Our lab’s focus is the functional characterization of complex host-microbe interactions in host diseases and behavior. Perhaps the grandest bioinformatics challenge of the genomics era is to place genes into functional disease pathways using data sets of limited sample size. Human genome studies have identified associations between our own genetics and disease, but in a surprising number of diseases, including cancer, autoimmune diseases, autism, HIV, and obesity, as well as aspects of animal behavior, our “second genome”–the mixture of genes in our resident microbes–has recently been implicated. In many of these cases we still understand little about the mechanisms of host-microbe interactions.
Although sequencing and other “omics” technologies now generate so much biological data we have to ship it on an airplane, many of the bioinformatics methods for analyzing these data are in their infancy. Furthermore, the data are high-dimensional and increasingly multi-omics, with many types collected for each sample, requiring tools from machine learning for data integration and the incorporation of prior knowledge. The methods our lab is developing will help lay the foundation for identifying host disease and behavior pathways across the host-microbe interface. Our research focuses include development of theory and tools for modeling genome-scale host-microbe interactions, predictive models of microbial community dynamics and genome variation, and data integration methods for high-throughput functional genomics assays. Read more...
Dr. Dan Knights
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 Michael C. 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.
Selected recent publications
- Smith MI, Yatsunenko T, Manary MJ, Trehan I, Mkakosya R, Cheng J, Kau AL, Rich SS, Concannon P, Mychaleckyj JC, Liu J, Houpt E, Li JV, Holmes E, Nicholson J, Knights D, Ursell LK, Knight R, Gordon JI. "Gut Microbiomes of Malawian Twin Pairs Discordant for Kwashiorkor"
Science, published online January 30 2013; 10.1126/science.1229000. [ article ]
The Human Microbiome Project Consortium. "Structure, Function and Diversity of the Healthy Human Microbiome"
Nature 486, 207--214 (2012). [ article ]
The Human Microbiome Project Consortium. "A framework for microbiome research".
Nature 486, 215--221 (2012). [ article ]
- Yatsunenko T, Rey F, Manary M, Trehan I, Dominguez-Bello MG, Baldassano RN, Anokhin AP, Heath AC, Warner B, Reeder J, Kuczynski J, Lozupone C, Lauber C, Clemente JC, Knights D, Knight R, Gordon JI. "Human gut microbiome differentiation viewed across age and geography".
Nature 486 (7402), 222-227. [ article ]
- Wu GD, Chen J, Hoffmann C, Bittinger K, Chen Y, Keilbaugh SA, Bewtra M, Knights D, Walters WA, Knight R, Sinha R, Gilroy E, Gupta K, Baldassano R, Nessel L, Li H, Bushman FD, Lewis JD. "Linking long-term dietary patterns with gut microbial enterotypes".
Science 2011 Oct 7;334(6052):105c8. [ article ]
- Knights D, Parfrey LW, Zaneveld J, Lozupone C, Knight R. "Human-associated microbial signatures: examining their predictive value".
Cell Host & Microbe. 2011 Oct 4;10(4):292-6. [ article ]
- Knights D, Kuczynski J, Charlson ES, Zaneveld J, Mozer MC, Collman RG, Bushman FD, Knight R, Kelley ST. 2011. "Bayesian community-wide culture-independent microbial source tracking".
Nature Methods 2011 Jul 17;8(9):761-3. [ article ] [ software ]
- Muegge BD, Kuczynski J, Knights D, Clemente JC, Peña AG, Fontana L, Henrissat B, Knight R, Gordon JI. 2011. "Diet Drives Convergence in Gut Microbiome Functions Across Mammalian Phylogeny and Within Humans".
Science 2011, May 20; 332(6032):970-974. [ article ]
- Dr. Knights's speedcubing records
- Dr. Knights's solutions to Rubik's cube
- "Seven Step Solution", Copyright 2003. Packaged with Rubik's Cube worldwide, over 1 million copies in print.
- "The Most Concise Understandable Solution to Rubik's Cube Ever" (using group theory), Copyright 2006.
- "Revolving Door Solution", Copyright 2005.
- Dr. Knights's 2010 essay on the cube
- Baby Names Clustering