Donald J. Zack

Genetic discovery using deep learning-derived optic nerve integrity phenotypes

The paper uses AI-derived retinal thickness phenotypes from 2D images to identify novel genetic loci for neurodegenerative diseases.

SureQuant IS-PRM Enables Cross-Species Targeted Quantification of Retinoid Metabolism and Signaling Proteins in the Heart

The paper develops a targeted proteomics method to quantify retinoid metabolism and signaling proteins across species and tissues, revealing tissue-specific networks and developmental changes in the heart.

Profiling miRNAs involved in Human Oligodendrocyte Precursor Cell Differentiation and Maturation

The paper identifies stage-specific miRNAs involved in human oligodendrocyte precursor cell differentiation and maturation through miRNA profiling of hESC-derived cells.

Internal limiting basement membrane inhibits functional engraftment of transplanted human retinal ganglion cells

This study shows that disrupting the internal limiting membrane enhances the survival and functional integration of transplanted human retinal ganglion cells in the retina.

Identification a Compact Promoter using a New Promoter Selection Strategy and Engineering Hybrid Pol II/III Enable Efficient Genome Editing in Human Retinal Ganglion Cells

The paper identifies a compact Pol II promoter and hybrid Pol II/III promoters to enable efficient single-AAV delivery of SpCas9 for genome editing in human retinal ganglion cells.

Recovery of retinal terminal fields after traumatic brain injury: evidence of collateral sprouting and sexual dimorphism

This study shows that retinal ganglion cell axons can re-establish terminal fields after traumatic brain injury through collateral sprouting, with sex differences in recovery.

Dynamic changes in mRNA isoform usage during human retinal organoid development

The paper uses long-read RNA sequencing to study dynamic mRNA isoform changes during human retinal organoid development, revealing splicing patterns and allelic imbalance.

Identification and functional characterization of an AMD associated c-ABL binding SNP streak within the ARMS2 gene promoter region

The paper identifies a 5-SNP block in the ARMS2 promoter that binds c-ABL and is associated with AMD, showing reduced transcriptional activity in reporter assays.

Distinctive cross-ancestry genetic architecture for age-related macular degeneration

This study identifies 63 AMD risk loci across multiple ancestries, highlighting ancestry-dependent genetic heterogeneity and potential therapeutic targets.

Intercellular communication atlas reveals Oprm1 as a neuroprotective factor for retinal ganglion cells

The paper constructs an intercellular communication atlas of the retina, identifying Oprm1 as a neuroprotective factor that enhances RGC survival through ligand-receptor interactions.

Regional Gene Expression in the Retina, Optic Nerve Head, and Optic Nerve of Mice with Experimental Glaucoma and Optic Nerve Crush

The paper examines regional gene expression differences in the retina, optic nerve head, and optic nerve of mice with glaucoma and optic nerve crush using bulk RNA-sequencing.

High-Throughput Screening for Myelination Promoting Compounds Using Human Stem Cell-derived Oligodendrocyte Progenitor Cells Identifies Novel Targets

The paper identifies novel pathways that enhance oligodendrocyte maturation and myelination through high-throughput screening of 2500 compounds using engineered human stem cell-derived OPCs.

Quantitative fate mapping: Reconstructing progenitor field dynamics via retrospective lineage barcoding

This paper introduces quantitative fate mapping to reconstruct progenitor field dynamics using lineage barcodes and validates it with simulations and experiments.

Human photoreceptors switch from autonomous axon extension to cell-mediated process pulling during synaptic marker redistribution.

This study investigates how human photoreceptor axons extend during development and regeneration, finding that they transition from autonomous growth to process pulling mediated by non-PR cells.

Large-scale Phenotypic Drug Screen Identifies Neuroprotectants in Zebrafish and Mouse Models of Retinitis Pigmentosa

The paper identifies neuroprotective compounds for retinitis pigmentosa using cross-species drug screens in zebrafish and mouse models, finding additive effects in some combinations.

Structural engraftment and topographic spacing of transplanted human stem cell-derived retinal ganglion cells

This study investigates how transplanted human stem cell-derived retinal ganglion cells integrate into the host retina and identifies the internal limiting membrane as a barrier to structural integration.

Single-Cell Transcriptomic Analysis Reveals Molecular Diversity of Human Oligodendrocyte Progenitor Cells

The paper uses single-cell transcriptomics to analyze human oligodendrocyte progenitor cells, revealing transcriptional heterogeneity and pathways involved in their differentiation.

Programmed Switch in The Mitochondrial Degradation Pathways During Human Retinal Ganglion Cell Differentiation from Stem Cells is Critical for RGC Survival

The paper shows that during human retinal ganglion cell differentiation, the mitochondrial degradation pathway shifts from the ubiquitine-proteasome system to the endo-lysosomal pathway, which is critical for cell survival.

PanoView: An iterative clustering for single-cell RNA sequencing data

PanoView is an iterative clustering method for scRNA-seq data that outperforms existing methods in detecting major and rare cell types without parameter tuning.

Single-cell analysis of human retina identifies evolutionarily conserved and species-specific mechanisms controlling development.

This study uses scRNA-Seq to analyze human and mouse retinal development, identifying conserved and species-specific gene expression patterns and a novel role for ATOH7 in photoreceptor specification.

Thyroid hormone signaling specifies cone subtypes in human retinal organoids

The paper shows thyroid hormone signaling controls the temporal switch between S and L/M cone fates in human retinal organoids.

A widespread decrease of chromatin accessibility in age-related macular degeneration

This study identifies global decreases in chromatin accessibility in AMD patients, linking epigenetic changes to disease progression and suggesting HDAC11 as a potential therapeutic target.

Axon Guidance Signaling Modulates Epithelial to Mesenchymal Transition in Stem Cell-Derived Retinal Pigment Epithelium

This study investigates EMT in stem cell-derived RPE cells, identifying dysregulated axon guidance molecules during the process.

Single Cell RNA Sequencing of stem cell-derived retinal ganglion cells.

The paper characterizes the transcriptome of human stem cell-derived retinal ganglion cells using single-cell RNA sequencing, identifying three subpopulations with varying maturity levels.

grID: A CRISPR-Cas9 guide RNA Database and Resource for Genome-Editing

The paper introduces grID, a CRISPR-Cas9 guide RNA database that compiles gRNA properties and integrates with other resources to aid in genome-editing design.