gr-eventstream is a set of GNU Radio blocks for creating precisely timed events and either inserting them into, or extracting them from normal data-streams precisely. It allows for the definition of high speed time-synchronous c++ burst event handlers, as well as bridging to standard GNU Radio Async PDU messages with precise timing easily.

Pathway Enrichment-Guided Activity Study of Alternative Splicing (PEGASAS)

PHOsphoproteomic dissecTiOn using Networks

(DRExM³L) Drug REpurposing using eXplainable Machine Learning and Mechanistic Models of signal transduction

Finding paths of interest in networks

Modeling signaling networks in cancer

Converting SBGN encoded pathways to the SIF file format

Converting KGML encoded KEGG pathways to the SIF file format

Code for analysis of single cell signaling network kinetics from flow cytometry (CyTOF) datasets

Code repository for the publication. Contains MATLAB codes and sequence data used for evolutionary analysis.

An integrative dynamic model of brain energy metabolism (Coultier et al 2009)

Code for modeling performed in Barney et al.

Computations required for https://doi.org/10.1103/PhysRevE.97.020402 and additional work

The functional analysis of genes provides relevant information to understand cellular function. Further, the mapping of genetic interactions sheds light on how genes act in the emergence of cellular complexity. Here, we present the most extensive genetic interaction and morphological profiling screen in a metazoan cell to date. We profiled 680 0…

Rescue of plasticity by a computationally predicted protocol (Liu et al. 2013)

Ligand-Receptor Interaction map based on scRNA-seq and pathway enrichment

Computational modeling of gephyrin-dependent inhibitory transsynaptic signaling (Lupascu et al 2020)

Structure learning for protein signaling pathways

Model of a BDNF feedback loop (Zhang et al 2016)