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 and Gut Microbiome Contributions to Obesity Risk in Golden Retriever Lifetime Study Participants” No budget. In-kind support for sample access and shipping of 400 veterinary samples and associated clinical and survey data. 2017 NSF Division of Environmental Biology, SBS, Proposal 1701970 (PI) 06/01/17 – 05/31/18; awarded Dissertation Research: Intra-population genomic and metabolic diversity among understudied archaea in methane-cycling wetlands $ 20,215 2017 Morris Animal Foundation, D17CLP-801 (PI) 02/01/17 – 01/31/2018; awarded “Examining the Association of Diet, Antimicrobial Exposure and Other Health Exposures with the Fecal Microbiome in Golden Retrievers: A CLHP Pilot Study” $ 4,946

CS Miller 4 2015 DOE Joint Genome Institute Community Science Program - Small Scale, Prop. 2049 (Co-PI) 10/01/2015 - 08/31/2018; awarded “Identifying key genomes and metabolisms responsible for near-surface methane cycling in freshwater wetlands.” (PI: Kelly Wrighton, OSU) in-kind support for DNA and transcriptome sequencing. 2015 DOE Environmental Molecular Sciences Laboratory, Proposal 48859 (Co-PI) 10/01/15 - 9/30/17; awarded “Biogeochemical and genomic determinants of methane cycling in freshwater wetland sediments” (PI: Kelly Wrighton, OSU) $ 136,061 estimated in-kind support for FTICR-MS, NMR metabolomics, transcriptomics, and proteomics Ranked 1st of 46 proposals. 2015 DOE Joint Genome Institute Community Science Program - Small Scale, Prop. 1849 (PI) 02/02/2015 - 03/31/2018; awarded “Developing a systems-level understanding of biotic and abiotic controls on microbial methane cycling in freshwater wetlands.” $ 196,763 estimated in-kind support for DNA sequencing. 2014 DOE Environmental Molecular Sciences Laboratory, Proposal 48641 (Co-PI) 12/23/2014 - 9/30/2015; awarded “High-resolution, parallel measurements of wetland organic carbon and microbial community metabolism under changing redox conditions” (PI: Kelly Wrighton, OSU) $ 41,792 estimated in-kind support for FTICR Mass Spectrometry.

Awarded, internal to CU Denver

2018 CU Denver Office of Research Services and College of Liberal Arts and Sciences (PI) 08/06/2017; awarded Dissemination Grant: Complex evolutionary history of translation Elongation Factor 2 and diphthamide biosynthesis in Archaea and parabasalids. $ 900 2017 CU Denver Office of Research Services and College of Liberal Arts and Sciences (PI) 10/11/2017; awarded Dissemination Grant: High-resolution sequencing reveals unexplored archaeal diversity in freshwater wetland soils. $ 404 2017 CU Denver College of Liberal Arts and Sciences, SITFAC (PI) 04/27/17-05/31/17; awarded High-Impact Practices with High-Performance Computing: an Infrastructure Request in Support of Course-Based Undergraduate Research and Directed Research in Bioinformatics $ 17,950

CS Miller 5 2016 Colorado Center for Personalized Medicine (PI) 09/09/2016-02/14/2017; awarded “Empirical quantification of primer bias in 16S rRNA gene surveys of microbiome samples” in-kind support for 18,000 CPU hours of compute time on Rosalind High Performance Computing System as part of competitive RFA for Beta Users Program 2015 CU Denver Office of Research Services (Co-PI) 07/01/2015; awarded “Linking E. coli toxin production and antibiotic resistance genes in rivers that pose a significant public health risk” (Co-PI: Annika Mosier, University of Colorado Denver) $ 17,183 2015 CU Denver Office of Research Services (PI) 02/18/2015 - 02/17/2015; awarded “Computational assembly of microbial community genomes from complex environments.” $ 25,000 requested, $ 10,000 funded 2014 CU Denver College of Liberal Arts and Sciences, Dissemination Grant (PI) 12/12/2014; awarded “Perturbation and restoration of the fathead minnow gut microbiome after low-level triclosan exposure” $ 2,000 requested, $1,300 funded 2013 CU Denver College of Liberal Arts and Sciences, SITFAC (Co-PI) 01/29/2013; awarded “Request for Funds to Purchase Laptop Computers in Support of Biology Instruction in Quantitative Reasoning” $ 110,448 2012 CU Denver ORS/ORDE Pilot Research Mentor Program Grant (PI) 10/01/2012 - 01/31/2014; awarded “Leveraging Complementary Strengths in Genomics and Applied Microbiology for the Study of Bioenergy-Relevant Microbial Communities.” $ 3,000 requested and funded.

