People

Lozupone Lab

 

Lozupone IMG

Catherine Lozupone

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.

 

 

 

Mike Shaffer

Mike Shaffer

Graduate Student: I am interested in exploring the effects of various diseases on human microbiomes such as the nose and gut.  By looking at varying data types, such as 16S sequencing, metabolomics and data from computational techniques, we can get ideas about what functional changes are happening in human microbial communities in response to disease.  I seek to develop computational methods and tools in order to integrate this information for better hypothesis generation and discovery of novel functional changes associated with disease.  I am also interested in CRISPR and the microvirome and how these interaction dynamics effect bacterial community structure in microbial communities.

 

 

Katie Arnolds

Katie Arnolds

Graduate Student: I am a second year  in the Microbiology Program. I did my undergraduate work in Cultural and Medical Anthropology at UCSC, and my Masters in Biology at USF. where I studied the interaction of viruses and hosts. This background inspired an interest in how microbes can be pathogenic but more often are vital commensal organisms. In the Lozupone lab I will be investigating how the microbiome interacts with host and how it is shifted in disease states, with a particular focus on the molecular mechanisms driving these complex and exciting interactions.​

 

 

 

Abigail Armstrong

Abigail Armstrong

Graduate Student Microbiology: I am interested in studying the connection between our external and internal environment and how that impacts health and behavior. As an undergrad I studied biology and scientific computing and modeling, and my previous research has been in developing software tools and lab techniques to make microbial ecology research more efficient. My research goals include providing a bridge between microbiologists and computer scientists in microbiome projects. I am also excited about discovering new aspects of our internal ecosystem that may lead to health interventions to increase the quality of life for ailing individuals.

 

 

Nichole Nusbacher

Nichole Nusbacher

Professional Research Assistant: 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.

 

 

Sam Li

Sam Li

Post-doctoral fellow: My graduate work was on host restriction factors against retroviral infections, and how these host genes impact adaptive immunity. Working mostly with a mouse model of retroviral infection, I was able to link the function of an intrinsic antiviral gene to enhanced T cell immune responses. I am excited now to be working with primary human samples in the labs of Dr. Lozupone and Dr. Brent Palmer, where I hope to continue learning about the interactions of retroviruses (particularly HIV) with the host gut environment. Specifically, I would like to know more about how commensal bacteria impact various stages of HIV infection, such as viral transmission, persistence, or the latent viral reservoir.

 

 

 

Cuining Liu

Cuining Liu

Graduate Student: After working in the NGS industry, I became enamored with both the tremendous potential and equally immense challenges of analyzing high-throughput ‘omics data, but wanted to extend those techniques to the research questions in microbiology and metabolic engineering I pursued as a wet lab scientist in undergrad. My path lead me to the Lozupone lab, where as a biostatistics graduate student I aim to develop better statistical methods for analyzing and visualizing the impacts of the human microbiome.

 

 

 

 

Keith Hazelton

Keith Hazelton: MD Fellow

I am a fellow in Pediatric Gastroenterology, Hepatology and Nutrition at Children’s Hospital Colorado. I completed my MD/PhD degrees at The Albert Einstein College of Medicine prior to coming to Colorado for my pediatrics residency. During my PhD research I studied the interactions between the purine salvage pathways of the malaria-causing parasite Plasmodium falciparum and their human host. This work sparked an interest in the metabolic interactions between humans and microbes and the role of those interactions in health and disease. My current interests are in investigating the role of bile acid metabolism in various disease states such as obesity, C. difficile colitis, inflammatory bowel disease and liver disease. I will be using various genetic manipulation techniques to assess the effect of modulating microbial bile acid metabolism in models of these diseases.

 

 

Elmar Pruesse

Elmar Pruesse: Postdoctoral Fellow

I am a computer scientist and bioinformatician interested in developing more effective tools for analyzing sequence data. As a graduate student, I developed the high-throughput multiple sequence alignment software SINA and was co-founder of the SILVA rRNA database project. My primary focus lies in creating production ready solutions for bioinformatical problems that are easy and safe to use, robust and scalable. Currently, I am working on methods for assembling and analyzing multi-sample metagenomic sequence data.

 

 

 

 

Nancy Morena Huizar

Nancy Moreno Huizar

Professional Research Assistant: I graduated from the University of Colorado Denver with a Bachelor’s of Science degree in Biology and Public Health in July 2016. I am looking forward to utilizing my degree and learning the computational side of the Lozupone lab.

 

 

 

 

 

Casey Martin

Casey Martin

Graduate Student Microbiology: 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.

 

 

Ansley

Ansley Tripp

Student Research Assistant: I am a Georgia native and am currently an undergraduate senior at the University of Colorado Denver completing a B.S. in Psychology. In 2015, I was diagnosed with stage IIB Hodgkin's Lymphoma. After completing six months of chemotherapy, I went into remission and have luckily remained so ever since. My personal health battles combined with my natural interests in the mind and body have directed me towards a path of research. In addition to being a research assistant in the Lozupone Lab, I am also a research assistant in the Kilbourn Lab at CU Denver. I am currently working on an honor's thesis project that is assessing the relationship between cognitive impairment (chemobrain) in breast cancer patients receiving chemotherapy and the microbiome. Outside of school and research, I enjoy seeing live music, taking my dogs on hikes, and giving back to the community. I am forever indebted to the research that has allowed me to beat cancer, and as a result, have worked very closely with The Leukemia & Lymphoma Society (LLS) to raise money for cancer research. Due to extensive fundraising, I was titled Woman of the Year 2018 for LLS's Rocky Mountain Chapter. In the Fall of 2019, I plan on applying to the Health Psychology PhD program at CU Denver in hopes of continuing my research all while bridging the gap between the mind and body.