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University of Colorado Denver College of Liberal Arts and Sciences

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Faculty & Staff Directory

Christopher Miller, Ph.D.

Dr. Christopher Miller

Assistant Professor


Office Location: SI 4098

Phone:  (303) 556-3107

Fax:  (303) 556-4352

Office hours: T 10:00a-11:00p and
W 3:00p-4:00p

Areas of Expertise:

Bioinformatics, Genomics of Microbial Communities


Ph.D., Molecular Biology, University of California, Los Angeles, 2008

B.A., Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, 2002


The Miller lab develops and uses bioinformatic and genome-enabled approaches to study microbial communities.  With the advent of new sequencing technologies, one can sequence billions or trillions of base pairs of DNA for relatively little money.  One of the most powerful applications of this new economy is the direct sequencing of microbial DNA and RNA from the environment.  The combination of deep sequencing and bioinformatics reveals that even “simple” natural microbial communities are in fact quite complex.  The Miller lab is interested in understanding this complexity at a systems level for microbial communities relevant to the environment, bioenergy production, and human health and disease.

Link to Google Scholar Profile page:
Miller, C.S., Handley, K.M., Wrighton, K.C., Frischkorn, K.R., Thomas, B.C., and Banfield, J.F. (2013). Short-Read Assembly of Full-Length 16S Amplicons Reveals Bacterial Diversity in Subsurface Sediments. PLoS ONE 8, e56018.
 Handly, K.M., N.C. VerBerkomes, C.I. Steefel, K.H. Williams, I. Sharon, C.S. Miller, K.R. Frischkorn, K. Chourey, B.C. Thomas, M.B. Shah, P.E. Long, R.L. Hettich, and J.F. Banfield. "Biostimulation induces syntrophic interactions that impact C, S and N cycling in a sediment microbial community. " The ISME Journal In press.
Wrighton, K.C., B.C. Thomas, I. Sharon, C.S. Miller, C.J. Castelle, N.C. VerBerkmoes, M.J. Wilkins, R.L. Hettich, M.S. Lipton, K.H. Williams, P.E. Long, and J.F. Banfield (2012). "Fermentation, Hydrogen and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla." Science. 337 (6102): 1661.
Justice, N.B., C. Pan, R.S. Mueller, S. Spaulding, V. Shah, C.L. Sun, A. Yelton, C.S. Miller, B.C. Thomas, M. Shah,  N.C. VerBerkmoes, R. Hettich, and J.F. Banfield (2012). "Hetertrophic Archaea Contribute to Carbon Cycling in Low-pH, Suboxic Biofilm Communities." Appl Environ Microbiol.
Fujishima, K., J. Sugahara, C. S. Miller, B. J. Baker, M. Di Giulio, K. Takesue, A. Sato, M. Tomita, J. F. Banfield and A. Kanai (2011). "A novel three-unit tRNA splicing endonuclease found in ultrasmall Archaea possesses broad substrate specificity." Nucleic Acids Res  39(22): 9695.
Gladden, J. M., M. Allgaier, C. S. Miller, T. C. Hazen, J. S. VanderGheynst, P. Hugenholtz, B. A. Simmons, and S. W. Singer (2011). "Glycoside Hydrolase Activities of Thermophilic Bacterial Consortia Adapted to Switchgrass." Appl Environ Microbiol 77(16): 5804.
Miller, C.S., B. J. Baker, B. C. Thomas, S. W. Singer and J. F. Banfield (2011). "EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data." Genome Biology 12(5): R44.
Miller, C. S. and D. Eisenberg (2008). "Using inferred residue contacts to distinguish between correct and incorrect protein models." Bioinformatics 24(14): 1575.
Cruz, D., A. D. Watson, C. S. Miller, D. Montoya, M. T. Ochoa, P. A. Sieling, M. A. Gutierrez, M. Navab, S. T. Reddy, J. L. Witztum, A. M. Fogelman, T. H. Rea, D. Eisenberg, J. Berliner and R. L. Modlin (2008). "Host-derived oxidized phospholipids and HDL regulate innate immunity in human leprosy." J Clin Invest 118(8): 2917.
Williamson, S. J., D. B. Rusch, S. Yooseph, A. L. Halpern, K. B. Heidelberg, J. I. Glass, C. Andrews-Pfannkoch, D. Fadrosh, C. S. Miller, G. Sutton, M. Frazier and J. C. Venter (2008). "The Sorcerer II Global Ocean Sampling Expedition: Metagenomic Characterization of Viruses within Aquatic Microbial Samples." PLoS ONE 3(1): e1456.
Yooseph, S., G. Sutton, D. B. Rusch, A. L. Halpern, S. J. Williamson, K. Remington, J. A. Eisen, K. B. Heidelberg, G. Manning, W. Li, L. Jaroszewski, P. Cieplak, C. S. Miller, H. Li, S. T. Mashiyama, M. P. Joachimiak, C. van Belle, J. M. Chandonia, D. A. Soergel, Y. Zhai, K. Natarajan, S. Lee, B. J. Raphael, V. Bafna, R. Friedman, S. E. Brenner, A. Godzik, D. Eisenberg, J. E. Dixon, S. S. Taylor, R. L. Strausberg, M. Frazier and J. C. Venter (2007). "The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families." PLoS Biol 5(3): e16.
Salwinski, L., C. S. Miller, A. J. Smith, F. K. Pettit, J. U. Bowie and D. Eisenberg (2004). "The Database of Interacting Proteins: 2004 update." Nucleic Acids Res 32(Database issue): D449.

BIOL 4024/5024 - Introduction to Biotechnology

BIOL4050/5050 - Advanced Biology Topics: Introduction to Genomics and Bioinformatics

BIOL 6010 - Topics in Integrative and Systems Biology