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

Cytoscape Clinic 2016

August 19, 2016

Wednesday, Sep 7, 2016 from 9:00 am – 1 pm UC San Diego Campus, BRF2 room 1102 Organized by Barry Demchak

In this workshop, the Cytoscape development team will try something completely new.

Attendees at our yearly Spring workshop have requested a non-lecture format ...

Cytoscape Workshop 2016

May 3, 2016

Thursday, May 19, 2016 from 1:30 pm – 6 pm Sanford Consortium for Regenerative Medicine Organized by Barry Demchak

Cytoscape is the most popular software for visualizing molecular networks and biological pathways and for integrating these networks with annotations, gene expression profiles and ...

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 ...

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Conferences & Workshops

Hands-on Cytoscape Clinic
September 7, 2016, from 9:30 – 1:00 pm
BRF2 (Room 1102) at UC San Diego
Organized by Dr. Barry Demchak
Register for the event here

Fall Systems-To-Synthesis (S2S) Meeting
October 13, 2016, from 1:30 – 6:00 pm
The Village 15 at UC San Diego
Registration begins in September 2016

CRISPR Screens Workshop
October 20, 2016, from 1:30 – 6:00 pm
Sanford Consortium for Regenerative Medicine
Organized by Dr. Olivier Harismendy
Registration begins in September 2016

Metabolomics Conference
October 27, 2016, from 1:30 – 6:00 pm
Sanford Consortium for Regenerative Medicine
Organized by Dr. Mohit Jain
Registration begins in September  2016

SDCSB Annual Scientific Retreat
January 20-22, 2017
UCLA Lake Arrowhead Conference Center
Registration begins in Fall 2016

IP Workshop
March 16, 2017, from 1:30 – 6:00 pm
Sanford Consortium for Regenerative Medicine
Organized by Kamala Janiyani
Registration begins in Winter 2017

Spring Systems-To-Synthesis (S2S) Meeting
April 6, 2017, from 1:30 – 6:00 pm
The Village 15 at UC San Diego
Registration begins in Spring 2017

 

Weekly Events

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

qBio Seminar Series (2015-2016)

Systems Biology Career Development Seminars (Spring 2016)

Monthly Events

San Diego Bioinformatics Users Series (SDBUS)

Systems Biology Club