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The New York State Center of Excellence in Bioinformatics & Life Sciences (CoE) involves faculty from our three primary research institutions, University at Buffalo, Roswell Park Cancer Center and Hauptman-Woodward Medical Research Institute. Below is brief information on the research interests of the faculty. For more detailed information, click on the scientist's name.

Dr. Albert’s research employs plant systems to study genomic and developmental problems from an evolutionary perspective. One area of current interest is genome sequencing of “primitive” flowering plant species and characterization relative to model organisms such as Arabidopsis and rice. Another active research area is evolutionary developmental biology, particularly involving a member of the sunflower family, the Gerbera daisy.

Almon,Richard

The central focus of the work in Dr. Almon's laboratory is developing mathematical models that describe complex phenomena in biological systems.  The prime vehicle for this work is the class of anti-inflammatory/immunosuppressive drugs known as corticosteroids.  This important class of drugs have severe side effects which include muscle atrophy, osteoporosis, insulin resistant diabetes, arthrosclerosis and, hypertension.

Dr. Ambrosone’s research focuses on molecular epidemiology and the role of genetic factors in modifying relationships between reproductive, dietary and environmental exposures and cancer risk. She is also interested in genetic and non-genetic factors that impact prognosis after a diagnosis of cancer.

Research in the Andreadis group focuses in the following areas: Cardiovascular tissue engineering, adult stem cells for tissue engineering, wound healing, biomaterials and gene delivery for tissue regeneration, gene modified skin for protein delivery, functional genomics in tissue engineering.

Dr. Balthasar's research, which is funded by the National Institutes of Health, utilizes pharmacokinetic and pharmacodynamic analyses to guide the development of new therapies. Current research focuses on the development of drug targeting strategies to improve the selectivity of cancer chemotherapy and on the development of new immunotherapies for the treatment of humoral autoimmune diseases.

Balu-Iyer, Sathy

Dr. Bittner's interests include the application of research from Philosophy and Artificial Intelligence to bio-medical ontologies and terminology systems, medical image analysis, and medical information systems. This includes work on formal ontology, qualitative reasoning, approximate reasoning, vagueness, and indeterminacy.

Research in Dr. Blumenthal's laboratory is directed at understanding basic questions concerning structure-function relationships in ion channels. He is especially interested in using a variety of naturally-occurring toxins as probes of both ion transport and gating processes in these transmembrane macromolecules. To better understand the nature of these toxin binding sites and their linkages to channel gating transitions, his laboratory analyzes the interactions of mutated channels and toxins by whole cell voltage clamp.

The primary philosophy that links all our research work is that significant improvements in analytical methods and materials will derive from a deeper understanding of the key molecular-level events and processes that are involved. Current efforts in our laboratories focus on Sensors, Arrays, and Detectors, Tailored Materials, Environmentally Friendly Chemistries, Chemical Analysis of Things As They Are, and Instrumentation.

Buck, Michael J.

The Buck Lab integrates both experimental and computational approaches to study transcription factor targeting in model organisms.  The DNA sequences recognized by transcription factors are located all over the genome but a tiny fraction is bound in living cells. Transcription factors are directed to their genomic targets by DNA sequence, epigenetic markers, and protein-protein interactions.  Understanding how these modulators affect transcription factor binding remains a major unsolved biological problem.

Dr. Campagnari’s research interests are primarily in microbial pathogenesis, particularly in identification and characterization of bacterial virulence components including colonization factors and putative vaccine antigens. Currently active projects include detailed analysis of both carbohydrates and proteins involved in adherence and biofilm formation for various human mucosal pathogens and microarray analysis of specifically defined mutations.

Dr. Canty's research interests involve Hibernating Myocardium and Sudden Cardiac Death. Chronic Adaptations to Myocardial Ischemia. High Throughput Proteomic Analysis in Health and Disease.

