CURRICULUM VITAE Christopher S. Miller Campus Address Department of Integrative Biology Campus Box 171 PO Box 173364 Denver, CO 80217-3364 Phone: 303-315-7665 [email protected] Education 2008 PhD University of California, Molecular Biology Los Angeles Dissertation: “Computational Inference of Protein Structure and Function from Microbial Genomes and Metagenomes” 2002 BA University of Colorado, Molecular, Cellular, and Developmental Biology Boulder minor: Computer Science Professional Experience 2012 – present Assistant Professor – University of Colorado Denver Department of Integrative Biology Computational Bioscience Program 2009 – 2012 Postdoctoral Researcher – University of California, Berkeley Department of Earth and Planetary Science: laboratory of Dr. Jillian Banfield. 2003 – 2008 Graduate Student Researcher– University of California, Los Angeles Molecular Biology Institute: laboratory of Dr. David Eisenberg. Peer Reviewed Publications (* Miller lab member) 2018 Narrowe, A.B.* †, Spang, A. †, Caceres, E.F., Baker, B.J., Miller, C.S. ^#, Ettema, T.J.G.#, 2018. Complex evolutionary history of Elongation Factor 2 and diphthamide biosynthesis in Archaea and parabasalids. Genome Biology and Evolution, in press. (†, # equal contributions; ^ Corresponding author). Advance Article available at https://academic.oup.com/gbe/advance-article/doi/10.1093/gbe/evy154/5060531 2017 Angle, J.C., Morin, T.H., Solden, L.M., Narrowe, A.B.*, Smith, G.J., Borton, M.A., Rey- Sanchez, C., Daly, R.A., Mirfenderesgi, G., Hoyt, D.W., Riley, W.J., Miller, C.S., Bohrer, G. & Wrighton, K.C., 2017. Methanogenesis in oxygenated soils is a substantial fraction of wetland methane emissions. Nature Communications, 8(1), p.1567. 1 2017 Narrowe, A.B.*, Angle, J.C., Daly, R.A., Stefanik, K.C., Wrighton, K.C. & Miller, C.S., 2017. High-resolution sequencing reveals unexplored archaeal diversity in freshwater wetland soils. Environmental Microbiology, 19(6), pp.2192-2209. 2016 Mosier, A.C., Miller, C.S., Frischkorn, K.R., Ohm, R.A., Li, Z., LaButti, K., Lapidus, A., Lipzen, A., Chen, C., Johnson, J., Lindquist, E.A., Pan, C., Hettich, R.L., Grigoriev, I. V, Singer, S.W. & Banfield, J.F., 2016. Fungi Contribute Critical but Spatially Varying Roles in Nitrogen and Carbon Cycling in Acid Mine Drainage. Frontiers in Microbiology, 7(238). 2015 Andrade, K., Logemann, J., Heidelberg, K.B., Emerson, J.B., Comolli, L.R., Hug, L.A., Probst, A.J., Keillar, A., Thomas, B.C., Miller, C.S., Allen, E.E., Moreau, J.W., Brocks, J.J. & Banfield, J.F., 2015. Metagenomic and lipid analyses reveal a diel cycle in a hypersaline microbial ecosystem. The ISME journal, 9(12), pp.2697–711. 2015 Narrowe, A.B.*, Albuthi-Lantz, M., Smith, E.P.*, Bower, K.J.*, Roane, T.M., Vajda, A.M. & Miller, C.S., 2015. Perturbation and restoration of the fathead minnow gut microbiome after low-level triclosan exposure. Microbiome, 3(1), p.6. 2015 Handley, K.M., Wrighton, K.C., Miller, C.S., Wilkins, M.J., Kantor, R.S., Thomas, B.C., Williams, K.H., Gilbert, J. A., Long, P.E. & Banfield, J.F., 2015. Disturbed subsurface microbial communities follow equivalent trajectories despite different structural starting points. Environmental microbiology, 17(3), pp.622-636. 2014 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. 2013 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. 2013 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. PLoS ONE, 8(3), p.e57819. 2013 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. 2012 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. 2012 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. CS Miller 2 2011 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. 2011 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. 2011 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. 2008 Miller, C.S. & Eisenberg, D., 2008. Using inferred residue contacts to distinguish between correct and incorrect protein models. Bioinformatics, 24(14), pp.1575–82. 2008 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. 2008 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. 2007 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. 2004 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. Non-Peer Reviewed Publications 2017 Narrowe, A.B.*, Miller, C.S. & Lozupone, C., 2017. Microbial Biodiversity: Straight from the Dolphin’s Mouth. Current Biology, 27(24), pp.R1307–R1309. (invited commentary) Non-Peer Reviewed Books and Book Chapters 2013 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. CS Miller 3 Publications/Creative Works in Preparation and Under Review Iyer, M.*, Miller, C.S. Dipeptide frequencies outperform other genomic and proteomic features in predicting microbial optimum growth temperature. Under review at Frontiers in Genetics, Section: Bioinformatics and Computational Biology. Narrowe, A.B.*, Borton, M.A., McGivern, B.B., Rodriguez-Ramos, J.A., Solden, L.M., Daly, R.A., Wrighton, K.C., Miller, C.S. Freshwater wetland metagenomes reveal expanded metabolic potential within the Bathyarchaeota. Manuscript in preparation. DeHay, K.*, Simpson, M, Wolfe, B.A., Miller, C.S. Golden Retriever Microbiome Composition is Associated with Canine Heath Status. Manuscript in preparation. Grants Awarded, external support 2018 DOE Joint Genome Institute Community Science Program, Proposal 504205 (Co-PI) 10/01/2018-09-30-2021; awarded “From genomes to methane production: targeting critical knowledge gaps in wetland soils” (PI: Kelly Wrighton, OSU) Substantial in-kind support for 11.5 Tbp of DNA library preparation, DNA sequencing, Transcriptomics, Informatics, and Metabolomics. 2018 DOE Environmental Molecular Sciences Laboratory, Proposal 50229 (Co-PI) 10/01/2018-09/30/2020; awarded “Methanogenesis in wetland soils: It may not always be as deep as we all thought” (PI: Kelly Wrighton, OSU) $154,418 estimated in-kind support for advanced metabolomics, proteomics, and micro- CT instrument time and staff support to characterize wetland soils. 2018 Morris Animal Foundation, Golden Retriever Lifetime Study Pilot Study Proposal (PI) 04/01/2018 - 03/31/2019; awarded “Determining Environmental