Dr. Bai’s research interests lie in development and refinement of bioinformatics algorithms/software and databases on next-generation sequencing (NGS data), development of statistical model for solving biological problems, bioinformatics analysis of clinical data, as well as other topics including, but not limited to, uncovering disease genes and variants using informatics approaches, computational analysis of cis-regulation and comparative motif finding, large-scale genome annotation, comparative “omics”, and evolutionary genomics.
Prof. Huan’s research broadly revolves around uncertainty quantification, data-driven modeling, and numerical optimization. He focuses on methods to bridge together models and data: e.g., optimal experimental design, Bayesian statistical inference, uncertainty propagation in high-dimensional settings, and algorithms that are robust to model misspecification. He seeks to develop efficient numerical methods that integrate computationally-intensive models with big data, and combine uncertainty quantification with machine learning to enable robust and reliable prediction, design, and decision-making.
Dr. Lee’s research in data science concerns biological questions in systems biology and network medicine by developing algorithms and models through a combination of statistical/machine learning, information theory, and network theory applied to multi-dimensional large-scale data. His projects have covered genomics, transcriptomics, proteomics, and metabolomics from yeast to mouse to human for integrative analysis of regulatory networks on multiple molecular levels, which also incorporates large-scale public databases such as GO for functional annotation, PDB for molecular structures, and PubChem and LINCS for drugs or small compounds. He previously carried out proteomics and metabolomics along with a computational derivation of dynamic protein complexes for IL-3 activation and cell cycle in murine pro-B cells (Lee et al., Cell Reports 2017), for which he developed integrative analytical tools using diverse approaches from machine learning and network theory. His ongoing interests in methodology include machine/deep learning and topological Kolmogorov-Sinai entropy-based network theory, which are applied to (1) multi-level dynamic regulatory networks in immune response, cell cycle, and cancer metabolism and (2) mass spectrometry-based omics data analysis.
Eric Michielssen, PhD, is Professor of Electrical Engineering and Computer Science, Director of the Michigan Institute for Computational Discovery and Engineering, and Associate Vice President for Advanced Research Computing. His research interests include all aspects of theoretical, applied, and computational electromagnetics, with emphasis on the development of fast (primarily) integral-equation-based techniques for analyzing electromagnetic phenomena. His group studies fast multipole methods for analyzing static and high frequency electronic and optical devices, fast direct solvers for scattering analysis, and butterfly algorithms for compressing matrices that arise in the integral equation solution of large-scale electromagnetic problems. Furthermore, the group works on plane-wave-time-domain algorithms that extend fast multipole concepts to the time domain, and develop time-domain versions of pre-corrected FFT/adaptive integral methods. Collectively, these algorithms allow the integral equation analysis of time-harmonic and transient electromagnetic phenomena in large-scale linear and nonlinear surface scatterers, antennas, and circuits. Recently, the group developed powerful Calderon multiplicative preconditioners for accelerating time domain integral equation solvers applied to the analysis of multiscale phenomena, and used the above analysis techniques to develop new closed-loop and multi-objective optimization tools for synthesizing electromagnetic devices, as well as to assist in uncertainty quantification studies relating to electromagnetic compatibility and bioelectromagnetic problems.
Professor Gull works in the general area of computational condensed matter physics with a focus on the study of correlated electronic systems in and out of equilibrium. He is an expert on Monte Carlo methods for quantum systems and one of the developers of the diagrammatic ‘continuous-time’ quantum Monte Carlo methods. His recent work includes the study of the Hubbard model using large cluster dynamical mean field methods, the development of vertex function methods for optical (Raman and optical conductivity) probes, and the development of bold line diagrammatic algorithms for quantum impurities out of equilibrium. Professor Gull is involved in the development of open source computer programs for strongly correlated systems.
I am a data scientist, with extensive and various experience drawing inference from large data sets. In education research, I work to understand and improve postsecondary student outcomes using the rich, extensive, and complex digital data produced in the course of educating students in the 21st century. In 2011, we launched the E2Coach computer tailored support system, and in 2014, we began the REBUILD project, a college-wide effort to increase the use of evidence-based methods in introductory STEM courses. In 2015, we launched the Digital Innovation Greenhouse, an education technology accelerator within the UM Office of Digital Education and Innovation. In astrophysics, my main research tools have been the Sloan Digital Sky Survey, the Dark Energy Survey, and the simulations which support them both. We use these tools to probe the growth and nature of cosmic structure as well as the expansion history of the Universe, especially through studies of galaxy clusters. I have also studied astrophysical transients as part of the Robotic Optical Transient Search Experiment.
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.
Bill Currie studies how physical, chemical, and ecological processes work together in the functioning of ecosystems such as forests and wetlands. He studies how human impacts and management alter key ecosystem responses including nutrient retention, carbon storage, plant species interactions, and plant productivity. Dr. Currie uses computer models of ecosystems, including models in which he leads the development team, to explore ecosystem function across the spectrum from wildland to heavily human-impacted systems. He often works in collaborative groups where a model is used to provide synthesis.
He is committed to the idea that researchers must work together across traditional fields to address the complex environmental and sustainability issues of the 21st century. He collaborates with field ecologists, geographers, remote sensing scientists, hydrologists, and land management professionals.