SDCSB began in 2005 as the San Diego Consortium for Systems Biology to bring together scientists across disciplines and institutions, to promote collaborative research and training, and to support the exchange of ideas and resources.

NCSB LogoIn 2010, we became one of the National Centers for Systems Biology funded by the National Institute of General Medical Sciences (NIGMS) (P50 GM085764). Over the past five years our research has led to significant systems biology advances, including genome-wide studies of how stress remodels transcriptional and genetic networks, discovery of an independent metabolic clock coordinating cell growth through cycles of TOR1 activity, demonstration that much of the Gene Ontology can be inferred directly from ‘omics data, prediction of cancer survival time and drug response by an approach called Network Based Stratification and a series of major feats in engineering of synthetic coupled genetic circuits.

The theme of our Center – “From Maps to Models” – addresses an important challenge in systems biology: traversing between network maps and mathematical models, two very successful but so far mostly separate biological representations and modes of study. Network maps tend to be global, static, abstract and descriptive, whereas mathematical models tend to be local, dynamic, detailed and predictive. Guided by this overarching theme, four SDCSB research projects seek to develop a general library of maps and models relevant to fundamental cellular and super-cellular processes, including the spatiotemporal architecture of the genome, protein turnover dynamics, cell-cell communication and heterogeneity and environment-genome interactions. These mapping and modeling activities are fueled by technologies advanced across three SDCSB core platforms.

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PQBP1 triggers innate immue responses to HIV-1

The innate immune response to HIV-1 is in part coordinated by dendritic cells, immune sentinels that themselves are targets of HIV-1 infection. Sumit Chanda’s lab recently discovered that immunogenic HIV-1 reverse transcripts are recognized in dendritic cells by PQBP1, which then initiates the innate immune response.

Read in Cell

Pulsing Signals Help to Overcome Noise

Pulsing Signals crop BBiological systems must transmit information in the face of both intrinsic noise inherent to biochemical reactions and extrinsic noise due to cell-to-cell variations. Using both experimental and theoretical approaches to, researchers in Roy Wollman’s group found that pulsed signals are more reliable at overcoming the effects of cell-to-cell variability that than just a single, one-off signal. 

Read in Science
Mutations in p53 Alone Don’t Explain Deadly Cancer

TP53-3p Survival Curves 2
Although mutations in p53 are associated with more aggressive forms of cancer, researchers in Trey Ideker’s lab have found evidence suggesting that the deleterious effects of the mutated gene may in large part be due to other genetic abnormalities, at least in squamous cell head and neck cancers. In a study published in Nature Genetics,  researchers found that the high mortality rates among head and neck cancer patients tends only to occur when mutations in p53 coincide with the loss of the short arm of chromosome 3.

Read in Nature Genetics

Registration for July’s SDBUS is now open

June 22, 2015

Join the Center for Computational Biology & Bioinformatics (CCBB) and the San Diego Center for Systems Biology (SDCSB) for our eleventh bioinformatics talk on Wednesday, 7/1/15 from 4-6PM.

Amanda Birmingham from The Center for Computational Biology & Bioinformatics will be giving ...

Registration for June’s San Diego Bioinformatics Users Series (SDBUS) is now open

June 2, 2015

Join the Center for Computational Biology and Bioinformatics (CCBB) and the San Diego Center for Systems Biology for our tenth bioinformatics talk on Wednesday, June 17, 2015, from 4 – 6 pm.

Roman Sasik from the CCBB will be giving a ...

The SDCSB’s Quarterly
Systems-to-Synthesis Meeting

April 2, 2015

Friday, April 10, 2015, from 1:30 pm – 6 pm Meeting Rooms on Fifteen, 15th Floor of Building 1, Village West

 

The SDCSB’s Quarterly Systems-to-Synthesis Meeting will feature short talks by graduate students and postdoctoral fellows from labs throughout the SDCSB followed ...

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