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Job Dekker, PhD

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Spatial Organization of Genomes
We study how a genome is organized in three dimensions inside the nucleus. The spatial organization of a genome plays important roles in regulation of genes and maintenance of genome stability. Many diseases, including cancer, are characterized by alterations in the spatial organization of the genome. How genomes are organized in three dimensions, and how this affects gene expression is poorly understood. To address this issue we study the genomes of human and yeast, using a set of powerful molecular and genomic tools that we developed.

Dekker Lab Website ››

 
Marian Walhout, Ph.D.

Faculty name tags Walhout.jpgMapping Gene Regulatory and Metabolic Networks in the Nematode C. elegans
We use a variety of experimental and computational systems biology approaches to map and characterize gene regulatory networks and to understand how regulatory circuitry controls animal development, function, and homeostasis. Ultimately, we aim to understand how dysfunctional networks affect or cause diseases like diabetes, obesity and cancer.

Walhout Lab Website ››

 
Robert Brewster, PhD

Faculty name tags brewster.jpgDissecting and Understanding the Implications of Resource Sharing to Cellular Decision Making
My group studies transcriptional regulation in bacteria through a combination of theory, using molecularly detailed statistical mechanics models to produce quantitative predictions, and the tools of modern synthetic biology to design and test these predictions using a wide range of microscopy techniques. In particular, I am interested in understanding how the interconnected environment of the cell, where most regulatory players (transcription factor proteins, regulatory RNAs, etc.) act on dozens or even hundreds of different genes, can influence the special and temporal patterns of gene expression.

Brewster Lab Website ››

 
Michael J. Lee, PhD

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Systems Pharmacology of Anti-Cancer Therapies  
Our interests exist within an emerging discipline called Systems Pharmacology, which is focused broadly on understanding principles in drug therapy and mechanisms underlying the therapeutic activity of drugs as well as complex drug combinations. Towards this end, our group uses a combination of experimental and computational approaches to study the organization and function of signaling networks controlling the growth, survival, and death of cancer cells. We are particularly interested in understanding the adaptive properties that cells engage when faced with anti-cancer drugs, as well as identifying genetic, non-genetic, and contextual factors that contribute to the therapeutic variability seen in cancer patients.

Lee Lab Website ››

 
Amir Mitchell, PhD

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Cellular Networks in Health and Disease - from Robust Function to Catastrophic Failure
Our lab studies the response of cellular networks to changing environments in health and disease. While the structure of regulatory pathways is studied extensively, far less is known about network re-organization under time-varying stimuli. Yet this under-explored dimension has broad implications – time-variant stimuli can culminate in extreme outcomes, from detrimental signaling catastrophes to anticipatory stress responses. We combine experimental and theoretical approaches to dissect network functionality and uncover its unique points of failure. We aim to exploit the network structure to therapeutically target subpopulations of diseased cells within a healthy host.

Mitchell Lab Website ››

 
Elizabeth A. Shank, PhD

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Microbial interspecies interactions
Microbes live everywhere, and their community activities can have profound impacts on their hosts as well as on ecosystem‐level processes. Our group is focused on dissecting microbial cell-cell interactions to understand how secreted specialized (or secondary) metabolites contribute to the establishment, dynamics, and stability of these microbial communities. We use traditional microbiology, fluorescent co-culture, bioinformatics, mass spectrometry imaging, and native-like microcosms to identify and dissect chemical signaling interactions between microbes in both natural and laboratory settings, with the long-term goal of rationally manipulating microbial communities to improve host health and the environment.

Shank Lab Website ››

 
Lutfu Yilmaz, PhD

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Metabolic Network Modeling with the Nematode C. elegans
We aim to develop a systems-level understanding of how animal metabolism converts nutrients into biomass, energy, and by-products. Specifically, we have reconstructed a metabolic network model of the nematode C. elegans, which allows flux balance analysis to explore how the network of annotated biochemical reactions in this organism work altogether as a whole system. We integrate this mathematical model with gene expression datasets to resolve metabolic function under tissue-specific contexts and other defined conditions.   
  

 

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Transitions Between Being Alive and Being Truly or Seemingly Dead
We are interested in identifying and studying the ways in which a cell or an organism transitions between being alive and being either truly or seemingly dead (e.g., dormancy). We hope to find common principles that underlie these transitions. We are particularly interested in principles that allow life to be restarted after it has nearly or completely ceased, as in the case of dormant spores in yeast and diapaused mouse embryos. Our studies can deepen our understanding of quiescent and senescent cells which, in turn, are important for understanding human diseases such as cancer and how and why organisms age. We use quantitative experiments that range from single-cell-level measurements on microscopes to transcriptome analyses.

