My main interest is developing and integrating computational tools into life sciences research.

Mechanisms and functions of ATP-dependent chromatin remodeling complexes and their place in genome regulation

Regulation of gene expression by RNA structure and RNA-binding proteins.

Chromatin structure and its role in gene regulation

RNA Chemistry. Biochemistry. Organic Chemistry. Computational Chemistry. Physical Chemistry.

Our group merges computational and experimental approaches to understand how host-associated microbes shape health.

The Du lab is interested in understanding how transcription machineries and regulatory DNA elements organize in 3D in the nucleus to regulate gene expression. Both healthy and cancerous cells acquire functional genomic features, including super-enhancers (SEs) to drive expression of prominent oncogenes and developmentally important genes. Mechanistically, how such super-enhancers control gene expression to affect different outcomes in develo

How do biomolecules know how to come together to form higher-order structures within the cells? How does the cell maintain this organization over time? The Feric lab studies the fundamental mechanisms underlying cellular organization, particularly in the context of aging and age-related diseases. We investigate how phenomena occurring on different scales - molecular, organellar, and cellular - are interconnected with each other.

Genetics of neurodevelopmental disorders.

The utilization of biochemical, molecular genetics, and spectroscopic approaches to decipher mechanisms of cellulose biosynthesis.

Structural studies of amyloids, viruses, and protein complexes using single particle cryo-EM; In situ structural biology with correlative light/electron microscopy (CLEM), volume EM, and electron tomography; Development of new methods to improve cryo-EM sample grid preparations, data collections, image analyses and 3D reconstructions.

The understanding of the molecular mechanisms involved in the replication and assembly of flaviviruses and alphaviruses.

We use Petunia inflata as a model to study biochemical, molecular, and structural bases of a self/non-self recognition mechanism between pollen and pistil adopted by flowering plants to prevent in breeding and promote outcrossing.

Structural biology of catalytic ribonucleoprotein complexes.

Growth Control and Cancer Genetics.

Computational analysis of protein structure, function, genomics and evolution.

We study how malaria parasites prepare for unpredictable moments of transmission between mammals and mosquitoes. We use transcriptomics, proteomics, gene editing, and high-resolution microscopy to determine mechanisms that control these preparations so that we can find weaknesses that can be exploited via future therapeutics.

The combination of tools from functional genomics, molecular biology, computational biology, biochemistry, and metabolomics to understand the fundamental molecular mechanisms underlying the development of this parasite.

We build machine learning applications to understand how transcription factors control cellular identity.

The McReynolds lab is broadly interested in understanding the biochemistry behind aging, and its intersection with stress, with the long-term goal of identifying strategies that promote healthier aging.

Developing computer science techniques for analysis of biological data and on answering fundamental biological questions using such methods.

Bacterial cell envelope biosynthesis.

We use microbial genetics, biochemistry, and cell biology approaches to determine the molecular mechanisms that enable bacteria to establish symbiosis with a eukaryotic host. The model system is the symbiosis formed between the bioluminescent bacterium Vibrio fischeri and the Hawaiian bobtail squid Euprymna scolopes. Our primary interests in this system include quorum sensing,contact-dependent killing mechanisms, and sulfur metabolism.

We apply cryo-EM and X-ray crystallography techniques to reveal three-dimensional structures of DNA and RNA polymerases for elucidating the mechanisms of DNA replication and RNA transcription.

Our lab is the birthplace of Galaxy. It is developed and maintained together with our collaborators and worldwide community. We also work on a variety of topics related to mutational dynamics and experimental evolution. We are also an integral part of the AnVIL project.

The structural mechanisms of signaling and regulation in protein complexes.

Understanding the host-metabolite-microbiota communication network‚ specifically how the manipulation of gut microbiota by diet and/or xenobiotics impacts host metabolites (e.g., bile acids, short chain fatty acids), their metabolism, and how these co-metabolites interact with host ligand-activated transcription factors.

The mechanism of tissue regeneration using the response to anemia as a model system.

The biochemical pathway of AHR activation and characterized species difference in AHR mediated transcriptional activation of target genes.

The biochemical pathway of AHR activation and characterized species difference in AHR mediated transcriptional activation of target genes.

Stress-induced gene expression and UV resistance pathways, Regulation of mRNAs from birth to death during stress responses, Targeted protein degradation during transcriptional stress and How RNA Polymerase II contends with barriers throughout the genome.

The Rolls lab aims to understand how neurons generate axons and dendrites with different microtubule organization, and how neurons respond to injury. Current projects focus on mechanisms that control microtubule polarity and dynamics and mechanisms that promote neuronal regeneration.

We study the signal transduction and vesicular trafficking processes that promote migration in epithelial cells. We seek to understand the role of these processes in normal homeostasis and in pathological processes.

Understanding the consequences of HSV latency for the neurons that harbor the HSV pathogen and the search for improved therapeutics using a combination of virology, neurobiology, next generation sequencing technologies, and bioinformatics.

The understanding of how genes are regulated by combining genetic, biochemical and structural descriptions.

Research Description coming soon (2/27/22) Full list of publications: https://www.ncbi.nlm.nih.gov/myncbi/1ZOLwVxR6x-/bibliography/public/

Our group is focused on understanding signaling pathways that allow bacteria to sense and respond to their environment. We use tools from chemistry, biochemistry, and molecular biology to develop a molecular level understanding of the proteins and small molecules involved in these systems, as well as their role(s) in bacterial growth and virulence.

Elucidating molecular structures relevant to chemists, biochemists, material scientists etc. and educating graduate students embarking in these fields, the technique of X-ray diffraction (crystal growth, data collection and structure solution and refinement, and interpretation).