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- person_outline denes
- person_outline Julio Saez-Rodriguez
Publication for OmniPath
Discriminate the response of Acute Myeloid Leukemia patients to treatment by using proteomics data and Answer Set Programming
[…] compiling signaling networks may be considered time demanding, many publicly available resources containing regulatory information currently exist such as KEGG , Reactome [, ], Pathway Commons , OmniPath  and NDEX . Some of these resources have available tools or Cytoscape  plug-ins to extract networks given a list of molecules, such as ReactomeFIViz  for Reactome, CyPath2  for Path […]
Integrative Computational Network Analysis Reveals Site Specific Mediators of Inflammation in Alzheimer's Disease
[…] ignaling interactions with direction (source-target relationship) and sign (activation or inhibition) as an input for our method. For this, we used publicly available signaling interactions databases OmniPath and ReactomeFI (Wu et al., ; Turei et al., ). We combined them by removing the redundant interactions commonly present in both databases (by removing the duplicate entry) to acquire only uniq […]
Logic Modeling in Quantitative Systems Pharmacology
[…] ted to many different other cases. Once we have chosen a system to model, the first step is to build a network based on what is known about the system (PKN). Here, public databases and resources like Omnipath help to gather and relate known information. When appropriate experimental data are available, they can be used to refine the PKN. Tools like CellNOpt help us in this process. Finally, with a […]
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