Dr. Aaron Best

Dr. Aaron Best began working at 麻豆视频网站 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 鈥� 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 鈥� 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 鈥� Aaron鈥檚 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 鈥� 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鈥檚 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鈥�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, 鈥溾€� (topic proposal approved by Frontiers In editor), acting as lead editor for the topic, 2014鈥損resent
Editorial board member (Microbiology section) for the Nature Publishing Group international open access journal, Scientific Reports, 2011鈥損resent

Selected grants

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

Selected publications

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