Dr. Aaron Best began working at Hope College in fall 2004 after completing graduate work and post-doctoral training in the fields of microbiology and microbial evolution at the University of Illinois at Urbana-Champaign. His research includes understanding the unique process of transcription in the human parasite Giardia lamblia, the integration of large scale data sets into models of metabolism for bacteria and the microbial ecology of the Macatawa Watershed. Each project hinges on the use of DNA sequences to guide questions and hypotheses. His teaching occurs through one-on-one interactions with students in research projects in his lab, classroom-based research laboratory experiences for first-year and upper-level students, and interactive courses in the area of microbiology and bioinformatics. 

AREAS OF INTEREST

• Microbial genomics — Comparative genomics, genome-scale metabolic modeling, transcriptional regulatory network modeling, identification of missing gene function, genome sequencing and microbial ecology of different ecosystems.
• Microbial evolution — Comparative analyses of transcription systems in eukaryotes, mechanisms of transcription in Giardia lamblia, evolution of metabolic and transcriptional networks in microbes.

Approach at a Primarily Undergraduate Institution

• Convergence — Aaron’s research interests are best approached using techniques ranging from targeted biochemical and molecular studies to modeling and interpretation of the large-scale data sets being produced in the biological sciences today. The techniques and questions sit at the interface among multiple disciplines. Therefore, his work is largely collaborative to bring multi-disciplinary perspectives and skills to the studies at hand. Working in the context of a primarily undergraduate institution in a biology department provides rich opportunities for investigating problems on multiple scales of biology and allows for fruitful collaboration with large research institutions.
• Integration of research into courses — Course-based research experiences (CREs) are beneficial to both the research program and to the students. CREs often produce useful preliminary data and provide recruiting opportunities for students trained in the project area. CREs allow more students to learn science by actually doing science. Many of the major areas of Aaron’s research interests have been implemented as CREs in courses that he teaches.

EDUCATION

• Post-doc, microbial evolution, University of Illinois at Urbana-Champaign (Carl R. Woese, Ph.D., advisor), 2002–2004
• Ph.D., microbiology, University of Illinois at Urbana-Champaign (Gary J. Olsen, Ph.D., advisor), 2001
  Thesis: Evolution of transcription in Archaea and the early-diverging eukaryote, Giardia lamblia
• M.S., microbiology, University of Illinois at Urbana-Champaign, (Gary J. Olsen, Ph.D., advisor), 1999
• B.A., biology, William Jewell College, Liberty, Missouri (Paul W. Gabrielson, Ph.D, thesis advisor), 1996
  Thesis: Assessing phylogenetic relationships among red algae using 18S ribosomal DNA

HONORS and AWARDS

• 2017 Watershed Stakeholder of the Year Award, Macatawa Watershed Project of the Macatawa Area Coordinating Council
• Inaugural holder of the Harrison C. and Mary L. Visscher Endowed Professorship in Genetics, Hope College
• Towsley Research Scholar, Hope College
• Visiting Research Scientist, The Sanford Burnham Medical Research Institute, La Jolla, California
• Argonne National Laboratory Guest Faculty Research Program
• Guest associate editor for Nature, Frontiers in Microbiology, hosting the research topic, “Towards Integrated Metabolic and Regulatory Models of All Microbial Life” (topic proposal approved by Frontiers In editor), acting as lead editor for the topic, 2014–present
• Editorial board member (Microbiology section) for the Nature Publishing Group international open access journal, Scientific Reports, 2011–present

Selected grants

• National Science Foundation, Award Number MCB-1716285, “Collaborative Research: RUI: Investigating microbial metabolic and regulatory diversity by modeling gene activity states inferred from transcriptome data,” PI: Best A  and DeJongh M, September 2017–August 2020, $488,522
• National Science Foundation, Award Number MCB-1616737, “RUI: Dynamics of Genomic Mosaicism in Non-Host Associated Escherichia Populations,” PI: Best A, August 2016–July 2019, $775,316
• Sawyer Products, “Global Survey of Microbial Populations and Chemical Contaminants in Water Sources,” PI: Best A, Peterson J, Pikaart M and Peaslee G, July 2016–December 2017, $314,000
• Herbert H. and Grace A. Dow Foundation, “Meeting the Persistent Challenges: Recruiting, Retaining, and Graduating Michigan STEM Students,” with C. Mader and G. Peaslee, December 2014–November 2017
• National Science Foundation, Award Number MCB-1330734, “Collaborative Research: RUI: Developing Integrated Metabolic Regulatory Models (iMRMs) for the Investigation of Metabolic and Regulatory Diversity of Sequenced Microbes,” with M. DeJongh, October 2013–September 2016
• National Science Foundation, Award Number DBI-1229585, “MRI: Acquisition of a Benchtop Next Generation Sequencing Platform to Enhance Undergraduate Research and Education at Hope College,” with J. Li, September 2012–August 2015
• Department of Energy, Subcontract Number 2F-30041, “KBase: An Integrated Knowledgebase for Predictive Biology and Environmental Research,” with M. DeJongh and N. Tintle, October 2011–September 2016
• National Science Foundation, Award Number ABI-0850546, “Extending the RAST Server to Support Reconstruction and Modeling of Cellular Networks,” with M. DeJongh, N. Tintle, D. Rodionov and R. Overbeek, September 2009–August 2012
• National Science Foundation, Award Number MCB-0745100, “RUI: Automated Metabolic Reconstruction for All Sequenced Microbial Genomes,” with M. DeJongh, August 2008–July 2012

