Dana-Farber Cancer Institute (DFCI)  | Dept of Cancer Biology (DFCI)  | Harvard Medical School (HMS)  | Dept of Genetics (HMS)     

Affiliated CCSB Core Members

 

 

Albert-László Barabási 
Center for Complex Network Research, Northeastern University

The CCNR researches how networks emerge, what they look like, how they evolve, and how networks provide explanations into the behavior of complex systems, biological and otherwise.

Barabási AL. The network takeover. Nat Physics 2012; 8:14-6.

Juan Fuxman Bass
Boston University

 
The Fuxman Bass lab studies the transcriptional regulation of immune genes ad their misregulation in disease by integrating orthogonal protein-DNA interaction mapping methods with computational and experimental approaches. The ultimate goal is to understand how immune responses are orchestrated and how gene expression can be modulated for therapeutic gains.

 

Jennifer Benanti
University of Massachusetts Medical School

 
The Benanti lab studies how transcription, phosphorylation and protein degradation contribute to the regulatory network that controls the cell cycle. The goal is to identify conserved properties of cell cycle control networks, and ultimately to understand how the cell cycle is misregulated in cancer cells.

 

Robert C. Brewster
University of Massachusetts Medical School

 
The Brewster lab 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 as way of 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.

 

Martha Bulyk
Harvard Medical School, Brigham & Women's Hospital

The Bulyk Lab investigates transcriptional regulation, particularly transcriptional enhancers and the interactions between sequence-specific transcription factors and their DNA binding sites. Genomic, proteomic, and computational technologies are applied to diverse biological organisms.

Busser BW, et al. Molecular mechanism underlying the regulatory specificity of a Drosophila homeodomain protein that specifies myoblast identity. Development 2012; 139:1164-74

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Job Dekker 
University of Massachusetts Medical School


The Dekker Lab studies how a genome is organized in three dimensions inside the nucleus. The spatial organization of a genome plays an important role in the regulation of genes and maintenance of genome stability. They study the genomes of human and yeast using a set of powerful molecular and genomic tools.

Sanyal A, Lajoie BR, Jain G, Dekker J. The long-range interaction landscape of gene promoters. Nature 2012; 489:109-13.


Suzanne Gaudet
Dana-Farber Cancer Institute

 
The focus of the Gaudet Lab is on the life-or-death decision making in cancer cells treated with Tumor Necrosis Factor or TNF, a pro-inflammatory cytokine that induces both pro-survival and pro-apoptotic signaling. By using single-cell measurement approaches combined with computational models, they aim to reach improved understanding of how cells make the life-or-death decision.

Gaudet S, Spencer SL, Chen WH, Sorger PK. Exploring the contextual sensitivity of factors that determine cell-to-cell variability in receptor-mediated apoptosis. PLoS Comput Biol 2012; 8:e1002482.


Alexander "Sasha" Gimelbrant
Dana-Farber Cancer Institute

 
Similar, neighboring human cells can vary from each other in their ability to process information and in their responses to physiological stimuli and drugs. Autosomal monoallelic expression (MAE) is a recently uncovered source of cell-to-cell variation. This epigenetic mechanism affects over 20% of all human genes, including key genes linked to cancer and other major diseases. The goal of the Gimelbrant lab is to understand the molecular mechanisms underlying the establishment and maintenance of MAE and to identify ways to manipulate MAE.

Nag A, Savova V, Fung HL, Miron A, Yuan GC, Zhang K, Gimelbrant AA. Chromatin signature of widespread monoallelic expression. eLife 2013;2:e01256.


Michael J. Lee
University of Massachusetts Medical School

 
The Lee lab investigates systems pharmacology of anti-cancer drug action, aiming towards producing better therapeutic options for breast cancer. The focus is on signaling pathways controlling the growth, survival, and death of cancer cells, identifying sources of therapeutic variability and clarifying the “rules” that underlie drug efficacy.

Lee MJ, Ye AS, Gardino AK, Heijink AM, Sorger PK, Macbeath G, Yaffe MB. Sequential application of anticancer drugs enhances cell death by rewiring apoptotic signaling networks. Cell 2012;149:780–94.


Amir Mitchell
University of Massachusetts Medical School

 
The Mitchell lab studies the response of cellular networks to changing environments in health and disease by combining 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.

 

Chad Myers
University of Minnesota

 
Research in the Myers’ lab focuses on machine learning approaches for integrating diverse genomic data to make inferences about biological networks. The main focus of our work is developing computational methods for analysis and interpretation of large-scale genetic interaction networks and methods for integration of diverse genomic data to predict gene function or infer biological networks. His lab is developing approaches for analyzing and leveraging interaction networks to answer biological questions in a variety of systems including yeast, plants, worm and human.

 

Arthur B. Pardee, emeritus
Dana-Farber Cancer Institute

 
Art Pardee can rightfully be acknowledged as a founding spirit of systems biology. His discovery of feedback inhibition in pyrimidine metabolism delineated the first regulatory circuit in biology, in effect the first biological 'system'. The reknowned PaJaMo experiments (Pa for Pardee) led to the development by Jacob and Monod of the model of operon regulation in bacteria. Later, Dr. Pardee established that the cell cycle has a 'Restriction Point', or 'Pardee Point', in the G1 phase where the cell commits to moving into S phase. Into his 90's Dr. Pardee remains active, with current interests lying in the characterization of clinically useful breast cancer markers.

Yates RA & Pardee AB. Control of pyrimidine biosynthesis in Escherichia coli by a feed-back mechanism. J Biol Chem 1956; 221:757-70.

Frederick "Fritz" Roth
Donnelly Centre, University of Toronto

Research at the Roth Lab involves designing and interpreting large-scale experiments to understand pathway structure and its relationship to phenotype and human disease, through both computational and experimental lines of research. 

Taşan M et al. A resource of quantitative functional annotation for Homo sapiens genes. Genes Genomes Genetics 2012; 2:223-33.

Daniel P. Silver
Thomas Jefferson University

The Silver lab undertakes large-scale high-throughput functional genomics approaches to isolate new cancer-relevant genes, and also participates in translational breast cancer research efforts. 

Silver DP, Livingston DM. Mechanisms of BRCA1 tumor suppression. Cancer Discov 2012; 2:679–84.

Marian Walhout
University of Massachusetts Medical School

 
The Walhout Lab uses experimental and computational systems biology approaches to map and characterize gene regulatory networks and to understand how regulatory circuitry controls animal development, physiological functions and homeostasis. The ultimate aim is to understand how dysfunctional regulatory networks relate to diseases like diabetes, obesity and cancer.

Reece-Hoyes et al. Yeast one-hybrid assays for gene-centered human gene regulatory network mapping. Nat Methods 2012; 8:1050-2.

Brandon Xia
McGill University

 
The Xia Lab uses and develops structural and systems biology approaches to build computer models of complex biomolecular systems, in order to elucidate the interdependencies between sequence, structure, function, and evolution of biomolecular systems.

Franzosa EA & Xia Y. Structural principles within the human-virus protein-protein interaction network. PNAS 2011; 108: 10538-43.

 

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