Faculty — UM Bioinformatics Graduate Program

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	Abecasis, Goncalo, D. Phil Associate Professor of Biostatistics The focus of my research is the identification and characterization of genes determining human variation and disease. In particular, I have focused on developing analytical methods and statistical tools that will facilitate the mapping of complex traits and allow geneticists to realize the benefits of new high-throughput technologies in the lab. Much of my research has focused on the use of linkage disequilibrium in the mapping of complex disease susceptibility genes. Linkage disequilibrium based mapping strategies search for short segments of ancestral chromosomes shared among present day individuals. High-throughput technologies allow fine-scale characterization of genetic variation and have made these searches possible.
	Abney, Steve, Ph.D. Associate Professor of Linguistics, Associate Professor of Electrical Engineering & Computer Science and Associate Professor in School of Information His research interests include parsing, corpora, statistical methods, documentation of endangered languages, human sentence processing, machine learning and language acquisition, information extraction, question answering, spoken dialogue systems, syntax, prosody, and semantics.
	Ackerman, Mark, Ph.D. Associate Professor of Information, and Associate Professor of Electrical Engineering & Computer Science Ackerman's research focuses on such areas as privacy, organizational memory or collaborative information access, collective information reuse, and online communities. He is part of the SocialWorlds research group that studies these areas of interest.
	Adams, Julian, Ph.D. Professor of Molecular, Cellular, and Developmental Biology Dr. Adams' laboratory studies a range of problems in the population genetics and evolution of microorganisms. Current projects concern (1) the analysis of the role of transposable elements and gross chromosomal rearrangements in the generation of adaptive genetic change in populations of S. cerevisiae, (2) the analysis of the evolutionary dynamics and physiological basis of polymorphisms arising in evolving populations of E. coli and S. cerevisiae, and (3) molecular and biochemical characterization of the process of adaptation in microbial populations. Dr. Adams also has interests in human population genetics, he is currently working with the genetic and demographic structure of human isolates.
	Al-Hashimi, Hashim, Ph.D. Assistant Professor of Chemistry and Assistant Research Scientist in Biophysics Our laboratory applies solution state NMR spectroscopy to investigate the molecular basis of RNA function in processes ranging from gene expression (e.g. transcriptional activation and translation) to virion functioning (e.g. genome packaging and reverse transcription). We make extensive use of new NMR techniques involving measurements of residual dipolar couplings in determining global aspects of RNA structure, dynamics and interaction.
	Andrews, Phil, Ph.D. Professor of Biological Chemistry, Research Professor of Biological Chemistry and Director of MLSC-Core Technology Alliance Bioactive peptides--structure and function; development of new technologies in proteome analysis and functional genomics for identifying gene function and characterizing gene products, including analysis of posttranslational modifications.
	Atchade, Yves, Ph.D. Assistant Professor of Statistics The central theme of my research is Monte Carlo methods; particularly methodological and theoretical aspects of Markov Chain Monte Carlo (MCMC). I'm also genuinely interested in statistical modeling (particularly form a Bayesian perspective). I have some applied ongoing projects in social science and biology.
	Athey, Brian, Ph.D. Professor of Bioinformatics and Computational Biology, Departments of Psychiatry and Internal Medicine, Associate Director, Center for Computational Medicine and Biology (CCMB), Principal Investigator, NIH National Center of Integrative Biomedical Informatics, Director, Biomedical Informatics Program, Michigan Institute for Clinical and Health Research "Integrative Biomedical Informatics" and "Translational Bioinformatics", and "Computational Multiscale Modeling and Simulation of Macroscopic and Microscopic Biological Systems"
	Baker, James, M.D. Ruth Dow Doan Professor of Biologic Nanotechnology, Professor of Internal Medicine, Chief, Division of Allergy, Associate Professor of Pathology, and Professor of Biomedical Engineering Autoimmune endocrine disease; host defense mechanisms and immunologic diseases; adjuvant vaccines; gene transfer; targeted drug delivery; biosensors, bio imaging, and biologic nanotechnology
	Balis, Ulysses, M.D. Associate Professor of Pathology, Director of Clinical Informatics, and Co-Director of Division of Pathology Informatics Numerical analysis and interpretation of digital histological (whole-slide) data sets in tandem with expression data and other high-order data, Vector Quantization (VQ) tools and Gallois Fields, design of support vector engines for automated region-of-interest based image repository query.
	Baveja, Satinder, Ph.D. Associate Professor of Electrical Engineering & Computer Science Research: My main research interest is in the old-fashioned goal of Artificial Intelligence (AI), that of building autonomous agents that can learn to be broadly competent in complex, dynamic, and uncertain environments. The field of reinforcement learning (RL) has focused on this goal and accordingly my deepest contributions are in RL. More recently, I have been taking seriously the challenge of building agents that can interact with other agents and even humans in both artificial and natural environments. This has led to research in: * human-computer interaction * computational game theory * mechanism design
	Beecher, Chris, Ph.D. Research Professor of Pathology The development of the science of Metabolomics. The lab focus is both on aspects of data generation and data interpretation.
	Berke, Joshua, Ph.D. Assistant Professor of Psychology and Neuroscience Scholar My primary interests concern the role of basal ganglia circuits in the learning, selection and performance of actions, and how such neural mechanisms are altered in psychiatric and neurological disorders such as drug addiction and Parkinson's Disease. My current studies use chronic electrophysiological recording in awake, freely-moving rats and transgenic mice. I examine how populations of neurons encode information and interact with one another, and how these neural representations are changed by learning experiences and by dopaminergic manipulations.
	Bhavnani, Suresh, Ph.D. Research Assistant Professor, Center for Computational Medicine and Biology My research focuses on developing biomedical applications based on the network analysis and visualization of biomedical datasets, and the systematic analysis of user needs. The goal is to identify general frameworks which map patterns in information, to effective and efficient algorithms and interfaces, with applications across biomedical domains.