Other Support

2018 NIH T15 Training Grant Supplement to 4T15LM009451-10 (Co-Investigator) 08/24/2018 - 06/30/2019; awarded “Native CUREs: Culturally Inclusive, Course-based Undergraduate Research Experiences in Data Science for Native Americans” (PI: Larry Hunter, CU Denver Anschutz Medical Campus) partial salary support for curriculum development and implementation

CS Miller 6 2013 NIH 1DP7OD018422-01 (Key Personnel) 09/20/2013 - 08/31/2018; awarded “Innovative Biomedical Graduate Training For Workforce Readiness” (PI: Inge Wefes, CU Denver Graduate School) partial summer salary support for 2014, 2015

Pending

2018 DOE Joint Genome Institute New Investigator Community Science Program, Proposal (Co-PI) submitted 09-03-2018; pending “Impacts of antibiotic pollution on freshwater nitrogen cycling” (PI: Annika Mosier, CU Denver) in-kind support for DNA library preparation, DNA sequencing

Unsuccessful

2016 DOE Office of Biological and Environmental Research, TES (Co-PI) 10/01/2016 - 09/30/2019; unsuccessful (submitted 01/21/2015) “Data-driven parameterization of factors controlling methane emissions in freshwater wetlands” (PI: Gil Bohrer, OSU) $ 599,937 requested; $ 64,942 to CU Denver 2016 DOE Office of Biological and Environmental Research, Genome Science (Co-PI) 08/01/2016 - 07/31/2019; unsuccessful (submitted 03/21/2016) “Genomes to Ecosystem function: Targeting critical knowledge gaps in microbial methane cycling” (PI: Kelly Wrighton, OSU) $ 350,030 requested to CU Denver 2015 NSF MCB Systems and Synthetic Biology (PI) 08/01/2016 - 07/31/2019; unsuccessful (submitted 11/16/2015) “Data-driven Inference of the Phylogenetic Distribution of Microbial Traits” $ 386,486 requested to CU Denver 2015 Gulf Of Mexico Research Initiative (Co-PI) Submitted 03/13/2015; unsuccessful “Elucidating metabolic pathways and microorganisms involved in petroleum degradation using high-resolution omic approaches” (PI: Brett Baker, UT Austin Marine Science Institute) $ 1,000,182 requested; $ 242,878 to CU Denver 2015 NSF Division of Environmental Biology, Ecosystem Science (Co-PI) Submitted 01/22/2015; unsuccessful “Biogeochemical and genomic determinants of methane cycling in freshwater wetland sediments” (PI: Kelly Wrighton, OSU) No budget submitted for preliminary proposal

CS Miller 7 2014 DOE Joint Genome Institute Community Science Program - Small Scale (PI) Submitted 05/23/2014; unsuccessful “Opening the microbial black box: characterizing the mechanistic role of dissolved organic carbon in freshwater wetlands methane flux.” in-kind award for services 2014 DOE Office of Biological and Environmental Research (Co-PI) Preliminary proposal submitted 09/03/2014; invited for full proposal, but withdrawn for strategic reasons (planned resubmission in fall 2015) “High-resolution, parallel measurements of organic carbon, geochemistry, and microbial communities to parameterize wetland methane emissions under changing climate scenarios.” (PI: Kelly Wrighton, OSU) $ 1,500,000 total costs requested, with $ 350,000 to CU Denver. 2014 NSF Division of Environmental Biology, Ecosystem Science (Co-PI) Preliminary proposal submitted 01/22/2014; unsuccessful “From genes to ecosystem function: Identifying the unknown microorganisms, pathways, and metabolic interdependencies controlling carbon turnover in freshwater wetlands” (PI: Kelly Wrighton, OSU) No budget submitted for preliminary proposal 2013 DOE Office of Biological and Environmental Research (Co-PI) Invited full proposal submitted 04/19/2013; unsuccessful “Influence of Viral Induced Microbial Lysis on Carbon Cycling” (PI: Karrie Weber, University of Nebraska Lincoln) $ 253,165 total costs requested for CU Denver 2013 NIH National Institute of Environmental Health Sciences (Co-PI) Full proposal submitted 01/16/2013; unsuccessful “Integrated systems analysis of gut microbiome disruption in fishes” (PI: Alan Vajda, University of Colorado Denver) $ 922,576 total costs requested 2013 NIH National Institute of General Medical Sciences (Co-PI) Full Proposal submitted 01/14/2013; unsuccessful “Microbiome Development and Functional Contributions of the Skin Bacterial Community to the Acid, Lipid Environment” (PI: Timberley Roane, University of Colorado Denver) $ 1,516,677 total costs requested

