More than 50 faculty and scientists participate in IGSB. Fellows include faculty from the University of Chicago and Argonne National Laboratory, as well as faculty from other CBC institutions who participate as Associate or Visiting Fellows. All Fellows are engaged in activities related to the IGSB mission and help development of IGSB goals in the future. Appointments into the IGSB are made for a renewable term of five years.
Fellows and their laboratories benefit from being part of a community engaged in both large-scale and small-scale collaborative science in Genomics and Systems Biology. IGSB offers an environment which attracts some of the best young researchers in the field. The Institute’s goals are being accomplished through a variety of mechanisms including logistical and infrastructure support for collaborative grant applications, development of a junior Fellows program, and supporting applications for pilot funding of high risk projects. Fellows also have priority access to IGSB facilities and infrastructure including the Cellular Screening Center (CSC) and the High-throughput Genome Analysis Core (HGAC).
Dr. Ahsan’s research interests focus on studying the inter-relationships between environmental and genomic factors in cancer and other diseases and exploiting information on these relationships at a population level in developing and evaluating prevention interventions in humans.
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.
Dr. Bell is using various genetic approaches to map and identify the genes that affect development of type 2 diabetes mellitus as well as diabetic complications. He carries out studies in both humans and mouse models to determine the mechanisms by which the diabetes genes they identify affect blood glucose levels. Their studies of pancreatic beta-cells are focused on understanding the transcriptional regulatory networks that determine normal cell function
Dr. Bergelson interested in the ecology and evolution of plant-enemy interactions. Her lab research focuses on the coevolutionary interactions between Arabidopsis thaliana and its bacterial pathogens.
Dr. Chen’s major research interests is to conduct integrated analyses of cancer-omics on both protein-coding and non-coding genes (particularly, microRNAs) regarding both genetic and epigenetic changes in the development of leukemia and lymphoma.
Dr. Cox research focus is on the identification and characterization of genetic variation influencing susceptibility to complex disorders. We work on both the localization of the genetic variation, via linkage studies and linkage disequilibrium mapping, as well as on the analytic component to positional cloning of genes for complex disorders.
Research in the Crispino lab is focused on investigating the regulatory mechanisms governing normal and malignant blood cell development,
John M. Cunningham, MD, is the Chief, Section of Pediatric Hematology/ Oncology at the University of Chicago. He is an internationally known expert in the treatment and research of childhood cancers and blood diseases. He has particular expertise in treating hemoglobinopathies, which are disorders that affect red blood cells, such as sickle cell disease and thalassemia. He is a recognized leader in the field of pediatric stem cell transplantation and has developed novel uses for this life-saving treatment.
The Dinner group develops and applies theoretical methods for relating cellular behavior to molecular properties. They are particularly interested in how proteins regulate access to genes in the context of the development of the immune system. Understanding how such complex behavior arises from physical and chemical features is a problem in fundamental statistical mechanics, but its solution has direct implications for treating autoimmune pathologies and improving gene therapy and vaccination strategies.
Ph.D. Department of Human Genetics- Dr. Di Rienzo’s group aims to characterize the amount and patterns of genetic variation in human populations, and to elucidate the forces that shape and maintain this variation. Forces such as demographic change or population structure exert genome-wide effects, while others, such as natural selection, result in locus-specific effects.
The major focus of Dr. Dolan’s research has been in the area of DNA damage/repair of anticancer agents that has been extended to the pharmacogenetics of DNA damaging agents.
Dr. Fehon interest center on the molecular mechanisms by which signal transduction pathways are organized into specialized membrane domains. In addition to their known role in organizing receptors and downstream effectors into functional signaling complexes, such organized complexes function to integrate signaling activities from multiple pathways and to segregate simultaneous but distinct functions of a single pathway.
Dr. Ian Foster, PhD, is Director of the Computation Institute, a joint institute of the University of Chicago and Argonne National Laboratory. He is also an Argonne Senior Scientist and Distinguished Fellow, and the Arthur Holly Compton Distinguished Service Professor of Computer Science. Ian received a BSc (Hons I) degree from the University of Canterbury, New Zealand, and a PhD from Imperial College, United Kingdom, both in computer science. His research deals with distributed, parallel, and data-intensive computing technologies, and innovative applications of those technologies to scientific problems in such domains as climate change and biomedicine. Methods and software developed under his leadership underpin many large national and international cyberinfrastructures. Dr. Foster’s honors include the Lovelace Medal of the British Computer Society and the Gordon Bell Prize for high-performance supercomputing.
