Systematic Ornithology —  As a first love in science, Peterson maintains active interests in systematic ornithology. Working with Robert Moyle and Mark Robbins, Peterson codirects the Division of Ornithology in the University of Kansas Biodiversity Institute. In particular, they codirect one of the most active graduate programs in systematic ornithology globally, and simultaneously one of the most active global bird sampling programs. Division research is  generally specimen based,  and explores diverse topics of the evolution, distribution, and diversity of birds worldwide.

Distributional Ecology — Over the past 20 years, Peterson has become intensely interested in the environmental, landscape, and biotic factors that together constrain and shape the geographic distributions of species.  With colleague Jorge Soberón and others, Peterson has explored conceptual dimensions of these questions, as well as many practical and applied  applications of deep understanding of distributional ecology to biodiversity-related questions. This work was summarized in a 2011 book, published by Princeton University Press,  entitled Ecological Niches and Geographic Distributions,  which was co-authored with six valued colleagues. Petersons distributional ecology work continues, largely in collaboration with members of the Biodiversity and Macroecology Laboratory.

Historical Biogeography —  Peterson has an intense interest in the historical processes of landscape and climate change that have shaped the evolution and distribution of biodiversity. This work has evolved out of exploration of the potential of ecological niche modeling to inform about paleodistributional patterns,  particularly in tandem with molecular sequence data and quantitative phylogeographic analyses. Currently,  Peterson is working with regionwide assessments of historical biogeographic patterns underlying phylogeographic patterns across the Amazon Basin,  in Southeast Asia, and in the tepui region of northern South America.

Disease Transmission — Over the past 15 years, Peterson has extended his interests in distributional ecology to reflect on mapping challenges in the area of disease transmission risk mapping. This work has led him to collaborate with specialists expert in dengue, malaria, Ebola, Chagas disease, hantavirus,  plague, tularemia, and many other zoonotic diseases. On a more conceptual level, this work has resulted in a new viewpoint on spatial epidemiology and mapping challenges related to disease transmission risk. Much of this work is now summarized in a book to be published by Johns Hopkins University Press,  as well as in many published scientific journal articles.

Online Learning Resources for Biodiversity — A major project that began in 2012 is the Biodiversity Informatics Training Curriculum,  which received major funding from the JRS Biodiversity Foundation. The program consists of developing detailed and comprehensive in-person training courses and the online digital training resources covering the entirety of the field of biodiversity informatics.  The project centers on Africa, and has already held training courses in Kenya, South Africa, Ghana, Uganda, and Cameroon, and has courses planned for Ethiopia and Taiwan.  Project information is coordinated via a Facebook page,  and all training resources are made available via a project website.

Chickens and Junglefowl —  A long-term project in which Peterson has been involved constitutes a 17 year collaboration with I. Lehr Brisbin, of the Savannah River Ecology Laboratories (now retired), and several other colleagues. The project centers on a population of Red Junglefowl  that appear to be the only, or one of very few, genetically pure populations of this most important bird species, which gave rise to the domestic chicken. This project has involved behavioral studies, hybridization experiments, phenotypic analyses, and now of genomic analyses of this unique population of junglefowl.

Virtual Vector Laboratory — With generous support from the Office of the Provost of the University of Kansas, Peterson has been working for the past two years in close collaboration with the Information and Telecommunication Technology Center and Spencer Art Museum of the University of Kansas, the University of Brasilia, and the National Public Health Institute of Mexico to develop automated identification systems for the vectors of Chagas’ disease. This project is presently in an advanced prototype stage, and is seeing active development, both in the area of technology development and data resource development, but also in active implementation of usable, real-world knowledge infrastructures for public health applications.