Bioinformatics; Genomics and proteomics; Molecular and Cellular Biology; Molecular genetics; Gene Expression; Transcription and Translation
Our research group is interested in how regulatory proteins are targeted to the correct DNA binding sites at the correct time. Transcription factors are directed to their genomic targets by DNA sequence, local chromatin structure, and protein-protein interactions. These modulators of transcription factor binding are not independent but function both cooperatively and competitively to regulate where transcription factors bind. Understanding how these modulators affect transcription factor binding in vivo remains a major unsolved biological problem. We use the model organism Saccharomyces cerevisiae to address the disconnect between the presence of the correct DNA binding sequence and true regulatory protein binding, integrating both experimental and computational approaches to: i) investigate transcription factor binding in response to environmental stress, ii) identify and characterize the mechanisms directing transcription factor target selection, and iii) and develop bioinformatics tools to analyze and interpret ChIP-seq experiments and chromatin structural patterns.
Autoimmunity; Bioinformatics; Genomics and proteomics; Immunology; Infectious Disease; Molecular and Cellular Biology; Molecular genetics; Neurobiology
My primary research is in the field of biomedical ontology development. An ontology is a controlled, structured vocabulary intended to represent knowledge within a particular domain. Terms in an ontology have logical relationships to each other and to terms in other ontologies, to allow for reasoning and inference across the ontology. Biomedical ontologies allow annotation and integration of scientific data within particular fields of science and medicine, and their careful curation and logical structure facilitate data analysis. My work in biomedical ontology is strongly informed by my earlier experience in laboratory research in immunology, genetics, molecular biology and virology. My research group works on ontologies for both basic and clinical applications, in collaboration with researchers both at UB and other institutions. I led efforts to revise and extend the Cell Ontology, which is intended to represent in vivo cell types from across biology. We worked extensively to bring it up to community-accepted standards in ontology development, placing particular emphasis on improving the representation of hematopoietic cells and neurons. We are developing the Cell Ontology as a metadata standard for annotation and analysis of experimental data in immunology in support of the National Institute of Allergy and Infectious Diseases (NIAID) ImmPort Immunology Database and Analysis Portal and Human Immunology Project Consortium. We have also developed ways to use the Cell Ontology in support of the analysis of gene expression data linked to cell types and have contributed to the Functional Annotation of the Mammalian Genome (FANTOM) 5 Consortium‘s work on identifying gene transcription start sites across multiple cell types and tissues. My research team is also developing the Neurological Disease Ontology to represent clinical and basic aspects of neurological diseases in order to support translational research in this area. In collaboration with clinical colleagues at UB, we are initially focusing on Alzheimer’s disease and dementia, multiple sclerosis and stroke. We have as well developed a companion ontology, the Neuropsychological Testing Ontology, to aid in the annotation and analysis of neuropsychological testing results used as part of the diagnosis of Alzheimer‘s disease and other neurological diseases. I am a long-term member of the Gene Ontology (GO) Consortium and have a particular interest in the representation of immunology and neuroscience in the GO. I am also involved in UB’s contribution to the Protein Ontology and contribute as well to the work of the Infectious Disease Ontology Consortium, Immunology Ontology Consortium and Vaccine Ontology Consortium. I teach and mentor students at the master’s and doctoral levels, and advise undergraduate, graduate, and medical students in summer research projects as well.
My research as technical imaging director of the Buffalo Neuroimaging Analysis Center focuses on developing and applying quantitative image analysis methods to neuroimaging data in order to characterize better the onset, progression, and treatment of neurological diseases. In particular, magnetic resonance imaging (MRI) can provide a vast amount of raw data about a variety of brain and spinal cord tissue characteristics, but extracting meaningful clinical and research metrics from these data is still challenging. Modern computer science techniques, however, can play a transformative role in helping physicians assess data they receive from neuroimaging techniques in order to deliver the best possible care to their patients. Highlights of my work include developing and validating a method for detecting and quantifying demyelination and remyelination in vivo, developing a method that dramatically improves the precision of conventional tissue-specific atrophy measurement and creating a technique for characterizing iron deposition in the basal ganglia. This work has had a substantial impact on our understanding of multiple sclerosis (MS) onset and progression, and the first two techniques have been successfully applied in clinical trials to understand better the impact of various therapeutic approaches in MS. My ongoing research in quantitative image analysis is aimed at increasing our understanding of the data available from state-of-the-art neuroimaging. This increased understanding can be directly translated to clinicians to better inform their patient diagnoses and treatment decisions.