	Boehnke, Michael, Ph.D. Richard G. Cornell Collegiate Professor of Biostatistics Design and analysis of human gene mapping studies of common multifactorial diseases. Linkage and linkage disequilibrium mapping. Applications to type 2 diabetes, schizophrenia, glaucoma.
	Booth, Victoria, Ph.D. Assistant Professor of Mathematics, Research Assistant Professor of Anesthesiology, and Research Fellow, Mathematics
	Brooks, Charles, Ph.D. Warner-Lambert/Parke-Davis Professor of Chemistry and Biophysics Research in the group of Charles L. Brooks III in the Department of Chemistry and Biophysics Program at the University of Michigan is focused on the application of statistical mechanics, quantum chemistry and computational methods to chemically and physically oriented problems in biology.
	Burant, Charles, M.D., Ph.D. Dr. Robert C. and Veronica Atkins Professor of Metabolism, Associate Professor of Internal Medicine and Associate Professor of Molecular and Integrative Physiology Our lab focuses on the study of Diabetes, with on-going research in many areas. We are interested in identifying the ways in which nutrients, drugs and biologics affect insulin sensitivity and the way that they lead to Type II Diabetes. We are evaluating these affects through clincal research, utilizing animal models of diabetes and insulin sensitivity, and through studying the underlying cellular pathways of energy metabolism. Additionally, we are interested in studying how new B-cells can be generated ex vivo for the treatment of both Type I and II Diabetes. We are utilizing novel techniques to prospectively isolate and differentiate adult pancreatic stem/progenitor cells into multiple pancreatic lineages.
	Burmeister, Margit, Ph.D. Research Professor in Molecular & Behavioral Neuroscience Institute, Professor of Human Genetic sand Professor of Human Genetics in Psychiatry This laboratory's research is aimed at finding genes involved in behavioral and neurological and psychiatric diseases, especially related to depression and drug abuse. With the Human Genome sequenced, unprecedented numbers of genetic variants identified, untangling these risk factors is now possible and has started in my laboratory. This includes work on the phenotypes, on novel techniques to score genetic variants in a high throughput manner, and on correlating microarray expression data with genotypes.
	Burns, Daniel, Ph.D. Professor of Mathematics and Director of Bioinformatics Dr. Burns' research interests center around DNA helix dynamics and gene regulation, especially the effects of supercoiling in the organization of chromatin and its nuclear membrane attachments. Other interests include de novo peptide sequencing, and transmembrane protein structure and topology prediction. Dr. Burns' continuing mathematical interests include complex analytic geometry and its relationship to symplectic geometry.
	Camper, Sally, Ph.D. Professor of Human Genetics and Internal Medicine, Chair of Human Genetics Camper lab focuses on development and function of the neuroendocrine system using transgenic mice, gene targeting, and molecular genetics analysis of mouse mutations. Bioinformatics projects ongoing in the lab include cross species DNA sequence comparisons to identify regulatory elements and analysis of 30,000 embryonic pituitary cDNA sequences in our database.
	Carlson, Heather, Ph.D. Associate Professor of Medicinal Chemistry and Chemistry Dr. Carlson focuses on understanding protein-ligand complexes through molecular mechanics simulations, quantum mechanics calculations, and database mining. Her lab has two major goals: (1) developing new methods that incorporate protein flexibility into computer-aided drug design and (2) creating Binding MOAD (Mother of All Databases), the definitive database for protein-ligand recognition. Keywords for research in her laboratory include structure-function relationships, molecular recognition, drug design, database, and biophysics.
	Cease, Kemp, M.D., M.B.A. Associate Professor of Internal Medicine Dr. Cease's research program is pursued in close collaboration with Dr. Jon Oscherwitz, a senior member of the research group and Research Investigator in the Division. The laboratory has continued to examine the structure-activity relationships of tandemly repeated epitopes. Such tandem repeats exist in nature and can serve as the target of T cell and B cell responses. Dr.'s Oscherwitz and Cease have conclusively demonstrated enhanced immunogenicity of these structures for both T cell and B cell responses, and have shown that this is a property of the tandem repeat architecture rather than simply of epitope dose. The lab has previously published these findings for T cell responses as well as for B cell responses as well using engineered vaccine constructs containing tandemly repeated HIV epitopes.
	Chinnaiyan, Arul, M.D., Ph.D. S.P. Hicks Collegiate Professor, Associate Professor of Pathology, Associate Professor of Urology and Director of Pathology Microarray Laboratory Dr. Chinniayan's research focuses on functional genomics approaches to study cancer and trancriptional memory. Genes identified using these strategies are then characterized using traditional biochemical methods. Projects span from basic science to translational research. Key words for his research include bioinformatics, DNA microarrays, prostate cancer, breast cancer, proteomics, genomics, biomarkers, transcriptional memory, and apoptosis.
	Crippen, Gordon, Ph.D. Professor of Pharmaceutical Chemistry Dr. Crippen's laboratory centers on theory of protein folding, including structure, thermodynamics, and kinetics. He also looks at molecular modeling, statistical mechanics, quantitative structure-activity relations, novel methods in conformational analysis including distance geometry; drug receptor site modeling; calculation of protein folding.
	Del Vecchio, Domitilla, Ph.D. Assistant Professor of Electrical Engineering & Computer Science My research interests are currently in two main areas: (1) State estimation and control in multi-agent decision and control systems; (2) Rational design of biomolecular systems using control theory.
	Douglas, Julie, Ph.D. Assistant Professor of Human Genetics Dr. Douglas' research involves statistical genetics and genetic mapping of complex human diseases and traits with an emphasis on the development, application, and evaluation of statistical methods.
