Bora Uyar

Oncogene inactivation-induced senescence facilitates tumor relapse

This study shows that oncogene inactivation-induced senescence both limits tumor growth and promotes relapse by creating a pro-recurrence microenvironment.

An atlas-scale generative model for unified representation learning of bulk RNA-seq data

The paper trains a supervised VAE on bulk RNA-seq data to learn a unified tissue-aware representation, achieving high tissue classification accuracy and demonstrating the impact of dataset scale.

Flexynesis: A deep learning framework for bulk multi-omics data integration for precision oncology and beyond

Flexynesis provides a versatile deep learning framework for integrating bulk multi-omics data, offering usability, adaptability, and benchmarking across diverse datasets.

Pathogenic mutations of human phosphorylation sites affect protein-protein interactions

The paper investigates how pathogenic mutations at phosphorylation sites affect protein-protein interactions, showing that such mutations disrupt phosphorylation-dependent motifs and alter cellular functions.

Multi-omics alleviates the limitations of panel-sequencing for cancer drug response prediction

This study shows that combining transcriptome data with gene panel features improves drug response prediction in cancer.

Multi-omics and deep learning provide a multifaceted view of cancer

This study uses deep learning to analyze multi-omics data and identify cancer-related biomarkers that can classify cancer types, predict survival, and guide clinical decisions.

Parallel genetics of regulatory sequences in vivo

The paper functionally analyzes regulatory sequences in C. elegans by introducing mutations and measuring their effects on gene expression and fitness.

HOT or not: Examining the basis of high-occupancy target regions

The paper investigates whether HOT regions are genuine transcription factor binding sites or ChIP-seq artifacts, finding they likely result from technical biases and specific sequence features.

Reproducible genomics analysis pipelines with GNU Guix

The paper presents reproducible genomics analysis pipelines using GNU Guix for RNA-seq, ChIP-seq, Bisulfite-seq, and single-cell RNA-seq, ensuring consistent results across different environments.

FACT sets a barrier for cell fate reprogramming in C. elegans and Human

The paper identifies FACT as a conserved reprogramming barrier in C. elegans and humans that maintains cell identity by modulating chromatin accessibility.