Deniz Dalkara

The paper identifies rod bipolar and AII amacrine cells as key to surround responses in OFF retinal ganglion cells through optogenetics and electrophysiology.

The paper uses AI to analyze the structural impact of 7-mer peptide insertions in AAV capsids, identifying viable modifications and their effects on capsid stability and function.

The paper develops and evaluates two synthetic fusion promoters, Pikali and Nocchu, for enhanced and balanced transgene expression in both rods and cones of retinal organoids.

This study compares immune responses to AAV-delivered CRISPR-Cas9 and RNP-delivered CRISPR-Cas9 in the retina, finding persistent inflammation with AAV and transient inflammation with RNP.

The paper compares CRISPR/Cas9 gene editing efficiency in retinal organoids, HEK293T cells, and mouse models, finding retinal organoids better mirror in vivo editing outcomes.

This study shows that expressing short-wavelength cone opsin in RGCs causes hyperpolarization, opposite to mid-wavelength opsin's depolarization, due to different G-protein activation.

The paper determines the optimal sequencing depth for accurately measuring barcode concentrations in combinatorial genetic experiments by analyzing NGS data and incorporating a mathematical model of PCR amplification.

The paper shows that immune responses to AAV-mediated ocular gene delivery vary across species and individuals, complicating reliable immunomonitoring.

The paper introduces tools to selectively enhance Gi/o-mediated GIRK currents in excitable cells using light-activated GPCRs.

The paper investigates why engineered AAV variants have lower titers and finds that DNAse digestion heat reduces their stability, leading to artificially low titers.

The paper introduces ACIDES, a method that improves performance estimation in directed evolution by combining statistical inference and in-silico simulations, tested on experimental and public datasets.

This study shows that optogenetic stimulation of AII amacrine cells restores both ON and OFF retinal responses and enables other retinal computations in degenerate retinas.

This study shows that Numb regulates Tau levels and prevents neurodegeneration in tauopathy models, with Numb-72 specifically reducing intracellular Tau.

This study shows chronic nicotine exposure shifts decision-making strategies toward increased exploitation in a foraging task, with optogenetic manipulation of dopamine neurons replicating this effect.

This paper demonstrates sonogenetic stimulation of the brain with high spatiotemporal resolution for visual restoration in rats and rodents.

This study identifies distinct dopamine circuits in the ventral tegmental area that mediate nicotine's reinforcing and anxiogenic effects through opposing responses in neurons projecting to the nucleus accumbens and amygdala.

This study uses optogenetics and functional ultrasound imaging to show that surface stimulation of the rat visual cortex activates a large volume of V1, including deep layers and areas beyond V1.

The paper evaluates an optogenetic construct for vision restoration in non-human primates, demonstrating high temporal resolution and visual acuity above legal blindness.

The paper investigates neural circuits in the mouse retina and finds that color-opponent cells are predominantly located in the ventral retina, supporting color vision in the upper visual field.

This study uses directed evolution to create AAV vectors with enhanced gene delivery to the outer retina in primates.

The paper develops a method to image the entire inner plexiform layer of the retina at once, revealing response speed gradients in bipolar cells and isolating experimental batch effects.

This study identifies YAP's role in Müller glia quiescence exit and regeneration by linking it to EGFR signaling and cell cycle re-entry in retinal injury.

The paper demonstrates that rod bipolar cells provide asymmetric input to direction selective ganglion cells, contributing to their direction selectivity through all-optical manipulation and imaging.

This study demonstrates that optogenetically activated ganglion cells in mouse and macaque retinas have high spatial resolution, predicting acuity above legal blindness limits.