My research is focused on developing efficient and effective statistical and computational methods for genetic and genomic studies. These studies often involve large-scale and high-dimensional data; examples include genome-wide association studies, epigenome-wide association studies, and various functional genomic sequencing studies such as bulk and single cell RNAseq, bisulfite sequencing, ChIPseq, ATACseq etc. Our method development is often application oriented and specifically targeted for practical applications of these large-scale genetic and genomic studies, thus is not restricted in a particular methodology area. Our previous and current methods include, but are not limited to, Bayesian methods, mixed effects models, factor analysis models, sparse regression models, deep learning algorithms, clustering algorithms, integrative methods, spatial statistics, and efficient computational algorithms. By developing novel analytic methods, I seek to extract important information from these data and to advance our understanding of the genetic basis of phenotypic variation for various human diseases and disease related quantitative traits.
Samuel K Handelman, Ph.D., is Research Assistant Professor in the department of Internal Medicine, Gastroenterology, of Michigan Medicine at the University of Michigan, Ann Arbor. Prof. Handelman is focused on multi-omics approaches to drive precision/personalized-therapy and to predict population-level differences in the effectiveness of interventions. He tends to favor regression-style and hierarchical-clustering approaches, partially because he has a background in both statistics and in cladistics. His scientific monomania is for compensatory mechanisms and trade-offs in evolution, but he has a principled reason to focus on translational medicine: real understanding of these mechanisms goes all the way into the clinic. Anything less that clinical translation indicates that we don’t understand what drove the genetics of human populations.
Jun Li, PhD, is Professor and Chair for Research in the department of Computational Medicine and Bioinformatics and Professor of Human Genetics in the Medical School at the University of Michigan, Ann Arbor.
Brenda Gillespie, PhD, is Associate Director in Consulting for Statistics, Computing and Analytics Research (CSCAR) with a secondary appointment as Associate Research Professor in the department of Biostatistics in the School of Public Health at the University of Michigan, Ann Arbor. She provides statistical collaboration and support for numerous research projects at the University of Michigan. She teaches Biostatistics courses as well as CSCAR short courses in survival analysis, regression analysis, sample size calculation, generalized linear models, meta-analysis, and statistical ethics. Her major areas of expertise are clinical trials and survival analysis.
Prof. Gillespie’s research interests are in the area of censored data and clinical trials. One research interest concerns the application of categorical regression models to the case of censored survival data. This technique is useful in modeling the hazard function (instead of treating it as a nuisance parameter, as in Cox proportional hazards regression), or in the situation where time-related interactions (i.e., non-proportional hazards) are present. An investigation comparing various categorical modeling strategies is currently in progress.
Another area of interest is the analysis of cross-over trials with censored data. Brenda has developed (with M. Feingold) a set of nonparametric methods for testing and estimation in this setting. Our methods out-perform previous methods in most cases.
Bhramar Mukherjee is a Professor in the Department of Biostatistics, joining the department in Fall, 2006. Bhramar is also a Professor in the Department of Epidemiology. Bhramar completed her Ph.D. in 2001 from Purdue University. Bhramar’s principal research interests lie in Bayesian methods in epidemiology and studies of gene-environment interaction. She is also interested in modeling missingness in exposure, categorical data models, Bayesian nonparametrics, and the general area of statistical inference under outcome/exposure dependent sampling schemes. Bhramar’s methodological research is funded by NSF and NIH. Bhramar is involved as a co-investigator in several R01s led by faculty in Internal Medicine, Epidemiology and Environment Health sciences at UM. Her collaborative interests focus on genetic and environmental epidemiology, ranging from investigating the genetic architecture of colorectal cancer in relation to environmental exposures to studies of air pollution on pediatric Asthma events in Detroit. She is actively engaged in Global Health Research.
Dr. Zeina Mneimneh is Assistant Research Scientist in the University of Michigan Survey Research Center.
Her research focuses on the use of social media and neighborhood contextual information to study social and health science topics and involves a collaboration between Michigan and Georgetown University.
Kai S. Cortina, PhD, is Professor of Psychology in the College of Literature, Science, and the Arts at the University of Michigan, Ann Arbor.
Prof. Cortina’s major research revolves around the understanding of children’s and adolescents’ pathways into adulthood and the role of the educational system in this process. The academic and psycho-social development is analyzed from a life-span perspective exclusively analyzing longitudinal data over longer periods of time (e.g., from middle school to young adulthood). The hierarchical structure of the school system (student/classroom/school/district/state/nations) requires the use of statistical tools that can handle these kind of nested data.
Dr. Raghunathan’s primary research interest is in developing methods for dealing with missing data in sample surveys and in epidemiological studies. The methods are motivated from a Bayesian perspective but with desirable frequency or repeated sampling properties. The analysis of incomplete data from practical sample surveys poses additional problems due to extensive stratification, clustering of units and unequal probabilities of selection. The model-based approach provides a framework to incorporate all the relevant sampling design features in dealing with unit and item nonresponse in sample surveys. There are important computational challenges in implementing these methods in practical surveys. He has developed SAS based software, IVEware, for performing multiple imputation analysis and the analysis of complex survey data. Raghunathan’s other research interests include Bayesian methods, methods for small area estimation, combining information from multiple surveys, measurement error models, longitudinal data analysis, privacy, confidentiality and disclosure limitations and statistical methods for epidemiological studies. His applied interests include cardiovascular epidemiology, social epidemiology, health disparity, health care utilization, and social and economic sciences. Raghunathan is also involved in the Survey Methodology Program at the Institute for Social Research, a multidisciplinary team of sociologists, statisticians and psychologists, provides an opportunity to address methodological issues in: nonresponse, interviewer behavior and its impact on the results, response or measurement bias and errors, noncoverage, respondent cognition, privacy and confidentiality issues and data archiving. The Survey Methodology Program has a graduate program offering masters and doctoral degrees in survey methodology.
My research focuses on developing and applying computational and data-enabled methodology in the broader area of sustainability. Main thrusts are as follows:
- Human mobility dynamics. I am interested in mining large-scale real-world travel trajectory data to understand human mobility dynamics. This involves the processing and analyzing travel trajectory data, characterizing individual mobility patterns, and evaluating environmental impacts of transportation systems/technologies (e.g., electric vehicles, ride-sharing) based on individual mobility dynamics.
- Global supply chains. Increasingly intensified international trade has created a connected global supply chain network. I am interested in understanding the structure of the global supply chain network and economic/environmental performance of nations.
- Networked infrastructure systems. Many infrastructure systems (e.g., power grid, water supply infrastructure) are networked systems. I am interested in understanding the basic structural features of these systems and how they relate to the system-level properties (e.g., stability, resilience, sustainability).
A network visualization (force-directed graph) of the 2012 US economy using the industry-by-industry Input-Output Table (15 sectors) provided by BEA. Each node represents a sector. The size of the node represents the economic output of the sector. The size and darkness of links represent the value of exchanges of goods/services between sectors. An interactive version and other data visualizations are available at http://mingxugroup.org/
My research focuses on developing statistical methods and software tools for the analysis of human genetic data and application of those methods to understand the genetic basis of human health and disease. Our methods and tools are used by statisticians and geneticists worldwide. My disease research is focused on type 2 diabetes (T2D) and related traits and on bipolar disorder and schizophrenia. Our studies are generating and analyzing genome or exome sequence data on 10,000s of individuals, requiring the efficient handling of petabyte-scale data.