Sinem K. Saka

This paper introduces a dual-photoreactive adapter to enable rapid, one-step DNA barcoding of antibody panels for multiplexed imaging.

ProPER enables multiplexed molecular-state analysis by converting spatial proximity into DNA readouts, revealing kinetic details of gene induction and splicing.

This study identifies a specific leukemic stem cell (LSC) subtype that drives niche remodeling in AML by altering fibroblast states and suppressing osteolineage differentiation.

The paper introduces faster variants of the Caprola tool for calcium-dependent fluorescent labeling, enabling more sensitive and efficient recording of neuronal activity in zebrafish.

This study shows that Eomes regulates UBC differentiation and migration in mice, mirroring human UBC development, and highlights conserved molecular mechanisms in cerebellar development.

This paper introduces a framework for high-plex spectral imaging using DNA-barcoded labeling and programmable signal amplification to improve panel design and unmixing accuracy.

This study identifies Nup153 as a docking point for splicing machinery at the nuclear pore, showing its role in mRNA processing and gene splicing.

SpatialData, a Zarr/OME-NGFF-based format plus Python library, unifies images, labels, points, shapes and tables across spatial omics platforms with coordinate alignment, lazy loading and cross-modal aggregation.

SABER enables highly multiplexed and amplified detection of DNA and RNA in cells and tissues by using oligo-based probes with long DNA concatemers for sensitive fluorescent detection.

OligoMiner designs genome-scale oligo FISH probes with customizable parameters and evaluates probe specificity using supervised learning, demonstrating scalability across model organisms.