Health Sciences Tower
Professor & Vice Chair for Research
Summary : Benveniste's Laboratory focuses on (1) exploring, characterizing and understanding diagnostic MR contrast parameters suitable to visualize neuro-pathology in neurodegenerative diseases; (2) investigate transgenic animal models were specific genes are modified to understand mechanism(s) and treatment of addiction and of drug-induced neurotoxicity using high resolution MR imaging, (3) advance technologies in molecular MR imaging.
Health Sciences Tower
Summary : Dr. Button's research work in the past has focused on Advanced Magnetic Resonance Mammography and Dynamic Infrared Imaging. His current research projects are infrared imaging, breast cancer detection, magnetic resonance and computer aided diagnosis (CAD).
Health Sciences Tower 10-020
Summary : Depression is a complex, heterogeneous disorder. It is most likely for this reason that neuroimaging has yet to uncover a clinically useful diagnostic or prognostic aid for people living with this disease, despite providing an unprecedented level of detail about the living human brain. As a biomedical engineers, we have the ability to incorporate the most current and technically advanced procedures in mathematics, image processing, and statistics in order to improve outcomes for patients diagnosed with Major Depressive Disorder (MDD) and other mental illnesses. My focus is to use advanced image processing algorithms to uncover the neurobiology of mental illness, and help improve both diagnosis and treatment. This includes: (1) developing algorithms to combine high dimensional multimodal data. Our group has a large repository of structural and functional Magnetic Resonance Images (MRI), Diffusion Tensor Images (DTI), and Positron Emission Tomography (PET) images of subjects with mental illness and controls. Fusing information from multiple modalities in a meaningful way may lead to personalized medicine options for those suffering from MDD and other illnesses; (2) Visualizing neurotransmitter systems in vivo. Examining neurotransmitter systems with PET can help us understand more about the pathophysiology of mental illness; and (3) Extracting the most accurate quantitative information from brain images using improved imaging sequences such as Diffusion Spectrum Imaging (DSI) and Arterial Spin Labeling (ASL). These high resolution imaging sequences can help us get the most complete and accurate view of the brain. Through advanced imaging techniques and image processing algorithms, we can help improve the lives of those suffering with MDD and other disorders.
Laufer Center - 5252
Summary : Ken A. Dill is interested in the physics of how proteins fold; the microscopic origins of the unusual physical properties of water; the foundations and applications of variational entropy-based principles in statistical physics; and how the laws of physics constrain and enable the biological properties and evolution of cells.
Stony Brook University Hospital
Summary : Dilmanian's main area of research has been experimental methods of radiation therapy with segmented beams. In particular, he has been applying arrays of parallel, thin planes of synchrotron x rays (microbeams) at the National Synchrotron Light Source (NSL), BNL, to spinal cord injury research, and arrays of parallel, thin planes of carbon ion beams at the NASA Space Radiation Laboratory (NSRL), BNL, to cancer research in a geometry called interleaved carbon minibeams. Hi imaging projects have included computed tomography with beams of narrow energy bandwidth, and the use of microCT for body composition studies. Finally, he has been collaborating James Hainfeld, PhD and others on experimental methods of radiation therapy with dose-enhancing agents, such as gold nanoparticles.
Professor, Vice Chair for Research
Summary : Our group consists MR physicists, MR engineers, image scientists and application scientists, working collaboratively to advance MRI technologies and their biomedical applications. Our primary research interests are: (1) Development of in-vivo MRI and optical imaging technologies for studying the brain and the retina, (2) Application of imaging technologies to study normal anatomy, physiology and function in animal models and humans, and (3) Application of imaging technologies to study stroke, retinal degeneration and retinopathy in animal models and humans.
Summary : The primary role of this laboratory is to study basic physiological flow phenomena, both experimentally and numerically, as well as cellular and tissue engineering as applied to the vascular system. and to suggest ways of improving the functioning of cells, tissues and organs in the body. These physiological flows include blood flow in the heart, blood flow in arteries, veins and the microcirculation, air flow in the respiratory airways, and urine flow in the kidney and urethra. This laboratory simulates systems through the use of computers, assisting life scientists to better understand physiological functions without having to rely entirely on living systems as experimental models. The use of mathematical analysis helps minimize animal experimentation. Other projects are the investigation of hemodynamics as a regulator of vascular biology, the mathematical modeling of the dynamic response of mammalian cells, the role of flow and the associated shear stress on vascular endothelial biology, prosthetic circulatory devices and the tissue engineering of blood vessel substitutes. The laboratory is also engaged in the evaluation of critical conditions that lead to failure of biological organs, such as the heart and the coronary circulation, failure of circulatory prosthetic devices as stents, heart valves and grafts. To facilitate in vitro and in vivo studies, the laboratory develops new investigative techniques, noninvasive diagnostic methods, and advance, multi-dimensional numerical modeling.
