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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

​2015 Spring Semester Office Hours:


Areas of Expertise:
The Miller Lab​
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.

Dr. Miller is core faculty in the Computational Bioscience Program​ at the University of Colorado Anschutz Medical Campus.

Brooks, B., Firek, B.A., Miller, C.S., Sharon, I., Thomas, B.C., Baker, R., Morowitz, M.J. & Banfield, J.F., 2014. Microbes in the neonatal intensive care unit resemble those found in the gut of premature infants. Microbiome, 2(1), p.1.

Handley, K.M., Verberkmoes, N.C., Steefel, C.I., Williams, K.H., Sharon, I., Miller, C.S., Frischkorn, K.R., Chourey, K., Thomas, B.C., Shah, M.B., Long, P.E., Hettich, R.L. & Banfield, J.F., 2013. Biostimulation induces syntrophic interactions that impact C, S and N cycling in a sediment microbial community. The ISME journal, 7, pp.800–816.

Miller, C.S., Handley, K.M., Wrighton, K.C., Frischkorn, K.R., Thomas, B.C. & Banfield, J.F., 2013. Short-Read Assembly of Full-Length 16S Amplicons Reveals Bacterial Diversity in Subsurface Sediments. PloS one, 8(2), p.e56018.

Miller, C.S., 2013. Assembling full-length rRNA genes from short-read metagenomic sequence datasets using EMIRGE. E. F. DeLong, ed. Methods in enzymology, 531, pp.333–52.

Wilkins, M.J., Wrighton, K.C., Nicora, C.D., Williams, K.H., McCue, L.A., Handley, K.M., Miller, C.S., Giloteaux, L., Montgomery, A.P., Lovley, D.R., Banfield, J.F., Long, P.E. & Lipton, M.S., 2013. Fluctuations in Species-Level Protein Expression Occur during Element and Nutrient Cycling in the Subsurface. K. Rockne, ed. PloS one, 8(3), p.e57819.

Justice, N.B., Pan, C., Mueller, R., Spaulding, S.E., Shah, V., Sun, C.L., Yelton, A.P., Miller, C.S., Thomas, B.C., Shah, M., Verberkmoes, N., Hettich, R. & Banfield, J.F., 2012. Heterotrophic Archaea Contribute to Carbon Cycling in Low-pH, Suboxic Biofilm Communities. Applied and environmental microbiology, 78(23), pp.8321–30.

Wrighton, K.C., Thomas, B.C., Sharon, I., Miller, C.S., Castelle, C.J., VerBerkmoes, N.C., Wilkins, M.J., Hettich, R.L., Lipton, M.S., Williams, K.H., Long, P.E. & Banfield, J.F., 2012. Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla. Science, 337(6102), pp.1661–5.

Fujishima, K., Sugahara, J., Miller, C.S., Baker, B.J., Di Giulio, M., Takesue, K., Sato, A., Tomita, M., Banfield, J.F. & Kanai, A., 2011. A novel three-unit tRNA splicing endonuclease found in ultrasmall Archaea possesses broad substrate specificity. Nucleic acids research, 39(22), pp.9695–704.

Gladden, J.M., Allgaier, M., Miller, C.S., Hazen, T.C., VanderGheynst, J.S., Hugenholtz, P., Simmons, B.A. & Singer, S.W., 2011. Glycoside hydrolase activities of thermophilic bacterial consortia adapted to switchgrass. Applied and environmental microbiology, 77(16), pp.5804–12.

Miller, C.S., Baker, B.J., Thomas, B.C., Singer, S.W. & Banfield, J.F., 2011. EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data. Genome biology, 12(5), p.R44.

Cruz, D., Watson, A.D., Miller, C.S., Montoya, D., Ochoa, M.-T., Sieling, P.A., Gutierrez, M.A., Navab, M., Reddy, S.T., Witztum, J.L., Fogelman, A.M., Rea, T.H., Eisenberg, D., Berliner, J. & Modlin, R.L., 2008. Host-derived oxidized phospholipids and HDL regulate innate immunity in human leprosy. The Journal of clinical investigation, 118(8), pp.2917–28.

Miller, C.S. & Eisenberg, D., 2008. Using inferred residue contacts to distinguish between correct and incorrect protein models. Bioinformatics, 24(14), pp.1575–82.

Williamson, S.J., Rusch, D.B., Yooseph, S., Halpern, A.L., Heidelberg, K.B., Glass, J.I., Andrews-Pfannkoch, C., Fadrosh, D., Miller, C.S., Sutton, G., Frazier, M. & Venter, J.C., 2008. The Sorcerer II Global Ocean Sampling Expedition: metagenomic characterization of viruses within aquatic microbial samples. PloS one, 3(1), p.e1456.

Yooseph, S., Sutton, G., Rusch, D.B., Halpern, A.L., Williamson, S.J., Remington, K., Eisen, J.A., Heidelberg, K.B., Manning, G., Li, W., Jaroszewski, L., Cieplak, P., Miller, C.S., Li, H., Mashiyama, S.T., Joachimiak, M.P., van Belle, C., Chandonia, J.-M., Soergel, D.A., Zhai, Y., Natarajan, K., Lee, S., Raphael, B.J., Bafna, V., Friedman, R., Brenner, S.E., Godzik, A., Eisenberg, D., Dixon, J.E., Taylor, S.S., Strausberg, R.L., Frazier, M. & Venter, J.C., 2007. The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS biology, 5(3), p.e16.

Salwinski, L., Miller, C.S., Smith, A.J., Pettit, F.K., Bowie, J.U. & Eisenberg, D., 2004. The Database of Interacting Proteins: 2004 update. Nucleic acids research, 32(Database issue), pp.D449–51.


BIOL 4024/5024 - Introduction to Biotechnology

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

BIOL 6010 - Topics in Integrative and Systems Biology