	Elenitoba-Johnson, Kojo, M.D. Associate Professor & Director, Division of Translational Research and Director, Molecular Diagnostics Laboratory Hematologic malignancies.
	Feldman, Eva, M.D., Ph.D. Russell N. DeJong Professor of Neurology and the Director, Neuropathy Center Dr. Feldman's laboratory focuses on the role of growth factors in neuronal growth and neuroprotection. The lab is specifically interested in the neurotrophic properties of the insulin-like growth factors I and II (IGF-I, IGF-II). They use molecular biology, gene therapy and protein biochemistry in their research. The lab primarily studies Amyotrophic Lateral Sclerosis (ALS) and Diabetic Neuropathy.
	Forger, Daniel, Ph.D. Assistant Professor of Mathematics Mathematical Biology
	Garikipati, Krishnakumar, Ph.D. Associate Professor of Mechanical Engineering My work draws from applied mathematics, numerical methods, nonlinear mechanics and materials physics. I am particularly interested in problems of mathematical biology, biophysics and the mechanics of biology. Current research interests include growth and remodelling of biological tissue, cell adhesion and cell mechanics.
	Glotzer, Sharon, Ph.D. Professor of Chemical Engineering, Professor of Materials Science & Engineering, Professor of Macromolecular Science & Engineering, and Professor of Physics Assembly of nanoscale systems; supercooled and metastable liquids and complex fluids, colloids, and complex fluids; biomimetic materials design; computer simulation.
	Gumucio, Deborah, Ph.D. Professor of Cellular & Molecular Biology Gumucio laboratory works on endoderm/mesoderm cross-talk during organogenesis of the small intestine, gastrointestinal progenitor cells, molecular etiology of familial Mediterranean fever. Other words describing her research include hedgehog signaling, gastric cancer, inflammation, innate immunity.
	Hanauer, David, M.D., M.S. Clinical Lecturer in Pediatrics and Communicable Diseases and Assistant Director of Comprehensive Cancer Center Bioinformatics Core Dr. Hanauer is primarily interested in clinical medical informatics, especially in working with clinical data in the electronic medical record.
	Hanlon, Philip, Ph.D. Donald J. Lewis Collegiate Professor of Mathematics, Professor of Mathematics and Associate Provost for Academic and Budgetary Affairs The Hanlon laboratory work is on combinatorics and new facets of the Macdonald Conjectures.
	He, Yongqun, Ph.D. Assistant Professor of Laboratory Medicine Dr. He's primary interests are in studying microbial pathogenesis and host-pathogen interaction using high-throughput technologies and developing vaccines against intracellular pathogens. Dr. He also has an active interest in using or developing bioinformatics systems to uncover fundamental principles of infectious diseases and host-pathogen relations.
	Hero, Alfred, Ph.D. Professor of Electrical Engineering & Computer Science and Professor of Biomedical Engineering Network topology discovery, statistical pattern recognition, multimodality information integration, spatio-temporal modeling and analysis.
	Hughes, Richard, Ph.D. Associate Professor of Orthopaedic Surgery and Associate Professor of Biomedical Engineering Hughes lab concentrates on mathematical modeling related to orthopaedic surgery. Approaches include optimization and Monte Carlo simulation.
	Innis, Jeffrey, Ph.D. Associate Professor of Human Genetics and Associate Professor of Pediatrics and Communicable Diseases Innis lab research focuses on molecular genetics of mammalian limb development; genetics of human limb malformation syndromes. Other keywords for his work include molecular genetics, limb development, Hox genes and human genetics.
	Jackson, Trachette, Ph.D. Associate Professor of Mathematics Dr. Jackson is interested in the application of ordinary and partial differential equations; especially to modeling the genesis, progression and treatment of cancer. In keeping with the belief that mathematical modeling should be a quantitative representation of some experimental paradigm, she actively seeks collaborations with experimentalists in both academia and in industry.
	Jagadish, Hosagrahar, Ph.D. Professor of Computer Science and Engineering Prof. Jagadish studies the integration of data from multiple sources, and the usability, by non-technical users, of complex databases. Some questions he asks are: What happens when you can connect many different databases that are autonomously organized and managed? How can you query and integrate and analyze all the information that you potentially have access to? How can one represent, and account for, variations in information structure and in information quality? What can you do as an information publisher to maximize public accessibility of your information while preventing undesirable access? His laboratory has built Timber, a hierarchical database from the ground up for storing and querying XML data. He has also led the creation of MiMI, the Michigan Molecular Interaction Index.
	Kaciroti, Niko, Ph.D. Associate Research Scientist, Center for Human Growth and Development Dr. Kaciroti's research interest is in analyzing longitudinal data, repeated measures and discrete data with missing values. Another area of his research is using complex and dynamic models within a hierarchical Bayesian framework to analyze cortisol circadian rhythm.
	Kalbfleisch, Jack, Ph.D. Professor of Biostatistics, and Professor of Statistics Dr. Kalbfleisch's interests include the development of statistical methodology; statistical analysis of failure time, event history and longitudinal data; design and analysis of clinical trials; and stochastic modeling. Primary application areas include the analysis of registry data on solid organ transplants associated with the Scientific Registry of Transplant Recipients and related work on End Stage Renal Disease.
	Kardia, Sharon, Ph.D. Associate Professor of Epidemiology and Director of Public Health Genetics Program Genetic epidemiology with a focus on genetics of common chronic diseases, especially cardiovascular disease and hypertension.
	Kim, Sinae, Ph.D. Assistant Professor of Biostatistics Bayesian variable selection, clustering, nonparametric bayes, wavelets, bioinformatics, DNA microarray analysis. Bayesian variable selection, clustering, nonparametric bayes, wavelets, bioinformatics, DNA microarray analysis.