Summary : Developing a thin, flexible, fiber optic device based on Diffuse Correlation Spectroscopy (DCS) and Diffuse Optical Spectroscopy (DOS) principles that allows for the immediate detection of changes in spinal cord blood flow and oxygenation, in real time.
Summary : A senior chemist at Brookhaven National Laboratory, she focuses on the biochemical effects of drugs, aging, and selected diseases on the brain. Fowler received a Jacob Javits Investigator Award in the Neurosciences, in 1986 and 1993; a Gustavus John Esselen Award for Chemistry in the Public Interest in 1988; Brookhaven Laboratory's R&D Award, in 1994; the Aebersold Award from the Society of Nuclear Medicine in 1997; and the Francis P. Garvan-John M. Olin Medal in 1998.
Cold Spring Harbor Labs
Howard Hughes Medical Institution Investigator
Summary : Dr. Hannon received a B.A. degree in biochemistry and a Ph.D. in molecular biology from Case Western Reserve University, where he trained in the laboratory of Tim Nilsen. From 1992 to 1995, he was a postdoctoral fellow of the Damon Runyon-Walter Winchell Cancer Research Fund in the laboratory of David Beach, where he explored cell cycle regulation in mammalian cells. Dr. Hannon, along with collaborators, was able to identify p21, p15 and p16. His work and that of others has linked each of these to major tumor suppressor pathways, with the two latter genes being tumor suppressors in their own right and p21 being a major effector of the p53 tumor suppressor. After becoming an Assistant Professor at Cold Spring Harbor Laboratory in 1996 and a Pew Scholar in Biomedical Sciences in 1997, in 2000, he began to make seminal observations in the emerging field of RNA interference. His laboratory identified the effector complex of RNAi, which is called RISC, and showed that it contained small RNAs, now known as siRNAs, that were similar in size to those originally observed by David Baulcombe in his study of plants that were silencing transgenes by co-suppression. The origin of such small RNAs was revealed with his discovery of the Dicer enzyme; an RNAseIII family member that cleaves dsRNAs into discretely sized small RNAs that enter RISC. In 2002 Dr. Hannon accepted a position as Professor at Cold Spring Harbor Laboratory where he continued his studies to reveal that endogenous non-coding RNAs, then known as small temporal RNAs and now as microRNAs, enter the RNAi pathway through Dicer and direct RISC to regulate the expression of endogenous protein coding genes. In recognition of his research, Dr. Hannon was appointed to the Faculty of 1000, received the U.S. Army Breast Cancer Research Programâ€™s Innovator Award and the American Association for Cancer Researchâ€™s Award for Outstanding Achievement in Cancer Research. He assumed his current position in 2005 and continues to explore the mechanisms and regulation of RNA interference as well as its applications to cancer research.
Chemistry - 479
Summary : I am interested in understanding the structural and morphological development and manipulation of complex polymer systems during preparation and processing in real time. The focus of my research projects is the design, preparation, characterization and application of nanostructured soft condensed materials, such as fibers (one-dimensional orientation), films (two-dimensional orientation) and bulk material systems (three-dimensional orientation), through precise control of molecular architecture and physical interactions including crystallization, molecular level mixing, deformation and flow. My particular interests in biomedical applications include the use nanostructured biodgredation materials for drug release and tissue engineering.
Computer Sciences - 203G
Distinguished Professor & Chair
Summary : Arie Kaufman is the director of the Center of Visual Computing (CVC) and the director of the Cube project for volume visualization supported by the National Science Foundation, Department of Energy, Office of Naval Research, Hughes Aircraft Company, Hewlett-Packard Company, Silicon Graphics Company, Howard Hughes Medical Institute, and many others. His research interests include computer graphics and specifically computer graphics architectures, algorithms, and languages; visualization including volume visualization and scientific visualization; user interfaces; virtual reality; and multimedia. Kaufman is the editor-in-chief of the IEEE Transaction on Visualization and Computer Graphics. He has lectured widely and published numerous technical papers in these areas, including the IEEE tutorial book on Volume Visualization. He has been the papers chair and program cochair for Visualization 1990-1994 and the chairman of the IEEE CS Technical Committee on Computer Graphics.