Dr. Elkin serves as Professor and Chair of the UB Department of Biomedical Informatics. He is also a Professor of Medicine at the University at Buffalo. Dr. Peter L. Elkin has served as a tenured Professor of Medicine at the Mount Sinai School of Medicine. In this capacity he was the Center Director of Biomedical Informatics, Vice-Chairman of the Department of Internal Medicine and the Vice-President of Mount Sinai hospital for Biomedical and Translational Informatics. Dr. Elkin has published over 120 peer reviewed publications. He received his Bachelors of Science from Union College and his M.D. from New York Medical College. He did his Internal Medicine residency at the Lahey Clinic and his NIH/NLM sponsored fellowship in Medical Informatics at Harvard Medical School and the Massachusetts General Hospital. Dr. Elkin has been working in Biomedical Informatics since 1981 and has been actively researching health data representation since 1987. He is the primary author of the American National Standards Institute’s (ANSI) national standard on Quality Indicators for Controlled Health Vocabularies ASTM E2087, which has also been approved by ISO TC 215 as a Technical Specification (TS17117). He has chaired Health and Human Service’s HITSP Technical Committee on Population Health. Dr. Elkin served as the co-chair of the AHIC Transition Planning Group. Dr. Elkin is a Master of the American College of Physicians and a Fellow of the American College of Medical Informatics. Dr. Elkin chairs the International Medical Informatics Associations Working Group on Human Factors Engineering for Health Informatics. Dr. Elkin is the Editor of the Springer Informatics Textbook, Terminology and Terminological Systems. He was awarded the Mayo Department of Medicine’s Laureate Award for 2005. Dr. Elkin is the index recipient of the Homer R. Warner award for outstanding contribution to the field of Medical Informatics.
Internal Medicine; Internal Medicine - General
I graduated from the University of Buffalo School of Medicine and completed a residency in Internal Medicine at UB as well. I was a Chief Resident in 1990 and subsequently joined the Department of Medicine as a faculty member in the Division of General Internal Medicine. I served as an Associate Program Director for the Internal Medicine resident training program until 2008. From 2002 until 2008 I became involved in hospital administration and served as the Chief Medical Officer for the Erie County Medical Center. From 2008 until 2011 I served as the Chief Medical Officer for the Seneca Nation Health Department. During that time I completed a Masters of Public Health at the Mailman School of Public Health at Columbia University. In 2011 I returned full time to the Department of Medicine as Division Chief of General Internal Medicine and to ECMCC as VP for Clinical Integration. Throughout my career I have been very interested in medical education, quality improvement and patient safety. In my role at ECMCC as Vice President for Clinical Integration I have been charged with improving the patient experience and have focused on patient and physician communication. We are currently assessing barriers to effective communication and developing interventions to improve the quality of physician and patient interactions. I have always maintained that physicians need to actively participate in their communities and for this reason I have been involved with the P2 Collaborative of Western NY and currently am Chair of its Board of Directors. P2 has recently been designated as Western NY‘s population health improvement collaborative and will be actively involved in helping to promote a health prevention agenda for our community.
Dr. Furlani serves as Director of the University at Buffalo‘s Center for Computational Research (CCR), a leading academic supercomputing center. As Director of CCR, Dr. Thomas Furlani, whose Ph.D. is in Computational Chemistry, manages the day-to-day operations of the center as well as oversees its research activities. A National Science Foundation Pre-doctoral Fellow, Dr. Furlani has more than 25 years experience in research computing and visualization, including high-performance computing, computational chemistry, and cloud computing. In addition to supporting research, Education and Outreach has been an important component of CCR‘s mission since its inception, with on-going K-12, undergraduate and graduate level programs. In terms of K-12 outreach, CCR each year runs the Eric Pitman Annual Summer Workshop in Computational Science.
