Research Interest: Computational Biology
| Name | PhD Program | Research Interest | Publications |
|---|---|---|
| Pielak, Gary J. WEBSITE PUBLICATIONS |
PHD PROGRAM RESEARCH INTEREST |
My graduate students and I use the formalism of equilibrium thermodynamics and the tools of molecular biology and biophysics to understand how nature designs proteins. |
| Redinbo, Matt WEBSITE PUBLICATIONS |
PHD PROGRAM RESEARCH INTEREST |
We are interested in unraveling the molecular basis for human disease and discover new treatments focused on human and microbial targets. Our work extends from atomic-level studies using structural biology, through chemical biology efforts to identify new drugs, and into cellular, animal and clinical investigations. While we are currently focused on the gut microbiome, past work has examined how drugs are detected and degraded in humans, proteins designed to protect soldiers from chemical weapons, how antibiotic resistance spreads, and novel approaches to treat bacterial infections. The Redinbo Laboratory actively works to increase equity and inclusion in our lab, in science, and in the world. Our lab is centered around collaboration, open communication, and trust. We welcome and support anyone regardless of race, disability, gender identification, sexual orientation, age, financial background, or religion. We aim to: 1) Provide an inclusive, equitable, and encouraging work environment 2) Actively broaden representation in STEM to correct historical opportunity imbalances 3) Respect and support each individual’s needs, decisions, and career goals 4) Celebrate our differences and use them to discover new ways of thinking and to better our science and our community |
| Snoeyink, Jack WEBSITE PUBLICATIONS |
PHD PROGRAM RESEARCH INTEREST |
My primary research area is computational geometry, in which one studies the design and analysis of algorithms for geometric computation. Computational geometry finds application in problems from solid modeling, CAD/CAM, computer graphics, molecular biology, data structuring, and robotics, as well as problems from discrete geometry and topology. Most of my work involves identifying, representing, and exploiting geometric and topological information that permit efficient computation. My current focus is on applications of computational geometry in Molecular Biology and Geographic Information Systems (GIS). Examples of the former include docking and folding problems, and scoring protein structures using Delaunay tetrahedralization. |
| Tropsha, Alexander WEBSITE PUBLICATIONS |
PHD PROGRAM RESEARCH INTEREST |
The major area of our research is Biomolecular Informatics, which implies understanding relationships between molecular structures (organic or macromolecular) and their properties (activity or function). We are interested in building validated and predictive quantitative models that relate molecular structure and its biological function using statistical and machine learning approaches. We exploit these models to make verifiable predictions about putative function of untested molecules. |
| Vision, Todd WEBSITE PUBLICATIONS |
PHD PROGRAM RESEARCH INTEREST |
Our lab uses computational and molecular tools to study the evolution of genome organization, primarily in the flowering plants. Areas of |
| Weeks, Kevin WEBSITE PUBLICATIONS |
PHD PROGRAM RESEARCH INTEREST |
One of the most amazing discoveries of recent years has been the profound role of RNA in regulating all areas of biology. Further, the functions of many RNA molecules require that an RNA fold back on itself to create intricately and complexly folded structures. Until recently, however, we had little idea of the broad contributions of RNA structure and function because there simply did not exist rigorous methods for understanding RNA molecules in cells and viruses. The vision of our laboratory is therefore, first, to invent novel chemical microscopes that reveal quantitative structure and function interrelationships for RNA and, second, to apply these RNA technologies to broadly important problems in biology. Mentoring and research in the lab are highly interdisciplinary. Students learn to integrate ideas and concepts spanning chemical and computational biology, and technology development, and extending to practical applications in virology, understanding biological processes in cells, and discovery of small molecule ligands targeted against medically important RNAs. Each student has a distinct project which they drive to an impactful conclusion, but do so as part of the lab team which, collectively, has shown an amazing ability to solve big problems in RNA biology. The overarching goal of mentoring in the lab is to prepare students for long-term leadership roles in science. |
| Yeh, Jen Jen WEBSITE PUBLICATIONS |
PHD PROGRAM RESEARCH INTEREST |
We are a translational cancer research lab. The overall goal of our research is to find therapeutic targets and biomarkers for patients with pancreatic cancer and to translate our results to the clinic. In order to accomplish this, we analyze patient tumors using a combination of genomics and proteomics to study the patient tumor and tumor microenvironment, identify and validate targets using forward and reverse genetic approaches in both patient-derived cell lines and mouse models. At the same time, we evaluate novel therapeutics for promising targets in mouse models in order to better predict clinical response in humans. |
| Zhang, Qi WEBSITE PUBLICATIONS |
PHD PROGRAM RESEARCH INTEREST |
Our laboratory is focusing on developing and applying solution-state NMR methods, together with computational and biochemical approaches, to understand the molecular basis of nucleic acid functions that range from enzymatic catalysis to gene regulation. In particular, we aim to visualize, with atomic resolution, the entire dynamic processes of ribozyme catalysis, riboswitch-based gene regulation, and co-transciptional folding of mRNA. The principles deduced from these studies will provide atomic basis for rational manipulation of RNA catalysis and folding, and for de novo design of small molecules that target specific RNA signals. Research program in the laboratory provides diverse training opportunities in areas of spectroscopy, biophysics, structural biology, computational modeling, and biochemistry. |
| Calabrese, J. Mauro WEBSITE PUBLICATIONS |
PHD PROGRAM RESEARCH INTEREST |
Our lab is trying to understand the mechanisms by which long noncoding RNAs orchestrate the epigenetic control of gene expression. Relevant examples of this type of gene regulation occur in the case of X-chromosome inactivation and autosomal imprinting. We specialize in genomics, but rely a combination of techniques — including genetics, proteomics, and molecular, cell and computational biology — to study these processes in both mouse and human stem and somatic cell systems. |
| Purvis, Jeremy WEBSITE PUBLICATIONS |
PHD PROGRAM RESEARCH INTEREST |
We study the behavior of individual cells with a specific focus on “irreversible” cell fate decisions such as apoptosis, senescence, and differentiation. Why do genetically identical cells choose different fates? How much are these decisions controlled by the cell itself and how much is influenced by its environment? We address these questions using a variety of experimental and computational approaches including time-lapse microscopy, single-molecule imaging, computational modeling, and machine learning. Our ultimate goal is to not only understand how cells make decisions under physiological conditions—but to discover how to manipulate these decisions to treat disease. |