Youk Lab Website››

 

 

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Jennifer A Benanti, PhD

Jennifer Benanti, PhD
Associate Professor, Molecular, Cell & Cancer Biology

Regulation of Cell Growth and Division
Misregulation of cell division is the underlying cause of a number of human diseases, including cancer. Our lab is interested in understanding the molecular mechanisms that control how cells grow and divide. We study how protein degradation by the ubiquitin-proteasome system controls both the cell cycle and metabolic transitions.

Benanti Lab Website ››

   

Vanni Bucci, PhD
Associate Professor, Microbiology & Physiological Systems

Systems Biology of Host-Microbial Interactions
We have pioneered the set of frequentist and Bayesian regression techniques to infer host-microbiome dynamics from time-series abundance data. We apply these methods with both unsupervised and supervised machine learning methods to (1) predict dynamics between intestinal commensal and enteropathogenic bacteria in both animal models and human clinical studies, (2) determine colonization potential and structural stability of bacterial therapeutics that induce potent anti-inflammatory responses in the context of IBD, (3) identify bacteria and related functions that play central role in Alzheimer’s Disease etiology via immune-systems modulation, and (4) determine how the microbiome reprograms systemic gene expression following anti-TB therapy.

Bucci Lab Website ››

   
Tom Fazzio, PhD

Thomas Fazzio, PhD
Associate Professor, Molecular, Cell & Cancer Biology

Regulation of gene expression and cell fate by chromatin structure
We are focused on two problems central to gene regulation and development: (1) What are the pathways and mechanisms by which chromatin structure modulates gene regulatory networks? (2) How is chromatin structure remodeled during cellular differentiation to promote cell fate changes? We take a range of approaches to address these problems, largely in mouse embryonic stem cells and mouse models.

Fazzio Lab Website ››

   
Manuel Garber, PhD

Manuel Garber, PhD
Associate Professor Bioinformatics & Integrative Biology

The Functional Genome
The functional characterization of genomic elements using genome-wide functional assays such as RNA-Seq and ChIP-Seq. Our methods have been critical to the discovery and characterization of a novel set of large intergenic non-coding RNAs (lincRNAs) and to our understanding of the immune transcriptional response to pathogens. To study lincRNAs and in particular their evolutionary history, as well as the systematic dissection of the transcriptional regulation of the immune response.

Garber Lab Website ››

   
Dohoon Kim, PhD

Dohoon Kim, PhD
Assistant Professor, Molecular, Cell & Cancer Biology

Cancer Metabolism and Metabolic Toxicity
Our goal is to understand how changes in metabolic pathways support cancer cells and their survival within the tumor environment and to exploit these changes for therapeutic purposes. Cancer cells are dependent on metabolic pathways that involve the formation of toxic metabolites. The lab aims to characterize and understand the function of such pathways, and to target these pathways to poison cancer cells with their own metabolites. Furthermore, as widespread changes in metabolism accompany physiological and pathological changes in cellular state, we would like to collaborate with other groups to explore the potential roles of toxic metabolite pathways in contexts outside of cancer.

Kim Lab Website ››

   
Rene Maehr, PhD

Rene Maehr, PhD
Assistant Professor, Program in Molecular Medicine, Diabetes Center of Excellence

Mechanisms of Human Immune Syndromes
Our laboratory is interested in dissecting the underlying mechanisms of human immune syndromes such as autoimmunity and immunodeficiency. In this context, we use human pluripotent stem cells to reconstruct aspects of human development in vitro and the immune disease process in humanized disease models.

Maehr Lab Website ››

   
Athma Pai, PhD

Athma Pai, PhD
Assistant Professor, RNA Therapeutics Institute

Kinetics of Gene Regulation
Our lab lies at the intersection of RNA biology, computational genomics, and systems biology. Our central goal is to understand the dynamic nature of gene regulation in eukaryotic systems, by dissecting the kinetics of mRNA biogenesis and maturation. Specifically, we study the speed and efficiency at which RNA molecules are created and processed to ensure proper cellular functions. To do so, we combine high-dimensional computational analyses with novel functional genomics approaches to address both fundamental mechanistic questions and predict cellular responses across changing environmental contexts.

Pai Lab Website ››