Modeling pro-death signaling pathways in cancer hepatocytes using multi-combinatorial treatments of inhibitors and stimuli. - Leonidas G. Alexopoulos; Douglas A. Lauffenburger; Peter K. Sorger (BIBE, 2008)

Flexible informatics for linking experimental data to mathematical models via DataRail. - Julio Saez-Rodriguez; Arthur Goldsipe; Jeremy Muhlich; Leonidas G. Alexopoulos; Bjorn Millard; Douglas A. Lauffenburger; Peter K. Sorger (Bioinform., 2008)

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)

The Logic of EGFR/ErbB Signaling: Theoretical Properties and Analysis of High-Throughput Data. - Regina Samaga; Julio Saez-Rodriguez; Leonidas G. Alexopoulos; Peter K. Sorger; Steffen Klamt (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)

Understanding the limits of animal models as predictors of human biology: lessons learned from the sbv IMPROVER Species Translation Challenge. - Kahn Rhrissorrakrai; Vincenzo Belcastro; Erhan Bilal; Raquel Norel; Carine Poussin; Carole Mathis; Rémi H. J. Dulize; Nikolai V. Ivanov; Leonidas G. Alexopoulos; John Jeremy Rice; Manuel C. Peitsch; Gustavo Stolovitzky; et al. (Bioinform., 2015)

Dynamics and heterogeneity of brain damage in multiple sclerosis. - Ekaterina Kotelnikova; Narsis Aftab Kiani; Elena Abad; Elena H. Martinez-Lapiscina; Magí Andorrà; Irati Zubizarreta; Irene Pulido-Valdeolivas; Inna Pertsovskaya; Leonidas G. Alexopoulos; Tomas Olsson; Roland Martin; Friedemann Paul; et al. (PLoS Comput. Biol., 2017)

DeepSIBA: Chemical Structure-based Inference of Biological Alterations. - Christos Fotis; Nikos Meimetis; Antonis Sardis; Leonidas G. Alexopoulos (CoRR, 2020)

Predicting single cell genotypes from single cell expression profiles in AML using deep learning. - Georgios Asimomitis; Maria Sirenko; Christos Fotis; Dan A. Landau; Leonidas G. Alexopoulos; Elli Papaemmanuil (ICBBB, 2023)

Multiscale networks in multiple sclerosis. - Keith E. Kennedy; Nicole Kerlero de Rosbo; Antonio Uccelli; Maria Cellerino; Federico Ivaldi; Paola Contini; Raffaele De Palma; Hanne F. Harbo; Tone Berge; Steffan D. Bos; Einar A. Høgestøl; Synne Brune-Ingebretsen; et al. (PLoS Comput. Biol., 2024)