Models, Theoretical

A versatile workflow to integrate RNA-seq genomic and transcriptomic data into mechanistic models of signaling pathways.

Submitted by jdopazo on Fri, 02/12/2021 - 18:24

Garrido-Rodriguez M, López-López D, Ortuno FM, et al. A versatile workflow to integrate RNA-seq genomic and transcriptomic data into mechanistic models of signaling pathways. PLoS Comput Biol. 2021;17(2):e1008748. doi:10.1371/journal.pcbi.1008748.

Formulating and testing hypotheses in functional genomics.

Submitted by iguillen on Fri, 06/28/2019 - 14:20

Dopazo J. Formulating and testing hypotheses in functional genomics. Artif Intell Med. 2009;45(2-3):97-107. doi:10.1016/j.artmed.2008.08.003.

Gene Expression Integration into Pathway Modules Reveals a Pan-Cancer Metabolic Landscape.

Submitted by jdopazo on Fri, 11/02/2018 - 11:31

Cubuk C, Hidalgo MR, Amadoz A, et al. Gene Expression Integration into Pathway Modules Reveals a Pan-Cancer Metabolic Landscape. Cancer Res. 2018;78(21):6059-6072. doi:10.1158/0008-5472.CAN-17-2705.

Models of cell signaling uncover molecular mechanisms of high-risk neuroblastoma and predict disease outcome.

Submitted by jdopazo on Fri, 11/02/2018 - 11:02

Hidalgo MR, Amadoz A, Cubuk C, Carbonell-Caballero J, Dopazo J. Models of cell signaling uncover molecular mechanisms of high-risk neuroblastoma and predict disease outcome. Biol Direct. 2018;13(1):16. doi:10.1186/s13062-018-0219-4.

Graph-theoretical comparison of normal and tumor networks in identifying BRCA genes.

Submitted by jdopazo on Wed, 04/18/2018 - 19:27

Dopazo J, Erten C. Graph-theoretical comparison of normal and tumor networks in identifying BRCA genes. BMC Syst Biol. 2017;11(1):110. doi:10.1186/s12918-017-0495-0.