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CCMB Affiliated Faculty

The U-M Center for Computational Medicine and Bioinformatics (CCMB) is a campus-wide interdisciplinary academic center with over 100 affiliated faculty members. The faculty membership of CCMB has a strong representation from diverse fields such as mathematics, computer science, and statistics, and is complemented by faculty with biological and biomedical expertise who are applying cutting-edge biomedical informatics to their work.

CCMB faculty may serve as co-mentors for University of Michigan Bioinformatics Program students as well as providing research opportunities for students and faculty.

The faculty list below may be filtered by research area and/or last name.

Name Research
Elizabeth (“Liz”) Speliotes, Goncalo Abecasis, Ph.D.

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...

Julia Adler-Milstein, Ph.D. Julia Adler-Milstein, Ph.D.

Julia Adler-Milstein is an Assistant Professor at the School of Information with a joint appointment in the School of Public Health (Health Management and Policy). Her research focuses on policy and management issues related to the use of IT in healthcare delivery. Her expertise is in health information exchange and she has conducted three national surveys of health information organizations....

Philip C. Andrews, Ph.D. Philip C. Andrews, Ph.D.

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.

Brian D. Athey, Ph.D.

Brian Athey is the Michael Savageau Professor and founding Chair of the Department of Computational Medicine and Bioinformatics in the U-M Medical School and co-director of the Michigan Institute for Data Science (MIDAS). He also has appointments as a Professor of Psychiatry and of Internal Medicine. Brian received his Ph.D. in Cell and Molecular Biology (Biophysics Concentration) at the...

Sara Aton, Ph.D. Sara Aton, Ph.D.

The effects of sensory experience and sleep on neural circuits, mechanisms underlying nervous system plasticity and memory formation.

James R. Baker Jr, M.D. James R. Baker Jr, M.D.

Autoimmune endocrine disease; host defense mechanisms and immunologic diseases; adjuvant vaccines; gene transfer; targeted drug delivery; biosensors, bio imaging, and biologic nanotechnology

Scott Barolo, Ph.D. Scott Barolo, Ph.D.

Transcriptional enhancers are the primary processors and integrators of patterning information during embryonic development. The Barolo lab focuses on enhancers that are directly regulated by major cell signaling pathways, such Hedgehog, Wnt, Notch, MAPK, and BMP. We use genetic, biochemical, transgenic, biochemical, evolutionary, and computational approaches to study these DNA sequences (...

Michael Boehnke, Ph.D. Michael Boehnke, Ph.D.

Statistical design and analysis of human gene mapping studies of common multifactorial diseases. Genome-wide association and sequencing studies.
Application to type 2 diabetes and related traits, and bipolar disorder.

Victoria Booth, Ph.D. Victoria Booth, Ph.D.

My research is in applying mathematical modeling to further our understanding of the brain. My modeling work addresses different spatial and temporal scales of brain function, from single neuron spiking, to activity of large-scale spiking neuron networks, to networks of interacting neuronal populations. A consistent theme of my research is to utilize mathematical modeling to understand the...

Dr. Alan Boyle Alan Boyle, Ph.D.

Dr. Boyle's reasearch group aims to combine both computational and wet lab strategies to answer questions related to the transcriptional regulatory control of human genes. We believe that a complex regulatory control determines the fates of individual non-coding regulatory elements and that the integration of diverse genetic, epigenetic, and disease data is the best way to explore this control...

charles L. Brooks III, Ph.D. Charles L. Brooks III, Ph.D.

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.

Charles F. Burant, M.D., Ph.D. Charles F. Burant, M.D., Ph.D.

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...

Margit Burmeister, Ph.D. Margit Burmeister, Ph.D.

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...

Daniel Burns Jr, Ph.D. Daniel Burns Jr, Ph.D.

Dr. Burns' research interests center around DNA structure and dynamics and gene regulation, especially the effects of supercoiling in the organization of chromatin and its nuclear matrix attachments, analysis of Hi-C data via dynamical models, relations to cell states. Other interests include dynamics of cell membranes and structure. Dr. Burns' continuing mathematical interests include complex...

Sally A. Camper, Ph.D. Sally A. Camper, Ph.D.

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

Heather A. Carlson, Ph.D. Heather A. Carlson, Ph.D.

