Rob Brewster

Robert Brewster, PhD
Assistant Professor Program in Systems Biology and Microbiology and 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, regulator RNAs, etc.) act on dozens or even hundreds of different genes, can influence the special and temporal patterns of gene expression.

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Job Dekker, PhD
Joseph J. Byrne Chair in Biomedical Research,
Co-Director Program in Systems Biology, Professor Biochemistry and 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.

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

Systems Pharmacology of Anti-Cancer Therapies  

Our interests exists 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.

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Amir Mitchell

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.

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AJ 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.

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Affiliated Faculty 


Victor Ambros, PhD. 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.  

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Jeffrey Bailey, MD, PhD. Assistant Professor Bioinformatics and Integrative Biology 

Computational and Experimental Analysis of the Role of Segmental Duplication and Copy Number Variation in Human Disease.

One focus of the lab is directed towards dissecting the role of copy number variation in the pathogenesis of malaria. Malaria has been one of the strongest selective forces affecting the human population and still accounts for an estimated two to three million deaths per year. Another focus of the lab is examining the role of copy number variation in amyotrophic lateral sclerosis (ALS) or Lou Gehrig disease. We are collaborating with Dr. Robert Brown here at UMass to identify copy number variants affecting susceptibility and/or disease progression.


Jennifer Benanti PhD. Assistant Professor Program in Gene Function & Expression 

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.


Manuel Garber, PhD. Associate Professor Bioinformatics and 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.

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Dohoon Kim   

Dohoon Kim, PhD. Assistant Professor  Department of Molecular, Cell and 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 which 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.

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Rene Maehr  

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

Mechanisms of Human Immune Syndromes

Our laboratory is interested in dissecting the underlying mechanisms of human immune syndromes such as autoimmunity and immuno-deficiency. 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.

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Allan Jacobson, PhD. Professor and Chair Department of Microbiology and 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 (see below), and independent studies in higher organisms have provided strong support for the general applicability of this model to all eukaryotes.


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.


Zhiping Weng, PhD. Professor and Director Program in Bioinformatics and Integrative Biology 

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 interaction. Our lab has three main projects: Gene Regulation, Protein Docking and Small Silencing RNAs


Phillip Zamore, PhD. Professor and Chair RNA Therapeutics 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.

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