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Robert Brewster, PhD

Robert C. Brewster, PhD
Assistant Professor, Program in Systems Biology and Microbiology & Physiological Systems

Dissecting 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 ››

Job Dekker, PhD

Job Dekker, PhD
Joseph J. Byrne Chair in Biomedical Research,
Co-Director Program in Systems Biology, Professor Biochemistry & Molecular Pharmacology, Investigator Howard Hughes Medical Institute

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 ››

Michael J. Lee, PhD

Michael J. Lee, PhD
Assistant Professor, Program in Systems Biology and Program in Molecular Medicine

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

Amir Mitchell, PhD
Assistant Professor, Program in Systems Biology and Program in Molecular Medicine

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

Elizabeth A. Shank, PhD
Associate Professor, Program in Systems Biology and Microbiology & Physiological Systems

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 ››

Marian Walhout, Ph.D.

A.J. Marian Walhout, PhD
Maroun Semaan Chair in Biomedical Research, Co-Director Program in Systems Biology, Professor Program in Molecular Medicine

Mapping 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 ››


Hyun Youk, PhD
Associate Professor, Program in Systems Biology and Program in Molecular Medicine (Starting in January 2021)

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››


Affiliated Faculty

Victor Ambros, PhD

Victor Ambros, PhD
Silverman Professor of Natural Sciences, Professor Program in Molecular Medicine

Molecular and Genetic Control of Animal Development; MicroRNA Regulatory Mechanisms
We are interested in the genetic regulatory mechanisms that control animal development and in particular the molecules that function during animal development to ensure the proper timing of developmental events. We have primarily employed the nematode Caenorhabditis elegans as a model system for studying the function of regulators of developmental timing, which in C. elegans are known as the “heterochronic genes,” in reference to the remarkable changes in relative timing of developmental event that are elicited by mutations in these genes.

Ambros Lab Website ››

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 ››

Allan Jacobson, PhD

Allan S. Jacobson, PhD
Professor and Chair, Microbiology & Physiological Systems

Cytoplasmic Aspects of the Post-transcriptional Regulation of Gene Expression
Using the yeast Saccharomyces cerevisiae as a model system, much of the work in my lab is targeted to understanding the mechanistic details of nonsense-mediated mRNA decay (NMD). Our experiments have led us to formulate the faux UTR model for NMD in yeast, and independent studies in higher organisms have provided strong support for the general applicability of this model to all eukaryotes.

Jacobson 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 ››

Oliver Rando, MD, PhD

Oliver Rando, MD, PhD
Associate Professor, Biochemistry & Molecular Pharmacology

Genomic Approaches to Chromatin Structure and Function and to Epigenetic Inheritance
Our lab is broadly interested in epigenetic inheritance, but most of our research focuses on one putative carrier of epigenetic information – the nucleoprotein complex known as chromatin. We utilize genomics tools such as DNA microarrays and high-throughput sequencing to measure chromatin structure over entire genomes at single-nucleosome resolution, with the eventual goal of determining how chromatin states are established and maintained.

Rando Lab Website ››

Zhiping Weng, PhD

Zhiping Weng, PhD
Director Program in Bioinformatics & Integrative Biology, Professor Biochemistry & Molecular Pharmacology

Explore and Understand Biological Data Through the Application and Development of Computational Tools
We focus our research on regulatory molecules and their interactions, such as regulatory proteins and their DNA/RNA target sites, small silencing RNAs and their RNA targets, and protein-protein interactions. Our lab has three main projects: gene regulation, protein docking and small silencing RNAs.

Weng Lab Website ››

Phillip Zamore, PhD

Phillip Zamore, PhD
Gretchen Stone Cook Professor of Biomedical Sciences, Chair RNA Therapeutics Institute, Professor Biochemistry & Molecular Pharmacology, Investigator Howard Hughes Medical Institute

Dissecting the RNAi and miRNA Pathways
We are passionately committed to understanding how small RNAs - small interfering RNAs (siRNAs), microRNAs (miRNAs), and PIWI-interacting RNAs (piRNAs) - regulate gene expression in plants, fungi, and animals.

Zamore Lab Website ››