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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.

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.

Sriram Chandrasekaran

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Sriram Chandrasekaran, PhD, is Assistant Professor of Biomedical Engineering in the College of Engineering at the University of Michigan, Ann Arbor.

Dr. Chandrasekaran’s Systems Biology lab develops computer models of biological processes to understand them holistically. Sriram is interested in deciphering how thousands of proteins work together at the microscopic level to orchestrate complex processes like embryonic development or cognition, and how this complex network breaks down in diseases like cancer. Systems biology software and algorithms developed by his lab are highlighted below and are available at http://www.sriramlab.org/software/.

– INDIGO (INferring Drug Interactions using chemoGenomics and Orthology) algorithm predicts how antibiotics prescribed in combinations will inhibit bacterial growth. INDIGO leverages genomics and drug-interaction data in the model organism – E. coli, to facilitate the discovery of effective combination therapies in less-studied pathogens, such as M. tuberculosis. (Ref: Chandrasekaran et al. Molecular Systems Biology 2016)

– GEMINI (Gene Expression and Metabolism Integrated for Network Inference) is a network curation tool. It allows rapid assessment of regulatory interactions predicted by high-throughput approaches by integrating them with a metabolic network (Ref: Chandrasekaran and Price, PloS Computational Biology 2013)

– ASTRIX (Analyzing Subsets of Transcriptional Regulators Influencing eXpression) uses gene expression data to identify regulatory interactions between transcription factors and their target genes. (Ref: Chandrasekaran et al. PNAS 2011)

– PROM (Probabilistic Regulation of Metabolism) enables the quantitative integration of regulatory and metabolic networks to build genome-scale integrated metabolic–regulatory models (Ref: Chandrasekaran and Price, PNAS 2010)

 

Research Overview: We develop computational algorithms that integrate omics measurements to create detailed genome-scale models of cellular networks. Some clinical applications of our algorithms include finding metabolic vulnerabilities in pathogens (M. tuberculosis) using PROM, and designing multi combination therapeutics for reducing antibiotic resistance using INDIGO.

Research Overview: We develop computational algorithms that integrate omics measurements to create detailed genome-scale models of cellular networks. Some clinical applications of our algorithms include finding metabolic vulnerabilities in pathogens (M. tuberculosis) using PROM, and designing multi combination therapeutics for reducing antibiotic resistance using INDIGO.

Qiang Zhu

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Dr. Zhu’s group conducts research on various topics, ranging from foundational methodologies to challenging applications, in data science. In particular, the group has been investigating the fundamental issues and techniques for supporting various types of queries (including range queries, box queries, k-NN queries, and hybrid queries) on large datasets in a non-ordered discrete data space. A number of novel indexing and searching techniques that utilize the unique characteristics of an NDDS are developed. The group has also been studying the issues and techniques for storing and searching large scale k-mer datasets for various genome sequence analysis applications in bioinformatics. A virtual approximate store approach to supporting repetitive big data in genome sequence analyses and several new sequence analysis techniques are suggested. In addition, the group has been researching the challenges and methods for processing and optimizing a new type of so-called progressive queries that are formulated on the fly by a user in multiple steps. Such queries are widely used in many application domains including e-commerce, social media, business intelligence, and decision support. The other research topics that have been studied by the group include streaming data processing, self-management database, spatio-temporal data indexing, data privacy, Web information management, and vehicle drive-through wireless services.

Michael Boehnke

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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.

Johann Gagnon-Bartsch

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Johann Gagnon-Bartsch, PhD, is Assistant Professor of Statistics in the College of Literature, Science, and the Arts at the University of Michigan, Ann Arbor.

Prof. Gagnon-Bartsch’s research currently focuses on the analysis of high-throughput biological data as well as other types of high-dimensional data. More specifically, he is working with collaborators on developing methods that can be used when the data are corrupted by systematic measurement errors of unknown origin, or when the data suffer from the effects of unobserved confounders. For example, gene expression data suffer from both systematic measurement errors of unknown origin (due to uncontrolled variations in laboratory conditions) and the effects of unobserved confounders (such as whether a patient had just eaten before a tissue sample was taken). They are developing methodology that is able to correct for these systematic errors using “negative controls.” Negative controls are variables that (1) are known to have no true association with the biological signal of interest, and (2) are corrupted by the systematic errors, just like the variables that are of interest. The negative controls allow us to learn about the structure of the errors, so that we may then remove the errors from the other variables.

Microarray data from tissue samples taken from three different regions of the brain (anterior cingulate cortex, dorsolateral prefrontal cortex, and cerebellum) of ten individuals. The 30 tissue samples were separately analyzed in three different laboratories (UC Davis, UC Irvine, U of Michigan). The left plot shows the first two principal components of the data. The data cluster by laboratory, indicating that most of the variation in the data is systematic error that arises due to uncontrolled variation in laboratory conditions. The second plot shows the data after adjustment. The data now cluster by brain region (cortex vs. cerebellum). The data is from GEO (GSE2164).

Microarray data from tissue samples taken from three different regions of the brain (anterior cingulate cortex, dorsolateral prefrontal cortex, and cerebellum) of ten individuals. The 30 tissue samples were separately analyzed in three different laboratories (UC Davis, UC Irvine, U of Michigan). The left plot shows the first two principal components of the data. The data cluster by laboratory, indicating that most of the variation in the data is systematic error that arises due to uncontrolled variation in laboratory conditions. The second plot shows the data after adjustment. The data now cluster by brain region (cortex vs. cerebellum). The data is from GEO (GSE2164).