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....

Andrew Chang Andrew Chang, M.D.

Dr. Andrew C Chang is currently working in collaboration with Dr. David Beer studying the pathogenesis of esophageal cancer. His particular interests include studying mechanisms of esophageal adenocarcinoma treatment resistance and chemoprevention.

Clinical projects under development include studies aimed at assessing outcomes after thoracic surgery among elderly patients and devising...

Vivian Cheung Vivian Cheung, M.D.

In the Cheung lab, we focus on human genetics and study gene regulation. We combine computational and experimental methods to study normal variation in human traits and genetics of complex diseases. We assess the extent of individual differences in cellular phenotypes such as gene expression and organelle function. Then, we treat the variable phenotypes as quantitative traits to map and...

Arul M. Chinnaiyan, M.D., Ph.D. Arul M. Chinnaiyan, M.D., Ph.D.

Dr. Chinniayan's research focuses on functional genomics, proteomic and bioinformatic approaches to study cancer for the purposes of understanding cancer biology as well as to discover clinical biomarkers.

Greg Dick, Ph.D. Greg Dick, Ph.D.

Our laboratory applies genomic and metagenomic analyses of microorganisms to problems in environmental and geological science. Applications in bioinformatics focus on comparative genomics and 'binning', whereby fragmentary metagenomic sequences of unknown origin are assigned to organisms on the basis of genome signatures. Of particular interest in this area are self-organizing maps of...

Ivo Dinov, Ph.D. Ivo Dinov, Ph.D.

Dr. Dinov is the Director of the Statistics Online Computational Resource (SOCR) and is an expert in mathematical modeling, statistical analysis, computational processing and scientific visualization of large datasets (Big Data). His applied research is focused on nursing informatics, multimodal biomedical image analysis, and distributed genomics computing. Examples of specific brain research...

Melissa Duhaime, Ph.D. Melissa Duhaime, Ph.D.

Dr. Duhaime uses (meta)genomic tools to investigate two realms of marine microbiology: (1) ocean plastic-microbe associations and the role of microbes in the fate of marine plastics, and (2) the evolution and ecology of ocean viruses and their microbial hosts, at both the community and single isolate level. Bioinformatic applications include developing strategies to manage large amounts of...

Eva L. Feldman, M.D., Ph.D. Eva L. Feldman, M.D., Ph.D.

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...

Daniel Forger Daniel Forger, Ph.D.

My research is devoted to understanding biological clocks. I use techniques from many fields, including computer simulation, detailed mathematical modeling and mathematical analysis, to understand biological timekeeping. My research aims to generate predictions that can be experimentally verified.

Peter Freddolino, Ph.D. Peter Freddolino, Ph.D.

The regulatory networks of bacteria play a key role in their information processing capabilities, coordinating and executing interactions with their environments. Quantitative, predictive models of these networks would be tremendously beneficial for facilitating the development of new antimicrobial therapies, enabling synthetic biology applications, and understanding bacterial evolution and...

Thomas W. Gardner, M.D., M.S. Thomas W. Gardner, M.D., M.S.

Our research is directed at understanding why diabetes damages the retina, with the goal of helping persons with diabetes maintain their vision.

Krishna Garikipati, Ph.D. Krishna Garikipati, Ph.D.

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.

Sharon C. Glotzer, Ph.D. Sharon C. Glotzer, Ph.D.

Assembly of nanoscale systems; supercooled and metastable liquids and complex fluids, colloids, and complex fluids; biomimetic materials design; computer simulation.

Pinghua Gong, Ph.D. Pinghua Gong, Ph.D.

Structured Sparsity Learning: Algorithms, Theories and Its Applications
Optimization Methods for Machine Learning
Feature Selection & Grouping
Multi-Task/Transfer Learning

Richard Gonzalez, Ph.D. Richard Gonzalez, Ph.D.

Primary areas of study are social psychology and judgment and decision making. I also work in the area of applied statistics to develop new analytic tools for social science.

Barry Grant, Ph.D. Barry Grant, Ph.D.

Our research involves the use of computational approaches, based on both biophysics and bioinformatics, to study the structure, function and evolution of biological macromolecules.

We are particularly interested in nature’s nanomachines: molecular motors and switches, which lie at the heart of biological processes, from the division and growth of cells...