Bioinformatics; Cell growth, differentiation and development; Genomics and proteomics; Molecular and Cellular Biology; Molecular Basis of Disease; Molecular genetics; Neurobiology; Gene Expression; Stem Cells; Transgenic organisms
My research goal is to gain a better understanding of how proteins that interact with DNA regulate RNA transcription, DNA replication and metazoan development. I mentor undergraduate and graduate students in my lab; we focus on the structure and function of the Nuclear Factor I (NFI) family of site-specific DNA binding proteins, and we are investigating their roles in development. Our work has been made possible by our development of loss-of-function mutations of the NFI genes in the mouse and C. elegans. We are addressing four major questions in my laboratory and in collaboration with a number of talented collaborators: What is the structure of the NFI DNA-binding domain? How does NFI recognize and interact with DNA? Does NFI change the structure of DNA when it binds? What proteins interact with NFI to stimulate RNA transcription and/or DNA replication? These research questions are explored in my lab through two major projects focused on the role of NFIB in lung development and the role of NFIX in brain development. When NFIB is deleted from the germline of mice the animals die at birth because their lungs fail to mature normally. This provides a good model for the problems that occur with premature infants, whose lungs also fail to mature normally. We are using this model to determine how NFIB promotes lung maturation with the goal of being able to stimulate this process in premature infants. In our NFIX knockout animals, the brains of the animals are actually larger than normal and contain large numbers of cells in an area known to be the site of postnatal neurogenesis. We have evidence that NFIX may regulate the proliferation and differentiation of neural stem cells, which produce new neurons throughout adult life. Our aim is to understand the specific target genes that NFIX regulates in the adult brain to control this process of neurogenesis.
Bioinformatics; Cell growth, differentiation and development; Gene Expression; Genomics and proteomics; Molecular genetics; Signal Transduction
Research in my laboratory investigates the genetic regulatory circuitry that controls how cell fates are determined during development. We focus on two key aspects, intercellular signaling and transcriptional regulation, using primarily the fruit fly Drosophila melanogaster due to its extremely well-annotated genome and amenability to experimental manipulation. All conclusions, however, are expected to relate directly to mammalian (including human) gene regulation. Recently, we have also started investigating the regulatory genomics of other insect species of both medical and agricultural importance, beginning with the development of methods for regulatory element discovery in species with fully sequenced genomes but little functional, experimental data. A defining feature of my laboratory is that it takes both wet-lab and computational/bioinformatics approaches to studying the same set of problems about development and transcriptional regulation; hypotheses and ideas generated using one set of methods are tested and explored using the other. Current research in the laboratory falls into two main areas: 1) discovery and characterization of transcriptional cis-regulatory modules (CRMs), and 2) mechanisms of specificity for receptor tyrosine kinase (RTK) signaling. The combined results of these studies will provide insight into gene regulation, genome structure, intercellular signaling, and the regulatory networks that govern embryonic development. My group is also heavily involved in biocuration through our development and maintenance of REDfly, an internationally-recognized curated database of known Drosophila transcriptional cis-regulatory modules (CRMs) and transcription factor binding sites (TFBSs). Despite more than 25 years of experimental determination of these elements, the data have never been collected into a single searchable database. REDfly seeks to include all experimentally verified fly regulatory elements along with their DNA sequence, their associated genes, and the expression patterns they direct. REDfly is by far the most comprehensive database of regulatory elements for the higher eukaryotes and serves as an important resource for the fly and bioinformatics communities.
