Ozgur Beker

This paper introduces waxMorph, a differentiable framework for simulating and reconstructing 3D morphogenesis, showing it can infer shape programs and trajectories from biological data.

The paper uses morphodynamic features from live imaging to predict cell fate during Xenopus mucociliary epithelial differentiation, showing that integrated time-resolved features outperform single features.

The paper develops Brendo, a resource identifying BMEC-specific genes using bulk RNA-seq data and provides a web platform for exploring these genes.

Patches decodes shared and condition-specific transcriptional programs in wound healing using scRNA-seq data, revealing universal patterns and treatment-specific changes.

This paper evaluates 31 cell-type deconvolution methods across human and mouse tissues, identifies regression-based methods as effective, and introduces the CATD pipeline for reproducible analysis.