	Kim, John, Ph.D. Assistant Professor of Human Genetics and Research Assistant Professor of Life Sciences Institute We study the mechanisms of small RNA function in C. elegans and mammalian systems using traditional and high-throughput methods, including massively-parallel sequencing, genome tiling microarrays, large-scale proteomics, and genome-wide RNAi screens. These projects provide great bioinformatic challenges to integrate diverse data and design computational predictions derived from these analyses.
	Kirschner, Denise, Ph.D. Associate Professor of Microbiology & Immunology The work in my laboratory focuses mainly on questions related to host-pathogen interactions in infectious diseases. The pathogens we focus on include both bacteria (Mycobacterium tuberculosis) and HIV-1. Such pathogens have evolved strategies to evade or circumvent the host-immune response and our goal is to understand the complex dynamic involved in host-pathogen interactions.
	Kondrashov, Alexey, Ph.D. Professor of Ecology and Evolutionary Biology and Research Professor in Life Sciences Institute Alexey Kondrashov is working on a variety of subjects in evolutionary genetics. His laboratory is trying to measure the rate of spontaneous mutation in Drosophila melanogaster, using several phenotype-based approaches. Also, he studies selection at the sequence level and parallelism in protein evolution using a comparative genomics approach.
	Krasny, Robert, Ph.D. Arthur F Thurnau Professor and Professor of Mathematics Dr. Krasny is developing grid-free particle methods for scientific computing. Fluid vortices are a topic of longstanding interest. Projects relevant to biomolecular dynamics include a multipole treecode algorithm for Coulomb interactions and a boundary integral method for the Poisson-Boltzmann model of implicit solvation.
	Kretzler, Matthias, M.D. Associate Professor of Internal Medicine Systems biology of renal diseases, including diabetes, hypertension and autoimmune diseases of the kidney. Coordination of an international consortium of renal biobanks for molecular analysis of renal disease: Anaylsis of genome wide expression data sets for molecular marker identification, transcriptional pathway mapping and promoter modelling.
	Kumar, Anuj, Ph.D. Assistant Professor of Molecular, Cell, Developmental Biology and Research Assistant Professor in Life Sciences Institute His research interests lie in the integrated application of functional genomics, proteomics, and bioinformatics towards the investigation of fundamental cellular processes in the budding yeast Saccharomyces cerevisiae. In particular, the scope of his research encompasses techniques of DNA microarray analysis, proteomic analysis of protein localization, and database development.
	Larson, Ronald, Ph.D. Chair and George Granger Brown Professor of Chemical Engineering, Professor of Macromolecular Science & Engineering, and Professor of Biomedical Engineering and Mechanical Engineering Our lab's research interests are in biopolymer dynamics, including dynamics of DNA, and DNA/protein interactions. We also use molecular dynamics methods to simulate lipid membranes, and interactions between lipid membranes and proteins, peptides, or nanoparticles. We also use microfluidic devices to study DNA/protein interactions or for genomic applications.
	Lastoskie, Christian, Ph.D. Associate Professor of Civil & Environmental Engineering and Associate Professor of Biomedical Engineering Dr. Lastoskie's laboratory's interests are in characterization of nanoporous materials, control of bacterial migration, methods of in situ bioremediation, and modeling of intracellular ion transport.
	Li, Jun, Ph.D. Assistant Professor of Human Genetics, and Research Assistant Professor, Center for Computational Medicine & Biology Genetic studies of complex human diseases, including psychiatric disorders,heart disease, and cancer, with emphases on genetic influence of gene expression, population structure, DNA copy number variation (eitherinherited or somatic), and application of next-generation sequencing methods to related problems.
	Lim, Megan, M.D., Ph.D. Associate Professor of Pathology and Director of Hematopathology The research interests of our lab is the study of molecular pathogenesis of hematologic malignancies. We utilize large-scale mass spectrometry-driven proteomics to study the signaling pathway deregulation in human lymphomas and leukemias. Translational research using transcriptome and proteomic analysis as tools to generate hypothesis regarding basic cellular mechanisms of cancer formation and progression are the aims of our research.
	Lin, Xiaoxia, Ph.D. Assistant Professor of Chemical Engineering The research goal of our lab is to unearth fundamental mechanisms underlying the diverse and complex functions of biological systems, and to engineer them for the development of beneficial biotechnologies, through a multidisciplinary approach integrating mathematical modeling, computer simulation and wet-lab experiments. More specifically, one part of our lab focuses on the quantitative investigation of the mechanisms for biological switching, which is a widespread feature of biological systems and is crucial for the regulation of numerous biological processes, such as cell cycle progression and cell fate decision. The other research area of our lab will be the study and engineering of microorganisms with the goal of developing new biotechnologies for important applications such as bio-energy and bio-remediation. Examples of interesting projects in this broad direction include system-level modeling of metabolic networks, design and construction of genetic circuits, and laboratory evolution of microbial consortia.
	Linderman, Jennifer, Ph.D. Professor of Chemical Engineering and Professor of Biomedical Engineering Quantitative studies and mathematical/computational modeling of receptor-mediated cell behavior, with application to G-protein coupled receptors, signal transduction mechanisms, pharmacology, immunology, and tissue engineering.
	Ljungman, Mats, Ph.D. Associate Professor of Radiation Oncology and Associate Professor of Environmental Health Sciences Dr. Ljungman works on mechanisms of p53 activation and cellular responses to DNA-damaging agents.
	Long, Jeffrey, Ph.D. Professor of Human Genetics Adjunct Professor of Biostatistics The research in this lab is focused on the analysis of human polymorphism, including human population genetics, the inheritance of complex diseases, and statistical genetics. One focus is on how levels of polymorphism and patterns of linkage disequilibrium are influenced by the interplay among diverse factors such as historical migrations, population size, gene flow, selective environment, mutation and recombination.
