Data & Models

The following data & models have been highlighted here for ease of access: Interaction Networks, Hierarchical Cell Models, and Aging Models. Additionally, specific data sets are listed with their corresponding paper on the Publications Page. 

Interaction Networks

The Ideker Laboratory has assembled and published many gene and protein interaction networks, which are available on the Network Data Exchange (NDEx) website. The NDEx Project provides an open-source framework where scientists and organizations can share, store, manipulate, and publish biological network knowledge.

The Network Data Exchange (NDEx)

Hierarchical Cell Models

Our computational analysis pipelines translate molecular networks and other data from genomics into hierarchical models of the cell. Web portals for each of these models are linked below:

Autophagy Ontology (AtgO)
DCell
Network Extracted Ontology (NeXO)

Aging Models

Hannum G, Guinney J, Zhao L, Zhang L, Hughes G, Sadda S, Klotzle B, Bibikova M, Fan JB, Gao Y, Deconde R, Chen M, Rajapakse I, Friend S, Ideker T*, Zhang K*., Genome-wide Methylation Profiles Reveal Quantitative Views of Human Aging Rates. Mol Cell. 2013 Jan 24;49(2):359-367. doi: 10.1016/j.molcel.2012.10.016. Epub 2012 Nov 21. [PDF] [PubMed] *Corresponding authors

"People Who Are HIV-Positive May Be Aging Faster Than Their Peers" (NPR)

Gross AM, et al. Methylome-wide Analysis of Chronic HIV Infection Reveals Five-Year Increase in Biological Age and Epigenetic Targeting of HLA. Mol Cell. 2016 Apr 21. [PDF] [PubMed]

Wang T, et al. Epigenetic aging signatures in mice livers are slowed by dwarfism, calorie restriction and rapamycin treatment. Genome Biology. 2017 Mar 28. [PDF] [PubMed]