Selected publications

• “The DOE Systems Biology Knowledgebase (KBase),” with A.P. Arkin, R.L. Stevens, R.W. Cottingham, S. Maslov, C.S. Henry, et al., Nature Biotechnology, in press
• “Identification and Analysis of Bacterial Genomic Metabolic Signatures,” with N. Bowerman, N. Tintle and M. DeJongh, Biocomputing 2017, World Scientific, 2017 
• “Characterization of Gut Microbiome Dynamics in Developing Pekin Ducks and Impact of Management System,” with A.L. Porter, S.M. Fraley and G.S. Fraley, Frontiers in Microbiology 7:2125, 2017
• “A Bayesian Framework for the Classification of Microbial Gene Activity States,” with C. Disselkoen, B. Greco, K. Cook, K. Koch, R. Lerebours, C. Viss, J. Cape, E. Held, Y. Ashenafi, K. Fischer, A. Acosta, M. Cunningham, M. DeJongh and N. Tintle, Frontiers in Microbiology 7:1191, 2016
• “Increased water contamination and grow-out Pekin duck mortality when raised with water troughs compared to pin-metered water lines using a United States management system,” with A. Schenk, A.L. Porter, E. Alenciks, K. Frazier, S.M. Fraley, et al., Poultry Science 95.4, 2016
• “Cautions about the reliability of pairwise gene correlations based on expression data,” with S. Powers, M. DeJongh and N.L. Tintle, Frontiers in Microbiology 6, 2015
• “Comparative genomics and functional analysis of rhamnose catabolic pathways and regulons in Bacteria,” with I.A. Rodionova, X. Li, V. Thiel, S. Stolyar, K. Stanton, J.F. Fredrickson, D.A. Bryant, A.L. Osterman and D.A. Rodionov, Frontiers in Microbiology 4, 2013
• “Inference of the Transcriptional Regulatory Network in Staphylococcus aureus by Integration of Experimental and Genomics-Based Evidence,” with D.A. Ravcheev, N. Tintle, M. DeJongh, A.L. Osterman, P.S. Novichkov and D.A. Rodionov,  Journal of Bacteriology 193, 2011
• “High-throughput generation, optimization and analysis of genome-scale metabolic models,” with C.S. Henry, M. DeJongh, P. Frybarger, B. Linsay and R.L. Stevens, Nature Biotechnology, 28, 2010
• “The RAST Server: Rapid Annotations using Subsystems Technology,” with R.K. Aziz, D. Bartels, M. DeJongh, T. Disz, R.A. Edwards, K. Formsma, S. Gerdes, E.M. Glass, M. Kubal, F. Meyer, G.J. Olsen, R. Olson, A.L. Osterman, R.A. Overbeek, L.K. McNeil, D. Paarmann, T. Paczian, B. Parrello, G.D. Pusch, C. Reich, R. Stevens, O. Vassieva, V. Vonstein, A. Wilke and O. Zagnitko, BMC Genomics, 9, 2008
• “Genomic minimalism in the early diverging, intestinal parasite, Giardia lamblia,” with H.G. Morrison, A.G. McArthur, F.D. Gillin, S.B. Aley, R.D. Adam, G.J. Olsen, W.Z. Cande, F. Chen, M.J. Cipriano, B.J. Davids, S.C. Dawson, H.G. Elmendorf, A.B. Hehl, M.E. Holder, S.M. Huse, U.U. Kim, E. Lasek-Nesselquist, G. Manning, A. Nigam, J.E.J. Nixon, D. Palm, N.E. Passamaneck, A. Prabhu, C.I. Reich, D.S. Reiner, J. Samuelson, S.G. Svard and M.L. Sogin, Science, 317, 2007

View a complete list of Aaron’s publications.