I direct the UB Behavioral Medicine Clinic (BMC), an internationally known clinic and research facility that provides short-term, state-of-the-art treatment for patients with painful medical disorders. These disorders include irritable bowel syndrome (IBS), low back pain, fibromyalgia, non-cardiac chest pain, temporomandibular disorder (TMD) and benign headaches such as migraine and tension headaches. A unique feature of our care is the use of evidence-based treatment protocols to help patients gain control of symptoms that have not adequately responded to standard medical treatments. Because our clinicians are active researchers, patients treated at the BMC receive cutting-edge treatments. My research, which is focused on developing and testing novel treatments for functional gastrointestinal (GI) disease, has been funded by the National Institutes of Health (NIH) since 1999. My research responsibilities include designing and conducting outcome clinical trials of novel treatments, which provide valuable research experiences for the medical, public health and psychology students I mentor. Students who work at my lab learn to design, write, conduct and analyze quality research projects with the goal of authoring at least one empirical study for publication in a first-tier journal. The academic skills my students learn at the BMC help them grow into independent researchers or academically oriented clinicians who value critical thinking and a scholarly approach to medicine. In addition, I routinely assist faculty and mentor GI fellows in research design and analysis. I lecture in several UB academic departments such as psychiatry, orthopedic surgery, neurosurgery and psychology with the aim of familiarizing trainees with the psychosocial aspects of chronic disease and ways to promote symptom self-management skills in patients coping with chronic illness. I present at the GI research conference on brain-gut interactions, outcome research, research methods and behavioral aspects of GI disease.
Infectious Disease; Bioinformatics; Microbial Pathogenesis
My clinical interest work focuses on infectious diseases, particularly those caused by Staphylococcus aureus. I practice medicine at the VA Western New York Healthcare System, where I am Chief of the Infectious Disease Section. The service here treats veterans with a wide variety of infectious diseases, including HIV and hepatitis C. I follow both inpatients and outpatients on this clinical service. Medical students, residents, and fellows evaluate and follow infectious disease consultations with me on the inpatient service. I teach extensively in the Medical School, and serve as Vice Chair for Education in the Department of Medicine. I enjoy working with students throughout the full spectrum of medical education, from first-year medical students to senior fellows in Infectious Disease. My research interests dovetail with my clinical work. I study Staphylococcal infections, particularly complications related to S. aureus bloodstream infections. My laboratory uses advanced molecular biology techniques to identify bacterial virulence factors. In collaboration with Steve Gill at the University of Rochester, we are analyzing three years of clinical data on S. aureus bacteremia in the Buffalo area and sequencing hundreds of bacteremia isolates of S. aureus to identify the genomic architectures associated with more severe complications and those associated with poor clinical outcomes. This work makes use of bioinformatics and database design, techniques that support my ongoing collaborations with other investigators on bioinformatics problems, particularly with Moraxella catarrhalis and Haemophilus influenzae. Prior to my studies in S. aureus, I conducted research on a fascinating pathogen, H. influenzae bio group aegyptius and Brazilian Purpuric Fever. Over that 10-year period my laboratory identified a unique epitope on a surface proteins associated with the disease. We were able to create the only isogenic mutant so far described with this pathogen that is highly refractory to genetic manipulation.
I work primarily at the Buffalo VA Medical Center (VAMC) where I served as the chief of nephrology for many years. I care for patients with a variety of kidney diseases, including acute and chronic kidney disease, end-stage renal disease, glomerulonephritis, polycystic disease and hypertension. I have a particular interest in the treatment of patients with resistant hypertension. I also care for patients with advanced chronic kidney disease. Together with a team of other health care professionals at the VAMC, I help patients to decide the optimal modality of dialysis for themselves and, when warranted, to consider the possibility of renal transplantation. I care for inpatients as a consultant on the nephrology consultation services. I see patients at outpatient clinics at the VAMC, and I follow patients in the VAMC outpatient dialysis unit. I participate in clinical trials related to treatment of diabetic kidney disease, treatment of anemia in chronic kidney disease and hypertension. My past research focused on understanding the response of cells to conditions of hypo- and hyperosmolality. I have published on hyponatremia and hypernatremia, and continue to have a clinical interest in these areas. I am the program director for the nephrology fellowship program and have served in this role since 1997. I oversee the nephrology fellowship training experience at the multiple clinical sites of UB’s Division of Nephrology, and I contribute to the development of the curriculum. I also serve as the coordinator of the four-week, organ-based “renal module” for first-year medical students: I plan the curriculum, identify speakers, organize the case-based small group sessions and write test questions. I also give 12 lectures and participate in four small-group sessions each year. I am committed to teaching and devote significant time in the medical school teaching medical students. In addition, I hold an adjunct appointment in the Department of Pharmacology and Toxicology, and I give lectures on renal pharmacology, hypertension and adverse drug reactions each year to students in that department. I also teach pharmacology and toxicology students in a recitation session focused on discussion of a clinical research paper.