As a Director of the Institute for Lasers, Photonics and Biophotonics (ILPB), Dr. Cartwright is responsible for the development of multidisciplinary research initiatives focused on photonics applications. Prof. Cartwright is also the director of the National Science Foundation sponsored Integrative Graduate Education and Research Traineeship (IGERT), focused on Biophotonics Materials and Applications.  In addition to his activities in the ILPB, Dr. Cartwright's laboratory has focused it's research on the development, fabrication and characterization of nanostructured III-Nitrides materials and devices, spintronic GaSb based devices, organic LEDs, and most recently, hybrid inorganic/organic flexible solar cell devices. Applications vary for the different material systems and fabricated devices but include biological and chemical sensors, solid state lighting, photovoltaics, optical imaging and optical microfabrication.  Prof. Cartwright's primary expertise is in the optical (CW and ultrafast) characterization of semiconductor materials and devices consisting of homo- and hetero-structures of III-V materials, such as GaAs/InGaAs/AlGaAs and GaN/AlGaN/InGaN, and II-VI materials such and ZnO. These studies provide essential information of carrier transport and recombination dynamics pertinent to device operation.  Finally, Dr. Cartwright's research group is active in the development of novel optical techniques in biosensing and non-destructive stress and strain analysis.

Dr. Ceacareanu’s lab focuses on elucidating the mechanisms of cancer invasion induced or exacerbated by hyperinsulinemia and nitric oxide. Besides opening new opportunities for targeted molecular treatment and cancer phenotype manipulation, Dr. Ceacareanu also coordinates translational research studies that investigate our abilities for early detection of aggressively invasive tumor potential. Her laboratory aims at developing predictive screening tools to forecast cancer recurrence and guide antineoplastic therapy to improve treatment outcomes.

Dr. Ceusters is advancing the referent tracking paradigm as a new ontology-based methodology for representing biomedical facts in electronic health records (EHR) following the principles of unqualified realism within an EHR regime based on the idea of faithfulness to clinical reality.

Dr. Chaudhary uses high-performance computers to provide neurosurgeons with the up-to-date visual information required in the operating room to ensure successful surgical outcomes.

Dr. Colon's research interests include general bioanalytical chemistry with emphasis on micro/nano-chemical analysis utilizing capillary separation technology (e.g., electrophoresis and capillary HPLC), the development and study of new materials for the fractionation and enrichment of biomolecues (e.g., pharmaceutical drugs and phosphorylated compounds), and the implementation of separation technology to study biochemical systems.

Dr. Detitta is interested in the phase problem in x-ray crystallography and the crystallization of macromolecules, and the development of crystal growth methods and techniques.

Dr. Disney's research centers on the development of a chemical code for molecular recognition of RNA.  Research projects are centered on the development of state-of-the-art combinatorial synthesis high-throughput screening techniques.  Applications of our studies may lead to better treatments of genetic diseases and cancer.

Research in Dr. Diver's group centers around the development of new synthetic methods to synthesize molecules that have unique biological properties. A major theme in their group is the efficient construction of complex molecules using transition metal catalysis. Recent work in their lab has been dedicated to developing new ways to make ring structures in complex molecules by using tandem enyne metathesis. Enyne metathesis produces products that readily engage in other reactions to rapidly build three-dimensional assemblies. Our current focus in anticancer natural products is on the amphidinolide group of polyketides and the epidithiadiketopiperazine group. Last, they have used ring-closing metathesis to make carbocyclic nucleoside analogs which may be useful antimicrobial agents and have anticancer potential.

Dr. Donahue's research interests lie in the intersection of diabetes and cardiovascular disease. He is particularly interested in the loss of the female protection that occurs in diabetes, as well as the role of insulin resistance in atherosclerosis in the non-diabetic condition. As the population ages, the impact of diabetes will assume greater public health importance.

Dr. Furlani serves as the Director of the Center for Computational Research, a leading academic supercomputing and visualization center, where his team is involved in building and maintaining the sophisticated computational resources necessary to support life sciences and bioinformatics initiatives.