Other Indicators of Scholarly and Creative Activity

Summary citation statistics (Google Scholar as of September 13, 2018): All citations 4272 (from 22 publications) h-index 15 (15 publications have at least 15 citations) i10-index 19 (18 publications have at least 10 citations)

CS Miller 8 Presentations at Meetings (* student authors)

2018 Narrowe, A.B.*, Solden, L.M., Angle, J.C., Borton, M.A., Daly, R.A., Miller, C.S., Wrighton, K.C. Genome-enabled resolution of archaeal phylogenetic and metabolic diversity in methanogenic freshwater wetlands. International Symposium on Microbial Ecology, Leipzig, Germany. Poster. 2017 DeHay, K.*, Simpson, M, Wolfe, B.A., Miller, C.S. Please pick up after your pet: composition and correlates with health of the golden retriever gut microbiome. Colorado Clinical and Translational Sciences Institute Microbiome Summit, Thornton, CO. Poster. 2017 Miller, C.S. Targeted assembly of genes and genomes for a deeper view into archaeal populations in microbial communities. Society for Industrial Microbiology and Biotechnology Annual Meeting, Denver, CO. Invited Talk. 2017 Narrowe A.B.*, Angle J.C., Daly R.A., Stefanik K.C., Wrighton K.C., Miller C.S. Targeted exploration of archaeal genomic, phylogenetic, and spatial diversity in freshwater wetland soils. DOE Joint Genome Institute Genomics of Energy & Environment Meeting, Walnut Creek, CA. Poster. 2017 Narrowe, A.B.*, Angle, J.C., Daly, R.C., Stefanik, K.C., Wrighton, K.C., Miller, C. S. Targeted exploration of archaeal genomic, phylogenetic, and spatial diversity in freshwater wetland soils. DOE JGI NeLLi 2017: From New Lineages of Life to New Functions, Walnut Creek, CA. Poster. 2016 Banks-Richardson, D.*, Narrowe, A.B.*, Miller, C.S. Insights into Bathyarcheota Ecology and Co-occurrence Patterns as Revealed by Public Metagenome Sequencing Data. ISCB Rocky Mountain Bioinformatics Conference, Snowmass, CO. Poster and Selected Talk. 2016 Iyer, M.R.*, Miller, C.S. Prediction of Prokaryotic Optimum Growth Temperature Based on Genomic and Proteomic Features. ISCB Rocky Mountain Bioinformatics Conference, Snowmass, CO. Poster. 2016 Narrowe, A.B.*, Angle, J.C., Daly, R.A., Stefanik, K.C., Borton, M.A., Wrighton, K.C., Miller, C.S. Archaeal and bacterial distribution and diversity across spatial and geochemical gradients within a methane-emitting freshwater wetland. International Symposium on Microbial Ecology, Montreal, Canada. Poster (student travel award). 2016 Narrowe A.B.*, Angle J.C., Daly R.A., Stefanik K.C., Wrighton K.C., Miller C.S. Recovering archaeal and bacterial community structure through reconstruction of 16S rRNA amplicon sequences Front Range Computational and Systems Biology Symposium, Fort Collins, CO. Poster. 2015 Narrowe, A.B.*, Angle, J.C., Daly, R.A., Stefanik, K.C., Wrighton, K.C., Miller, C.S. Genome level insights into methane cycling communities across temperate freshwater wetlands biogeochemical gradients. General Meeting of the American Society for Microbiology, New Orleans, LA. Poster (student travel award). 2014 Narrowe, A.B.*, Bleeker, C.*, Liu, C.*, Miller, C.S. EMIRGE 2: Improved Resolution of Microbial Community Structure. ISCB Rocky Mountain Bioinformatics Conference, Snowmass, CO. Poster and Selected Talk.

