard Pfeiffer, et al. “Fragment-Based De Novo Design Reveals a Small-Molecule Inhibitor of Helicobacter Pylori HtrA.” Angewandte Chemie (International Ed. in English) 54, no. 35 (August 2015): 10244–48. https://doi.org/10.1002/anie.201504035.

Reker, Daniel, and Gisbert Schneider. “Active-learning strategies in computer-assisted drug discovery.” Drug Discovery Today 20, no. 4 (April 2015): 458–65. https://doi.org/10.1016/j.drudis.2014.12.004.

Miyao, Tomoyuki, Daniel Reker, Petra Schneider, Kimito Funatsu, and Gisbert Schneider. “Chemography of natural product space.” Planta Medica 81, no. 6 (April 2015): 429–35. https://doi.org/10.1055/s-0034-1396322.