Critical Care Medicine; Pulmonary & Critical Care Medicine; Internal Medicine; Pulmonary Disease; Pulmonary; Bioinformatics
I am engaged in clinical, teaching and research responsibilities related to the evaluation and treatment of patients with pulmonary disease or patients who are critically ill. My inpatient practice is primarily located at the medical intensive care unit (MICU) at the Buffalo General Medical Center (BGMC). The MICU provides ongoing medical care to patients who are critically ill and require significant life support therapies to sustain life or vital bodily functioning. I am specifically interested in asthma, COPD and lung cancer, but deal with a variety of disease. I evaluate patients with pulmonary disorders including shortness of breath, lung masses, abnormal chest imaging, abnormal pulmonary function tests, chronic obstructive pulmonary disease (COPD), asthma, interstitial lung disease, pulmonary hypertension and lung cancer, at the lung and heart outpatient clinic located in BGMC. The pulmonary team to which I belong also provides inpatient pulmonary consultation at both BGMC and Roswell Park Cancer Institute. Currently I am pursuing additional training in the analysis of Big Data in medical/healthcare fields. I am particularly focused on the application of drug repurposing in translation and clinic research. I also am heavily focused on the specific analysis of large VA associated clinical and genomic data sets as a fellow in the VA and NCI sponsored Big-Data Scientist Enhancement Program. I am engaged in the study of the human airways microbiome and metagenome. The human microbiome is the the collection of all the microbial organisms in a human body, and the corresponding metagenome is the collection of the genes, and gene products of the microbes. Due the potential impact of the microbiome on human health and disease, I am interested in studying the putative effects the interaction with human hosts, specifically innate immunity interaction with the metagenome in lung disease. Additionally, I collaborate with the Division of Allergy and Immunology and the Institute of Laser, Photonics and Biophotonics to elucidate immune cell function in airway diseases such as asthma and COPD. Our research focuses on the development of therapeutics aimed at novel targets identified as important in the molecular basis of pulmonary disease; efficacious laboratory results will generate more effective treatment plans for patients. I am actively involved in teaching medical students, residents and fellows about the appropriate care of the critically ill patient, as these trainees rotate in the MICU.
Over the past 30 years, my outpatient focus has been the care and management of patients with complex glomerular and autoimmune diseases. I serve as attending physician on the renal consult services for UBMD Nephrology at Buffalo General Medical Center, Roswell Park Cancer Institute and Erie County Medical Center (ECMC). I am also an attending physician on the inpatient Medicine A (General Medicine) and D (Renal Medicine) services at ECMC. My research concentrates on understanding mechanisms that underlie kidney disease, including the role of the complement system, a major factor in the body‘s immune response. My lab has developed and studied animal models of systemic lupus erythematosus, diabetic nephropathy, glomerulonephritis, obstructive nephropathy and acute renal failure. In addition to modeling disease in animals, we also have performed clinical studies both for promising new therapies and for those that focus on examining gene profiles from diseased renal tissue. To answer questions that arise in the course of our research, our work spans a number of disciplines and utilizes state-of-the-art approaches such as mouse kidney transplantation, 15-color flow cytometry and magnetic resonance imaging. My original degree is in mathematics, which remains a passion of mine. I also am interested in computational biology and founded the Computation Biology Core Facility at the University of Chicago. The core strength and emphasis of UB in the area of clinical informatics was a key factor in my decision to accept a position here so that I can continue to contribute to projects related to this field. In collaboration with leadership from other disciplines at UB, I helped establish one of the first clinical informatics fellowship programs in the United States. As a result, we accepted in 2014 the first joint nephrology/clinical informatics trainee in the country. As an educator, I am committed to the career development of the students, trainees and faculty working with me in my lab, in clinical research areas, in clinical informatics and in the clinical arena. Over the course of my career, I have mentored many outstanding students, fellows and faculty. Under my leadership and guidance, a number have received nationally competitive awards, and many have gone on to become academic leaders--including one who became a medical school dean. I serve on the Kidney, Urologic and Hematologic Diseases Subcommittee of the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), which critically evaluates training in nephrology. Through this commitment, I help ensure continued quality improvement in nephrology training, both nationally and at UB.