CS Miller 9 2013 Miller, C.S. et al. Data-Driven Microbiology. American Society for Microbiology Conference for Undergraduate Educators, Englewood, CO. Invited Talk. 2013 Lantz M.A.*, Narrowe A.B.*, Roane T.M., Miller C.S., Vajda A.M. Gut Microbiome Disruption by Environmental Toxicants in Fish. General Meeting of the American Society for Microbiology, Denver, CO. Poster. 2012 Miller, C.S., Handley, K.M., Wrighton, K.C., Frischkorn, K.R., Thomas, B.C., Banfield, J.F. Deep Sequencing and Assembly of Targeted Amplicons in Microbial Communities. ISCB Rocky Mountain Bioinformatics Conference, Snowmass, CO. Invited Keynote Talk. 2012 Miller, C.S. Mosier, A.C., Grigoriev, I.V., Pan, C., Hettich, R.L., Singer, S.W., Banfield J.F. Fungal Metabolism at pH 1: Genomic, Transcriptomic, and Proteomic Analyses of a Natural Microbial Community. General Meeting of the American Society for Microbiology, San Francisco, CA. Selected Talk. 2012 Miller, C.S., Brooks, B.B., Sharon, I, Wrighton, K.C., Handley, K.M., Thomas, B.C., Banfield, J.F. EMIRGE: Sensitive, quantitative microbial community characterization via deep sequencing and assembly of full-length 16S amplicons. International Human Microbiome Congress, Paris, France. Poster (travel award). 2006 Miller, C.S. Li, H., Eisenberg, D. Annotation of Environmental Sequencing Data with Non-Homology Methods. Microbial Community Genomics in Animals and in the Environment, Tahoe City, CA. Poster. 2004 Miller, C.S., Salwiński, Ł., Riley, R., Eisenberg, D. Extracting High Confidence Protein- Protein Interactions From Large Scale Mass Spectrometry Data. Biological Discovery Using Diverse High-Throughput Data, Steamboat Springs, CO. Poster (travel award).

Invited Seminars/Workshops Presented

2017 Unearthing deep archaeal diversity in methane-emitting freshwater wetlands. Microbiome Network, Colorado State University. Ft. Collins, CO. 2017 The Microbial Communities Within Our Dogs. Morris Animal Foundation Board of Trustees Meeting, Denver, CO. 2015 Targeted rRNA gene assembly for high-resolution inference of microbial community structure. The Center for Applied Plant Sciences Seminar Series, The Ohio State University, Columbus, OH. 2015 Mud and Guts: Assembling Genes and Genomes to Gain Insights Into Diverse Microbial Communities. The Power of Informatics to Advance Health Mini-Symposium, University of Colorado Anschutz Medical Campus, Aurora, CO. 2015 Using EMIRGE for assembly of full-length rRNA genes from short-read data. University of Colorado Boulder EBIO 5460: Molecular Methods in Microbial Ecology, Boulder, CO. 2014 Mud, fish guts, and acid mine drainage: microbe-hunting after the Eisenberg lab. David Eisenberg Symposium, UCLA, Los Angeles, CA. 2013 Microbial communities through the lens of high-throughput sequencing and computation. University of Colorado Denver Tri Beta Biological Honors Society Meeting, Denver, CO

CS Miller 10 2012 Bioinformatic and genome-enabled approaches for the study of microbial communities. University of Colorado Denver AMC Computational Biosciences Program, Aurora, CO. 2012 Getting to know the members of your community: High-throughput sequencing and computation for microbial community systems biology. University of Colorado Denver Department of Integrative Biology, Denver, CO. 2011 Deep sequencing of genes and genomes from microbial communities. OPX Biotechnologies, Boulder, CO. 2011 Next-generation sequencing tools for getting to know the members of your community. University of California, Berkeley ESPM 112: Microbial Ecology, Berkeley, CA.

