Identifying Drug Effects via Pathway Alterations using an Integer Linear Programming Optimization Formulation on Phosphoproteomic Data. - Alexander Mitsos; Ioannis N. Melas; Paraskeuas Siminelakis; Aikaterini D. Chairakaki; Julio Saez-Rodriguez; Leonidas G. Alexopoulos (PLoS Comput. Biol., 2009)

Modeling signaling pathways in articular cartilage. - Ioannis N. Melas; Aikaterini D. Chairakaki; Alexander Mitsos; Zoe Dailiana; Christopher G. Provatidis; Leonidas G. Alexopoulos (EMBC, 2011)

Combined logical and data-driven models for linking signalling pathways to cellular response. - Ioannis N. Melas; Alexander Mitsos; Dimitris E. Messinis; Thomas S. Weiss; Leonidas G. Alexopoulos (BMC Syst. Biol., 2011)

Identification of signaling pathways related to drug efficacy in hepatocellular carcinoma via integration of phosphoproteomic, genomic and clinical data. - Ioannis N. Melas; Douglas A. Lauffenburger; Leonidas G. Alexopoulos (BIBE, 2013)

Detecting and Removing Inconsistencies between Experimental Data and Signaling Network Topologies Using Integer Linear Programming on Interaction Graphs. - Ioannis N. Melas; Regina Samaga; Leonidas G. Alexopoulos; Steffen Klamt (PLoS Comput. Biol., 2013)

A crowd-sourcing approach for the construction of species-specific cell signaling networks. - Erhan Bilal; Theodore Sakellaropoulos; Challenge Participants; Ioannis N. Melas; Dimitris E. Messinis; Vincenzo Belcastro; Kahn Rhrissorrakrai; Pablo Meyer 001; Raquel Norel; Anita Iskandar; Elise Blaese; John Jeremy Rice; et al. (Bioinform., 2015)