My group performs research to understand, through multiscale modelling, how organismal metagenomes specify their behavior and characteristics in conjunction with their environments. We accomplish this by developing novel computational biology and bioinformatics algorithms for predicting protein and proteome structure, function, interaction, design and evolution. We apply these basic science techniques to important practical problems in medicine, genetic and genomic engineering and nanobiotechnology. I received the 2010 National Institutes of Health (NIH) Director‘s Pioneer Award to develop the Computational Analysis of Novel Drug Opportunities (CANDO) platform (http://protinfo.org/cando/) to repurpose drugs approved for other indications in a shotgun manner. Our integrated informatics platform determines interactions between and among all drugs and all protein structures to create compound-proteome interaction signatures. The compound-proteome interaction signatures are weighted using pharmacological, physiological and chemoinformatics data and compared and analyzed to predict the likelihood of the corresponding compounds being efficacious for all indications simultaneously, in effect inferring homology of drug behavior at a proteomic level. Using this approach, we have made predictions for all the indications that our library of drugs maps to, with benchmarking accuracies that are two orders of magnitude better than what is observed when using random controls. We have performed prospective in vitro validations of our predictions, demonstrating comparable or better inhibition than existing drugs approved for clinical use in indications such as dengue, dental caries, diabetes, hepatitis B, herpes, lupus, malaria and tuberculosis. Our approach may be generalized to compounds beyond those approved by the FDA, and it can as well consider mutations in protein structures to enable precision medicine. We have also applied our computational techniques to design peptides for vaccines, antibacterial activity and inorganic substrate adhesion and model the structures, functions and interactions of all tractable proteins encoded by several rice genomes. A consistent theme in our research is the combination of in virtuale simulation and homology inference, followed by in vitro and in vivo verification and application, directed toward holistic multiscale modelling of complex biological systems.
Internal Medicine - General
I am Research Associate Professor of Biomedical Informatics in the Department of Biomedical Informatics (BMI), Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, SUNY (UB). Prior to joining BMI, I was a health sciences librarian focusing on instructing health care professionals and biomedical scientists of the importance of evidence-based practice, medical informatics, and lifelong learning. I taught learners and practitioners in all health care disciplines how to conduct quality searches of the literature, how to use information to create new knowledge, and how to value, use and recognize the expertise of the health sciences librarian. I have practiced a non-traditional form of librarianship as a result of my work at UB where I served as a faculty member embedded in the educational domain of the medical school; teaching medical students and residents, conducting research, serving on university committees, writing grants, and publishing the results of my work. As a hospital librarian I made a major commitment to developing educational programs for patients and families to ensure that they had access to quality, reliable, understandable health information. I was a member of a multidisciplinary team of health care professionals who taught refugee mothers from Somalia best practices for managing the health and wellness of their children. With funding from the National Network of Libraries of Medicine, Middle Atlantic Region, I created a program to teach diabetic patients with limited health literacy skills, how to find quality, reliable, and understandable health information to enable them to better manage their disease. I designed outreach programs for hospitalized patients to deliver information to their bedside, and also mailed material to patient’s homes. I persuaded the hospital’s CEO to provide space and support for a Wellness Center Library in the new vascular institute to meet the information needs of outpatients seeking day treatment for their disease. I will always apply the knowledge, skills and expertise that I have acquired throughout my career to my current appointment.
My work focuses on putting patient safety at the heart of medical education and practice. I care for inpatients at the Erie County Medical Center (ECMC) as well as in nursing home settings. I conduct research on patient safety and quality of care, focusing especially on the role of system science and information technology in improving safety in primary care. I have served as a co-investigator on grants from the Agency for Healthcare Research and Quality (AHRQ) and as the principal investigator on various other grants, including a Health Resources and Services Administration (HRSA) grant that examined adopting health information technology in primary care offices and its current and potential impacts on patient safety. I bring together methods from diverse fields, including systems and reliability theory, complexity science and management science to create unique approaches to improving care. I mentor medical students on research projects. I also supervise master’s and doctoral students in UB’s School of Management who are interested in the field of management in health care settings. As vice chair for research in the Department of Family Medicine and director of the Primary Care Research Institute, my goal is to foster high quality health services research aimed at improving patient care and patient health while keeping costs down. My teaching of medical students and residents also focuses on patient safety, including medication safety and medical error disclosure. I teach these topics during clerkship, in lectures and small groups. I also teach clinical skills and supervise medical students in both outpatient and inpatient settings. I supervise family medicine residents on the inpatient service at ECMC and in nursing homes.
