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Arvind Rao

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Arvind Rao is an Associate Professor in the Department of Computational Medicine and Bioinformatics, and Radiation Oncology in the School of Medicine. 

His research is in:

1. Transcriptional Genomics: A bioinformatics framework that identifies tissue‐specific enhancers by integrating multi‐modal genomic data has been developed previously [Rao2010]. There is interest to integrate other sources of information (like epigenomic and ChIP datasets) to improve the efficacy of enhancer prediction. We have also participated in the TCGA Glioma groups’ work [Brat2015, Ceccarelli2016] on identifying transcriptional regulators underlying gliomagenesis.

2. Image Informatics: In order to quantify the phenotypic aspects of disease and their relationships with outcome and their genetic context, we have developed methods for the analysis of histopathology [ Mousavi2015, Vu2016] and radiology [Yang2015] images, focusing on tumor heterogeneity. One direction of our group is to develop image analysis tools to delineate tumor image features from radiology data and to develop predictive models to relate them along with underlying genomic measurements to outcomes in low grade gliomas. Further, we have also investigated methodologies to link tumor imaging, genetics and immune status in gliomas. More recently, my group has been studying the relationship between image-derived features, genetics and cognitive status in glioblastoma patients. Further, we have also developed methods for the analysis of multiparametric MR datasets in Radiation Oncology.

3. Heterogeneous Data Integration: Integrative decision making in the clinical domain involves the need for principled formalisms that can integrate pathology, imaging and genomic data sets to drive hypothesis generation and clinical action. We have focused on developing high throughput measurement pipelines from this diverse array of data sources and methods for their integration. Simultaneously, methods for visualization are also under investigation. A more recent interest of our group is to integrate genomics, imaging and (online) behavioral data from patient to assess their evolving response to treatment, in the context of learning healthcare platforms. This could also enable the development of hybrid diagnostics.

4. Informatics for Combinatorial Drug Screens: the availability of multimodal data sources (cell line genomics, drug assays) coupled with high throughput, high content imaging platforms have created the need for informatics frameworks to identify rational drug combinations capable of modulating disease-associated phenotype. In this context, we have worked with the Gulf Coast Consortium to create analysis platforms that jointly mine imaging and genomics data for combinatorial drug discovery.

 

The overall goal is to link different data sources, such as imaging-derived phenotypes with genomic alteration for clinical predictive models. This has prompted work in AI/ML models for image processing &computer vision, data integration and genomic analysis.

 

Camille Avestruz

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Dr. Avestruz is a computational cosmologist. She uses simulations to model, predict, and interpret observed large-scale cosmic structures. Her primary focus is to understand the evolution of galaxy clusters. These are the most massive gravitationally collapsed structures in our universe, comprised of hundreds to thousands of galaxies. Other aspects of her work prepare for the next decade of observations, which will produce unprecedented volumes of data. In particular, she is leading software development efforts within the clusters working group of the Large Synoptic Survey Telescope to calibrate galaxy cluster masses from simulation data. Dr. Avestruz also incorporates big data methods, including machine learning, to extract gravitational lensing signatures that probe the mass distribution of massive galaxies and galaxy clusters.

[Click on image to see video] Image projection of various components and properties of a simulated galaxy cluster in its last 8 gigayears of formation. The top left panel shows the underlying dark matter content, the top middle image shows the distribution of stars, and the remaining four panels are properties of the gas content: density, temperature, entropy, and metallicity. To model the evolution of galaxy clusters in a cosmological volume, the simulation uses adaptive refinement in space and time in order to span the relevant dynamic range of the system.

Fernanda Valdovinos

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Fernanda Valdovinos is an Assistant Professor in the department of Ecology and Evolutionary Biology and Complex Systems. She received her Ph.D. in Ecology and Evolutionary Biology from the Faculty of Science, University of Chile in 2008. Before joining the University of Michigan, she was a researcher in the Estación Biológica de Doñana, Spain, at the Pacific Ecoinformatics and Computational Lab in Berkeley, CA and at the department of Ecology and Evolutionary Biology at the University of Arizona.

Her lab studies the structure and dynamics of ecological networks at ecological and evolutionary scales; including their resilience to biodiversity loss, biological invasions, climate change, and exploitation by humans. She is a principal investigator in MICDE Catalyst Grant: “Embedded Machine Learning Systems To Sense and Understand Pollinator Behavior”.

Jianzhi (George) Zhang

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Jianzhi (George) Zhang is a Professor of Ecology and Evolutionary Biology interested in the relative roles of chance and necessity in evolution. He got his B. S. from Fudan University in Shanghai, China, and his Ph. D. in Genetics from Pennsylvania State University. He was a  Fogarty postdoctoral fellow at the National Institute of Allergy and Infectious Diseases before moving to the University of Michigan.

