The University of Chicago
The overriding research interest of the lab is trying to disentangle the relationship between genotype and phenotype, and to understand the forces shaping functional genetic variation in humans. We approach this broad topic through a combination of experimental and computational approaches: We employ high-throughput functional genomics and genome-wide association analysis (GWAS) to identify variable regions of the genome with functional effects on aspects of the transcription profile (expression levels, splicing, etc.), and to investigate how these patterns are altered in different contexts. At the same time, we examine the levels and patterns of segregating nucleotide variation within human populationss (population genetics) and between human and other species (comparative genomics) to identify regions of the genome with patterns of variation suggestive of natural selection or selective constraint over time, as such patterns may be indicative of function.
Dr. Grossman is the Director of Informatics at IGSB, a Senior Fellow at the Computation Institute, Chief Research Informatics Officer for the Division of the Biological Sciences, University of Chicago, and Professor of Medicine in the Section of Genetic Medicine at the University of Chicago. His research group focuses on bioinformatics, data mining, cloud computing, data intensive computing, and related areas. Current research projects include: Bionimbus (http://www.bionimbus.org), a cloud-based system for managing, analyzing and sharing genomic data and Sector/Sphere (sector.sourceforge.net), a cloud-based system for data intensive computing. He is also interested in developing new algorithms for the large scale analysis of genomic and phenotypic data.
Dr. Jones was jointly appointed Assistant Professor of the IGSB and the Ben May Institute for Cancer Research in September 2006. As a postdoc at Harvard, Jones pioneered the use of protein microarrays to study complex molecular signaling networks involved in human cancers and other diseases. His new IGSB laboratory utilizes advanced proteomics and genomics technologies to better understand the complex signal transduction mechanisms that result in cancer, diabetes, and other human disease. An understanding of these processes at the molecular level should enable the identification of many new therapeutic targets
The Rust lab is interested in elucidating how information processing and decision-making functions in a live cell arise robustly from the stochastic interactions of individual molecules, and how these systems malfunction in diseased states. To this end, we employ quantitative fluorescence microscopy and biochemical measurements closely coupled with data-driven mathematical modeling. We have recently been interested in a three-protein clock found in photosynthetic bacteria. The post-translational interactions between these proteins (KaiA, KaiB and KaiC) generate a self-sustained 24 hour oscillation capable of predicting the time of day based on previous environmental cues.
Dr. Rzhetsky’s interest is in (asymptotic) understanding how phenotypes, such as human healthy diversity and maladies, are implemented at the level of genes and networks of interacting molecules. To harvest as much information about known molecular interactions as possible, his group runs a large-scale text-mining effort aiming at analysis of a vast corpus of biomedical publications. Currently they can extract from text automatically about 500 distinct flavors of relations among biomedical entities (such as bind, activate, merystilate, and transport)
Dr. White is a pioneer in combining experimental and computational techniques to understand the networks of factors that control biological systems during development and evolution. He has developed novel integrated systems biology approaches for studying complex diseases and identifying new diagnostic biomarkers for a variety of cancer types.
Argonne National Laboratory
Dr. Antonopoulos joined the IGSB and Biosciences Division at Argonne National Laboratory in June 2008 and holds a joint appointment in the Department of Medicine, Section of Gastroenterology, at the University of Chicago. Dr. Antonopoulos is a microbiologist interested in studying the formation and development of microbial communities. His interest in understanding mammalian gastrointestinal function has been complemented by ongoing research in environmental systems (subsurface and topsoil systems). Although the scales are vastly different between the two, many of the approaches used in both GI and field research are steeped in classical ecological theory and serve to circumnavigate the complex nature of the microbial communities underlying system function.
My primary research interest revolves around modeling microbial ecosystem dyanmics using high-throughput sequencing data that describes the taxonomic and functional diversity of the system. Combined with physical, chemical and other biology variables measured in each ecosystem, I am working towards generating bioclimatic models of microbial ecosystems, that enable prediction of taxonomic and metabolic potential from remote sensing data (satellites and aircraft) across broad geographic and temporal space. Fundamentally I adhere to a system biology model, within which I aim to describe the community dynamics that yield the ecosystem services that humanity has come to rely on.
Dr. Meyer is a computational biologist with research interest in metagenomics. He currently has joint appointment with the Mathematics and Computer Science Divison, and the Computation Institute. He is working closely with researchers in the Biosciences Division at Argonne National Laboratory and the medical school at the University of Chicago. Dr. Meyer is the IGSB Associate Director who is responsible on the administrative unit at ANL