Barry Smith is a prominent contributor to both theoretical and applied research in ontology, especially in the biomedical domain. He is the author of some 500 publications on ontology and related topics, and editor of The Monist: An International Quarterly Journal of General Philosophical Inquiry. His research has been funded by the National Institutes of Health, the US, Swiss and Austrian National Science Foundations, the US Department of Defense, the Volkswagen Foundation, and the European Union. In 2002 he received the 2 million Euro Wolfgang Paul Award of the Alexander von Humboldt Foundation and in 2010 he was awarded the first Paolo Bozzi Prize in Ontology by the University of Turin. Smith is SUNY Distinguished Professor in the Department of Philosophy and Director of the National Center for Ontological Research in the University at Buffalo (UB). He is also Adjunct Professor in the UB Departments of Biomedical Informatics, Computer Science and Neurology. Smith’s pioneering work on the science of ontology led to the formation of the OBO (Open Biomedical Ontologies) Foundry, a suite of resources designed to support information-driven research in biology and biomedicine. He is ontology lead for the NIAID ImmPort project, one of the principal scientists of the National Center for Biomedical Ontology, a Scientific Advisor to the Gene Ontology Consortium, and a PI on the Protein Ontology and Infectious Disease Ontology projects. He also provides ontology support to the United Nations Environment Program, the US Army Intelligence and Information Warfare Directorate (I2WD) and other defense agencies. Since 2009 Smith has also served as ontology consultant to Hernando de Soto of the Institute of Liberty and Democracy (ILD) supporting the work of the ILD on creating modern legal frameworks that help the poor of the developing and ex-communist world access property and business rights.
Bioinformatics; Gene Expression; Genomics and proteomics
The recent development of high-throughput genomics technologies is revolutionizing many aspects of modern biology. However, the lack of computational algorithms and resources for analyzing massive data generated by these techniques has become a rate-limiting factor for scientific discoveries in biology research. In my laboratory, we study machine learning, data mining and bioinformatics and their applications to cancer informatics and metagenomics. Our work is based on solid mathematical and statistical theories. The main focus of our research is on developing advanced algorithms to help biologists keep pace with the unprecedented growth of genomics datasets available today and enable them to make full use of their massive, high-dimensional data for various biological enquiries. My research team is working on two major projects. The first is focused on metagenomics, currently funded by the National Institutes of Health (NIH), the National Science Foundation (NSF) and the Women’s Health Initiative. Our goal is to develop an integrated suite of computational and statistical algorithms to process millions or even hundreds of millions of microbial genome sequences to: 1) derive quantitative microbial signatures to characterize various infectious diseases, 2) interactively visualize the complex structure of a microbial community, 3) study microbe-microbe interactions and community dynamics and 4) identify novel species. We collaborate with researchers throughout the University at Buffalo, notably those in the School of Medicine and Biomedical Sciences, the School of Public Health and Health Professions and the College of Arts and Sciences. The second project focuses on cancer progression modeling. We use advanced computational algorithms to integrate clinical and genetics data from thousands of tumor and normal tissue samples to build a model of cancer progression. Delineating the disease dynamic process and identifying the molecular events that drive stepwise progression to malignancy would provide a wealth of new insights. Results of this work also would guide the development of improved cancer diagnostics, prognostics and targeted therapeutics. The bioinformatics algorithms and software developed in our lab have been used by more than 200 research institutes worldwide to process large, complex data sets that are core to a wide variety of biological and biomedical research.