Yuanfang Guan, Ph.D. Yuanfang Guan, Ph.D.

Functional genomic data, such as RNA-seq, microarray, protein-protein interactions, are growing exponentially these days. The research in Guan Lab focuses on developing novel and high-accuracy algorithms that integrate these data for predicting gene functions and networks. We have the following ongoing projects in the lab:

1. Modeling dynamic networks: Biological networks may rewire...

Deborah Gumucio, Ph.D. Deborah Gumucio, Ph.D.

The Gumucio laboratory works on endoderm/mesoderm cross-talk during organogenesis of the small intestine. An important signaling molecule is hedgehog, which is secreted by the endoderm and acts on several different cell types in the mesoderm. We are developing mouse models to explore this signaling and we are investigating in silico tools for the identification of hedgehog target genes and...

David A. Hanauer, M.D., M.S. David A. Hanauer, M.D., M.S.

Dr. Hanauer is primarily interested in clinical medical informatics, especially in working with clinical data in the electronic medical record.

Yongqun "Oliver" He, Ph.D. Yongqun "Oliver" He, Ph.D.

Dr. He's primary bioinformatics interests are development of biomedical ontologies and their applications in literature mining, Bayesian network modeling, microbial genomics, and vaccine informatics. His primary wet-lab research interests are in studying microbial pathogenesis and host-pathogen interaction using high-throughput technologies and developing vaccines against intracellular...

Alfred Hero, Ph.D. Alfred Hero, Ph.D.

Network topology discovery, statistical pattern recognition, multimodality information integration, spatio-temporal modeling and analysis.

Gerry Higgins Gerald A. Higgins, M.D., Ph.D.

My research focuses on pharmacogenomics to optimize medication selection and dosage for patients who have been diagnosed with psychiatric disorders and neurological disease. Emphasis is placed on noncoding regulatory pathways in the human epigenome for discovery of novel brain pathways that mediate the pharmacodynamics of drugs such as mood stabilizers, anticonvulsants, antipsychotics,...

Richard E. Hughes, Ph.D. Richard E. Hughes, Ph.D.

Hughes lab concentrates on mathematical modeling related to orthopaedic surgery. Approaches include optimization and Monte Carlo simulation.

Jeffrey W. Innis, M.D., Ph.D. Jeffrey W. Innis, M.D., Ph.D.

Early Post-Implantation Mammalian Body Patterning

Post-implantation development requires precisely coordinated cellular movements in preparation for gastrulation. We have characterized and genetically mapped a spontaneous X-linked mouse mutant, Polypodia (Ppd), which we discovered and established as a mutant line using in vitro fertilization and genetic crosses to explore early post-...

Trachette L. Jackson, Ph.D. Trachette L. Jackson, Ph.D.

The main focus of Dr. Jackson's research is combining mathematical modeling, numerical simulation and in vivo experiment to gain deeper understanding of tumor growth and vascular development at the molecular, cellular, and tissue levels.

Hosagrahar V. Jagadish, Ph.D. Hosagrahar V. Jagadish, Ph.D.

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...

Hui Jiang, Ph.D. Hui Jiang, Ph.D.

Hui Jiang is interested in developing statistical and computational methods for the analysis of large-scale biological data generated using modern high-throughput technologies.

Olivier Jolliet, Ph.D. Olivier Jolliet, Ph.D.

Professor Jolliet's research and teaching programs aim to assess environmental risks and impacts of chemicals and of innovative technologies. He co-initiated the UNEP (United Nations Environment Program)/SETAC Life Cycle Initiative and is the scientific manager of its Life Cycle Impact Assessment program. He is editor and reviewer for several scientific journals.

Wenjun Ju Wenjun Ju

My research interests include investigating the role of cell-type-specific genes in kidney disease initiation and progression, and applying systems biology approach to develop non-invasive molecular markers that can predict disease progression at early stage using large multi-center study cohorts.

Niko Kaciroti, Ph.D. Niko Kaciroti, Ph.D.

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.

Hyun Min Kang, Ph.D. Hyun Min Kang, Ph.D.