	Lubensky, David, Ph.D. Norman M Leff Assistant Professor of Physics and Assistant Professor of Physics My lab is broadly interested in mathematical modeling of biochemical and genetic networks. Cell fate specification and pattern formation in development are one focus, but topics of current interest also include everything from noise in biochemical oscillators to the evolution of genetic networks. A newer related direction is the mechanical control of cell shape and morphogenesis.
	Lubman, David, Ph.D. Maude T Lane Professor of Surgical Immunology, Professor of Surgery and Professor of Pathology The Lubman Research Lab is involved in developing novel biotechnologies to solve difficult biological problems. The focus of the work has been in the field of Proteomics and Cancer Research. Proteomics involves the study of the protein expression of a cell, where proteins are the entities that perform the functions of the cell. Dr. David M. Lubman's work has involved developing methods to profile large numbers of proteins expressed by cancer cells and to understand how these proteins are different than those observed from normal cells. Proteins that are modified or overexpressed in cancer cells often result in new protein pathways that lead to tumorogenesis and metastasis of the cancer.
	Macoska, Jill, Ph.D. Associate Professor of Urology and Director of UMCCC Affymetrix and cDNA Microarray Core The Macoska laboratory is focused on the activation or repression of signaling mechanisms involved in cellular proliferation, cellular motility, and gene transcription by inflammatory mediators, particularly cytokines and chemokines, secreted consequent to aging.
	Maddock, Janine, Ph.D. Associate Professor of Molecular, Cellular, and Developmental Biology Dr. Maddock's work is aimed at understanding basic developmental questions using approaches in molecular genetics, biochemistry, and cell biology complemented by bioinformatics, genomics and proteomics. Two major areas of ongoing projects in the laboratory are under study: (1) to understand how a new class of GTP-binding proteins function in Caulobacter crescentus and Saccharomyces cerevisiae, and (2) to understand how asymmetry is established and maintained in bacteria, particularly in C. crescentus and Escherichia coli.
	McInnis, Melvin, M.D. Thomas B. and Nancy Upjohn Woodworth Professor of Bipolar Disorder and Depression and Professor of Psychiatry Genetics of bipolar disorder, genetics of major depression, longitudinal outcomes and translational research in mood disorders. Dr. McInnis directs a large clinical research enterprise focused on bipolar disorder genetics and longitudinal outcomes. Patients are cared for in a large clinic with 4 nurse practitioners, 2 social workers, 3 residents, and 3 attending psychiatrists. We are have an NIMH funded project to identify adolescents at risk for BP disorder. An NIMH funded research project is focused on fine mapping of a region of interest on chromosome 8q24.
	Meng, Fan, Ph.D. Research Assistant Professor of Psychiatry
	Merajver, Sofia, M.D., Ph.D. Professor of Internal Medicine, Director, Breast and Ovarian Cancer Risk Evaluation Program, Co-Director Breast Oncology Program Molecular genetics of breast cancer, BRCA1 gene function, angiogenesis, cancer risk assessment.
	Michailidis, George, Ph.D. Associate Professor of Statistics and Electrical Engineering and Computer Science Dr. Michailidis works on computational problems in genomics and proteomics, modeling of biological networks, machine learning, applied probability, stochastic processing networks, and network tomography.
	Miller, Richard, M.D., Ph.D. Professor of Pathology and Associate Director, Geriatrics Center Dr. Miller's research is on genetics and cell biology of aging in mice, with emphasis on gene mapping and mechanisms of cellular stress resistance in long-lived mouse mutants. His lab also works on immunology of aging, emphasizing T cell signal transduction, and protein kinase pathways and surface glycosylation.
	Nair, Vijay, Ph.D. Donald A. Darling Professor of Statistics and Professor of Industrial and Operations Engineering I have a broad range of interests in methodology, theory, and applications. I have worked in Engineering Statistics, Reliability and Degradation Modeling, Network Tomography, Design and Analysis of Experiments (including applications in Behavioral Intervention Research), and Quality Improvement.
	Nelson, Patrick, Ph.D. Assistant Professor of Mathematics and Research Assistant Professor, Center for Computational Medicine and Biology Mathematical Biology, specifically modeling of infectious diseases. Work focuses on HIV and HBV. Our group also studies Type 1 Diabetes and Immunology.
	Nesvizhskii, Alexey, Ph.D. Assistant Professor of Pathology Dr. Nesvizhskii's research interest is in the field of quantitative proteomics, with a focus on the development of computational methods for processing and extracting biological information from complex proteomic datasets. Similar to other global high throughput technologies such as microarray gene expression analysis, proteomics is extremely dependent on the ability to quickly and reliably analyze large amounts of experimental data. One of the aims of Dr. Nesvizhskii's research is to close the critical gap between the development of high throughput quantitative proteomics methods and the ability to deal with the resulting data deluge and to convert it into new biological knowledge or to develop new disease biomarkers. The efforts in his lab range from the development of computational tools and statistical methods for mass spectrometry-based peptide and protein identification and quantification, to the establishment of guidelines and standards for proteomic data analysis and publication, to the creation of public databases and proteomic data repositories and integration of proteomic with genomic and other types of biological data.
	Neubig, Richard, M.D., Ph.D. Professor of Pharmacology Molecular mechanisms of adrenergic receptors; role of guanine nucleotide proteins in cell responses; biochemical and biophysical approaches to the study of drug receptor interactions.
	Norman, Joseph, M.D., Ph.D. Clinical Lecturer in Internal Medicine Medical informatics, decision analysis.
