Possible Projects
Dr. Bernie Daigle
Associate Professor of Biological Sciences
How does genomics help us integrate biological molecule data? Discovering subtype-specific prognostic biomarkers for post-traumatic stress disorder from omics data. Daigle’s research uses omics data and bioinformatics to discover disease biomarkers. REU participants will apply Hidden Markov modeling (HMM) to longitudinal psychiatric assessment score data from the Systems Biology of Post-Traumatic Stress Disorder (PTSD) Consortium Fort Campbell active-duty military cohort. The goal is to discover prognostic PTSD subtypes that show interesting biological differences. Students will learn practical computing skills, exploratory data analysis, HMM, and other approaches to analyze human clinical and molecular data from PTSD positive and negative individuals. By applying these techniques to large molecular datasets including psychological, genomic, transcriptomic, and proteomic measurements, students will identify candidate prognostic PTSD subtypes and characterize their association with a diverse set of omics data.
For more information on Dr. Daigle, click here.
Dr. Shawn Brown
Assistant Professor of Biological Sciences
How does genomics help us understand gene transfer events in populations? Probing the genomes of snow fungi for signatures of viruses and viral mediated gene transfer. Brown studies microbial ecology including community composition and function by applying genomic and bioinformatic approaches. REU participants will develop novel analytical student driven questions on snow fungi DNA-based viral associates and discover signatures of previous viral mediated gene transfer events using cutting-edge analyses. Student projects will build upon hypotheses that the evolution of the snow fungal lifestyle may be facilitated by active or previous viral infection and associated gene transfer events. Students will gain familiarization with snow fungi through primary literature and instruction from Dr. Brown. Projects will leverage Brown’s extensive library of pure cultures and assembled genomes to test these viral mediated adaptation hypotheses.
For more information on Dr. Brown, click here.
Dr. Duane McKenna
Professor of Biological Sciences
How does genomics help us understand how novel genes generate evolutionary innovation? Characterizing the genomic basis of lignocellulose digestion in plant-feeding beetles. McKenna’s research addresses insect systematics, genomics, evolution, and biodiversity in beetles with a particular focus on the evolution of specialized plant-feeding. REU students will learn how to manually annotate putative plant cell wall degrading enzymes (PCWDEs) encoded in the genome of the red milkweed beetle, Tetraopes tetrophthalmus, a specialized plant-feeder whose genome is being sequenced by the McKenna Lab along with 14 other phytophagous beetle genomes as part of an existing NSF-funded project (DEB: 2110053). Specifically, the student will identify the genes encoding putative PCWDEs in the genome of T. tetrophthalmus, likely microbial donors, and the diversity (copy numbers) of PCWDEs via de novo genomics. This work will engage students in identifying the diversity and phylogenetic distribution of genes encoding PCWDEs in beetle genomes in an understudied group.
For more information on Dr. McKenna, click here.
Dr. Yongmei Wang
Professor of Chemistry
How does genomics help us study interactions among proteins involved in disease? Omics data mining and discovery of integrin biomarkers for cancer metastasis. Wang’s research addresses computational and theoretical studies at the interface of macromolecular systems and nanomedicine particularly in cancer diseases. Students will interrogate integrin gene expression in tumors from cancer patients presenting metastasis. Integrins are a family of transmembrane proteins responsible for interactions between cells and the extracellular matrix and have key functional roles during metastasis. Students will develop and test hypotheses to identify significant differential expression of integrins that can serve as potential biomarkers for cancer metastasis predictions. Students will engage in the use of machine learning algorithms to interrogate integrins expression by accessing publicly available genomic data at Cancer Cell Line Encyclopedia and The Cancer Genome Atlas. Students will also gain experience in using Python/Jupyter notebooks to analyze datasets and gain the experience of using deep learning tools to identify top features in classifying datasets.
For more information on Dr. Wang, click here.
Dr. Amy Abell
Associate Professor of Biological Sciences
How does genomics help us understand cell phenotypes? Quantitative ChIP studies to understand the epigenomics of fetal growth restriction. Dr. Abell uses genomics to understand the functional mechanisms and epigenomic regulation of cell phenotypes. In her lab, REU participants will use genomics tools to understand the epigenomic regulation of fetal growth and how genetic perturbations lead to fetal growth restriction. Students will use undifferentiated and differentiated stem cells that form the placenta and placental tissue with genetic disruption of the enzymes MAP3K4, CBP, and/or HDAC6. Students will gain experience in bioinformatics approaches using mapped RNAseq and ChIPseq data and Easeq to predict regions in genes of interest and in the design of primers to examine these regions. Students will gain wet bench experiences in chromatin isolation, DNA shearing, chromatin immunoprecipitation, and droplet digital PCR.
