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, whole-cell proteome 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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Translating Gentoypes to Phenotypes

CELS_COVER-1The challenge of predicting biological outcomes based on underlying genetic features has vexed biologists for decades. A recent paper from Trey Ideker and colleagues described a new approach based on machine learning that leverages prior knowledge about how cells are organized. Instead of just considering which genes are mutated, this approach takes into account how combinations of mutated genes interact with one another such as in an organelle or as joint participants in a biochemical pathway.


Read in Cell Systems
Electricity Coursing through Biofilms

The endogenous role of ion channels in bacteria has long been a mystery. Recent work from the Suel lab has revealed that ion channels allow for long-range electrical communication in bacterial biofilms. These electrical signals play a key role coordinating growth. Perhaps then one way to control the growth of these largely antibiotic resistant biofilms is to disrupt these signals leading to unregulated growth and the eventual collapse of the entire community.

Read in Nature
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

The SDCSB’s Quarterly Systems-to-Synthesis Meeting: Spring 2016

March 21, 2016

Thursday, April 14, 2016, from 1:30 pm to 5:30 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 ...

Intellectual Property and Licensing Workshop 2016

January 28, 2016

Thursday, March 24, 2016 from 12:30 pm – 7 pm Main Auditorium at the Sanford Consortium for Regenerative Medicine Organized by Kamala Janiyani

This workshop will bring together intellectual property professionals, entrepreneurs, researchers and students to discuss the recent developments in the area ...

Annual Scientific Retreat 2016

September 29, 2015

The annual San Diego Center for Systems Biology Retreat will take place at the UCLA Lake Arrowhead Conference Center from Friday, January 29th, through Sunday, January 31st. The Retreat will feature talks by faculty members from each of the four ...

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Conferences & Workshops

Cytoscape Workshop
May 19, 2016 @ 1:30 – 6:00 pm
Sanford Consortium for Regenerative Medicine
Organized by Dr. Barry Demchak, UCSD
Registration begins in early April


Weekly Events

Genetics, Bioinformatics and Systems Biology Colloquium (2015-16)

qBio Seminar Series


Monthly Events

Career Development Seminar Series

San Diego Bioinformatics Users Series (SDBUS)

Systems Biology Club