His research interests lie in areas of medical genetics and population genetics, including the analysis of next-generation sequencing data, genetic association mapping of rare variants, genetics of polygenic traits, genetics-driven approach to drug discovery, association studies with unstratified population, confounding-conscious analysis of high-throughput biological data, fine-scale...

Sharon L.R. Kardia, Ph.D. Sharon L.R. Kardia, Ph.D.

Genetic epidemiology with a focus on genetics of common chronic diseases, especially cardiovascular disease and hypertension.

Alla Karnovsky, Ph.D. Alla Karnovsky, Ph.D.

My research interests involve the analysis of high throughout omics data, focusing primarily on metabolomics, and the development of computational methods and tools for the analysis and integration of metabolomics data with other types of genomic data. I am also interested in biomedical ontologies and one of my current projects involves the development of Informed Consent Ontology.

My...

Jeff Kidd, Ph.D. Jeff Kidd, Ph.D.

We apply a genome-wide approach to understanding the processes that shape the structure, content, and sequence variation of genomes among human populations and between species. We seek to understand how biological and historic population processes act to shape genomic variation and how this variation leads to the wide range of phenotypic diversity observed in the natural world.

We take...

Aaron Alan King, Ph.D. Aaron Alan King, Ph.D.

In the King Lab, we use sophisticated mathematical, computational, and statistical tools to advance theoretical ecology and evolution. We formalize scientific hypotheses as mathematical models to make precise predictions and powerful inference. One major focus of our research is the ecology and evolution of infectious diseases. We formulate mathematical models and confront them with data to...

Denise E. Kirschner, Ph.D. Denise E. Kirschner, Ph.D.

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.

Kitzman Jacob Kitzman, Ph.D.

We develop genome-scale technologies to comprehensively identify sequence variants, resolve genomic structures, and dissect their functional impacts with respect to molecular and cellular phenotypes.

1. Haplotype-resolved sequencing. We have developed new sequencing methods to experimentally resolve the haplotype phase of variants, which is almost entirely discarded during conventional...

Robert Krasny, Ph.D. Robert Krasny, Ph.D.

My research involves developing particle methods for scientific computing. Several projects are relevant to biomolecular dynamics including: a multipole treecode algorithm for screened Coulomb interactions, a treecode/Ewald method for periodic systems, and a boundary integral method for the Poisson-Boltzmann model of solvated biomolecules.

Matthias Kretzler, M.D. Matthias Kretzler, M.D.

Systems biology of renal diseases, including nephrotic syndrome, diabetes, hypertension and autoimmune diseases of the kidney. Coordination of NIH ORDR rare disease Nephrotic Syndrome Study Network for multi scalar analysis of glomerular disease: Anaylsis of genome wide expression data sets for molecular marker identification, transcriptional pathway mapping, promoter modeling and systems...

Anuj Kumar, Ph.D. Anuj Kumar, Ph.D.

Research interests in the Kumar Lab lie in the integrated application of functional genomics, proteomics, and bioinformatics towards the investigation of fundamental cellular processes in the budding yeast Saccharomyces cerevisiae and related fungal pathogens. In particular, the scope of this research encompasses techniques of systematic phenotypic screens, proteomic analyses of protein...

Ronald G. Larson, Ph.D. Ronald G. Larson, Ph.D.

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.

Christian Lastoskie, Ph.D. Christian Lastoskie, Ph.D.

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.

jun Li, Ph.D. Jun Li, Ph.D.

Genetic and genomic analyses of complex phenotypes, including bipolar disorder, cancer, blood clotting disease, and traits involving animal models and human microbiomes. Our approach emphasizes statistical analysis of genome-scale datasets (e.g, gene expression and genotyping data, results from next-generation sequencing), evolutionary history, bioinformatics, and pattern recognition.

Xiaoxia (Nina) Lin, Ph.D. Xiaoxia (Nina) Lin, Ph.D.

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...

Jennifer Linderman, Ph.D. Jennifer Linderman, Ph.D.

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.

Mats Ljungman, Ph.D. Mats Ljungman, Ph.D.

We have developed four techniques based on bromouridine labeling of nascent RNA that allow us to estimate both the rate of transcription (Bru-seq) and the rate of degradation and splicing kinetics (BruChase-seq) of any RNA. In addition, the use of UV light to introduce random transcription-blocking lesions allowing us to map transcription start sites and active enhancer elements genome-wide (...

