Brian S. Clark

This study improves killifish retinal transcriptome annotation using long-read sequencing, identifying thousands of previously unannotated transcripts and enhancing gene naming accuracy.

This study identifies the lncRNA Peanut as promoting rod photoreceptor differentiation and neurogenesis by inhibiting Notch signaling and regulating Tox2 expression in retinal progenitor cells.

The paper shows that Dicer/miRNAs in late retinal progenitor cells are essential for proper postnatal retinal development and function.

The paper shows that DNA demethylation, mediated by TET enzymes, is essential for rod-photoreceptor fate determination during retinal development.

This study uses bulk and single-cell RNA-seq to analyze age-related transcriptome changes in the African turquoise killifish retina, identifying oxidative stress, gliosis, and inflammageing, and highlighting dysregulation of retinal disease genes.

The paper uses single-cell transcriptomics to show Evf2 lncRNA guides Dlx5/6UCE to many enhancer-gene guidance sites, with subpopulation-specific effects and long-range gene regulation.

This study identifies gene regulatory networks controlling retinal development by integrating single-cell RNA and ATAC-seq data from mouse and human retinas, revealing transcription factors that regulate temporal patterning and cell fate.

The paper introduces scProject and projectionDrivers to identify gene-wise differences in latent space projections across cell types and species in single-cell data, validated on mouse and human retinal development.

This study shows that Atoh7 is essential for RGC survival but not for their specification, as RGCs can develop without Atoh7 when apoptosis is inhibited.

This study identifies Casz1's role in regulating temporal identity transitions in neural progenitors through interactions with the NuRD and polycomb repressor complexes during retinal neurogenesis.

ASCOT identifies key regulators of neuronal subtype-specific splicing by analyzing public RNA-Seq data and demonstrating the role of PTBP1, MSI1, and PCBP2 in rod photoreceptor splicing.

The paper introduces scCoGAPS and projectR to decompose cell identity into shared and species-specific factors, enabling transfer learning across datasets and species.

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.

The paper uses single-cell RNA sequencing to analyze retinal development stages and identifies NFI factors as regulators of late progenitor cell specification and mitotic exit.

The paper shows that Lhx2, with its coactivator Ldb1 and corepressor Rnf12, regulates the balance between neurogenesis and gliogenesis in the retina by controlling cell cycle exit, Notch signaling, and expression of neurogenic factors.

The paper develops a collection of 1406 validated monoclonal antibodies against human transcription factors and identifies factors contributing to their successful generation.