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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 亚洲色吧� 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 亚洲色吧� 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 亚洲色吧� Aaron亚洲色吧檚 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 亚洲色吧� 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亚洲色吧檚 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亚洲色吧�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, 亚洲色吧溠侵奚�吧� (topic proposal approved by Frontiers In editor), acting as lead editor for the topic, 2014亚洲色吧損resent
• Editorial board member (Microbiology section) for the Nature Publishing Group international open access journal, Scientific Reports, 2011亚洲色吧損resent

Selected grants

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

Selected publications

• 亚洲色吧淭he DOE Systems Biology Knowledgebase (KBase),亚洲色吧� with A.P. Arkin, R.L. Stevens, R.W. Cottingham, S. Maslov, C.S. Henry, et al., Nature Biotechnology, in press
• 亚洲色吧�,亚洲色吧� with N. Bowerman, N. Tintle and M. DeJongh, Biocomputing 2017, World Scientific, 2017 
• 亚洲色吧�,亚洲色吧� with A.L. Porter, S.M. Fraley and G.S. Fraley, Frontiers in Microbiology 7:2125, 2017
• 亚洲色吧�,亚洲色吧� 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
• 亚洲色吧�,亚洲色吧� with A. Schenk, A.L. Porter, E. Alenciks, K. Frazier, S.M. Fraley, et al., Poultry Science 95.4, 2016
• 亚洲色吧�,亚洲色吧� with S. Powers, M. DeJongh and N.L. Tintle, Frontiers in Microbiology 6, 2015
• 亚洲色吧�,亚洲色吧� 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
• 亚洲色吧�,亚洲色吧� with D.A. Ravcheev, N. Tintle, M. DeJongh, A.L. Osterman, P.S. Novichkov and D.A. Rodionov,  Journal of Bacteriology 193, 2011
• 亚洲色吧�,亚洲色吧� with C.S. Henry, M. DeJongh, P. Frybarger, B. Linsay and R.L. Stevens, Nature Biotechnology, 28, 2010
• 亚洲色吧�,亚洲色吧� 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
• 亚洲色吧� Giardia lamblia,亚洲色吧� 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

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