Dr. Gilad research focuses on inter-primate comparisons at the sequence and expression levels with the long-term goals of identifying genomic regions of functional importance, understanding human gene regulatory processes and elucidating the genetic architecture of human-specific traits
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. Conrad Gilliam, PhD, is the Dean for Research and Graduate Education at the University of Chicago Biological Sciences Division (BSD). Dr. Gilliam completed his postdoctoral training in human genetics at the University of London before joining the faculty at Harvard Medical School in 1983. He moved to Columbia University in 1986, where he was a Professor in the Departments of Psychiatry and Genetics & Development and was named Director of the Columbia Genome Center in 2000. He came to the University of Chicago in 2004 as chair of human genetics. He is an authority on the identification and characterization of heritable mutations that affect the nervous system.
The main goal of Dr. Glick’s is to understand the processes that generate Golgi stacks. The cisternal maturation model provides a conceptual framework for studying Golgi formation. This model postulates that new Golgi elements arise at transitional ER (tER) sites, which are specialized for the production of ER-to-Golgi transport vesicles.
Dr. Glotzer is interested in cell cycle regulation of central spindle assembly and function. Central spindle assembly begins at the metaphase to anaphase transition, when chromosomes move polewards on shrinking kinetochore microtubules. At this time, non-kinetochore spindle microtubules become bundled to form the central spindle. His lab discovered an evolutionarily conserved protein complex, centralspindlin, consisting of a Rho family GAP, CYK-4, and a kinesin like protein, ZEN-4, that is directly involved in central spindle assembly.
The overall goal of Dr. Green’s research is to determine the molecular mechanisms by which female steroid hormones regulate development, differentiation and/or cellular proliferation and survival in hormone responsive tissues and cancers.
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. Hudson’s research concerns primarily on the analysis and interpretation of molecular variation within and between populations. The goal is to understand the evolutionary forces that have produced the observed patterns of variation within populations and between species. My work is entirely theoretical, focusing on the stochastic processes relevant to evolution in finite populations in which genetic drift, mutation, migration and selection may all be important. Monte Carlo computer simulations and methods of statistical inference are important aspects of the work
Dr. Joachimiak is a biophysicist who works in the area of protein structure, a critical aspect of drug design. Dr. Joachimiak and his team at ANL are working to improve methods that determine protein structures including new techniques in protein production, crystal growth, X-ray crystallographic structure.
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 major goals of Dr. Koide research are to understand the molecular mechanisms underlying protein function at the atomic level and to exploit such knowledge to engineer proteins with novel shape and/or function.
Dr. Kossiakoff’s research interests centers around studying at atomic resolution the structural and functional properties that define molecular recognition systems that activate and regulate biological properties. In particular, we study the energetics of hormone-induced receptor activation and regulation of growth hormone and its receptor using X-ray crystallography, site-directed mutagenesis, phage display mutagenesis and biophysical analysis.
Dr. Thomas Krausz is an expert pathologist with broad interests in tumor pathology including melanocytic tumors, soft tissue tumors, breast tumors, lung tumors and mesothelioma.
Dr. Kreitman’s lab focuses on issues in molecular evolution, and especially on identifying forces governing the evolutionary process. The central effort has been to understand the evolution of the alcohol dehydrogenase locus (Adh) in Drosophila. We are studying the evolutionary process on three different time scales—-affecting populations, affecting species, and affecting long-term molecular evolution.
The Kron laboratory is a highly collaborative group of cell biologists, geneticists, biochemists and chemists. Their major basic research efforts are directed at 1) dissecting cyclin dependent kinase structure and function in yeast, 2) defining roles for chromatin modifications in DNA damage response, and 3) developing novel mass spectrometry methods for phosphoproteomics and high throughput screening.
Dr. Michelle Le Beau, PhD, is the Director of the Comprehensive Cancer Center and the Cancer Cytogenetics Laboratory at the University of Chicago. For nearly a decade, Dr. Le Beau served as the head of cytogenetic studies of lymphoma for the Children’s Cancer Group (now COG), and was a member of the Cytogenetics Review Committee for Cancer and Leukemia Group B (CALGB). She also served as a member of the Board of Directors of the American College of Medical Genetics. She was a member of the NIH Pathology B Study Section (1996-2001) and CAMP Study Section (2001-2006), served as the Chair of this Study Section from 2004-2006, and was a member of the NCI Cancer Centers Review Parent Committee (2005-2009). Dr. Le Beau is an international leader in cancer cytogenetics and genetics, and is recognized for her work in identifying recurring cytogenetic abnormalities, in defining the clinical, morphological, and cytogenetic subsets of leukemia, in identifying the genetic pathways that lead to myeloid leukemias, and on the application of fluorescence in situ hybridization (FISH) technology for clinical diagnostics and gene mapping.
