Hacking the microbiome
1.Writing or refining computer programs skillfully.
2.Seeking and exploiting weaknesses in a complex system in order to change its behavior for one's benefit.
Our computational microbiology lab develops methods that bring precision medicine to the microbiome. We apply those methods to find patterns in microbial communities that predict and diagnose human diseases.
Dr. Dan Knights is an Assistant Professor in the Department of Computer Science and Engineering and the BioTechnology Institute at the University of Minnesota. He obtained his Ph.D. in Computer Science under Rob Knight and Mike Mozer at the University of Colorado at Boulder, with a certificate in Interdisciplinary Quantitative Biology from the University of Colorado's BioFrontiers Institute. He came to the University of Minnesota from a post-doctoral fellowship in the lab of Ramnik Xavier at Harvard Medical School and the Broad Institute of MIT and Harvard.
Ward TL, Dominguez-Bello MG, Heisel T, Al-Ghalith G, Knights D, Gale CA. Development of the Human Mycobiome over the First Month of Life and across Body Sites. mSystems. 2018 Jun 26;3(3):e00140-17. [article]
Shields-Cutler RR, Al-Ghalith GA, Yassour M, Knights D. SplinectomeR enables group comparisons in longitudinal microbiome studies. Frontiers in microbiology. 2018;9:785. [article]
Ward TL, Knights D, Gale CA. Infant fungal communities: current knowledge and research opportunities. BMC medicine. 2017 Dec 1;15(1):30. [article]
Clayton JB, Vangay P, Huang H, Ward T, Hillmann BM, Al-Ghalith GA, Travis DA, Long HT, Van Tuan B, Van Minh V, Cabana F. Captivity humanizes the primate microbiome. Proceedings of the National Academy of Sciences. 2016 Aug 29:201521835. [article]
Al-Ghalith GA, Montassier E, Ward HN, Knights D. NINJA-OPS: fast accurate marker gene alignment using concatenated ribosomes. PLoS computational biology. 2016 Jan 28;12(1):e1004658. [article]
Livanos AE, Greiner TU, Vangay P, Pathmasiri W, Stewart D, McRitchie S, Li H, Chung J, Sohn J, Kim S, Gao Z. Antibiotic-mediated gut microbiome perturbation accelerates development of type 1 diabetes in mice. Nature microbiology. 2016 Aug 22;1:16140. [article]
Maldonado-Gómez MX. Stable engraftment of Bifidobacterium longum AH1206 in the human gut depends on individualized features of the resident microbiome. Cell Host & Microbe. 2016 Oct 12;20(4):515-26. [article]
Knights D, et al. Advances in inflammatory bowel disease pathogenesis: linking host genetics and the microbiome.
Gut, 62 (10), 1505-1510 (2013). [ article ]
Smith MI, et al. Gut Microbiomes of Malawian Twin Pairs Discordant for Kwashiorkor.
Science, published online January 30 2013; 10.1126/science.1229000. [ article ]
Huttenhower C, et al. Structure, Function and Diversity of the Healthy Human Microbiome.
Nature 486, 207--214 (2012). [ article ]
Yatsunenko T, et al. Human gut microbiome differentiation viewed across age and geography.
Nature 486 (7402), 222-227. [ article ]
Knights D, et al. Human-associated microbial signatures: examining their predictive value.
Cell Host & Microbe. 2011 Oct 4;10(4):292-6. [ article ]
Knights D, et al. Bayesian community-wide culture-independent microbial source tracking.
Wu GD, et al. Linking long-term dietary patterns with gut microbial enterotypes.
Science 2011 Oct 7;334(6052):105c8. [ article ]