Professional Organizations (current)

American Society for Microbiology

Courses Taught

Advanced Biology Topics: Introduction to Genomics and Bioinformatics (BIOL 4050/5050) Advanced Biology Topics: Personalized Medicine and Bioinformatics (BIOL 4050/5050) Biology Seminar (BIOL 4990/6655) Genomics and Bioinformatics (BIOL 4225/5225) Introduction to Biotechnology (BIOL 4024/5024) Methods and Tools in Biomedical Informatics (CPBS 7711; co-taught, 1 lecture / year) Research Methods in Biomedical Informatics (CPBS 7712; co-taught, 2 lectures / year) Research Seminar (BIOL 4990/6655) Topics in Integrative and Systems Biology (BIOL 7010, BIOL 6010)

Service

2008-present Reviewer for Bioinformatics, Frontiers in Microbiology, The ISME Journal, Microbiome, Molecular Ecology Resources, Molecular Phylogenetics and Evolution, Nature Communications, PLoS Computational Biology, PeerJ, Scientific Reports 2018-present Department of Integrative Biology, Curriculum Committee 2015-present Department of Integrative Biology, Biotechnology Certificate Faculty Advisor 2013-present Department of Integrative Biology, Graduate Advisory Committee 2011-present Maintain and support open source microbial ecology software, EMIRGE. 2018 Department of Integrative Biology, Tenure Track Faculty Search Committee Chair for Systems Biologist in Physiology 2018 Proposal Reviewer for Department of Energy Joint Genome Institute Community Science Program New Investigator Proposals 2018 CU Denver College of Liberal Arts and Sciences Capital Equipment Fund Grant Review Committee 2018 CU Denver Faculty Assembly (1 semester)

CS Miller 11 2017-2018 Department of Integrative Biology, Tenure Track Faculty Search Committee for Quantitative Biologist 2017 Proposal Reviewer for Department of Energy Joint Genome Institute Community Science Program Annual Call 2017 Session Convener for Society for Industrial Microbiology and Biotechnology Annual Meeting: “Computational techniques for studying the microbiome” 2017 Abstract Reviewer for American Society of Microbiology Microbe 2017 meeting, Systems Biology sub-track 2014-2018 CU Denver, Grant Reviewer for Undergraduate Research Opportunities Program 2014-2018 CU Denver, Organizing committee for the Mini-Symposium on The Power of Informatics to Advance Health 2016, 2017 Department of Integrative Biology, PhD in Integrative and Systems Biology preliminary exam committee 2016 Proposal Reviewer for Department of Energy Joint Genome Institute Small-Scale Community Science Program: Microbial / Metagenome program 2016 Public lecture for CU Denver Mini-STEM School: Using Cheap DNA Sequencing to See the Microbial Communities All Around Us. 2013-2015 CU Denver, Curriculum Development for Professional Science Masters degrees in Biotechnology and Bioinformatics (partially compensated via NIH BEST award) 2015 Computational Bioscience Program, PhD admissions committee 2015 CU Denver, Professional Science Masters in Biomedical Sciences and Biotechnology Admissions Committee 2014-2015 CU Denver, Graduate School Dean Search Committee 2014 Computational Bioscience Program, Preliminary Exam Committee 2014 Computational Bioscience Program, Annual Retreat Organizer 2014 Department of Integrative Biology, Ad-hoc committee on Quantitative Reasoning curriculum development 2012-2013 Department of Integrative Biology, Tenure Track Faculty Search Committee for Microbiologist 2013 CU Denver, Poster Judge, Research and Creative Activities Symposium 2013 Department of Integrative Biology, PhD in Integrative and Systems Biology recruitment weekend 2013 Computational Bioscience Program, PhD in Computational Bioscience recruitment weekend 2013 Department of Integrative Biology, SITFAC Fund Application (awarded), Laptop Computers in Support of Biology Instruction in Quantitative Reasoning 2012 Department of Integrative Biology, Steering Committee for PhD Program in Integrative and Systems Biology

CS Miller 12