PSB Primary Faculty

 job_dekker

 

Job Dekker, PhD. Professor and Co-Director 

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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 Albertha J Walhout, PhD. Professor and Co-Director   

Mapping Transcription Regulatory Circuits 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.

   

 

 

Lee Photo   

Michael J. Lee, PhD, Assistant Professor

Systems Pharmacology of Anti-Cancer Therapies


Treatment of many human diseases, including cancer, typically involves modulation of signal transduction pathways. These pathways are functionally integrated, very plastic, and incredibly sensitive to environmental context. 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.

   

 

 

PSB Affiliated Faculty 

 

Ambros

Victor Ambros, PhD. Professor and Co-director RNA Therapeutics Institute

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.  

   
Baily_2  

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.

   
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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.

   
Garber  

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.

   
Jacobson  

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.

   
/uploadedImages/MaPS/Faculty/LitvakV.jpg Vladimir Litvak, PhD, Assistant Professor Microbiology & Physiological Systems
   
Rando  

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.

   
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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

   
 Zamore  

Phillip Zamore, PhD. Professor and Co-Director of 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.