Dan Knights - Publications

My curriculum vitae is here.

Peer-reviewed journals - updated January 4, 2011

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 cultures, ages and families". Nature (in press).

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 ]

McNulty NP, Yatsunenko T, Hsiao A, Faith JJ, Muegge BD, Goodman AL, Henrissat B, Oozeer R, Cools-Portier S, Gobert G, Chervaux C, Knights D, Lozupone CA, Knight R, Duncan AE, Bain JR, Muehlbauer MJ, Newgard CB, Heath AC, Gordon JI. "The impact of a consortium of fermented milk strains on the human gut microbiome: a study involving monozygotic twins and gnotobiotic mice". Science Translational Medicine 2011 Oct 26;3(106):106ra106. [ article ]

Verhulst NO, Qiu YT, Beijleveld H, Chris Maliepaard C, Knights D, Schulz S, Berg-Lyons D, Lauber CL, Verduijn W, Haasnoot GW, Mumm R, Bouwmeester HJ, Claas FH, Dicke M, van Loon JJ, Takken W, Knight R, Smallegange RC. "Composition of human skin microbiota affects attractiveness to malaria mosquitoes". PLoS One 6(12): e28991. [ article ]

Flores GE, Bates ST, Knights D, Lauber CL, Stombaugh J, Knight R, Fierer N. "Microbial Biogeography of Public Restroom Surfaces". PLoS ONE 2011;6(11):e28132. Epub 2011 Nov 23. [ 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 ]

Zaneveld JR, Parfrey LW, van Treuren W, Lozupone C, Clemente JC, Knights D, Stombaugh S, Kuczynski J, Knight R. "High-Throughput Studies of Microbial Habitat Adaptation: Principles and Progress". Trends in Microbiology 2011 Oct;19(10):472-82. [ article ]

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, 332(6032):970-974. [ article ]

Caporaso JG, Lauber CL, Costello EK, Berg-Lyons D, Gonzalez A, Stombaugh J, Knights D, Gajer P, Ravel J, Fierer N, Gordon JI, Knight R. "Moving pictures of the human microbiome". Genome Biology 2011 May 30;12(5):R50 (Epub ahead of print). [ article ]

Werner JJ, Knights D, Garcia ML, Scalfone NB, Smith S, Yarasheski K, Cummings TA, Beers AR, Knight R, Angenent LT. 2011. "Bacterial Community Structures are Unique and Resilient in Full-Scale Bioenergy Systems". PNAS 108, 4158-4163. [ article ]

Yilmaz, P. et al. 2011. "Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications". Nature Biotech 29, 415-420. [ article ]

Knights D, Costello EK, Knight R. 2010. "Supervised Classification of Human Microbiota". FEMS Microbiology Reviews 35, 343-359. [ article ] [ data ]

Lozupone C, Lladser ME, Knights D, Stombaugh J, Knight R. 2010. "UniFrac: an effective distance metric for microbial community comparison". The ISME Journal 5, 169-172. [ article ]

Knights D, Kuczynski J, Koren O, Ley RE, Field D, Knight R, DeSantis TZ, Kelley ST. 2010. "Supervised classification of microbiota mitigates mislabeling errors". The ISME Journal 5, 570-573. [ article ] [ tutorial ]

Kuczynski J, Costello EK, Nemergut DR, Zaneveld J, Lauber CL, Knights D, Koren O, Fierer N, Kelley ST, Ley RE, Gordon JI, Knight R. 2010. "Direct sequencing of the human microbiome readily reveals community differences". Genome Biology 11(5):210. [ article ]

Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R. 2010. "QIIME allows analysis of high-throughput community sequencing data". Nature Methods 7(5):335-6. [ article ] [ software ]

Peer-reviewed conference proceedings

Werner J. J., Knights D. B., Garcia M. L., Scalfone N., Cummings T. A., Beers A. R., Knight R. and Angenent L. T. (2010). "Phylogenetic dynamics of bacterial communities in a time series of nine full-scale granular upflow digesters treating brewery". In: Proc. of the 12th World Conference on Anaerobic Digestion, October 31-November 4, 2010, Guadalajara, Mexico.

Knights D, Mozer MC, Nicolov N. "Detecting Topic Drift with Compound Topic Models". 2009 International AAAI Conference on Weblogs and Social Media. [ pdf ]

Knights D, Mytkowicz T, Sweeney PF, Mozer MC, Diwan A. Blind Optimization for Exploiting Hardware Features. In: Proc. of the 18th International Conference on Compiler Construction, pages 251-265, Berlin, Heidelberg, 2009. Springer-Verlag. [ pdf ]

Selected Other Publications

Over 1 million copies in print.

Michael Otte, Daniel Knights, Joseph Pfeiffer III, Jane Mulligan and Gregory Grudic. New Techniques for Path Planning in Image Space. Department of Computer Science, University of Colorado at Boulder. Technical report, 2009. [ pdf ]

Knights, D, Mozer, MC, Nicolov, N. "Detecting Topic Drift". (2009). In N. Nicolov et al. (Eds.), Recent Advances in Natural Language Processing (Vol. 5, pp. 113-130). Amsterdam: John Benjamins.

Knights, D. and Lanza, J. Localization and identification of visual landmarks (poster summary) in Journal of Computing Sciences in Colleges, Volume 16, Issue 4 (2001). and in Consortium for Computing Sciences in Colleges, Proceedings of the sixth annual CCSC northeastern conference, Middlebury, VT (2001). [ ACM ] [alt: pdf ]

Das, S, Wu, C, Knights, D, and W. Truszkowski. Distributed Intelligent Planning and Scheduling (DIPS). NASA Goddard Space Flight Center (Agents Division) (1999). [Similar version in Proceedings of the 2001 AAAI Spring Symposium Series, Palo Alto, CA (March, 2001)]. [ pdf ] [alt: pdf ]

Programs and Projects

Featured in "Best of the Web", PC World Magazine (August 2002).

Dan Knights, Laura Matefy, Victor Dan. Computer-assisted solution of the 15-Puzzle by video stream. Course project, Computer Vision with Daniel Scharstein, 2000. [ details ]

Knights, D. mnp Virtual cube - pre-release version (Shockwave movie). Copyright 2003.
Play with any dimension of cuboid puzzle from 1x1x1 to 5x5x5! Requires Shockwave plug-in. This version is only half finished. There are plenty of bugs. [ play here ]

Knights, D. Rubik's Cube: The Simple Solution by Dan Knights (video) at rubiks.com. Copyright 2002.

Knights, D. Revolving Door Solution (pamphlet). Copyright 2004.
My solution to Rubik's Cube using only group theory and the concept of "Revolving Doors". Unlike most solutions, this solution requires no special notation, and it is designed to be fully "understandable" at every step. [ pdf ]

Knights, D. Beginner/Intermediate Solution (pamphlet). Copyright 2004. I designed this solution for beginning and intermediate solvers. Beginners can learn just one algorithm per step, intermediate solvers can use the extra algorithms (marked with an asterisk) to solve faster. [ pdf ]