	Omenn, Gilbert, M.D., Ph.D. Professor of Internal Medicine, Professor of Human Genetics, Professor of Public Health, and Director of Center for Computational Medicine and Biology Dr. Omenn's research focuses on cancer proteomics and informatics. He leads the Proteomics Alliance for Cancer Research, the HUPO Plasma Proteome Project, the Driving Biological Problems Core of the National Center for Integrative Biomedical Informatics, and the Center for Computational Medicine and Biology. There are datasets for application of analytical tools, and there are research teams eager to engage in collaborative studies in each of these initiatives. He has long-standing interests in mechanisms of genetic predispositions to risks from environmental and occupational exposures, pharmacogenetics and pharmacogenomics, and science-based risk analyses.
	Pascual, Mercedes, Ph.D. Associate Professor of Ecology and Evolutionary Biology I am a theoretical ecologist interested in population and community dynamics. My research areas encompass: (1) The spatio-temporal dynamics of nonlinear ecological systems for antagonistic interactions (predator-prey, host-parasite, and disturbance-recovery), particularly approaches to scale-up systems from small, individual, levels to more aggregated, population, levels, and approaches to incorporate implicitly in simple (highly aggregated) temporal models the effect of smaller scales. Similar questions are being addressed on the dynamics of infectious diseases in networks. (2) The response of nonlinear ecological systems to environmental variability and the application of nonlinear time series analysis to identify key environmental drivers and to predict responses. In particular, the nonlinear dynamics of infectious diseases in response to climate variability and climate change, including aspects of evolutionary change in pathogens. The main disease under study is cholera, but work is also underway on malaria and influenza. (3) The relationship between structure and dynamics in large networks of ecological interactions (consumer-resource and parasitic links).
	Patel, Jignesh, Ph.D. Associate Professor of Electrical Engineering & Computer Science Bioinformatics, spatial query processing, architecture-conscious database management systems, XML query processing.
	Pennathur, Subramanium, M.B.B.S. Assistant Professor of Internal Medicine We focus on exploring the role of hyperglycemia in promoting vascular inflammation and oxidative stress, leading to diabetic end organ damage. The overall goals of my research are to elucidate the biochemical pathways through which hyperglycemia accelerates glycoxidative reactions and to identify the major proteins targeted for glycoxidation in the diabetic state in vivo. We plan to determine the chemical nature of diabetic tissue damage and the relative contributions of oxidative pathways through the following concurrent experiments using mass spectrometry based techniques: i) studies of model systems to elucidate the chemical nature of the reaction pathways in vitro; ii) studies of diabetic animal models to identify oxidative pathways that operate in vivo; and iii) studies of cultured cells to identify proteins that are vulnerable to glyoxidation. Understanding such pathways would facilitate the rational design of drugs for preventing diabetic complications. We also seek to determine oxidative and metabolomic biomarkers in patients with diabetes, atherosclerosis and renal disease
	Pienta, Kenneth, M.D. Professor of Internal Medicine and Urology and Director, Urologic Oncology Dr. Pienta's laboratory focuses on defining cancer as a complex adaptive system, with a special emphasis on understanding the biology of prostate cancer metastasis. The laboratory defines metastasis as a set of defined steps encompassing emigration, migration, and immigration of the cancer cells. Within each of these steps there exist Boolean network nodes that can be identified and targeted for the development of new therapeutic strategies for the treatment of hormone refractory prostate cancer.
	Pietropaolo, Massimo, M.D. Associate Professor of Internal Medicine, Pediatrics, Director, Laboratory of Immunogenetics and Brehm Scholar, Brehm Center for Type 1 Diabetes Research and Analysis Islet cell autoimmunity in Type 1 and Type 2 Diabetes; identification of novel molecular targets of autoimmune diabetes; prediction of Type 1 Diabetes; epidemiology of islet cell autoimmunity in Type 2 diabetes; genetics of Type 1 Diabetes; proteomics in Type 1 Diabetes
	Qin, Zhaohui, Ph.D. Assistant Professor of Biostatistics Modeling and computation in statistical genetics and genomics, applications in bioinformatics, Monte Carlo methods.
	Radev, Dragomir, Ph.D. Associate Professor in School of Information, Associate Professor of Electrical Engineering & Computer Science and Associate Professor of Linguistics Dr. Radev's research interests include graph algorithms, semi-supervised machine learning, natural language processing, information retrieval, lexical networks, and applications to bioinformatics, political science, and webometrics.
	Richardson, Rudy, Sc.D., D.A.B.T. Professor of Environmental Health Sciences, Dow Professor of Toxicology and Associate Professor of Neurology We are interested in understanding mechanisms of chemically induced neurological and vascular diseases, and developing biomarkers of exposure and disease. In our lab and through collaborations, we study interactions of small molecules with target proteins using computational molecular modeling, kinetics, optical and fluorescence spectroscopy, protein mass spectrometry, quantitative structure-activity relationships, and x-ray crystallography.
	Rosania, Gus, Ph.D. Assistant Professor of Pharmaceutical Sciences Dr. Rosania's laboratory studies the mechanism of action of emerging chemotherapeutic agents for treating cancer and degenerative diseases. Dr. Rosania's research is providing a fresh, new approach to the development of novel chemotherapeutic strategies, by combining knowledge of the mechanism of action of small molecules together with mechanistic insights into molecular process of fundamental biological significance.
	Rosenberg, Noah, Ph.D. Assistant Professor of Human Genetics, Research Assistant Professor of Human Genetics, Biostatistics, and Ecology and Evolutionary Biology, and Research Assistant Professor in Life Sciences Institute Mathematical models in genetics and evolution, human population genetics, statistical methods for inference of human genetic history, role of human genetic variation in disease-gene mapping, statistical genetics, genetic variation in pathogens, gene trees and species trees, phylogenetics
	Sartor, Maureen, Ph.D. Research Assistant Professor of Center for Computational Medicine and Biology, Adjunct Research Assistant Professor of Biostatistics My main research interests involve empirical and hierarchical Bayesian models, as well as other statistical modeling, applied to the analysis of high-thoughput genomic data, and understanding and assessing the biological significance of results and molecular pathways involved. With the advent of tiling arrays and next-generation sequencing, many new biases and issues surround the question of biological significance and functionality.