Research is directed towards understanding the mechanisms of virulence of mucosal pathogens. Adherence is a critical first step in the pathogenesis of mucosal diseases, as it is important in interactions with mammalian cells, can activate macrophages and play a role in invasion of epithelial cells. The molecular basis of adherence and fimbrial and nonfimbrial-associated adhesins are investigated. Adhesins for binding of pathogenic bacteria to mucous-covered surfaces have been studied at the molecular level. Studies of fimbrial adhesins of P. gingivalis have shown that protein interactions with salivary components are critical. Investigation of binding domains of fimbrial adhesin-associated proteins, their synthesis, and assembly, and expression of this organelle are among our current projects. We are exploring the immunogenicity of adhesins as well, using synthetic peptides in order to evaluate their usefulness as vaccines. Studies of S. gordonii as a vector for these vaccines are proceeding through genetic engineering of strains and testing in animal and human studies.

Louis J. Goldberg pursued a research career in the neuroscience of motor control at UCLA and received a MERIT Award from the NIH in recognition of this research. Since 2003 he has been active in the field of biomedical ontology, working closely with Dr. Barry Smith of the Ontology Research Group, and his colleagues on a number of projects ranging from critical analysis of the SNOMED Dental Vocabulary to ontology-supported radiological image analysis.

Dr. Hakansson's lab is focused on investigating the pathogenesis of Streptococcus pneumoniae. We are specifically looking at how it interacts with host cells in the respiratory tract during colonization and transition to infection. The lab also focuses on HAMLET, a protein that induced apoptosis in tumor cells without affecting healthy cells. Current projects are aimed at understanding the mechanism of HAMLET-induced bacterial death and the potential use of HAMLET in preventing and treating established pneumococcalinfections. Understanding these mechanisms may also help us define how HAMLET kills tumor cells.

Dr. Halfon's laboratory investigates the genetic regulatory circuitry responsible for assigning cell fates during development, using the Drosophila embryonic mesoderm as our primary model system. His work combines genomics and bioinformatics with the traditional molecular and genetic techniques of Drosophila research to investigate two key components of developmental regulatory networks, intercellular signaling and transcriptional regulation.

Dr. Hua's group is working on the development of microfluidic devices and systems for applications in biology and physiology. They use the lab chips to study various cellular activities and cell response to different chemicals, pharmaceutical agents, and environmental toxicity. One of her main interests is to study time resolved ion transport in renal cells and cell volume regulation.

As a Mathematician, Dr. Hauptman is interested in the development of mathematical methods to determine the structure of substances of biological importance. He received the Nobel Prize for his groundbreaking work in x-ray crystallography.

Dr. Hu’s main research lies in the analysis of experimental data from areas in the biomedical sciences, including RNA profiling, genomics, systems biology, and proteomics.  Much of the work occurs through collaborative projects with other faculty members in the university and RPCI. Dr. Hu also develops computational and statistical methodology and approaches for expression analysis, comparative analysis of genomic DNA sequence, and the study of genetic networks.

Dr. Jusko's research program involves theoretical, mechanistic, and in vivo studies of the pharmacokinetics, pharmacodynamics, and pharmacogenomics of various drugs including corticosteroids, immunosuppressive agents, and biotech products such as erythropoietin.

The CUBRC laboratory, of which Dr. Karalus is Director, focuses on a variety of biodefense related issues including biodetection, the development of novel therapeutics, decontamination, and aerosol biology modeling.  The laboratory helps develop prototype integrated devices that can rapidly perform sample preparation and detect threat agents using molecular biology techniques.   The laboratory is also pursuing novel technology using the principles of bioconformatics to develop therapeutics against infectious agents and other diseases.

Dr. Knight is the Chair of the Anesthesiology Department at UB, in addition to his professorships in Anesthesiology and Microbiology. Dr. Knight’s research focuses on pathogenesis of aspiration pneumonitis, host response to post-operative pneumonia, pulmonary inflammatory response in COPD surgery patients, bacterial modulation of lung inflammatory response, and brain-derived Tumor Necrosis Factor (TNF) and adrenergic responses in neuropathic pain. Dr. Knight’s lab resides in UB’s Witebsky Center for Microbial Pathogenesis and Immunology.