Health Sciences Tower
Summary : Jerome Liang focuses his attention on the development of quantitative SPECT systems, 3D virtual endoscopy, and computer aided diagnosis. This work includes creating a quantitative SPECT imaging modality as a cost-effective means for patient diagnosis as well as developing a high resolution PET as a functional research imaging modality. Liang is also striving to create a virtual colonoscopy as a cost-effective procedure for colon screening and to construct an automatic method for brain-tissue segmentation for diagnosis of disorders. In addition, he plans to build various models, in terms of physics, mathematics, and statistics, to simulate the practical problems above and then to validate the models by experiments. Liang has published his findings in journals such as Magnetic Resonance Medicine.
Health Sciences Tower 12-080
Summary : I believe that the role of biomedical engineers is to help nature help itself. My research interests revolve around hemodynamics. This includes not only the exploration of what is, but also create what does not exist. Our laboratory is involved in the study of blood flow to the brain and the creation of therapeutic devices both retractable and implantable to restore blood flow to normal physiological conditions. Some example include the analysis of blood flow from radiographic images, the application of mathematical tools to simulate blood flow in vasculature of interest, creation of silicone replicas of blood vessels both with and without pathologies for both elucidation of flow within and for the testing of new tools for blood flow restoration and navigation of access tools. Coils for the treatment of brain aneurysms and flow diverters are examples of mechanical devices that have been investigated extensively in our laboratory. Histoacryl, the predecessor of NBCA and Onyx for the treatment of arteriovenous malformation have all been investigated extensively in our lab.
500 Sunnyside Blvd
Summary : Our lab is taking a proactive approach to the genome information explosion by developing databases, data-analysis tools, and user interfaces to organize, manage, and visualize that vast body of information. One current project is the development of a third-party annotation system for the Caenorhabditis elegans genome sequence. This system will allow researchers to add comments and observations to the C. elegans database and to conveniently view the annotations of others with a Web browser. The system uses the ACEDB database in conjunction with the Java and Perl interfaces that have been developed in our lab. A second project is the development of a genome informatics tool kit, a modular collection of database query tools, sequence-analysis programs, and user interfaces that will allow biologists to solve data-management problems without the assistance of a computer programmer.
Brookhaven National Lab
Summary : Lisa Miller is the Life and Environmental Sciences group leader at the NSLS. She is also spokesperson for Beamline U10B and X27A. Beamline U10B specializes in mid-infrared microspectroscopy of materials such as biological tissues, polymers, coated and corroded surfaces, soils, minerals, and plants. Beamline X27A specializes in x-ray fluorescence microprobe analysis of trace metals in similar materials. Lisa Miller's research focuses on the study of the chemical makeup of tissue in disease using high-resolution infrared and x-ray imaging at the NSLS. Her work has two primary research areas: (1) examination of the chemical composition of bone tissue in diseases such as osteoarthritis and osteoporosis, and (2) correlation of metal ion content and protein structure in brain tissue in protein-folding diseases such as Alzheimer's disease and scrapie.
Cold Spring Harbor Labs
Summary : I am interested in gaining a fundamental understanding of the behavior of complex biological systems, both from a mechanistic, physico-chemical perspective, and from an engineering perspective emphasizing function. I am also interested in applying this knowledge to help improve therapies for brain disorders. My research combines a number of approaches, including theoretical work, informatics, and experimental work. My theoretical interests are primarily in formalizing the treatment of biological function using ideas and methods from engineering. The informatics component of my research is devoted to the development of computational tools for analyzing neurobiological data, particularly electrophysiological data from experiments designed to probe cognitive phenomena. In addition, I am working on building knowledge bases to integrate information from the neuroscientific literature, both for the research and medical communities. I have an experimental research program studying memory formation in the fruitfly, integrating information across genetic, neural and behavioral levels. In collaborative research, I study song development in the zebra finch. My research is highly interdisciplinary and has a broad scope. I am also interested in the communication of science to a general audience.
Computer Sciences - 261
Summary : Klaus Mueller's areas of interest are medical, scientific and information visualization, visual analytics, medical imaging, computer graphics, virtual and augmented reality, and high-performance computing. He has pioneered the use of programmable commodity graphics hardware boards (GPUs) for the acceleration of a wide variety of computer tomographic (CT) reconstruction algorithms and medical physics phenomena. Applications include diagnostic imaging, radiotherapy, electron microscopy, ultrasound tomography for breast mammography, and others. In the visual analytics area he works on devising new high-dimensional data visualization frameworks and combining them with statistical pattern recognition and machine learning to create intuitive interactive analytical reasoning environments for medical professionals. He is also working towards a comprehensive visual data mining environment for neuroscientists, called BrainMiner, to enable a more targeted and experiential derivation of brain functional models from large collections of knowledge and data.
