Students (past & present)

PhD 2025, Civil and Environmental Engineering

Laboratory Mentor: Lutgarde Raskin

Population/Modeling Mentor: Steven Skerlos

CV (provided 8/8/2023)

Previous Institution: University of Hong Kong (B.Eng in Civil Engineering)

Research interest(s) and project(s) at U of M: I am developing a biomembrane filtration system which combines the membrane aerated biofilm reactor (MABR) and a dynamic membrane bioreactor (DMBR) to remove nitrogen and solids in wastewater. DMBR uses the biofilm to metabolize nitrate and retain the suspended solids in the wastewater, I am trying to engineer the biofilm, or dynamic membrane, to be more sustainable for long-term use. We have a pilot scale system which is running at Ann Arbor wastewater treatment to demonstrate the feasbility of the concept of "biomembrane filtration" process. In the meanwhile, I am developing a multiplex biofilm investigation system using optical coherence tomagraphy to investigate the biofilm structure at mesoscale and manipulate the predation pressure and see how different predation pressure impacts the biofilm structure. 

Math modeling aspect(s) of the research. I am developing a process model of the biomembrane filtration process of the dynamic membrane bioreactor using SIMBA# (a process engineering software) 

Laboratory aspect(s) of the research. I will monitor the biochemical parameters including ammonia, nitrate, total nitrogen, biological oxygen demand, etc. in the influent and effluent to evaluate the performance of biomembrane filtration system. 

Population Sciences aspect(s) of the research. I will use metagenomics and 16S rRNA sequencing to investigate the bacterial and eukaryotic community, as well as the co-occurrence of different species in anoxic dynamic membrane bioreactor designed for denitrfication. 

Graphical abstract of the research: https://drive.google.com/open?id=1c17tjHRhaXSqhy278Z-RGQB6dOCcNa0B 

PhD 2025, Microbiology and Immunology

Laboratory Mentor: Robert Woods

Population/Modeling Mentor: Aaron King

Previous Institution: Loyola University Chicago 

Research interest(s) and project(s) at U of M: My research is focused on vancomycin resistant enterococcus faecium (VRE) and the role of bacteriocins in its transmission through the Michigan Medicine hospital system.

Math modeling aspect(s) of the research. The modeling aspects of my research includes transmission modeling of VRE and evaluating the influence of bacteriocin presence on transmission predictions.

Laboratory aspect(s) of the research. My lab work includes microbe culturing, assessment of bacteriocin activity, and various molecular biology techniques.

Population Sciences aspect(s) of the research. Population sciences are integrated into my work by studying the evolutionary and ecological impacts of VRE bacteriocins on the gut microbiome.

Career Experience

2024 

ITiMS Experience

PhD 2022, Epidemiology

Laboratory Mentor: Kelly Bakulski

Population/Modeling Mentor: Betsy Foxman

Previous Institution: University of Michigan

Research interest(s) and project(s) at U of M: My research interests focus on incorporating concepts from evolution and ecology to understand how human health and disease is shaped by the microorganisms with which we share our environment. I'm particularly interested in integrating analysis of host, microbe and environmental factors in order to understand multifactorial diseases for which single causal agents are lacking or poorly understood (such as dental caries, gingivitis, preterm birth and metabolic syndromes). Through my participation in two training fellowships, the Genome Science Training Program and the Integrated Training Program in Microbial Systems, I use methods in mathematical modeling and population sciences to analyze high-dimensional and compositional data. 

Math modeling aspect(s) of the research. I study microbial systems using genomic techniques, including 16S rRNA amplicon based sequencing and metagenomic methods. The data produced by these methods is high-dimensional, sparse, and compositional.  I attempt to reduce the dimensionality of this data while retaining complexity using techniques from mathematics and data science such as weighted network analysis and latent class analysis. As I continue in my PhD I am interested in translating these techniques to time-series analyses, potentially involving dynamic mode decomposition or dynamic Bayesian networks.

Population Sciences aspect(s) of the research. As an epidemiologist, I work with large cohorts of individuals to draw inference on causal mechanisms in populations. I am particularly involved with Center for Oral Health Research in Appalachia (COHRA) study, investigating microbial agents in oral disease within a large, longitudinal cohort of American children.