Dr. Miecznikowski's expertise is in image analysis within the realm of bio-imaging systems. His main area of research is in the design and consequent analysis of two-dimensional difference gel electrophoresis experiments. He has also worked on applying nonlinear models and estimation procedures to microarrary images.

Dr. Morse, whose research focuses on the design and analysis of new clinical and translational trials for HIV treatment, directs UB's Laboratory for Antiviral Research and the Antiviral Clinical Pharmacology Laboratory Unit in the Erie County Medical Center, the only facility in the Buffalo area that offers pharmacologic research protocols for HIV-infected patients. He studies how the pharmacology of anti-HIV drugs and patient pharmacogenetics influence treatment outcomes.

Timothy focuses in three broad, related areas: pathogenesis of infection by Haemophilus influenzae and Moraxella catarrhalis, bacterial infection in chronic obstructive pulmonary disease, and vaccine development for H. influenzae and M. catarrhalis. The approach is to apply basic laboratory methods to study the pathogenesis of respiratory tract bacterial pathogens. 

Dr. Nowak's research interests and laboratory involve global comparative genomic and differential gene expression analyses. She was a contributor in creating the BAC libraries used to sequence the human genome, and she continues extensive genomics work today, including her role as Director of Roswell Park Cancer Institute's Microarray and Genetics Facility, which provides extensive testing capabilities. Dr. Nowak also serves as the CoE's Director of Science and Technology.

Dr. Patel's research is to investigate the structure-function relationships, gene regulation, genetic defects and gene targeting of the mammalian pyruvate dehydrogenase complex (PDC). His research interests include metabolic programming and the development of obesity, and the relationship between the structure and function of components that make up an enzyme group called the human pyruvate dehydrogenase complex. A deficiency of any of the components of the complex results in severe neurological disabilities.

To understand how the brain works, the lab focuses on the structure, function and regulation of synaptic receptors, with emphasis on NMDA receptors at excitatory synapses. Electrophysiology and other state-of-the-art approaches are used to build quantitative, mechanistic models to describe synaptic responses to a variety of conditions/stimuli. This research may contribute new insights into mechanisms of synaptic transmission, information processing, learning and memory (LTP and LTD). It may also provide more effective therapies for stroke, brain and spinal cord injuries, or schizophrenia, Alzheimer’s, ALS and Parkinson’s, respectively.

Dr. Qu’s major research interests include the proteomic investigation of the levels of drug/therapy responsive proteins and their biological meaningful post-translational modifications (PTMs), cellular signaling pathways and protein drug PK/PD, in a variety of biological systems. Current works are directed toward proteomic-scale profiling of proteins that are regulated by a number of drugs, including certain steroids and anti-cancer drugs. He uses cutting-edge analytical technologies for proteomic-scale identification and quantification of effector proteins/biomarkers/drugs in highly complex biological samples, such multi-dimensional chromatography, nano-spray ionization linear ion trap mass spectrometry, high-resolution LTQ-Orbitrap, etc. Additional interests include the development of novel analytical strategies for pharmaceutical and biological analysis using LC/MS/MS technology such as: ultra-sensitive identification/quantification of small molecular drug/metabolites in highly complex biological samples using micro-LC/MS/MS, high-resolution protein PTM determination, etc. 

Dr. Ramanathan's research interest is the treatment of multiple sclerosis (MS) and other demylelinating diseases. Ongoing research includes work on the patient-centered projects such as molecular mechanisms of disease and treatment effects in MS, genomics of therapy optimization, gene expression profiling and proteomics and mathematical models for pharmacogenomics. The bioinformatics research program is focused in the areas of integration of clinical and genomic data, biomarker optimization, multi-dimensional visualization, and modeling genomics and proteomics time series.