David K. Lubensky, Ph.D. David K. Lubensky, Ph.D.

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.

David M. Lubman, Ph.D. David M. Lubman, Ph.D.

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...

Brent Martin, Ph.D. Brent Martin, Ph.D.

Our group aims to explore the function and physiological role of novel enzymes and lipids involved in the development of neurological diseases and cancer. To achieve these goals, we propose to bridge chemical, analytical, and biological approaches to identify novel disease targets and develop chemical approaches for therapeutic intervention. Our expertise in cell and molecular biology,...

Richard C. McEachin, Ph.D. Richard C. McEachin, Ph.D.

My research interests revolve around the development and application of computational approaches to understanding the genetic etiology underlying complex disease. I emphasize the use of statistical approaches that allow us to mine the extensive resources available in public databases, analysis of high-throughput data types (e.g. microarray, next generation sequencing, genome wide association...

Melvin McInnis, M.D. Melvin McInnis, M.D.

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...

Fan Meng, Ph.D. Fan Meng, Ph.D.

Algorithms and advanced genomic and transcriptomic analyses of complex datasets, especially from studies of the central nervous system.

Rajasree Menon, Ph.D. Rajasree Menon, Ph.D.

My main research is focused on studying alternative splice isoforms/variants that are involved in different types of human cancers. I have developed an approach to integrate transcriptomic data with mass-spectrometric data for the identification of splice isoforms. The functional role of the distinct splice variant of a gene is not well understood. I use different computational tools to...

Sofia D. Merajver, M.D., Ph.D. Sofia D. Merajver, M.D., Ph.D.

Molecular genetics of breast cancer, BRCA1 gene function, angiogenesis, cancer risk assessment.

Richard A. Miller, M.D., Ph.D. Richard A. Miller, M.D., Ph.D.

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.

Ryan E. Mills, Ph.D. Ryan E. Mills, Ph.D.

Our research group is primarily focused on the analysis of whole genome sequence data to identify genetic variation (primarily structural variation) and examine their potential functional impact in disease phenotypes. We are particularly interested in analyzing complex regions of the genome that are not easily resolved through modern sequencing approaches and which may exhibit interesting...

John V Moran, Ph.D. John V Moran, Ph.D.

The goal of our laboratory is to understand how an abundant class of jumping genes, known as retrotransposable elements, impacts the structure and function of human genomes. In particular, we study Long INterspersed Element-1 (LINE-1 or L1) retrotransposons. The average human genome is estimated to contain roughly 80-100 LINE-1 elements that are able to mobilize (i.e., retrotranspose) to new...

Kayvan Najarian, Ph.D. Kayvan Najarian, Ph.D.

The focus of Dr. Najarian’s research is on the design of signal/image processing and machine learning methods to create computer-assisted clinical decision support systems that improve patient care and reduce the costs of healthcare. Dr. Najarian’s lab also designs sensors to collect and analyze physiological signals and images. In particular, Dr. Najarian’s research focuses on creating...

Alexey Nesvizhskii, Ph.D. Alexey Nesvizhskii, Ph.D.

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...

Joseph Norman, M.D., Ph.D. Joseph Norman, M.D., Ph.D.

Medical informatics, decision analysis.

Gilbert S Omenn, M.D., Ph.D. Gilbert S Omenn, M.D., Ph.D.

Dr. Omenn's research focuses on cancer proteomics and informatics. He is especially interested in the role of differential expression of alternative splice isoforms of proteins and transcripts in specific cancer-related pathways. He chairs the Human Proteome Organization (HUPO) global Human Proteome Project (www.thehpp.org). There are datasets for...

Petros Papagerakis, B.D.S., B.Sc., M.Sc., Ph.D. Petros Papagerakis, Ph.D.

The Papagerakis lab is interested in several aspects of tooth development and dental cells differentiation including the regulation of cell lineage commitment and stage-specific gene expression as well as the developmental control of matrix deposition and maturation. Our main focus is to link basic science and mathematical modeling with clinically applicable research in the areas of Medical...

Stephen Parker, Ph.D. Stephen CJ Parker, Ph.D.

