Building the mega single-cell transcriptome ocular meta-atlas

Probabilistic harmonization and annotation of single‐cell transcriptomics data with deep generative models

(2021) Chenling Xu et al.   Molecular Systems Biology

PARC: ultrafast and accurate clustering of phenotypic data of millions of single cells

(2020) Shobana V Stassen et al.   BIOINFORMATICS

Single-Cell Transcriptomic Comparison of Human Fetal Retina, hPSC-Derived Retinal Organoids, and Long-Term Retinal Cultures

(2020) Akshayalakshmi Sridhar et al.   Cell Reports

Single-Cell RNA Sequencing in Human Retinal Degeneration Reveals Distinct Glial Cell Populations

(2020) Andrew P. Voigt et al.   Cells

Single-Cell Analysis of Human Retina Identifies Evolutionarily Conserved and Species-Specific Mechanisms Controlling Development

(2020) Yufeng Lu et al.   DEVELOPMENTAL CELL

Single-cell profiling reveals an endothelium-mediated immunomodulatory pathway in the eye choroid

(2020) Guillermo L. Lehmann et al.   JOURNAL OF EXPERIMENTAL MEDICINE

MOUSE RETINAL CELL ATLAS: MOLECULAR IDENTIFICATION OF OVER SIXTY AMACRINE CELL TYPES

(2020) Wenjun Yan et al.   JOURNAL OF NEUROSCIENCE

Generalizing RNA velocity to transient cell states through dynamical modeling

(2020) Volker Bergen et al.   NATURE BIOTECHNOLOGY

Cell Atlas of The Human Fovea and Peripheral Retina

(2020) Wenjun Yan et al.   Scientific Reports

Cell Types of the Human Retina and Its Organoids at Single-Cell Resolution

(2020) Cameron S. Cowan et al.   CELL

Bulk and single-cell gene expression analyses reveal aging human choriocapillaris has pro-inflammatory phenotype

(2020) Andrew P. Voigt et al.   MICROVASCULAR RESEARCH

Jointly defining cell types from multiple single-cell datasets using LIGER

(2020) Jialin Liu et al.   Nature Protocols

A clustering-independent method for finding differentially expressed genes in single-cell transcriptome data

(2020) Alexis Vandenbon et al.   Nature Communications

Microglial Function Is Distinct in Different Anatomical Locations during Retinal Homeostasis and Degeneration

(2019) Emily G. O’Koren et al.   IMMUNITY

Molecular Classification and Comparative Taxonomics of Foveal and Peripheral Cells in Primate Retina

(2019) Yi-Rong Peng et al.   CELL

The barcode, UMI, set format and BUStools

(2019) Páll Melsted et al.   BIOINFORMATICS

Efficient integration of heterogeneous single-cell transcriptomes using Scanorama

(2019) Brian Hie et al.   NATURE BIOTECHNOLOGY

Single-Cell RNA-Seq Analysis of Retinal Development Identifies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specification

(2019) Brian S. Clark et al.   NEURON

Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data

(2019) Samuel L. Wolock et al.   Cell Systems

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Molecular characterization of foveal versus peripheral human retina by single-cell RNA sequencing

(2019) A.P. Voigt et al.   EXPERIMENTAL EYE RESEARCH

Current best practices in single‐cell RNA‐seq analysis: a tutorial

(2019) Malte D Luecken et al.   Molecular Systems Biology

Dissecting the transcriptome landscape of the human fetal neural retina and retinal pigment epithelium by single-cell RNA-seq analysis

(2019) Yuqiong Hu et al.   PLOS BIOLOGY

Single-cell transcriptional logic of cell-fate specification and axon guidance in early-born retinal neurons

(2019) Quentin Lo Giudice et al.   DEVELOPMENT

A single‐cell transcriptome atlas of the adult human retina

(2019) Samuel W Lukowski et al.   EMBO JOURNAL

Fast, sensitive and accurate integration of single-cell data with Harmony

(2019) Ilya Korsunsky et al.   NATURE METHODS

Single-cell transcriptomics of the human retinal pigment epithelium and choroid in health and macular degeneration

(2019) Andrew P. Voigt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degeneration

(2019) Madhvi Menon et al.   Nature Communications

Single-Cell Profiles of Retinal Ganglion Cells Differing in Resilience to Injury Reveal Neuroprotective Genes

(2019) Nicholas M. Tran et al.   NEURON

Recovering Gene Interactions from Single-Cell Data Using Data Diffusion

(2018) David van Dijk et al.   CELL

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

(2018) Laleh Haghverdi et al.   NATURE BIOTECHNOLOGY

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Deep generative modeling for single-cell transcriptomics

(2018) Romain Lopez et al.   NATURE METHODS

A test metric for assessing single-cell RNA-seq batch correction

(2018) Maren Büttner et al.   NATURE METHODS

Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics

(2016) Karthik Shekhar et al.   CELL

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Snakemake--a scalable bioinformatics workflow engine

(2012) J. Koster et al.   BIOINFORMATICS

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

The Neuronal Organization of the Retina

(2012) Richard H. Masland   NEURON

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT