The Systems Biology Lab applies methods of multiscale modeling to problems of cancer and cardiovascular disease, and examines the systems biology of angiogenesis, breast cancer and peripheral artery disease (PAD). Using coordinated computational and experimental approaches, the lab studies the mechanisms of breast cancer tumor growth and metastasis to find ways to inhibit those processes. We use bioinformatics to discover novel agents that affect angiogenesis and perform in vitro and in vivo experiments to test these predictions. In addition we study protein networks that determine processes of angiogenesis, arteriogenesis and inflammation in PAD. The lab also investigates drug repurposing for potential applications as stimulators of therapeutic angiogenesis, examines signal transduction pathways and builds 3D models of angiogenesis. The lab has discovered over a hundred novel anti-angiogenic peptides, and has undertaken in vitro and in vivo studies testing their activity under different conditions. We have investigated structure-activity relationship (SAR) doing point mutations and amino acid substitutions and constructed biomimetic peptides derived from their endogenous progenitors. They have demonstrated the efficacy of selected peptides in mouse models of breast, lung and brain cancers, and in age-related macular degeneration.

The Pathak lab is within the Division of Cancer Imaging Research in the Department of Radiology and Radiological Science. We develop novel imaging methods, computational models and visualization tools to ‘make visible’ critical aspects of cancer, stroke and neurobiology. Our research broadly encompasses the following areas: Functional and Molecular Imaging; Clinical Biomarker Development; Image-based Systems Biology and Visualization and Computational Tools. We are dedicated to mentoring the next generation of imagers, biomedical engineers and visualizers. Additional information can be found at www.pathaklab.org or by emailing Dr. Pathak.

The Systems neurobiology Laboratory is a group of laboratories that all study various aspects of neurobiology. These laboratories include: (1) computational neurobiology Laboratory: The goal of their research is to build bridges between brain levels from the biophysical properties of synapses to the function of neural systems. (2) computational Principles of Natural Sensory Processing: Research in this lab focuses on the computational principles of how the brain processes information. (3) Laboratory for Cognitive neuroscience: This laboratory studies the neural and genetic underpinnings of language and cognition. (4) Sloan-Swartz Center for Theoretical neurobiology: The goal of this laboratory is develop a theoretical infrastructure for modern experimental neurobiology. (5) Organization and development of visual cortex: This laboratory is studying the organization and function of neural circuits in the visual cortex to understand how specific neural components enable visual perception and to elucidate the basic neural mechanisms that underlie cortical function. (6) Neural mechanism of selective visual attention: This laboratory studies the neural mechanisms of selective visual attention at the level of the individual neuron and cortical circuit, and relates these findings to perception and conscious awareness. (7) Neural basis of vision: This laboratory studies how sensory signals in the brain become integrated to form neuronal representation of the objects that people see.

The Karakousis Lab is primarily focused on understanding the molecular basis of Mycobacterium tuberculosis persistence and antibiotic tolerance. A systems biology-based approach, including the use of several novel in vitro and animal models, in combination with transcriptional, proteomic, genetic, imaging, and computational techniques, is being used to identify host cytokine networks responsible for immunological control of M. tuberculosis growth, as well as M. tuberculosis regulatory and metabolic pathways required for bacillary growth restriction and reactivation. In particular, we are actively investigating the regulatory cascade involved in the mycobacterial stringent response. Another major focus of the lab is the development of host-directed therapies for TB, with the goal of shortening treatment and improving long-term lung function. Additional research interests include the development of novel molecular assays for the rapid diagnosis of latent TB infection and active TB disease, and for the detection of drug resistance.