The Parker laboratory uses an integrative research approach in the general fields of computational biology and functional genomics. The major goal of the lab is to generate mechanistic knowledge about how disease susceptibility is encoded in the non-coding portion of the genome, with a focus on type 2 diabetes. We accomplish this through an interdisciplinary combination of molecular/cellular...

Subramaniam Pennathur, M.B.B.S. Subramanium Pennathur, M.B.B.S.

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...

Indika Rajapakse, Ph.D. Indika Rajapakse, Ph.D.

My research is on the structure and function of networks that shape the dynamics of genome organization in the interphase nucleus in three dimensional space and time. I apply mathematical and statistical approaches derived from theory of networks, systems and control theory, and multivariate statistics.

Rudy J. Richardson, Sc.D., D.A.B.T. Rudy J. Richardson, Sc.D., D.A.B.T.

Dr. Rudy J. Richardson received his B.S. (magna cum laude) in Chemistry from Wichita State University. Upon achieving Ph.D. candidacy in Chemistry at SUNY Stony Brook, he transferred to Harvard, where he earned the Sc.M. and Sc.D. degrees in Physiology/Toxicology. After postdoctoral work in Neurochemistry at the Medical Research Council Toxicology Unit in Carshalton, England, he joined the...

Gus Rosania, Ph.D. Gustavo Rosania, Ph.D.

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...

Maureen Sartor, Ph.D. Maureen Sartor, Ph.D.

Dr. Sartor’s laboratory focuses on developing methods and tools for analysis of genomic and epigenomic data. This includes Bayesian models for prioritizing peaks in ChIP-Seq data, and methods for functional enrichment testing for proteomic, metabolomics, and ChIP-Seq (regulatory and epigenomic) data. The lab’s main biological focus is cancer, concentrating on oral cancers. Research ranges...

Robert Savit, Ph.D. Robert Savit, Ph.D.

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,...

Amr H. Sawalha, M.D. Amr H. Sawalha, M.D.

My research interest is in the genetics and epigenetics of complex autoimmune and inflammatory diseases, with a particular focus on lupus and systemic vasculitis. We apply state-of-the-art genomic and epigenomic methodologies, and subsequent functional studies using both in vitro and in vivo systems to identify and characterize genetic loci and pathways involved in the pathogenesis of immune-...

Patrick Schloss Patrick Schloss, Ph.D.

Dr. Schloss's research looks at resistance of the gut microbiota to perturbations such as colonization by exogenous pathogens and to mutations in host genes that give rise to tumors. To address these biological questions we develop computer software to process and analyze next generation sequencing data.

Santiago Schnell, Ph.D. Santiago Schnell, Ph.D.

Dr. Schnell investigates physiological systems comprising many interacting components, where modeling and theory may aid the identification of the key mechanisms underlying the behavior of the systems as a whole. Dr. Schnell's lab is particularly interested in investigating the molecular mechanisms of pancreatic beta-cells turnover and dysfunction in diabetes, the dynamics of metabolic...

Jessica Schwartz, Ph.D. Jessica Schwartz, Ph.D.

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.

Clayton Scott, Ph.D. Clayton Scott, Ph.D.

Machine learning, data mining, statistical signal and image processing, anomaly detection, and applications in bioinformatics.

Laura Scott, Ph.D. Laura Scott, Ph.D.

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,...

Srijan Sen, M.D., Ph.D. Srijan Sen, M.D., Ph.D.

Epidemiological studies indicate that genes and life stress are two of the most important factors in the etiology of depression. The goal of our laboratory is to shed light on how human genetic variation and stress interact to create the pathophysiological architecture underlying major depression.

While there has been growing interest in gene x stress interactions in depression over the...

David Sept, Ph.D. David Sept, Ph.D.

Research in the Sept lab covers four primary areas. The first focuses on the molecular interactions underlying cell migration, a process central to many aspects of development, differentiation and the cellular response to diseases such as cancer. Related to this is work characterizing and developing drugs that target sub-cellular filaments to treat parasitic diseases like toxoplasmosis,...

Kerby Shedden, Ph.D. Kerby Shedden, Ph.D.

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.

David Sherman, Ph.D. David Sherman, Ph.D.

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...

Carl Simon, Ph.D. Carl Simon, Ph.D.

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.

Stephen A. Smith, Ph.D. Stephen A. Smith, Ph.D.