Cold Spring Harbor Labs
Summary : One of the major barriers to progress in systems neuroscience has been the lack of assays to survey the whole brain at cellular level of resolution, either with respect to anatomy or function. The Osten lab has established several automated microscopy and bioinformatics methods for whole-brain analysis in the mouse. These methods allow us to study cell type-defined neuronal circuits in normal brain and in genetic models of neurodevelopmental and psychiatric disorders. These disorders are becoming increasingly well understood at the genetic level, but what has been lacking is a reproducible and robust means to locate the impact of the genetic lesions on specific brain regions or neuronal cell types.
Health Sciences Tower
Professor and Chair
Summary : The Center for Understanding Biology using Imaging Technology (CUBIT), under the guidance of Dr. Ramin Parsey and Christine Delorenzo, uses state-of-the-art imaging modalities to investigate psychiatric and neurological disorders. The goal of the lab is to develop, refine and apply brain-imaging techniques including positron emission tomography/magnetic resonance imaging (PET/MRI) to understand the biological causes of neuropsychiatric disorders and to improve their diagnosis and treatment. Several areas of focus of the lab include: 1) identifying biomarkers for diagnosis and predictors of treatment; 2) developing methods and modeling for neuroimaging; 3) understanding the serotonin system, specifically serotonin 1A and serotonin transporter systems, in major depression, bipolar disorder other mood disorders, and suicide; and 4) developing novel radio tracers. Using PET/MRI, we can better understand the neurotransmission deficits in psychiatric and neurological disorders that may aid diagnosis, identification of biomarkers and treatment targets to facilitate treatment development and ultimately to assist in treatment selection for precision medicine. Dr. Parsey has already established links with scientists at Brookhaven National Laboratory and with other departments at Stony Brook and aims to work collaboratively.
Cold Spring Harbor Labs
Summary : My laboratory is interested in the identification and functional characterization of cancer genes (oncogenes and tumor suppressors). Our main motivation for studying cancer genes is their proven practical value in serving as targets for new cancer therapies and as biomarkers that can guide treatment decisions. Additionally, cancer genes have normal functions and their characterization can often lead to deeper understanding of basic biology. In the past, our focus has been on the use of high-resolution genome arrays to pinpoint candidate oncogenes that are amplified in human cancer. We have validated many of these amplified genes as functional oncogenes in model systems and some of these validated oncogenes have served as starting points for cancer drug discovery programs. More recently, weâ€™ve branched out to include analysis of additional genomic alterations relevant to human cancer. Weâ€™ve also begun purely functional genomic approaches to identify genes involved in important cancer-related processes such as response to specific therapeutics.
Old Engineering - 314
Summary : Surface and interface properties of polymer thin films, nanocomposite materials, phase segregation in polymer blends, polymer dynamics in confined geometries, wetting in multilayer polymer films, fracture toughness of polymer interfaces, polymer adhesion, nanopatterning using polymer self assembly, nanotribiology of polymer film surfaces, nanopatterning with magnetic impregnates in glass. Experimental specialization: SIMS, X-ray and Neutron Reflection, Lateral, magnetic and atomic force microcopy TEM, RBS, and Mossbauer Spectroscopy.
Mathematics Tower 1-111
Summary : Rob Rizzo works in Computational Structural Biology. His research group seeks to understand the atomic basis for molecular recognition for specific biological systems involved in human disease such as HIV/AIDS, cancer, and influenza with the ultimate goal of developing new and improved drugs. Computational methods are used to model how molecules interact at the atomic level with a given drug target. The resultant 3D structural and energetic information is used to quantify and rationalize drug-binding for known systems and to make new predictions.
Professor and Associate Director
Summary : The Simmerling lab at Stony Brook University carries out research in the area of computational structural biology. In particular, the lab focuses on understanding how dynamic structural changes are involved in the behavior of biomoleculs such as proteins and nucleic acids.