Issam El Naqa

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Our lab’s research interests are in the areas of oncology bioinformatics, multimodality image analysis, and treatment outcome modeling. We operate at the interface of physics, biology, and engineering with the primary motivation to design and develop novel approaches to unravel cancer patients’ response to chemoradiotherapy treatment by integrating physical, biological, and imaging information into advanced mathematical models using combined top-bottom and bottom-top approaches that apply techniques of machine learning and complex systems analysis to first principles and evaluating their performance in clinical and preclinical data. These models could be then used to personalize cancer patients’ chemoradiotherapy treatment based on predicted benefit/risk and help understand the underlying biological response to disease. These research interests are divided into the following themes:

  • Bioinformatics: design and develop large-scale datamining methods and software tools to identify robust biomarkers (-omics) of chemoradiotherapy treatment outcomes from clinical and preclinical data.
  • Multimodality image-guided targeting and adaptive radiotherapy: design and develop hardware tools and software algorithms for multimodality image analysis and understanding, feature extraction for outcome prediction (radiomics), real-time treatment optimization and targeting.
  • Radiobiology: design and develop predictive models of tumor and normal tissue response to radiotherapy. Investigate the application of these methods to develop therapeutic interventions for protection of normal tissue toxicities.

Jieping Ye

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Jieping Ye, PhD, is Associate Professor of Computational Medicine and Bioinformatics in the Medical School at the University of Michigan, Ann Arbor.

The Ye Lab has been conducting fundamental research in machine learning and data mining, developing computational methods for biomedical data analysis, and building informatics software. We have developed novel machine learning algorithms for feature extraction from high-dimensional data, sparse learning, multi-task learning, transfer learning, active learning, multi-label classification, and matrix completion. We have developed the SLEP (Sparse Learning with Efficient Projections) package, which includes implementations of large-scale sparse learning models, and the MALSAR (Multi-tAsk Learning via StructurAl Regularization) package, which includes implementations of state-of-the-art multi-task learning models. SLEP achieves state-of-the-art performance for many sparse learning models, and it has become one of the most popular sparse learning software packages. With close collaboration with researchers at the biomedical field, we have successfully applied these methods for analyzing biomedical data, including clinical image data and genotype data.

Jeremy M G Taylor

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Jeremy Taylor, PhD, is the Pharmacia Research Professor of Biostatistics in the School of Public Health and Professor in the Department of Radiation Oncology in the School of Medicine at the University of Michigan, Ann Arbor. He is the director of the University of Michigan Cancer Center Biostatistics Unit and director of the Cancer/Biostatistics training program. He received his B.A. in Mathematics from Cambridge University and his Ph.D. in Statistics from UC Berkeley. He was on the faculty at UCLA from 1983 to 1998, when he moved to the University of Michigan. He has had visiting positions at the Medical Research Council, Cambridge, England; the University of Adelaide; INSERM, Bordeaux and CSIRO, Sydney, Australia. He is a previously winner of the Mortimer Spiegelman Award from the American Public Health Association and the Michael Fry Award from the Radiation Research Society. He has worked in various areas of Statistics and Biostatistics, including Box-Cox transformations, longitudinal and survival analysis, cure models, missing data, smoothing methods, clinical trial design, surrogate and auxiliary variables. He has been heavily involved in collaborations in the areas of radiation oncology, cancer research and bioinformatics.

I have broad interests and expertise in developing statistical methodology and applying it in biomedical research, particularly in cancer research. I have undertaken research  in power transformations, longitudinal modeling, survival analysis particularly cure models, missing data methods, causal inference and in modeling radiation oncology related data.  Recent interests, specifically related to cancer, are in statistical methods for genomic data, statistical methods for evaluating cancer biomarkers, surrogate endpoints, phase I trial design, statistical methods for personalized medicine and prognostic and predictive model validation.  I strive to develop principled methods that will lead to valid interpretations of the complex data that is collected in biomedical research.

Laura Balzano

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Professor Balzano and her students investigate problems in statistical signal processing and optimization, particularly dealing with large and messy data. Her applications typically have missing, corrupted, and uncalibrated data as well as heterogeneous data in terms of sensors, sensor quality, and scale in both time and space. Her theoretical interests involve classes of non-convex problems that include Principal Components Analysis (or the Singular Value Decomposition) and many interesting variants such as PCA with sparse or structured principal components, orthogonality and non-negativity constraints, nonlinear variants such as low-dimensional algebraic variety models, and even categorical data or human preference data. She concentrates on fast gradient methods and related optimization methods that are scalable to real-time operation and massive data. Her work provides algorithmic and statistical guarantees for these algorithms on the aforementioned non-convex problems, and she focuses carefully on assumptions that are realistic for the relevant applications. She has worked in the areas of online algorithms, real-time computer vision, compressed sensing and matrix completion, network inference, and sensor networks.

Real-time dynamic background tracking and foreground separation. At time t = 101, the virtual camera slightly pans to right 20 pixels. We show how GRASTA quickly adapts to the new subspace by t = 125. The first row is the original video frame; the middle row is the tracked background; the bottom row is the separated foreground.

Real-time dynamic background tracking and foreground separation. At time t = 101, the virtual camera slightly pans to right 20 pixels. We show how GRASTA quickly adapts to the new subspace by t = 125. The first row is the original video frame; the middle row is the tracked background; the bottom row is the separated foreground.