Evangelia Petsalaki

Biological Network Organization, Not Generic Graph Topology, Drives Graph-Based Gene Essentiality Prediction

This study evaluates whether graph-based gene essentiality prediction relies on biological network structure or generic graph topology, finding that biological connectivity is critical for performance.

Signalome-wide mapping of the NFκB pathway in T-cells reveals novel targets for immunotherapy

This study maps the NFκB pathway in T-cells using CRISPR screens and identifies novel regulators that enhance cytotoxicity and cytokine production.

T-cell signaling relies on partial CD45-exclusion at sub-micron sized cellular contacts

The paper shows that T-cell activation is initiated by partial CD45 exclusion at sub-micron contacts, leading to strong activation and cytotoxicity through small signaling changes.

Comprehensive evaluation of phosphoproteomic-based kinase activity inference

This paper evaluates kinase activity inference methods using phosphoproteomics data and benchmarking approaches, finding that curated kinase-substrate libraries significantly impact results.

Data-driven extraction of human kinase-substrate relationships from omics datasets

This study develops a machine learning model to predict kinase-substrate relationships from omics data, improving upon existing methods and providing a web tool for analysis.

Subcellular proteomics and iPSC modeling uncover reversible mechanisms of axonal pathology in Alzheimer's disease

The paper uses subcellular proteomics and iPSC models to identify mTOR pathway activation in axonal spheroids and show its reversible role in Alzheimer's disease pathology.

Decoding MASLD Progression: A Molecular Trajectory-Based Framework for Modelling Disease Dynamics

This paper develops a molecular trajectory-based framework to model MASLD progression using transcriptomic and proteomic data, identifying novel biomarkers and mechanistic insights.

ARID1A-induced transcriptional reprogramming rewires signalling responses to drug treatment in melanoma

This study reveals how ARID1A-mediated transcriptional rewiring drives resistance to MAPK inhibitors in melanoma by altering signalling pathways, immune interactions, and receptor dynamics, highlighting potential targets for combinatorial therapies.

PhosX: data-driven kinase activity inference from phosphoproteomics experiments

PhosX infers kinase activity changes from phosphoproteomics data using substrate sequence specificity, outperforming existing methods without requiring prior kinase-substrate knowledge.

Differential regulation of the proteome and phosphosproteome along the dorso-ventral axis of the early Drosophila embryo

The paper investigates proteome and phosphoproteome changes along the dorso-ventral axis of Drosophila embryos, revealing differential regulation and functional roles of proteins and phosphorylation events.

phuEGO: A network-based method to reconstruct active signalling pathways from phosphoproteomics datasets

phuEGO reconstructs active signalling pathways from phosphoproteomics data by combining network propagation and decomposition to improve functional interpretation.

Phosphoproteomics data-driven signalling network inference: does it work?

This study evaluates six pairwise measures for predicting kinase-substrate and substrate-substrate associations from phosphoproteomics data, finding poor performance but improved results with sequence similarity filtering.

In silico network-based screening reveals candidates for endothelial dysfunction therapy

The paper identifies 17 candidate genes for endothelial dysfunction therapy using computational network analysis and in silico perturbation, with one target showing anti-inflammatory and antioxidant effects.

Use of viral motif mimicry improves the proteome-wide discovery of human linear motifs

The paper identifies human linear motifs by analyzing viral protein interactions, finding 8,400 motif instances with 105 supported by multiple filters.

Identification of phenotype-specific networks from paired gene expression-cell shape imaging data

The paper integrates gene expression and cell shape imaging data to identify phenotype-specific gene networks and signaling pathways involved in breast cancer cell morphology.

CEN-tools: An integrative platform to identify the contexts of essential genes

CEN-tools identifies context-specific essential genes using CRISPR screen data, revealing gene dependencies across biological contexts and integrating with protein-protein interaction networks.

Proteome-wide inference of protein kinase regulatory circuits

The paper predicts human kinase-kinase regulatory relationships and their effects using data-driven methods, revealing a sparse but denser network than typically considered.

Decoding the functional Fes kinase signaling network topology in a lymphocyte model

The paper identifies c-Fes kinase substrates and shows how c-Fes and Src signaling balance regulates CD19 levels and influences B-cell receptor signaling.