James W
- Research Program Mentor
PhD at Washington University in St. Louis
Expertise
Computational Biology, Genetics, Genomics, Microbiology, Microbiome, Undernutrition, Virology, Protein Evolution, Evolutionary Biology, Biochemistry, Machine Learning, AI, Bioinformatics
Bio
Driven by a lifelong fascination with complex ecosystems, my scientific journey has evolved from studying evolutionary genomics to earning my doctorate at Washington University. During my postdoctoral research, I investigated the intricate microbial dynamics of animal models and the human virome to uncover how these communities impact health. Today, as a Senior Software Engineer at the Mayo Clinic, I apply my interdisciplinary background to tackle challenging biological problems through code. I am deeply passionate about the scientific process and am excited to mentor students on diverse computational biology projects, providing the guidance needed to turn their ideas into polished products. When I step away from my computational work, I love spending time outdoors with my wife, our young daughter. I am an avid angler who particularly enjoys tying my own flies and fly fishing in cold, clear water. I am currently spending my free time transforming our yard into a native plant meadow garden and attending local theater. Having benefited from excellent mentors throughout my career, I am committed to creating a supportive, fun, and productive environment where my students can see their own projects flourish.Project ideas
Good vs Evil: Are there 'good' and 'bad' actors in the human microbiome?
Many studies of the human microbiome attempt to identify a handful of microbial strains/species that are responsible for a certain phenotype or observed trait. These species are then highlighted as being good guys, important for a healthy microbiome, or bad guys, that are key contributors to a dysbiotic or unhealthy microbiome. However, in a system as complex as most human associated microbiomes, reality is rarely this simple. There are multiple organisms that are claimed to be important in promoting a healthy state in one article and then found to contribute to a disease or unhealthy state in another. A review of the evidence of the good and bad actors of the microbiome, and the context dependence of these findings, would be useful for researchers and a solid introduction to the topic for someone new to the field. Individual projects could be limited in scope to specific diseases or habitats/ecosystems of interest to the student.