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Vangay P, Johnson AJ, Ward TL, Al-Ghalith GA, Shields-Cutler RR, Hillmann BM, Lucas SK, Beura LK, Thompson EA, Till LM, Batres R. US immigration westernizes the human gut microbiome. Cell. 2018 Nov 1;175(4):962-72.

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, Lassen KG, Xavier RJ. Advances in inflammatory bowel disease pathogenesis: linking host genetics and the microbiome.

Gut, 62 (10), 1505-1510 (2013). [ 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. 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. Diet Drives Convergence in Gut Microbiome Functions Across Mammalian Phylogeny and Within Humans.

Science 2011, May 20; 332(6032):970-974. [ article ]


Werner JJ, Knights D, Garcia ML, Scalfone NB, Smith S, Yarasheski K, Cummings TA, Beers AR, Knight R, Angenent LT. Bacterial Community Structures are Unique and Resilient in Full-Scale Bioenergy Systems.

PNAS 108, 4158-4163. [ article ]

Other publications

Dan Knights. Rubik's Cube: 7-Step Solution Guide.

Packaged with Rubik's Cube. Copyright 2003. Booklet. Over 1 million copies in print.


Dan Knights. "The Most Concise Understandable Solution to Rubik's Cube Ever" (using group theory), Copyright 2006.


Dan Knights. "Revolving Door Solution", Copyright 2005.


Dan Knights. "The 7-Step Solution, with Extras", Copyright 2005.


Dr. Knights's 2010 essay on the cube.



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