D. Reker, Y. Rybakova, A. R. Kirtane, R. Cao, J. W. Yang, N. Navamajiti, A. Gardner, R. M. Zhang, T. Esfendiary, J. L'Heureux, T. von Erlach, E. M. Smekalova, D. Leboeuf, K. Hess, A. Lopez, J. Rogner, J. Collins, S. Tamang, K. Ishida, P. Chamberlain, D. S. Yun, A. Lytoon-Jean, C. K. Soule, J. H. Cheah, A. M. Hawayrd, R. Langer, G. Traverso†. Computationally guided high-throughput design of self-assembling drug nanoparticles. (2020), preprint available at bioRxiv,, in revision.



D. Reker. Active learning for drug discovery and automated data curation. (2020) Artificial Intelligence in Drug Discovery (Royal Chemical Society), in press.



D. Reker. Practical Considerations for Active Machine Learning in Drug Discovery. (2020) Drug Discov Today Tech.,



N. Brown*, P. Ertl*, R. A. Lewis*,†, T. Luksch*,†, D. Reker*,†, N. Schneider*.Editorial - Artificial intelligence in chemistry and drug design. (2020) JCAMD,



T. v. Erlach, S. Saxton, Y. Shi, D. Minahan, D. Reker, F. Javid, Y.-A. L. Lee, C. Schoellhammer, T. Esfandiary, C. Cleveland, L. Booth, J. Lin, H. Levy, S. Blackburn, A. Hayward, R. Langer†, G. Traverso†. Whole tissue robotic interface system for oral drug formulation development. (2020) Nat. Biomed. Eng, 4, 544–59.



D. Reker, Y. Shi, A. R. Kirtane, K. Hess, G. J. Zhong, E. Crane, C.-H. Lin, R. Langer, G. Traverso†. Machine learning uncovers food- and excipient-drug interactions. (2020) Cell Rep., 30(11), 3710-16.e4.



D. Reker†, R. A. Lewis.Advanced Editorial to announce a JCAMD Special Issue on Artificial Intelligence and Machine Learning. (2019) JCAMD, 33(11), 941.



D. Reker. Chemoinformatic analysis of natural product fragments. (2019) Chemoinformatics in Natural Product Research, Progress in the Chemistry of Organic Natural Products 110 (Springer Nature), 143-75.



L. Li, C. C. Koh, D. Reker,J.B. Brown, H. Wang, N. K. Lee, H.-H. Liow, H. Dai, H.-M. Fan, L. Chen, D-Q. Wei†. Predicting protein-ligand interactions based on bow-pharmacological space and Bayesian additive regression trees. (2019) Sci. Rep. 9, 7703.



D. Reker*, S. M. Blum*, C. Steiger, K. E. Anger, J. M. Sommer, J. Fanikos, G. Traverso†. "Inactive" ingredients in oral medications. (2019) Sci. Trans. Med. 11(483), eaau6753. (Highlighted in MIT News March 13 2019 and by NPR, Yahoo, Fortune, CNBC)



D. Reker†,G.J. L. Bernardes, T. Rodrigues†. Computational advances in combating colloidal aggregation in drug discovery.  (2019) Nat. Chem., 11, 402–18.



D. Reker,G.J. L. Bernardes†, T. Rodrigues†. Evolving and Nano Data Enabled Machine Intelligence for Chemical Reaction Optimization. (2018), in review, preprint available atChemRxiv.



D. Reker†, J. B. Brown. Selection of informative examples in chemogenomic datasets. (2018) Methods Mol. Bio., 1825, 369-410.



C. Rakers, D. Reker, J. B. Brown†. Small random forest models for effective chemogenomic active learning. (2017) J. Comput. Aided Chem., 18, 124-42.



D. Reker, P. Schneider, G. Schneider, J. B. Brown†. Active learning for computational chemogenomics. (2017) Fut. Med. Chem, 9 (4), 381-402.



J. Cui, M. Hollmén, L. Li, Y. Chen, S. T. Proulx, D. Reker, G. Schneider, M. Detmar†. New use of an old drug: inhibition of breast cancer stem cells by benztropine mesylate. (2017) Oncotarget, 8 (1), 1007-22.



G. Schneider†, D. Reker, T. Chen, K. Hauenstein, P. Schneider, K.-H. Altmann. Deorphaning the macromolecular targets of the natural anticancer compound doliculide. (2016) Angew. Chem. Int. Ed., 55 (40), 12408-11.



F. Grisoni*, D. Reker*, P. Schneider, L. Friedrich, V. Consonni, R. Todeschini, A. Koeberle, O. Werz, G. Schneider†. Matrix‐based molecular descriptors for prospective virtual compound screening. (2016) Mol. Inf., 36 (1-2).



D. Reker, P. Schneider, G. Schneider†. Multi-objective active machine learning rapidly improves structure-activity models and reveals new protein-protein interaction inhibitors. (2016) Chem. Sci., 7, 3919-27.



