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Patrick Schloss

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The Schloss lab is broadly interested in beneficial and pathogenic host-microbiome interactions with the goal of improving our understanding of how the microbiome can be used to reach translational outcomes in the prevention, detection, and treatment of colorectal cancer, Crohn’s disease, and Clostridium difficile infection. To address these questions, we test traditional ecological theory in the microbial context using a systems biology approach. Specifically, the laboratory specializes in using studies involving human subjects and animal models to understand how biological diversity affects community function using a variety of culture-independent genomics techniques including sequencing 16S rRNA gene fragments, metagenomics, and metatranscriptomics. In addition, they use metabolomics to understand the functional role of the gut microbiota in states of health and disease. To support these efforts, they develop and apply bioinformatic tools to facilitate their analysis. Most notable is the development of the mothur software package (https://www.mothur.org), which is one of the most widely used tools for analyzing microbiome data and has been cited more than 7,300 times since it was initially published in 2009. The Schloss lab deftly merges the ability to collect data to answer important biological questions using cutting edge wet-lab techniques and computational tools to synthesize these data to answer their biological questions.

Given the explosion in microbiome research over the past 15 years, the Schloss lab has also stood at the center of a major effort to train interdisciplinary scientists in applying computational tools to study complex biological systems. These efforts have centered around developing reproducible research skills and applying modern data visualization techniques. An outgrowth of these efforts at the University of Michigan has been the institutionalization of The Carpentries organization on campus (https://carpentries.org), which specializes in peer-to-peer instruction of programming tools and techniques to foster better reproducibility and build a community of practitioners.

The Schloss lab uses computational tools to integrate multi-omics tools in a culture-independent approach to understand how bacteria interact with each other and their host to drive processes such as colorectal cancer and susceptibility to Clostridium difficile infections.

Mousumi Banerjee

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My research is primarily focused around 1) machine learning methods for understanding healthcare delivery and outcomes in the population, 2) analyses of correlated data (e.g. longitudinal and clustered data), and 3) survival analysis and competing risks analyses. We have developed tree-based and ensemble regression methods for censored and multilevel data, combination classifiers using different types of learning methods, and methodology to identify representative trees from an ensemble. These methods have been applied to important areas of biomedicine, specifically in patient prognostication, in developing clinical decision-making tools, and in identifying complex interactions between patient, provider, and health systems for understanding variations in healthcare utilization and delivery. My substantive areas of research are cancer and pediatric cardiovascular disease.

Samuel K Handelman

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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.

Antonios M. Koumpias

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Antonios M. Koumpias, Ph.D., is Assistant Professor of Economics in the department of Social Sciences at the University of Michigan, Dearborn. Prof. Koumpias is an applied microeconomist with research interests in public economics, with an emphasis on behavioral tax compliance, and health economics. In his research, he employs quasi-experimental methods to disentangle the causal impact of policy interventions that occur at the aggregate (e.g. states) or the individual (e.g. taxpayers) level in a comparative case study setting. Namely, he relies on regression discontinuity designs, regression kink designs, matching methods, and synthetic control methods to perform program evaluation that estimates the causal treatment effect of the policy in question. Examples include the use of a regression discontinuity design to estimate the impact of a tax compliance reminders on payments of overdue income tax liabilities in Greece, matching methods to measure the influence of mass media campaigns in Pakistan on income tax filing and the synthetic control method to evaluate the long-term effect of state Medicaid expansions on mortality.

Evolution of Annual Changes in All-cause Childless Adult Mortality in New York State following 2001 State Medicaid Expansion

Brenda Gillespie

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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.

Ding Zhao

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Ding Zhao, PhD, is Assistant Research Scientist in the department of Mechanical Engineering, College of Engineering with a secondary appointment in the Robotics Institute at The University of Michigan, Ann Arbor.

Dr. Zhao’s research interests include autonomous vehicles, intelligent/connected transportation, traffic safety, human-machine interaction, rare events analysis, dynamics and control, machine learning, and big data analysis

 

Peter Adriaens

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My research focus is on the development and application of machine learning tools to large scale financial and unstructured (textual) data to extract, quantify and predict risk profiles and investment grade rating of private and public companies.  Example datasets include social media and financial aggregators such as Bloomberg, Pitchbook, and Privco.

Adriene Beltz

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The goal of my research is to leverage network analysis techniques to uncover how the brain mediates sex hormone influences on gendered behavior across the lifespan. Specifically, my data science research concerns the creation and application of person-specific connectivity analyses, such as unified structural equation models, to time series data; these are intensive longitudinal data, including functional neuroimages, daily diaries, and observations. I then use these data science methods to investigate the links between androgens (e.g., testosterone) and estradiol at key developmental periods, such as puberty, and behaviors that typically show sex differences, including aspects of cognition and psychopathology.

A network map showing the directed connections among 25 brain regions of interest in the resting state frontoparietal network for an individual; data were acquired via functional magnetic resonance imaging. Black lines depict connections common across individuals in the sample, gray lines depict connections specific to this individual, solid lines depict contemporaneous connections (occurring in the same volume), and dashed lines depict lagged connections (occurring between volumes).

A network map showing the directed connections among 25 brain regions of interest in the resting state frontoparietal network for an individual; data were acquired via functional magnetic resonance imaging. Black lines depict connections common across individuals in the sample, gray lines depict connections specific to this individual, solid lines depict contemporaneous connections (occurring in the same volume), and dashed lines depict lagged connections (occurring between volumes).

Kai S. Cortina

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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.

 

Rie Suzuki

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Dr. Suzuki is a behavioral scientist and has major research interests in examining and intervening mediational social determinants factors of health behaviors and health outcomes across lifespan. She analyzes the National Health Interview Survey, Medical Expenditure Panel Survey, National Health and Nutrition Examination Survey as well as the Flint regional medical records to understand the factors associating with poor health outcomes among people with disabilities including children and aging.