I have deep roots in biology and computer science. My primary research focuses on phylogenetic dataset construction, rates of evolution (molecular and character), and large- and small-scale biogeographic evolution.

Evan Snitkin, Ph.D. Evan Snitkin, Ph.D.

Our lab is primarily focused on the application of genomics to study the evolution and epidemiology of hospital associated pathogens. In particular, we are interested in integrating genomics with clinical and epidemiological data to better understand how healthcare practices impact transmission and evolution of drug-resistant organisms.

Elizabeth K. Speliotes Elizabeth K. Speliotes, M.D., Ph.D., M.P.H.

Nonalcoholic fatty liver disease, obesity and related metabolic diseases.

Chandra Sripada, Ph.D. Chandra Sripada, M.D., Ph.D.

Dr. Sripada's research examines the cognitive and neural mechanisms underpinning regulation of emotion, attention, and motoric responses in attention-deficit/hyperactivity disorder (ADHD) and substance use disorders (SUDS). Recent work emphasizes neurodevelopmental perspectives. He has a special interest in neuroimaging methodology, including machine learning, pattern classification, whole-...

Kathleen Stringer, Pharm.D. Kathleen Stringer, Pharm.D.

There are more than 130 different therapeutic proteins or peptides that are used to treat a broad range of illnesses. One of these proteins, tissue plasminogen activator (tPA), has been used to treat myocardial infarction and stroke. Dr. Stringer's laboratory has determined that in addition to its proteolytic function, tPA has anti-inflammatory activity. The combination of these two...

Zeeshan Syed Zeeshan Syed, Ph.D.

Application of machine learning and signal processing to problems in clinical medicine and developing world health care. Specific areas include computational biomarkers to predict cardiovascular and neurological disorders; addressing information overload in multi-model long-term data sets; treatment planning for cancer and surgery; low-cost software-based surrogates for expensive diagnostic...

Jeremy Taylor, Ph.D. Jeremy Taylor, Ph.D.

Longitudinal and survival analysis, cure models, missing data, Box-Cox transformations, statistical methods for bioinformatics, surrogate and auxiliary variables, statistical modelling of biomedical data.

Muneesh Tewari, Ph.D. Muneesh Tewari, Ph.D.

• Biology of circulating, cell-free microRNAs and translational applications
• Developing the next generation of biomarker approaches for cancer early detection, disease monitoring and treatment response prediction
• Bioinformatics and computational biology, high-throughput sequencing
• Point-of-care technologies for nucleic acid analysis

Dr. Tewari is a world-renowned...

Scott Tomlins, Ph.D. Scott Tomlins, M.D., Ph.D.

My research has focused on using high-throughput techniques to characterize the cancer genome and transcriptome to identify cancer-specific aberrations to better understand cancer biology and identify clinically relevant biomarkers and therapeutic targets. My most important contribution has been discovering TMPRSS2:ETS gene fusions in prostate cancer, which play a fundamental role in prostate...

Lam "Alex" Tsoi Lam "Alex" Tsoi, Ph.D.

Dr. Tsoi completed his PhD in biomedical science at the Medical University of South Carolina, supervised by Dr. W Jim Zheng. He then worked as a research fellow in the Center for Statistical Genetics from the Department of Biostatistics at the University of Michigan, under the mentorship of Dr. Goncalo Abecasis. He joined the Department of Dermatology and Department of Computational Medicine...

Michael Uhler, Ph.D. Michael Uhler, Ph.D.

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...

Angela Violi, Ph.D. Angela Violi, Ph.D.

Multiscale simulations of complex systems, nanoscience, interactions of nanoparticles with biomolecular assembly, nanoparticle growth and self-assembly.

Nils Walter, Ph.D. Nils Walter, Ph.D.

The Walter group explores the world of non-protein coding RNAs such as ribozymes, riboswitches, microRNAs and long non-coding RNAs (lncRNAs) as well as the processes of pre-mRNA splicing, mRNA transcription, translation, gene regulation and lncRNA-mediated epigenomics, using single-molecule fluorescence and molecular dynamics simulation tools. In addition, we use Monte-Carlo simulation,...

Zheng Wang, Ph.D. Jie Wang, Ph.D.
Shaomeng Wang, Ph.D. Shaomeng Wang, Ph.D.