	Sastry, Ann Marie, Ph.D. Professor of Materials Science and Engineering, Professor of Biomedical Engineering, and Professor of Mechanical Engineering Numerical and experimental work in disordered materials systems, including biological tissues and energetic materials. Design of batteries, including engineered and bioengineered constructs, and optimization of power supplies.
	Savit, Robert, Ph.D. Professor of Physics, and Faculty Associate, Research Center for Group Dynamics, Institute for Social Research Professor Savit's current research interests are in the area of nonlinear and adaptive systems. His group examines two types of issues. First, they study the nature of adaptive competition for scarce resources. They examine the deep phase structure that such systems exhibit, and explore the application of their insights to problems in group decision making in business, in social systems, resource allocation problems, and evolutionary systems. Professor Savit also engages in a series of experiments with groups of human subjects that study the problem of resource allocation, competition and emergent coordination. Second, his research group considers data analysis problems of nonlinear systems. Using new techniques developed in the context of dynamical systems, Professor Savit's group studies a number of intrinsically nonlinear systems. Among these are both mechanical and biological systems. In particular, he is working on the problem of understanding and predicting epileptic seizures.
	Schnell, Santiago, D. Phil. (Oxon) Associate Professor of Molecular and Integrative Physiology and Research Associate Professor of Computational Medicine and Biology The Schnell lab is developing models for the quantitative analysis of biological pathways and applying these models to problems in cell physiology. We are particularly interested in investigating the molecular mechanisms of beta-cell dysfunction in diabetes mellitus, the physiological role of the segmentation clock in embryogenesis, and the key mechanism of cellular guidance in cell migration.
	Schwartz, Jessica, Ph.D. Professor of Molecular and Integrative Physiology, Director of Cellular and Molecular Biology Dr. Schwartz's research interests include regulation of gene expression by growth factors, including: induction of expression of early response proto-oncogenes - molecular mechanisms by which transcription is stimulated, synergism among growth factors in such induction, consequences of altered expression of oncogenes on cell function.
	Scott, Clayton, Ph.D. Assistant Professor of Electrical Engineering and Computer Science Machine learning, data mining, statistical signal and image processing, anomaly detection, and applications in bioinformatics
	Scott, Laura, Ph.D. Assistant Research Scientist, Biostatistics Identification of genetic variants for type II diabetes and bipolar disease: My primary research interest is the identification of genetic variants that increase the risks of common diseases. For type II diabetes, as part of the Finland-United States Investigation of NIDDM genetics (FUSION) study, and for bipolar disease, as part of the Pritzker Neuropsychiatric Disorders Research Consortium, I am involved in genome-wide association studies of e300K SNP variants. Analysis of the SNP variants in the context of their biological function(s) will provide information on the spectrum of disease causing variants for common diseases.
	Shedden, Kerby, Ph.D. Associate Professor of Statistics and Associate Professor of Biostatistics Dr. Shedden's work focuses on statistical inference in gene expression analysis, and statistical analysis of cell-based assays of drug activity. Areas of emphasis include gene/drug interactions, gene expression changes associated with cancer, gene expression changes during the cell cycle, drug structure/activity relationships, and chemoinformatics.
	Sherman, David, Ph.D. John G. Searle Professor of Medicinal Chemistry, Professor of Medicinal Chemistry, Professor of Microbiology & Immunology, Professor of Chemistry, and Research Professor in Life Sciences Institute My research efforts over the past decade have evolved into several programs that are distinct in focus, yet coalesce into an overriding theme that include molecular genetic, biochemical and bioorganic chemical studies of microbial natural product biosynthesis. Metabolic engineering and combinatorial biosynthesis are powerful approaches for harnessing the tremendous metabolic capabilities of microorganisms, including primary and secondary pathways. New genomic-based technologies are enhancing considerably our ability to understand and manipulate complex biosynthetic systems and will enable vast new opportunities in medicine and industry. My laboratory is exploring fundamental aspects of the systems described below, as well as pursuing drug discovery opportunities in the area of infectious diseases and cancer.
	Simon, Carl, Ph.D. Director of Center of the Study of Complex Systems, Professor of Mathematics, Professor of Economics and Professor of Public Policy Dr. Simon's research work centers on the theory and application of dynamical systems, especially in modeling the epidemiology of HIV and influenza at the population and at the cellular levels. He also works with compartmental systems in biology and ecology. His current research focus is the evolution and spread of antibiotic resistant bacterial infection in health care facilities.
	Sreekumar, Arun, Ph.D. Assistant Professor of Pathology Cancer Proteomics. The major focus of my research is to identify diagnostic and prognostic biomarkers for prostate cancer. The research involves use of protein microarrays, multidimensional liquid phase protein fractionations and MS/MS analysis. One of the other areas we are developing is to monitor the autoantibody response or humoral response elicited by the immune system against tumor antigens. These we feel could be used as sensitive and specific biomarkers for early detection of prostate cancer.
	States, David, M.D., Ph.D. Professor of Human Genetics Dr. States' research focus is on computational analysis of genome regulatory elements. Techniques include simulation, classification, database construction and analysis, machine learning and parallel computation. Projects include: transcription factor binding site clusters, transcript reconstruction and analysis, genome contig assembly and analysis, megaclass sequence classification, and nucleosome binding modeling.
