Bülent Arman Aksoy

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

Cytokit processes and analyzes large-scale fluorescent microscopy data to quantify cell properties, validated through experiments and public datasets.

The paper optimizes T cell activation by identifying key culture factors and uncovering artifacts in bead-based activation methods.

Coral provides an interactive web tool for visualizing human kinome data with customizable features and high-resolution outputs.

The paper describes a computational pipeline for a personalized neoantigen vaccine trial, including tools for variant calling, peptide selection, and sequence reconstruction.

The paper introduces a set of open-source workflow management tools for bioinformatics, emphasizing reliability and flexibility.

This study explores factors influencing response and resistance to atezolizumab in urothelial cancer using multi-omic data, finding associations between TCR clonality and clinical outcomes.

Cycledash provides a web tool for validating and analyzing somatic variants by integrating existing tools and workflows.

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

The paper identifies rare functional mutations in cancer by mapping them to protein domain hotspots across 22 tumor types, revealing both known and novel mutations with functional implications.

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

The paper identifies recurrent DICER1 mutations in cancer that disrupt miRNA processing and cause mRNA expression imbalances, contributing to oncogenesis.

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