Biochemistry and Cell Biology and Pathology
Summary : Acute and chronic inflammatory responses are important host defenses against foreign substances or pathogens. These responses are largely mediated by neutrophils and macrophages, which release proteases, cytokines, and a number of other mediators of inflammation in the course of defending the host. We study the mechanisms of action of serine proteases and metalloproteases from activated neutrophils and develop specific inhibitors to control the tissue destruction which may otherwise injure the host during an inflammatory response. Because invasiveness and metastatic spread of tumor cells involves tissue degradation by the same families of proteinases as is seen in inflammation, we have extended our studies to include evaluation of agents intended to block tumor spread or tumor-stimulated vessel growth (angiogenesis). Our methods include biophysical probes of enzyme active sites and kinetic measurements. We also measure neutrophil and macrophage phagocytic activity and release of oxidants by flow cytometry. We have made extensive use of a complete interstitial extracellular matrix from rat smooth muscle cells which we label biosynthetically and employ as a substrate for inflammatory cells and tumor cells and their proteases. We employ matrices on porous membrane filters to quantitate inhibition of invasive migration of neutrophils, macrophages, endothelial cells, and tumor cells by proteinase inhibitors and other modulatory agents. Our collaboration with colleagues in the Department of Oral Biology and Pathology has led to a series of clinical trials on a class of proteinase inhibitors with additional pleiotropic downregulatory actions on inflammatory and tumor cells. The trials of these inhibitors, which are nonantimicrobial derivatives of tetracyclines, target potential applications in management of cancer, acute respiratory distress syndrome, periodontal disease, and cardiovascular complications of smoking. To understand how inflammatory cells communicate we study paracrine mechanisms of activation by cytokines, using immunofluorescence and flow cytometry to measure levels of expression of cell surface receptors and other marker proteins which are sensitive to the state of activation of the cells.
Computer Science Department
Distinguished Teaching Professor
Summary : Steven Skiena is a Distinguished Teaching Professor of Computer Science at Stony Brook University. He is a co-founder and the Chief Science Officer of General Sentiment, a social media and news analytics company. His research interests include algorithm design and its applications to biology. Skiena is the author of several popular books in the fields of algorithms, programming, and mathematics. The Algorithm Design Manual is widely used as an undergraduate text in algorithms and within the tech industry for job interview preparation.
Cold Spring Harbor Labs
Summary : Two challenges in cancer biology guide my work: first, how do tumors become addicted to certain gene products, and second, how do tumors develop resistance to anti-cancer drugs. I focus on the epidermal growth factor receptor (EGFR), which is both addictive when mutated and a common source of drug resistance.
Summary : Our group conducts cutting-edge research in electrochemistry, batteries and their intersection with human health. Specifically, our interests include studying batteries for medical applications such as implantable devices. Understanding and controlling factors that limit the lifetime of batteries are of particular interest including parasitic reactions and mechanisms that lead to internal depletion. The research is multi-disciplinary involving materials, electrochemistry and the use of advanced characterization techniques.
350 Community Drive
Director, Feinstein Institute for Medical Research
Summary : Systemic inflammation is an important process in the development of shock, rheumatoid arthritis, inflammatory bowel disease, stroke, and other diseases. Our research focuses on the roles of individual mediators of systemic inflammation, and their regulation by interactions between the brain and the innate immune system. Our discovery of the inflammatory action of TNF in non-malignant disease led directly to clinically approved treatments for rheumatoid arthritis and inflammatory bowel disease. To discover new mediators of systemic inflammation, we screened products of endotoxin-stimulated macrophage cultures. This resulted in the discovery that HMG-1, a DNA binding protein that was widely studied for its intracellular roles, is a mediator of endotoxin lethality. In contrast to TNF and IL-1, which are released early after endotoxin exposure, HMG-1 is released late after exposure to endotoxin. Antibodies to HMG-1 completely protect mice from endotoxin lethality, even when treatment is delayed several hours. In critically ill patients, the highest serum HMG-1 levels exist in lethal cases, indicating that HMG-1 may be a therapeutic agent. Ongoing research addresses the mechanisms of HMG-1 toxicity and action, as well as the identification of signal transduction pathways.
NIH National Human Genome Research Institute
Summary : The Organic Acid Research Section (OARS) studies a group of inborn errors of metabolism, the hereditary methylmalonic acidemias (MMA), and disorders of intracellular cobalamin metabolism. What has remained both perplexing and challenging is the wide spectrum of clinical phenotypes presented by the patients and the generally untreatable nature of many of the complications they display, such as renal disease in patients with isolated MMA and progressive visual deterioration in those with cobalamin C (cblC) deficiency.
Health Sciences Tower 4-120
Summary : Wei Zhao's main research interest is in the development of novel detector concept and new clinical applications for early detection of cancer. Her current research projects include (1) the characterization and optimization of a high-resolution flat-panel detector for digital mammography (imaging of the breast) through prototype development, image analysis, and computer modeling; (2) the development of detector technology and imaging system for three-dimensional imaging of the breast, which is aimed at achieving better detection of abnormality than existing two dimensional projection images; and (3) feasibility investigation of a large area flat-panel detector with amplification at each pixel for very low dose x-ray imaging applications.