Immunopathology; Surgical Pathology; Renal Pathology
Patient care for a Pathologist is centered on assisting patients and clinicians in the understanding and the use of clinical laboratory data for the planning of therapeutic decisions. My personal specialty focus areas are in renal pathology, immunopathology, and urological pathology. I provide tissue biopsy and clinical laboratory diagnose , prognoses, and therapeutic advice to patients and clinicians on medical and surgical diseases of the kidney (including kidney transplants), bladder, prostate , and testis. These services include the interpretation of biopsies and pathology specimens, consultations on the ordering and/or the results of clinical laboratory lab tests. Raised in Philadelphia, PA I received my undergraduate education from LaSalle College in Philadelphia in 1973. I attended the University Of Pennsylvania School Of Medicine and received my MD in 1977. After finishing medical school I did an internship in Internal Medicine at Pennsylvania. I completed my Pathology Residency in anatomic and clinical pathology at the Hospital of the University of Pennsylvania in 1982. During that training I had special concentrations in immunology, HLA testing, and nephropathology. I was a Fellow in Surgical Pathology in 1982-1983. I joined the faculty in the Department of Pathology and Laboratory Medicine at the University of Pennsylvania in 1983. In my first year of appointment I was given the opportunity to do a specially arranged fellowship with Dr Conrad Pirani in Nephropathology at Columbia University. At Penn I rose through the ranks to become Professor, Vice Chair for Anatomic Pathology-Hospital Services, and Interim Chair of the Department of Pathology and Laboratory Medicine My research interests are translational and have been focused in the domain of genitourinary pathology. Over the last decade I have had the great opportunity to work collaboratively with a group of image scientists in the development of quantitative image analysis tools tailored to the needs of the digital pathology community. Our vision is to create a new analytic paradigm fusing the data from the quantitative analysis of high resolution images with multidimensional molecular data. This “fused diagnostics” approach will support personalized predictive modeling of disease and its response to therapy. Our collaborative group is funded and is working hard to develop platforms which will support this new way of addressing complex multivariable testing. Over the years I have had the great good fortune to teach many classes of undergraduate medical students in nephropathology and genitourinary pathology. I have been Program Director of the Surgical Pathology and Immunopatholgy Fellowships at the Hospital of the University of Pennsylvania and instructed 56 Fellows. I have been a member of 9 PhD and 1 MS candidates’ thesis committees. I continue to instruct at the UME, GME, and Graduate student levels. I have been active in the work of many Pathology societies both as a speaker and in varied leadership roles. My volunteer work has been with the ACSP, USCAP, CAP, Pathology Informatics, ASIP, ICPI, and APC. I was a member of the ASCP Board of Directors for many years and rose through the leadership sequence to be elected ASCP President for 2010-2011. My society work has helped me understand both the challenges and the opportunities which face our profession in these times of great change. In 2011 I moved from Philadelphia to Buffalo to become Chair of Pathology and Anatomical Sciences at the University at Buffalo, State University of New York. I continue to maintain an active collaborative research program in image science and focus my efforts as Chair on building our clinical, educational, and research programs at UB. I am excited to be part of this great University which is on the rise.
Pediatrics; General Pediatrics
I am a physician executive with extensive experience in medical management, medical informatics – including big data and data science − financial analysis and computer modeling. I serve as the executive director of the University at Buffalo Institute for Healthcare Informatics (IHI), as chief medical informatics officer (CMIO) of UBMD, a multispecialty faculty practice of over 500 UB physicians, and as CMIO of Kaleida Health, the largest health care provider in Western New York The IHI supports big data health care research and economic development at UB and its partner institutions in the Buffalo Translational Consortium by providing a secure computing environment, data science and security consulting and extensive health care datasets. The IHI provides a secure data center with a state-of-the-art data repository infrastructure that can be used to generate knowledge that improves the health of the Western New York community, New York State and the nation. As CMIO my goal is to implement and optimize electronic health records (EHRs) and other systems so that they will collect data that can simultaneously provide clinical decision support, manage patient populations and feed data repositories. I have served in multiple medical and informatics leadership roles, and my background in clinical, administrative and technological medicine enables me to interface effectively with multiple health care environment stakeholders, including physicians, nurses, other clinical and administrative staff, information technology personnel and vendors. As a result, I have been able to lead physician practices through transformative changes, including the adoption of electronic health records. I have published and presented extensively in the field of informatics; my particular interest is ethical issues in informatics. I am a board-certified pediatrician and continue to practice general pediatrics in inner-city Buffalo.