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...

Zheng Wang, Ph.D. Zheng Wang, Ph.D.

Active Learning, Transfer Learning, Sparse Learning,
Big Data and Efficient Learning Algorithms, Matrix Completion and Recommendation,
Computational Learning Theory, Statistical Learning Theory.
Machine Learning Application in Social Computing

Naisyin Wang, Ph.D. Naisyin Wang, Ph.D.

Longitudinal Data Analysis, Model Based Clustering, Measurement Error Models, Mixed Effects Models, Missing Data Issues, Non- and Semiparametric Modeling, Applications in Biological and Medical Fields.

Stanley J. Watson, M.D., Ph.D. Stanley J. Watson, M.D., Ph.D.

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...

Thomas Werner, Ph.D. Thomas Werner, Ph.D.

Molecular pathways and networks underlying the changes causing diseases, especially various forms of cancer and immunological disturbances (e.g inflammatory diseases). Part of several international research consortia dealing with approaches to personalized medicine. Analysis and biological interpretation of high- through-put data especially microarrays and next generation sequencing (NGS)....

Andrzej Wierzbicki, Ph.D. Andrzej Wierzbicki, Ph.D.

Our lab is focused on understanding how RNA produced from non-coding sequences (non-coding RNA) controls genome activity on the chromatin level. This includes DNA methylation, histone modifications, nucleosome positioning and three-dimensional organization of chromosomes. Our work may be described as an interface of RNA biology and epigenomics.

Cristen J. Willer, Ph.D.

I'm interested in studying complex genetic diseases, particularly the genetics of quantitative traits such as lipid levels and human obesity. I've also been recently working on imputation of ungenotyped markers, population genetics, bioinformatics, and understanding the function behind genetic associations.

John A. Williams, M.D., Ph.D. John A. Williams, M.D., Ph.D.

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...

Patricia Wittkopp, Ph.D. Patricia Wittkopp, Ph.D.

Evolutionary genetics and genomics, evolution of development

Qiong Yang, Ph.D.

The broad focus of the Yang lab is on the quantitative understanding of early embryo development, a complex pattern formation process that involves proliferation, differentiation, and migration of indivldual cells, and cell-cell communications through mechanical and chemical signaling. Our strategy is to connect these multi-scale mechanisms by developing complementary in vitro and in vivo...

Jieping Ye, Ph.D. Jieping Ye, Ph.D.

Dr. Ye's research group focuses on conducting fundamental research in machine learning and data mining, developing computational methods for analysis of large-scale, high-dimensional, heterogeneous and complex biomedical data, and building informatics software.

John Younger, M.D., M.S. John Younger, M.D., M.S.

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...

Jianzhi Zhang, Ph.D. Jianzhi Zhang, Ph.D.

Molecular and genomic evolution

Yang Zhang, Ph.D. Yang Zhang, Ph.D.

Determining structure and function of protein molecules is a cornerstone of modern biology and medicine. The main focus of the Zhang lab is to develop bioinformatics approaches to predict the three-dimensional structures of proteins from amino acid sequences and then deduce the biological functions based on the sequence-to-structure-to-function paradigm. They are especially interested in the...

Xiang Zhou, Ph.D. Xiang Zhou, Ph.D.

My research is focused on developing statistical and computational methods to address interesting biological problems in genetic and genomic studies. These studies often involve large-scale and high-dimensional data sets, and examples include genome-wide association studies and functional genomic sequencing studies (RNAseq, ChIPseq etc.). Through developing novel analytic methods to extract...

Ji Zhu, Ph.D. Ji Zhu, Ph.D.

Statistical learning, data mining, high-dimensional data, network analysis, and applications in bioinformatics.

Michal Zochowski, Ph.D. Michal Zochowski, Ph.D.

The research done in our laboratory focuses on understanding the dynamical underpinnings of neural activity that is underlying brain cognitive function as well as its pathologies. That is, we would like to understand generic principles of the formation of spatiotemporal patterns in coupled dynamical systems that mediate neuronal communication and facilitate formation of different cognitive and...

Sebastian Zöllner, Ph.D. Sebastian Zöllner, Ph.D.

Genetic modeling, particularly the inheritance process; gene mapping.