T. Rodrigues*, D. Reker*, P. Schneider*, G. Schneider*,†. Counting on natural products for drug design. (2016) Nat. Chem., 8, 531-41.



P. Schneider, M. Röthlisberger, D. Reker, G. Schneider. Spotting and designing promiscuous ligands for drug discovery. (2016) Chem. Commun., 52, 1135-8.



T. Rodrigues*, D. Reker*, M. Welin, M. Caldera, C. Brunner, G. Gabernet, P. Schneider, B. Walse, G. Schneider†. De novo fragment design for drug discovery and chemical biology. (2015) Angew. Chem. Int. Ed., 54 (50), 15079-83. (selected by editor as “very important paper (VIP)”)



T. Rodrigues, D. Reker, J. Kunze, P. Schneider, G. Schneider†. Revealing the macromolecular targets of fragment-like natural products. (2015) Angew. Chem. Int. Ed., 54 (36), 10516-20.



A. M. Perna*, T. Rodrigues*, T. P. Schmidt, M. Böhm, K. Stutz, D. Reker, B. Pfeiffer, K.-H. Altmann, S. Backert, S. Wessler, G. Schneider†. Fragment-based de novo design reveals a small molecule inhibitor of Helicobacter pylori HtrA. (2015) Angew. Chem. Int. Ed., 54 (35), 10244-8. (selected by editor as "hot paper")



T. Miyao*, D. Reker*, P. Schneider, K. Funatsu, G. Schneider†. Chemography of natural product space. (2015) Planta Med., 81 (6), 429-35.



D. Reker, G. Schneider. Active-learning strategies in computer-assisted drug discovery. (2015) Drug Discov. Today, 20 (4), 458-65.



T. Rodrigues*, N. Hauser*, D. Reker, M. Reutlinger, T. Wunderlin, J. Hamon, G. Koch, G. Schneider†. Multidimensional de novo design reveals 5-HT2B receptor-selective ligands. (2015) Angew. Chem. Int. Ed., 54 (5), 1551-5.



D. Reker, A. M. Perna, T. Rodrigues, P. Schneider, M. Reutlinger, B. Mönch, A. Koeberle, C. Lamers, M. Gabler, H. Steinmetz, R. Müller, M. Schubert-Zsilavecz, O. Werz, G. Schneider†. Revealing the macromolecular targets of complex natural products. (2014) Nat. Chem., 6 (12), 1072-8. (Highlighted in ETH Life November 12 2014 and CHIMIA 2015, 69, No. 3, p153. Recommended article by the F1000 Faculty Review)



G. Schneider†, D. Reker, T. Rodrigues, P. Schneider. Coping with polypharmacology by computational medicinal chemistry. (2014) CHIMIA, 68 (9), 648-53.



D. Reker*, M. Seet*, M. Pillong, C. P. Koch, P. Schneider, M. C. Witschel, M. Rottmann, C. Freymond, R. Brun, B. Schweizer, B. Illarionov, A. Bacher, M. Fischer, F. Diederich, G. Schneider†. Deorphaning pyrrolopyrazines as potent multi‐target antimalarial agents. (2014) Angew. Chem. Int. Ed., 53 (27), 7079-84.



D. Reker, T. Rodrigues, P. Schneider, G. Schneider†. Identifying the macromolecular targets of de novo-designed chemical entities through self-organizing map consensus. (2014) Proc. Natl. Acad. Sci. USA, 111 (11), 4067-72. (Highlighted in ETH Life March 17 2014)



J. Lötsch, G. Schneider, D. Reker, M. J. Parnham, P. Schneider, G. Geisslinger, A. Doehring†. Common non-epigenetic drugs as epigenetic modulators. (2013) Trends Mol. Med., 19 (12), 742-53.



T. Rodrigues, F. Roudnicky, C.P. Koch, T. Kudoh, D. Reker, M. Detmar, and G. Schneider†. De novo design and optimization of Aurora A kinase inhibitors. (2013) Chem. Sci., 4 (3), 1229-33.



M. Reutlinger*, C.P. Koch*, D. Reker*, N. Todoroff, P. Schneider, T. Rodrigues, and G. Schneider†. Chemically advanced template search (CATS) for scaffold-hopping and prospective target prediction for 'orphan' molecules. (2013) Mol. Inf., 32 (2), 133-8.



D. Reker, L. Malmström†. Bioinformatic challenges in targeted proteomics. (2012) J. Proteome Res., 11 (9),  4393-402.



C. Fritz, C. Kirschner, D. Reker, A. Wisplinghoff, H. Paulheim, and F. Probst†. Geospatial web mining for emergency management. (2010) GIScience 2010 - Extended Abstracts.



D. Reker, S. Katzenbeisser, K. Hamacher†. Computation of mutual information from Hidden Markov Models. (2010) Comput. Biol. Chem., 34 (5), 328-33.