	Taylor, Jeremy, Ph.D. Pharmacia Research Professor of Biostatistics, Professor of Radiation Oncology and Associate Director for Biostatistics, Comprehensive Cancer Center Longitudinal and survival analysis, cure models, missing data, Box-Cox transformations, statistical methods for bioinformatics, surrogate and auxiliary variables, statistical modelling of biomedical data.
	Uhler, Michael, Ph.D. Professor of Biological Chemistry and Research Professor in Molecular and Behavioral Neuroscience Institute The research in our laboratory addresses the role of protein phosphorylation in the regulation of cell function, particularly the regulation of cells within the nervous system. The second messenger cyclic AMP (cAMP) and the protein kinase cAMP-dependent protein kinase have been shown to play key roles in the biochemical mechanisms which form the basis for learning and memory in invertebrate organisms. Our laboratory studies the role of cAMP and cAMP-dependent protein kinase in the regulation of neuronal gene transcription and ion channel function in the mammalian nervous system.
	Violi, Angela, Ph.D. Assistant Professor of Mechanical Engineering, Biomedical Engineering and Chemical Engineering Multiscale simulations of complex systems, nanoscience, interactions of nanoparticles with biomolecular assembly, nanoparticle growth and self-assembly.
	Walter, Nils, Ph.D. Associate Professor of Chemistry and Associate Research Scientist, Biophysics We explore the world of such catalytic RNAs, or "ribozymes", as well as other non-protein coding RNAs by using single-molecule and bulk-solution biochemical and biophysical tools. Which means that we work on fascinating biological catalysts at the interface of Chemistry, Biology, and Physics.
	Wang, Shaomeng, Ph.D. Professor of Internal Medicine and Pharmacology and Professor of Medicinal Chemistry Dr. Wang's focus is on the development of new computational methods for drug design and discovery, chemo-informatics and bioinformatics, and protein folding. He works on discovery, design, synthesis, and development of new small molecule therapeutics for treatment of cancer and neurological diseases by targeting crucial regulators of apoptosis, signal transduction molecules and dopamine transportor and GPCR proteins.
	Watson, Stanley, M.D., Ph.D. Ralph Waldo Gerard Professor of Neurosciences, Professor of Psychiatry, Co-Director and Research Professor, Molecular and Behavioral Neuroscience Institute Emotional regulation of complex behaviors such as reinforcement, feeding, and stress are central to proper functioning of both animals and humans. This laboratory focuses on CNS circuits and cellular systems that participate and regulate these states and related pathological conditions. Using a variety of molecular, anatomical, behavioral and pharmacological approaches, it is possible to focus on key circuits and molecules of interests.
	Williams, John, M.D., Ph.D. Professor and Chair of Molecular & Integrative Physiology and Professor of Internal Medicine Research in this laboratory focuses on the regulation of pancreatic function by hormones and neurotransmitters and is carried out at the cellular, molecular and integrative levels. Isolated cells from the pancreas of normal and transgenic animals as well as cell lines are being used. Several main areas are being studied. These include mechanisms of secretion of digestive enzymes by exocytosis, regulation of digestive enzyme synthesis to match the need, regulation of pancreatic growth, and abnormalities of function in experimental pancreatitis.
	Wittkopp, Trisha, Ph.D. Assistant Professor of Ecology and Evolutionary Biology Evolutionary genetics and genomics, evolution of development
	Woolf, Peter, Ph.D. Assistant Professor of Chemical Engineering and Biomedical Engineering Systems biology, computational biology, bioinformatics, pharmacogenomics, high-throughput screening, developmental biology, complex systems
	Young, Matthew, Ph.D. Assistant Professor of Biological Chemistry and Research Assistant Professor of Bioinformatics Dr. Young's laboratory utilizes a combination of experimental and computational approaches to study problems in protein kinases and cell signaling. In an example of regulation in a family of proteins we study, the Cyclin Dependent family of Kinases (CDKs), these kinases have evolved to require the binding of additional proteins, the cyclins, in order to activate their catalytic activity. Some examples of additional molecular mechanisms that have evolved to regulate catalytic activity in protein kinases include the interactions of additional domains with the catalytic core, phosphorylation-stabilized conformational transitions, the binding of external inhibitory proteins, and protein kinase localization. His laboratory's goal is to understand these regulatory mechanisms from a structural perspective, using the CDK family as a model.
	Younger, John, M.D., M.S. Associate Chair for Research, Department of Emergency Medicine and Associate Professor of Emergency Medicine We study the pathophysiology of and investigate new treatments for acute lung injury and acute respiratory failure. Particular interests include the mechanisms leading to lung edema and functional failure and laboratory techniques that can be used to quantify such changes. We are particularly interested in the role of complement activation in the development of injury and interactions between complement and bacterial pathogens in the lung. We are using the knowledge gained in this work to examine potential new therapies for lung injury.
	Zhang, Jianzhi, Ph.D. Associate Professor of Ecology and Evolutionary Biology Molecular and genomic evolution
	Zhang, Lixin, Ph.D., M.S. Assistant Research Scientist, Epidemiology Emergence and maintenance of infectious diseases, integrated approach to study urinary tract infection using epidemiologic, molecular, statistic, simulation, and informatic tools, and mechanisms of microbial pathogenesis.
	Zheng, Kai, Ph.D. Assistant Professor of Health Management and Policy and Assistant Professor of Information Information systems, health informatics, technology adoption and acceptance, evaluation of impact of technologies, human factors and HCI issues.
	Zhu, Ji, Ph.D. Assistant Professor of Statistics Machine learning, data mining, and their applications in bioinformatics, engineering, finance and physics
	Zoellner, Sebastian, Ph.D. Assistant Professor of Biostatistics and Psychiatry Genetic modeling, particularly the inheritance process; gene mapping.

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