Current and Former Lab Members
Our interdisciplinary team is composed of research professionals, graduate students and postdoctoral fellows in both computational and wet lab research roles.
Catherine Lozupone, Ph.D.
Principal investigator: I am a computational microbiologist who spent most of my time as a graduate student and postdoctoral researcher developing tools for analyzing microbial sequence data (such as UniFrac), and applying these tools to interesting datasets. My primary focus is on understanding the complex community of microorganisms that inhabit the human gut, the ways in which these microbes interact with our immune system, the functions that different microbial compositions may confer (e.g. in producing various metabolites from our food) and how these activities impact our health.
Lab Manager Extraordinaire: I completed my Master’s degree research in a microbial ecology lab investigating bacterial bioremediation. If you ever want to distract me, ask about the connection between Native American artifacts, mercury, and bacteria. While working for an alternative energy company, I developed a strong interest in the tools of molecular microbiology and metabolic engineering. I brought my skills to the Lozupone lab in May 2015 where I prepare and analyze our next-generation sequencing and investigate microbial metabolisms. I have a diverse research background, but that seems to be the norm for the field of Microbiome research and it provides me with good story-telling material.
Casey Martin, Ph.D.
Post Doc: As an undergraduate at the University of Tennessee, I developed biosensors for monitoring watersheds and agricultural systems for toxins and microbial contaminants. After graduation, I served as a program analyst for the National Human Genome Research Institute at the NIH where I helped coordinate genomic medicine research consortia. These experiences have cultivated an interest in microbial community assembly and function and how these attributes are impacted during infection. My work in the Lozupone lab will explore the dynamics of the host-pathogen-microbiome triad through a combination of benchwork and computational approaches. When not in lab, I may be found on my porch, irritating my neighbors with my banjo.
I am pursuing my PhD in Computational Bioscience and funded as an NIH/NLM T15 Informatics trainee. My current research involves development of novel computational methods to identify important features in longitudinal microbiome studies using machine learning methods. My projects include microbiome studies on autism spectrum disorder and a diet intervention in HIV-infected individuals.
Graduate Student in Computational Bioscience: I joined the Lozupone lab in 2021, and my research focuses on incorporating knowledge of microbial interactions with biological systems into knowledge bases to better understand mechanisms of the gut microbiome in disease. I studied Biophysics with a minor in Mathematics in undergrad at the University of San Diego, after which I spent 4 years working as a Software Test then Software Systems Engineer at Illumina. I am co-advised by Dr. Lozupone and Dr. Hunter.
Graduate Student in Microbiology: I graduated from and worked as a research assistant at the University of Oregon, where I became interested in the intersection of bacterial-bacterial and bacterial-host interactions. My research in the Lozupone lab will be focused on applying macroscale ecological ideas such as successional theory to the gut microbiome. I plan to investigate traits that are potentially beneficial to pioneer species as well as whether we can use synbiotic strategies to restore complex communities after disturbance events.
Graduate student in Integrative Physiology and Interdisciplinary Quantitative Biology (CU Boulder): I am interested in methods for integrating multi-omics datasets, particularly for studying the gut microbiome-brain axis in mood and stress-related disorders. My main focus is on utilizing dual (host/microbiome) transcriptomics at the gut mucosa to understand how pathobionts such as Helicobacter influence the development of colitis during chronic psychosocial stress. I hold a BS in nutrition from East Tennessee State University, and I am co-advised by Dr. Chris Lowry at CU Boulder.
Angela Sofia Burkhart Colorado
Graduate Student Computational Biology: I graduated from Wesleyan University with a BA in Biology and French minoring in Informatics and Modeling. Throughout that time, I was able to participate in a summer program at Anschutz Medical Campus which introduced me to various branches of research being performed on campus. As a graduate student I was able to rotate in the Lozupone lab where my research led to insights in the impact that diet may have on a patient with HIV’s response to treatment. By joining the lab I hope to continue this type of research and apply the skills I have learned to investigate the impact that diet has on the human gut microbiome using new workflows and software.
Research Coordinator: After graduating from the University of Arkansas with a B.S. in Biology, I went on to complete my Master’s of Public Health at the University of Minnesota. While in grad school I completed my internship at the Minnesota Department of Health with a study looking at the relationship between IBS and C. diff. This research got me further interested in the microbiome and its various roles in human health. I then spent three years as an environmental consultant Minneapolis, until I realized that that my true passions involved something related to medicine and the microbiome…and the mountains. When not in the lab you can find me somewhere outdoors, most likely with my mini-Bernedoodle – Enzo.
Professional Research Assistant: I graduated from Drake University in 2018 with degrees in Neuroscience and Biochemistry. Following graduation, I served as a volunteer with Peace Corps in Paraguay working in sustainable agriculture and environmental education. I have worked in research centered on neuropharmacology and modeling drug addiction as well as reproductive diseases and their interaction with the microbiome and the immune system. I am interested in the intersection between the nervous system, the immune system, and the microbiome, and how these systems operate together in states of health and disease. I am also interested in using computational techniques to better investigate and understand systems biology.
After graduating from Loyola University Chicago with a B.S. in Biology, I moved back to my hometown of Denver and began my professional career. I worked at Leprino Foods in the microbiology lab, studying and testing over 20 pathogens in dairy products. During a trip to Mexico, I was inspired by the agriculture and became interested in plants. I then worked as a Microbiologist in the cannabis industry, assessing grow sites across the United States. I quickly realized that not all plants are created equal. How and where they are produced has a tremendous impact on our health and the planet. Aside from genetics and external factors, a large part of who we are is what we consume, and it all starts in the gut. Outside of work, you can find me playing every sport in the book at a local park or rec center, or biking and hiking the beautiful trails of Colorado.