Dr. Russo’s research focuses on extraintestinal pathogenic isolates of Escherichia coli (ExPEC), which cause urinary tract infection, pulmonary infection, bacteremia, and other infections outside of the intestinal tract. Dr. Russo’s ExPEC studies focus on: 1) identification of new virulence determinants, 2) ExPEC-host interactions, and 3) vaccine development. Dr. Russo has also begun a new COE-based project in collaboration with Drs. Gill and Campagnari. These studies involve Acinteobacter, which is a bacterium that causes nosocomial infections and combat-related infections. Acinetobacter-related studies include: 1) Identification and initial assessment of potential vaccine candidates, 2) Molecular epidemiologic assessment of military and civilian healthcare associated Acinetobacter strain collections, 3) Genome sequencing of representative military and civilian associated A. baumannii strains, and 4) Comparative prevalence of virulence factors, antibiotic resistance genes, and genes that encode surface-exposed epitopes between military and civilian healthcare associated A. baumannii isolates by microarray analysis.

The Sachs Lab research focuses on cell mechanics and the mechanisms by which mechanical forces are transduced into cellular signals. This direction began when Dr. Sach's lab team discovered mechanosensitive ion channels in 1983. Since then they have studied the channels and the corresponding cell biophysics. Their methodologies includes patch clamp, high resolution light microscopy, fluorescence microscopy, high speed microscopy, TIRF, digital image analysis, high voltage EM with tomography, AFM, molecular biology, natural product and recombinant protein biochemistry and structural NMR.

Dr. Schultz's lab focuses on structural characterization of proteins from SARS coronavirus (SARS-CoV) and mouse hepatitis virus (MHV); identification and characterization of virus:host protein interactions involved in animal to human transmission; enzymatic mechanism of light emission and pH-regulation of luciferases from marine dinoflagellates; sensing cellular oxygen levels by prolyl-hyroxylases.

Dr. Smith's work focuses on ontology, which involves the classification of entities in areas including medicine and health care, where informatics, data mining and computational science can integrate such classifications.

Dr. Titus is the director of the Analog VLSI Laboratory at UB. His research involves optoelectronics, VLSI analog design, and neural networks to create novel silicon-based neuromorphic visual processing systems. Also, his work in these areas has led to new developments in chemical and bio-sensors in which integrated circuits are used to create small, efficient, low power sensor systems for various environments.

Tzanakakis, Emmanouhl

Dr. Tzanakakis' research activities are focused on the engineering of cells and tissues for reconstituting physiological processes. In particular, his laboratory utilizes facets of stem cell biotechnology towards the development of tissues for diabetes therapies. He is also interested in cellular signals regulating the functions of pancreatic insulin-producing cells.

Dr. Wood's research program is dedicated to the development and use of modern mass spectrometry techniques for the advancement of biomedicine. This includes advances in mass spectrometry instrumentation, structural proteomics, biomarker identification, and the use of mass spectrometry for investigating non-covalent molecular associations.

The goal of Dr. Yan's research is to understand the molecular and cellular mechanisms for neuromodulators to regulate ion channel functions and synaptic transmission in the central nervous system under normal and pathological conditions. A combination of electrophysiological, biochemical, pharmacological and molecular biological approaches are used. The two major research areas are: (1) To understand how serotonin and dopamine signaling regulate cortical neuronal activity and how the aberrant serotonin and dopamine function contributes to neuropsychiatric disorders including depression and schizophrenia. (2) To understand how the acetylcholine system is involved in the regulation of cognitive processes and how the deficient acetylcholine function is implicated in Alzheimer’s disease.

Human trisomy 21 (Down syndrome) causes mental retardation, increases the risks for heart defects, childhood leukemia, and Alzheimer’s disease, yet reduces the risks for solid tumors and atherosclerosis. Dr. Yu’s laboratory is generating precise mouse models of Down syndrome trisomic for all three human chromosome 21 syntenic regions by using chromosome engineering. They are also generating mouse strains carrying smaller trisomic segments to identify the critical genomic regions associated with the phenotypes of Down syndrome as well as compound mutant mice carrying both trisomic segments and knockouts of candidate genes to isolate the causative genes for these phenotypes.