For more information on Dr. Abell, click here.
Dr. Leigh Boardman
Assistant Professor of Biological Sciences
How does genomics help us understand whole-organism physiology and adaptation? Sequencing and assembling mitochondrial genomes of invasive insects. Boardman’s research addresses invasive insect physiology and mitochondrial genomics especially as related to organismal physiology. Students will participate in sequencing and assembling mitochondrial genomes from populations of invasive insect species that lack mitogenome resources and will be sourced from the UofM Meeman Biological Station and the AgriCenter International in Memphis, TN. Students will learn wet lab skills including extracting and quantifying DNA, preparing genomic libraries, and carrying out long-read real-time genomic sequencing. They will also learn bioinformatic skills to assemble and annotate complete mitogenomes and conduct comparative genomic analyses with publicly available, closely related mitogenomes. Students will engage with lab members in readings and discussions on invasive species, insect physiology, and emerging insect mitogenome research.
For more information on Dr. Boardman, click here.
Dr. Philip Kohlmeier
Assistant Professor of Biological Sciences
How does genomics help us understand novel behaviors in organisms? The evolution and functionalization of novel genes for division of labor in social hymenopterans. Kohlmeier’s research is aimed at understanding the neurogenetic mechanisms involved in the evolution of division of labor (DOL) in social hymenopterans. The focus will be on the emergence and subsequent functionalization of novel genes. REU students in his lab will analyze studies in which the genetic mechanisms of DOL have been investigated in different ant species to test the hypothesis that novel genes emerged early in the evolution of DOL and were then repeatedly co-opted to fulfill DOL-related functions. REU students will gain experience working with NCBI databases, BLAST, and phylogenetic analyses. Within this project, students will be trained in the theory of social evolution, in developing their own code for cross-species ortholog identifications, and in using these newly developed skills to understand the evolution of complex social phenotypes.
For more information on Dr. Kohlmeier, click here (coming soon).
Dr. Jennifer Mandel
Associate Professor of Biological Sciences
How does genomics help us understand how organisms are related to one another? Phylogenomic studies to resolve evolutionary relationships in the sunflower family. Mandel’s research centers on understanding how genetic and genomic variation generate patterns of plant biodiversity including broad questions related to how novel traits influence evolution in the sunflower family. REU participants will collaborate with a graduate student or postdoc in the lab to give students the opportunity to contribute to phylogenomic research as a part of an existing NSF-funded project (IOS: 2214472). Students will gain wet lab skills of extracting DNA, genomic library preparation, targeted sequence capture (Hyb-Seq), and long-read sequencing. Students will engage in experimental design making decisions about appropriate wet-lab protocols and methods for analysis through engaged interaction with the Mandel lab prior to and during the experience.
For more information on Dr. Mandel, click here.
Dr. Emily Puckett
Assistant Professor of Biological Sciences
How does genomics help us understand how populations adapt to their environment? Genomic changes in brown rats associated with adapting to harsh environmental conditions. Puckett’s research focuses on the evolutionary and conservation genomics of mammals including bears, rats, and chipmunks. The REU student will use existing genomic datasets to employ genotype-environment associations (GEA) for investigating genomic regions correlated with environmental variables, particularly winter and summer temperatures, and precipitation. Students will learn basic GIS skills to download, display, and extract data from WorldClim layers from each coordinate where a rat was sampled. Students will perform a multivariate GEA using redundancy analyses. Students will compare and interpret the output, specifically in light of evolutionary history of rats. Finally, they will return to the GIS and generate both point and kriged allele frequency estimates of derived and putatively adaptive variants across the rat range. Through this REU experience, the student will learn to use the Unix command line, PLINK, ArcGIS, and R to analyze and visualize genomic data.
For more information on Dr. Puckett, click here.
Dr. Vinhthuy Phan
Assicate Professor of Computer Science
How does genomics help us understand the biodiversity of communities? Developing coding skills for analyses of metagenomic data from microbial communities. Phan’s research incorporates computer science, bioinformatics, and data science in developing computational methods to analyze sequencing data. REU students will develop a bioinformatics project aimed at discovering species in microbial communities, leveraging publicly available genomic datasets. Students will be trained in techniques for reading and writing different biological file formats, querying the NCBI online databases, and retrieving biological records from the web. Students will be introduced to the Python language and the basic elements of the language, enabling them to write small programs independently. Students will also gain experience pipelining and executing bigger programs using techniques to write well-organized, efficient, and error-free code. Finally, they will use data visualization tools to plot data and draw figures to enable the effective presentation of data results.
For more information on Dr. Phan, click here.