Hi, I'm Daniel, a research scientist with interests in bioinformatics, genome biology, and research software engineering. I am committed to open, transparent, and reproducible research, and to established software engineering practices to the extent that they facilitate these ends. I also enjoy mentoring and teaching, both in the classroom and in less structured settings.
My research focuses primarily on leveraging annotated genome sequences to better understand eukaryotic genome composition and organization. I split my research effort between developing tools for managing and querying genome annotations, and applying these tools to characterize genomic features. I am especially interested in comparative genomics, and in species of agricultural significance—most of my work has focused on plant and insect genomics.
I recently joined Titus Brown's Lab for Data Intensive Biology at the University of California, Davis after completing a Ph.D. in the research groups of Volker Brendel (Indiana University) and Amy Toth (Iowa State University). See my curriculum vitae for additional details about my education and scholarship.
My approach to teaching mirrors the way I personally learn: teach fundamental principles with very basic exercises, and then provide space to extend those principles and synthesize new knowledge, building on the basics. I have been involved in a teaching capacity in variety of courses and workshops, with content ranging from computational genomics to basic biology to scientific computing.
See my teaching statement for additional details on my teaching and training activities.
Software & Databases
Creating software and databases is a big part of my research. I work hard to make these resources accessible, reliable, and re-purposeable, as a matter not only of obligation as a publicly funded scientist, but also of scientific integrity.
See my software/database catalog for more details.
I have used blogs, wikis, and web documents for several years to keep an electronic "lab notebook" of my research activities. I am transitioning to a new platform that will allow me to more easily integrate code, data visualization, and related discussion.
Watch this space for updates!