Özgün Babur

GSPlot: Visualizing gene set similarity in enrichment results

GSPlot visualizes gene set similarity in enrichment results by displaying gene sets in a 2D space based on their enriched content similarity.

Capturing scientific knowledge in computable form

The paper introduces Biofactoid, a tool that crowdsources structured biological knowledge from authors, enabling efficient human-computer interaction and expanding existing pathway databases.

COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms

The paper describes the development of a computational knowledge repository, the COVID-19 Disease Map, which curates SARS-CoV-2 virus-host interaction mechanisms and provides tools for their analysis and application.

Causal interactions from proteomic profiles: molecular data meets pathway knowledge

The paper introduces a computational method to generate causal explanations for proteomic profiles by integrating molecular data with prior biological pathway knowledge, demonstrating its application in various biological contexts.

Targeting Adaptation to Cancer Treatment by Drug Combinations

This paper introduces TargetScore, a method to identify adaptive responses and predict drug-induced vulnerabilities in cancer cells, validated through experiments on breast cancer cells.

Pathway Commons: 2019 Update

Pathway Commons updates its resource with integrated pathway data, tools, and software for biological pathway analysis.

Mutually exclusive autism mutations point to the circadian clock and PI3K signaling pathways

The paper identifies mutual exclusivity patterns in de novo mutations in autism spectrum disorder, linking them to circadian clock and PI3K/AKT signaling pathways.

PaxtoolsR: Pathway Analysis in R Using Pathway Commons

PaxtoolsR provides R access to pathway data from Pathway Commons, enabling extraction, merging, validation, and integration with local BioPAX datasets.

Systematic identification of cancer driving signaling pathways based on mutual exclusivity of genomic alterations

The paper identifies cancer driver pathways by detecting mutual exclusivity patterns in genomic alterations across TCGA datasets, revealing previously unreported driver events.

Perturbation biology models predict c-Myc as an effective co-target in RAF inhibitor resistant melanoma cells

The paper uses perturbation biology to predict c-Myc as a co-target with BRAF/MEK inhibitors to overcome RAF inhibitor resistance in melanoma.