Phosphoproteomics in drug discovery

MK Morris, A Chi, IN Melas, LG Alexopoulos - Drug discovery today, 2014 - Elsevier
Highlights•Phosphoproteomic technologies deliver highly informative data to aide drug
discovery.•Technologies include mass spectrometry and suspension and planar protein …

Integrative biological analysis for neuropsychopharmacology

MR Emmett, RA Kroes, JR Moskal, CA Conrad… - …, 2014 - nature.com
Although advances in psychotherapy have been made in recent years, drug discovery for
brain diseases such as schizophrenia and mood disorders has stagnated. The need for new …

Detecting and removing inconsistencies between experimental data and signaling network topologies using integer linear programming on interaction graphs

IN Melas, R Samaga, LG Alexopoulos… - PLoS computational …, 2013 - journals.plos.org
Cross-referencing experimental data with our current knowledge of signaling network
topologies is one central goal of mathematical modeling of cellular signal transduction …

[HTML][HTML] Modeling of signaling pathways in chondrocytes based on phosphoproteomic and cytokine release data

IN Melas, AD Chairakaki, EI Chatzopoulou… - Osteoarthritis and …, 2014 - Elsevier
Objective Chondrocyte signaling is widely identified as a key component in cartilage
homeostasis. Dysregulations of the signaling processes in chondrocytes often result in …

caspo: a toolbox for automated reasoning on the response of logical signaling networks families

S Videla, J Saez-Rodriguez, C Guziolowski… - …, 2017 - academic.oup.com
We introduce the caspo toolbox, a python package implementing a workflow for reasoning
on logical networks families. Our software allows researchers to (i) learn a family of logical …

Non Linear Programming (NLP) formulation for quantitative modeling of protein signal transduction pathways

A Mitsos, IN Melas, MK Morris, J Saez-Rodriguez… - PLoS …, 2012 - journals.plos.org
Modeling of signal transduction pathways plays a major role in understanding cells' function
and predicting cellular response. Mathematical formalisms based on a logic formalism are …

Association of gene polymorphisms in ABO blood group chromosomal regions and menstrual disorders

Y Su, GL Kong, YL Su, Y Zhou… - Experimental and …, 2015 - spandidos-publications.com
This study aimed to investigate whether single nucleotide polymorphisms (SNPs) located
near the gene of the ABO blood group play an important role in the genetic aetiology of …

Designing experiments to discriminate families of logic models

S Videla, I Konokotina, LG Alexopoulos… - … in bioengineering and …, 2015 - frontiersin.org
Logic models of signaling pathways are a promising way of building effective in silico
functional models of a cell, in particular of signaling pathways. The automated learning of …

Pathway analysis for RNA-Seq data using a score-based approach

YH Zhou - Biometrics, 2016 - academic.oup.com
A variety of pathway/gene-set approaches have been proposed to provide evidence of
higher-level biological phenomena in the association of expression with experimental …

Network‐based analysis of nutraceuticals in human hepatocellular carcinomas reveals mechanisms of chemopreventive action

M Michailidou, IN Melas, DE Messinis… - CPT …, 2015 - Wiley Online Library
Chronic inflammation is associated with the development of human hepatocellular
carcinoma (HCC), an essentially incurable cancer. Anti‐inflammatory nutraceuticals have …