The broad goal of Dr. Licht’s research program is to understand how mutations of transcriptional regulators may set up patterns of aberrant gene expression that yield cancer. This requires a detailed understanding of the normal function of these transcription factors. Such information includes an understanding of the role of these factors in cell growth, differentiation and developmental, the normal DNA binding and transcriptional activity of these proteins, identification of the critical protein partners of the factors and elucidation of the downstream targets of these genes. By modeling the function of both the normal and mutated forms of these factors, Dr. Licht and his group hope to better understand the molecular basis of cancer and potentially identify new therapeutic targets and pathways in this disease.
Our lab primary interest is to understand the connection between genetic factors and human psychiatric disorders or behaviors. Current research project is the genetic studies of bipolar disease (BD) using molecular genetics, genomics and bioinformatics approaches.
A fundamental problem in evolutionary biology is how genes with novel functions originate. My research focuses on this problem, although I am also interested in other issues of molecular evolution.
My research at the University of Chicago (in collaboration with Martin Kreitman) takes an evolutionary perspective to investigate the structure/function of eukaryotic cis-regulatory modules. Our approach has been to use transgenic analysis to functionally characterize evolved changes in the structure of a well-characterized enhancer controlling embryonic expression of even-skipped pair-rule stripe two in Drosophila.
The Lussier research group conducts research in the emerging field of phenomics, using computation to model phenotypes, integrate genomic with phenotypic datasets, and analyze phenomes in order to accurately individualize the understanding, the prediction, and the treatment of diseases.
My major scientific interest is the development of the approaches for representation and analysis of complex biological systems and how these approaches can be applied to the discovery of the molecular mechanisms contributing to complex heritable disorders.
Dr. McLeod, is internationally recognized for her expertise and extensive research in toxoplasmosis. She specializes in the comprehensive care of congenital toxoplasmosis and other Toxoplasma gondii infections.
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
Dr. Morimoto is interested in the fundamental events that underlie the appearance of misfolded proteins and their consequence to protein homeostasis, cellular function, and organismal adaptation and survival.
Our laboratory investigates the molecular basis of cardiac morphogenesis and Congenital Heart Disease. Congenital Heart Disease, or structural malformations of the heart present at birth, is the most common class of human birth defects. We employ forward and reverse genetic approaches in the mouse to address the genetic basis of structural heart disease. We use genetic, molecular, and biochemical methods to investigate the specific aspects of cardiac morphogenesis involved in Congenital Heart Disease.
Our group is interested in dissecting the architecture and function of gene regulatory networks. We investigate how the multiple transcription activators, repressors, boundary elements connected to a gene interact and orchestrate the precise tissue-specific and temporal-specific expression pattern of that gene.
The major research objectives of my laboratory are to identify genes that influence complex phenotypes, to understand their evolutionary history, and to elucidate how variation in these genes influences function. Our laboratory focuses on phenotypes related to fertility and to common diseases, and are conducted in a founder population, the Hutterites, and in outbred patient populations.
My research interests are diverse and include: treatment of breast cancer, especially in young or pregnant women; familial cancers; molecular genetics of cancer; cancer risk assessment and chemoprevention; breast cancer and minority populations and disparities in health outcomes.
My lab studies the genetic basis of cancer susceptibility. Genetically, we are all very similar, but not identical. Some of this normal variation is insignificant, but some may have important functional consequences. Our goal is to discover the critical sources of functional heterogeneity in the pathways that are the barriers against the cellular transition from normal to cancer.
My lab developed a microarray methods that measure tRNA abundance, its fraction of aminoacylation and misacylation at the genomic scale. We are exploring roles of tRNA in translational control in yeast and in mammalian cells including cancer.
My laboratory is engaged in a long term project to understand how DNA sequence specifies biological form. We are interested not only in the specification of typical form by a typical genome, but also in the effects of variability. Such variability might take the form of genetic variation in a population or intrinsic fluctuations in an individual
My laboratory works at the interface between signal transduction and developmental biology. The long term goal of our research is to understand how complex developmental decisions are controlled in time and space by multiple signaling pathways.
The focus of my laboratory is to determine the critical mechanisms that regulate cell growth and differentiation in response to growth factor or oncogenic stimulation and identify key targets for therapeutic intervention.
