Systems Biology Center New York: Databases and Datasets

Funding SBCNY is supported by Grant Number P50GM071558 from the National Institute of General Medical Sciences.

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Bromberg KD, Ma'ayan A, Neves SR, Iyengar R. Design logic of a cannabinoid receptor signaling network that triggers neurite outgrowth. Science 2008;320(5878):903-9.

PubMed Abstract

Berger SI, Posner JM, Ma'ayan A. Genes2Networks: Connecting lists of gene symbols using mammalian protein interactions databases. BMC Bioinformatics 2007;8:372.

PubMed Abstract

PHARMACOGENOMICS:

Powerpoint presentations of lectures from the Spring 2008 course.

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DATABASES AND DATASETS

Publicly available databases and datasets

DOQCS (Database of Quantitative Cellular Signaling) is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions.

PubMed Abstract

Regulatory Networks Represented as Directed Graphs

Description	Sig flat file format
Dataset version used in the paper (Ma'ayan et al. published in Science Aug. 12 2005) for the analysis and visualization of CA1 neuron cellular network. The dataset is dated 9.22.2004	9.22.2004.txt
The current updated version of the CA1 neuron cellular network dated 6.1.2006	6.1.2006.txt
Ma'ayan A, Jenkins SL, Neves S, Hasseldine A, Grace E, Dubin-Thaler B, Eungdamrong NJ, Weng G, Ram PT, Rice JJ, Kershenbaum A, Stolovitzky GA, Blitzer RD, Iyengar R. Formation of regulatory patterns during signal propagation in a Mammalian cellular network. Science 2005 Aug; 309(5737): 1078-1083.