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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.

Srijan Sen

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Srijan Sen, MD, PhD, is the Frances and Kenneth Eisenberg Professor of Depression and Neurosciences. Dr. Sen’s research focuses on the interactions between genes and the environment and their effect on stress, anxiety, and depression. He also has a particular interest in medical education, and leads a large multi-institution study that uses medical internship as a model of stress.

Jun Li

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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.

 Prof. Li’s areas of interest include 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.

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.

Sebastian Zoellner

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Sebastian Zöllner is a Professor of Biostatistics. He also holds an appointment in the Department of Psychiatry. Dr. Zöllner joined the University of Michigan after a postdoctoral fellowship in the Department of Human Genetics at the University of Chicago. His research effort is divided between generating new methods in statistical genetics and analyzing data. The general thrust of his work is problems from human genetics, evolutionary biology and statistical population biology.

Gilbert S. Omenn

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Gilbert Omenn, MD, PhD, is Professor of Computational Medicine & Bioinformatics with appointments in Human Genetics, Molecular Medicine & Genetics in the Medical School and Professor of Public Health in the School of Public Health and the Harold T. Shapiro Distinguished University Professor at the University of Michigan, Ann Arbor.

Doctor Omenn’s current research interests are focused on cancer proteomics, splice isoforms as potential biomarkers and therapeutic tar- gets, and isoform-level and single-cell functional networks of transcripts and proteins. He chairs the global Human Proteome Project of the Human Proteome Organization.

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.

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.