Dr. Janet Rowley, MD, is the Blum Riese Distinguished Service Professor of Medicine, Molecular Genetics & Cell Biology and Human Genetics at the University of Chicago. She is internationally renowned for her work in the discovery of molecular genetic alterations found in human malignancies, Rowley has studied chromosome abnormalities in leukemia and lymphoma to provide critical scientific insights that have led to cures for previously untreatable cancers. Her discoveries have resulted in more accurate diagnostic techniques and the development of effective treatment protocols targeted to particular patient subgroups. Among her numerous honors, Rowley was awarded the 2009 Presidential Medal of Freedom, the 1998 Albert Lasker Clinical Research Award, the 1998 National Medal of Science, the 1989 Charles S. Mott Prize from General Motors Cancer Research Foundation, and the AACR’s G.H.A. Clowes Memorial Award in 1989 and the Dorothy P. Landon-AACR Prize for Translational Cancer Research in 2005. She is a member of numerous honorary societies including the National Academy of Sciences, the Institute of Medicine, the American Philosophical Society and the American Academy of Arts and Sciences.
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. Ruvinsky is interested in the evolution of development (Evo-Devo), evolutionary genomics and molecular evolution. The goal of his lab is to integrate developmental, genomic and computational approaches to understand the evolution of genes and gene functions.
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. Schabacker’s current research includes the development of 1) a point-of-care human diagnostic respiratory biochip capable of rapidly identifying both bacterial and viral pathogens, 2) Veterinary diagnostic biochips capable of identifying causative organism(s) as well as antibiotic resistance for bovine respiratory syndrome and bovine mastitis, 3) Threat agent detection systems for rapid analysis (<15 minutes sample-to-answer) of multiple targets providing diagnostic confidence level outputs, 4) Biochips and systems for biomarker discovery.
My laboratory examines the mechanisms and strategies whereby pathogenic bacteria cause human disease.
Dr. Silverstein’s research focuses on the integration of advanced computing and communication technologies into biomedicine, particularly applying Grid computing, and on the design, implementation, and evaluation of high-performance collaboration environments for anatomic education and surgery.
Dr. Neil Shubin, PhD, is the Robert R. Bensley Professor, Organismal Biology and Anatomy at the University of Chicago. He is a paleontologist, evolutionary biologist, and science writer. Dr. Shubin is best know in the popular media as being one of three principal investigators who in 2004 discovered the fossil tetrapodomorph fish Tiktaalik roseae. Dr. Shubin’s research interests center around trying to better understand how and why new anatomical features and faunas arose throughout evolutionary history. His studies focus primarily on two critical time periods during the history of our planet, the Devonian and the Triassic.
We focus on integrating technologies to sustainably produce biofuels and biobased products. The goal is to design fermentation and enzymatic conversion systems that will facilitate continuous product recovery. Currently we work on organic acids and alcohols.
Dr. Solway’s laboratory addresses molecular mechanisms underlying airway constrictor hyperresponsiveness in asthma.
My general interests include Bayesian and computational statistics, particularly when applied to problems in population genetics.
Dr. Rick Stevens, PhD, is the Associate Laboratory Director for Computing, Environment, and Life Sciences at Argonne National Laboratory. He heads Argonne’s advanced computing initiative targeting the development of exascale computing technology and systems and computational biology. He is also a Professor of computer science at the University of Chicago and is a Senior Fellow of the University of Chicago & Argonne National Laboratory Computation Institute (CI), a multidisciplinary institute aimed at connecting computing to all areas of inquiry at the University and the Laboratory. In addition, he is the co-Director of the Argonne Futures Lab, a research group he started in 1994 to investigate problems in large-scale scientific visualization and advanced collaboration environments. His group in the Futures Lab has developed the widely deployed Access Grid collaboration system.
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.
Everett Vokes, MD, is the John E. Ultmann Professor of Medicine and Radiation Oncology at the University of Chicago. He is an internationally renowned expert in the treatment of head and neck cancer. Born in New York City, Dr. Vokes was educated in West Germany, receiving his medical degree from the University of Bonn Medical School. He served his residency in internal medicine at Ravenswood Hospital Medical Center in Chicago and at the University of Southern California in Los Angeles. He arrived at the University of Chicago as a hematology/oncology fellow in 1983 and was promoted to professor in 1995. For eleven years he served as chief of the Section of Hematology/Oncology, before his appointment as chair of the Department of Medicine in March 2009. In October 2009, Dr. Vokes was named interim dean of the Division of Biological Sciences and the Pritzker School of Medicine and interim vice president for medical affairs at the University of Chicago. He served in these roles for one year.
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.
My lab is interested in molecular genetics of species differentiation