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.

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:

Publications with cover-art featuring our work in Hierarchical Cell Models

Nature Methods, Volume 15 Issue 4, April 2018
On the cover: a cellular model learned by an artificial neural network. Cover design by Erin Dewalt, based on a concept by Jianzhu Ma, Samson Fong, Michael Yu and Trey Ideker. p290
Nature Biotechnology, Volume 31 Issue 1, January 2013
On the cover: A fractal-like hierarchy of network clusters extracted from the interaction networks of budding yeast. Dutkowski et al. use cellular components and processes embedded in molecular networks to derive a gene ontology (p 38). Credit: Janusz Dutkowski

Aging Models

Hannum G, et al. Genome-wide Methylation Profiles Reveal Quantitative Views of Human Aging Rates. Mol Cell. 2013 Jan 24 (Epub 2012 Nov 21). [PDF] [PubMed]

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]