  | Heinken, A. K., Ravcheev, D., Baldini, F., Heirendt, L., Fleming, R. M., & Thiele, I. (2019). Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease. Microbiome. doi:10.1186/s40168-019-0689-3  Peer Reviewed verified by ORBi |
 | Baldini, F., Heinken, A. K., Heirendt, L., Magnusdottir, S., Fleming, R., & Thiele, I. (2018). The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities. Bioinformatics. doi:10.1093/bioinformatics/bty941 Peer reviewed |
 | Noronha, A., Modamio Chamarro, J., Jarosz, Y., Guerard, E., Sompairac, N., Preciat Gonzalez, G. A., Danielsdottir, A. D., Krecke, M., Merten, D., Haraldsdottir, H., Heinken, A. K., Heirendt, L., Magnusdottir, S., Ravcheev, D., Sahoo, S., Gawron, P., Friscioni, L., Garcia Santa Cruz, B., Prendergast, M., ... Thiele, I. (2018). The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Research. doi:10.1093/nar/gky992 Peer Reviewed verified by ORBi |
  | Greenhalgh, K., Ramiro Garcia, J., Heinken, A. K., Baginska, J., Letellier, E., Halder, R., Frachet Bour, A., Ullmann, P., Thiele, I., Haan, S., & Wilmes, P. (16 February 2018). Cominatorial effect of dietary fibre and Lactobacillus rhamnosus in the context of colorectal cancer therapy [Poster presentation]. Cell Immunology symposium. |
 | Brunk, E., Sahoo, S., Zielinski, D. C., Altunkaya, A., Drager, A., Mih, N., Gatto, F., Nilsson, A., Preciat Gonzalez, G. A., Aurich, M. K., Prlic, A., Sastry, A., Danielsdottir, A. D., Heinken, A. K., Noronha, A., Rose, P. W., Burley, S. K., Fleming, R. M., Nielsen, J., ... Palsson, B. O. (2018). Recon3D enables a three-dimensional view of gene variation in human metabolism. Nature Biotechnology, 36 (3), 272-281. doi:10.1038/nbt.4072 Peer Reviewed verified by ORBi |
 | Thiele, I., Clancy, C., Heinken, A. K., & Fleming, R. M. (August 2017). Quantitative systems pharmacology and the personalized drug–microbiota–diet axis. Current Opinion in Systems Biology, 4, 43-52. doi:10.1016/j.coisb.2017.06.001 Peer reviewed |
 | Rowland, I., Gibson, G., Heinken, A. K., Scott, K., Swann, J., Thiele, I., & Tuohy, K. (2017). Gut microbiota functions: metabolism of nutrients and other food components. European Journal of Nutrition. doi:10.1007/s00394-017-1445-8 Peer Reviewed verified by ORBi |
 | Magnusdottir, S., Heinken, A. K., Kutt, L., Ravcheev, D., Bauer, E., Noronha, A., Greenhalgh, K., Jäger, C., Baginska, J., Wilmes, P., Fleming, R. M., & Thiele, I. (2016). Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota. Nature Biotechnology. doi:10.1038/nbt.3703 Peer Reviewed verified by ORBi |
Heinken, A. K., Ravcheev, D., & Thiele, I. (2016). Systems biology of bacteria-host interactions. In L. Nibali & B. Henderson (Eds.), The Human Microbiota and Chronic Disease: Dysbiosis as a Cause of Human Pathology. Hoboken, New Jersey, United States: John Wiley & Sons, i nc. doi:10.1002/9781118982907.ch7 Peer reviewed |
 | Heinken, A. K., & Thiele, I. (2015). Anoxic conditions promote species-specific mutualism between gut microbes in silico. Applied and Environmental Microbiology, 81 (12), 4049-4061. doi:10.1128/AEM.00101-15 Peer Reviewed verified by ORBi |
 | Heinken, A. K., & Thiele, I. (2015). Systematic prediction of health-relevant human-microbial co-metabolism through a computational framework. Gut Microbes, 6 (2), 120-130. doi:10.1080/19490976.2015.1023494 Peer Reviewed verified by ORBi |
 | Heinken, A. K., & Thiele, I. (2015). Systems biology of host-microbe metabolomics. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. doi:10.1002/wsbm.1301 Peer reviewed |
 | Heinken, A. K., Khan, M. T., Paglia, G., Rodionov, D. A., Harmsen, H. J., & Thiele, I. (September 2014). A functional metabolic map of Faecalibacterium prausnitzii, a beneficial human gut microbe. Journal of Bacteriology, 196 (18), 3289-3302. doi:10.1128/JB.01780-14 Peer Reviewed verified by ORBi |
 | Thiele, I., Heinken, A. K., & Fleming, R. M. (2013). A systems biology approach to studying the role of microbes in human health. Current Opinion in Biotechnology, 24 (1), 4-12. doi:10.1016/j.copbio.2012.10.001 Peer Reviewed verified by ORBi |
 | Heinken, A. K., Sahoo, S., Fleming, R. M., & Thiele, I. (2013). Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut. Gut Microbes, 4 (1), 28-40. doi:10.4161/GMIC.22370 Peer Reviewed verified by ORBi |
 | Sigurdsson, G., Fleming, R. M., Heinken, A. K., & Thiele, I. (2012). A systems biology approach to drug targets in Pseudomonas aeruginosa biofilm. PLoS ONE, 7 (4), 34337. doi:10.1371/journal.pone.0034337 Peer Reviewed verified by ORBi |