Professor Zhang’s research focuses on two main research areas:  (1) yeast as an experimental system for studying evolution, where his research group uses the budding yeast Saccharomyces cerevisiae and its relatives as model organisms to understand a variety of evolutionary processes such as the genetic basis of phenotypic variations among strains and species, or molecular and genomic bases of heterosis; and (2) computational evolutionary genomics where they use evolutionary, genomic, and/or systemic approaches to analyze publicly available data to characterize and understand pleiotropy, robustness, epistasis, gene-environment interaction, gene expression noise, translational regulation, RNA editing, convergent evolution, adaptation, origin of new genes, among-protein evolutionary rate variation, and other important genetic and evolutionary phenomena. Projects may also involve modeling and simulation, including the MICDE catalyst grant project where the team is using deep neural networks to infer molecular phylogenies and extract phylogenetically useful patterns from amino acid or nucleotide sequences, which will help understand evolutionary mechanisms and build evolutionary models for a variety of analyses.

Xun Huan

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Xun (Ryan) Huan is an Assistant Professor in the Department of Mechanical Engineering. His research broadly revolves around uncertainty quantification, data-driven modeling, and numerical optimization. His expertise focuses on bridging models and data: optimal experimental design, Bayesian methods for statistical inference, uncertainty propagation in high-dimensional settings, and methods that are robust to model misspecification. He seeks to develop efficient computational methods that integrate realistic models with big data, and combine uncertainty quantification with machine learning to enable robust prediction, design, and decision-making. He is interested in collaborative opportunities in various applications that can benefit from a better understanding of uncertainty and modeling. Current research activities include assessing uncertainty in deep neural networks, and developing sequential experimental design methods for improving autonomy.

Optimal experimental design seeks to identify experiments that produce the most valuable data, and can lead to substantial resource savings. For example, in the design of a shock-tube combustion experiment, design condition A maximizes the expected information gain. When Bayesian inference is performed on data from this experiment, we obtain “tighter” posteriors (with less uncertainty) compared to those obtained from suboptimal design conditions B and C.

Raed Al Kontar

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Rael Al Kontar is an Assistant Professor in the department of Industrial & Operations Engineering. His research broadly focuses on developing data analytics and decision-making methodologies specifically tailored for Internet of Things (IoT) enabled smart and connected products/systems. He envisions that most (if not all) engineering systems will eventually become connected systems in the future. Therefore, his key focus is on developing next-generation data analytics, machine learning, individualized informatics and graphical and network modeling tools to truly realize the competitive advantages that are promised by smart and connected products/systems.

Towards smart and connected systems

Stephen Smith

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Stephen Smith is an Associate Professor in the Department of Ecology and Evolutionary Biology. The Smith lab group is primarily interested in examining evolutionary processes using new data sources and analysis techniques. They develop methods to address questions about the rates and modes of evolution using the large data sources (e.g., genomes and transcriptomes) that have become more common in the biological disciplines over the last ten years. In particular, they use DNA sequence data to construct phylogenetic trees and conduct analyses about processes that shape the evolution of lineages and their genomes using these trees. In addition to this research program, they also address how new data sources can facilitate new research in evolutionary biology. To this end, they sequence transcriptomes, primarily in plants, with the goal of better understanding where, within the genome and within the phylogeny, processes like gene duplication and loss, horizontal gene transfer, and increased rates of molecular evolution occur.

Alex Gorodetsky

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Alex Gorodetsky is an Assistant Professor in the Department of Aerospace Engineering. His research includes using applied mathematics and computational science to enhance autonomous decision making under uncertainty. His research has an emphasis on controlling systems that must act in complex environments that are often represented through expensive computational simulations. His research uses tools from wide ranging areas including uncertainty quantification, statistical inference, machine learning, numerical analysis, function approximation, control, and optimization. Several of the key areas he focuses on are: optimal planning by solving large scale Markov decision processes, fast Bayesian estimation for nonlinear dynamical systems, high-dimensional compression and approximation of physical quantities of interest, and fusion of information from varying simulation fidelities and data through multi-fidelity modeling.

Bryan Goldsmith

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Bryan Goldsmith is an Assistant Professor in the Department of Chemical Engineering. His works focus on the development of novel catalysts and materials. The world is facing a growing population, mass consumerism, and rising greenhouse gas levels, all the while people strive to increase their standard of living. Computational modeling of catalysts and materials, and making use of its synergy with experiments, facilitates the process to design new systems since it provides a valuable way to test hypotheses and understand design criteria. His research team focuses on obtaining a deep understanding of catalytic systems and advanced materials for use in sustainable chemical production, pollution abatement, and energy generation. They use first-principles modeling (e.g., density-functional theory and wave function based methods), molecular simulation, and data analytics tools (e.g., statistical learning and data mining) to extract key insights of catalysts and materials under realistic conditions, and to help create a platform for their design.

A computational prediction for a group of gold nanoclusters (global model) could miss patterns unique to nonplaner clusters (subgroup 1) or planar clusters (subgroup 2)

A computational prediction for a group of gold nanoclusters (global model) could miss patterns unique to nonplaner clusters (subgroup 1) or planar clusters (subgroup 2)

Matthew Kay

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Matthew Kay is an Assistant Professor in the School of Information. His research focus in on human–computer interaction and information visualization. He tackles problems using a multi-faceted approach, including qualitative and quantitative analysis of behavior, building and evaluating interactive systems, and designing and testing visualization techniques.