[HTML][HTML] Automated methods for cell type annotation on scRNA-seq data

G Pasquini, JER Arias, P Schäfer… - Computational and …, 2021 - Elsevier
The advent of single-cell sequencing started a new era of transcriptomic and genomic
research, advancing our knowledge of the cellular heterogeneity and dynamics. Cell type …

Human pluripotent-stem-cell-derived organoids for drug discovery and evaluation

JJ Vandana, C Manrique, LA Lacko, S Chen - Cell Stem Cell, 2023 - cell.com
Human pluripotent stem cells (hPSCs) and three-dimensional organoids have ushered in a
new era for disease modeling and drug discovery. Over the past decade, significant …

Transfer learning enables predictions in network biology

CV Theodoris, L Xiao, A Chopra, MD Chaffin… - Nature, 2023 - nature.com
Mapping gene networks requires large amounts of transcriptomic data to learn the
connections between genes, which impedes discoveries in settings with limited data …

[HTML][HTML] Organoid intelligence (OI): the new frontier in biocomputing and intelligence-in-a-dish

L Smirnova, BS Caffo, DH Gracias, Q Huang… - Frontiers in …, 2023 - frontiersin.org
Biological computing (or biocomputing) offers potential advantages over silicon-based
computing in terms of faster decision-making, continuous learning during tasks, and greater …

Evolution of neuronal cell classes and types in the vertebrate retina

J Hahn, A Monavarfeshani, M Qiao, AH Kao, Y Kölsch… - Nature, 2023 - nature.com
The basic plan of the retina is conserved across vertebrates, yet species differ profoundly in
their visual needs. Retinal cell types may have evolved to accommodate these varied needs …

[HTML][HTML] Human brain organoids assemble functionally integrated bilateral optic vesicles

E Gabriel, W Albanna, G Pasquini, A Ramani… - Cell stem cell, 2021 - cell.com
During embryogenesis, optic vesicles develop from the diencephalon via a multistep
process of organogenesis. Using induced pluripotent stem cell (iPSC)-derived human brain …

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

Y Lu, F Shiau, W Yi, S Lu, Q Wu, JD Pearson… - Developmental cell, 2020 - cell.com
The development of single-cell RNA sequencing (scRNA-seq) has allowed high-resolution
analysis of cell-type diversity and transcriptional networks controlling cell-fate specification …

Retinal organoids: a window into human retinal development

M O'Hara-Wright, A Gonzalez-Cordero - Development, 2020 - journals.biologists.com
Retinal development and maturation are orchestrated by a series of interacting signalling
networks that drive the morphogenetic transformation of the anterior developing brain …

Charting human development using a multi-endodermal organ atlas and organoid models

Q Yu, U Kilik, EM Holloway, YH Tsai, C Harmel, A Wu… - Cell, 2021 - cell.com
Organs are composed of diverse cell types that traverse transient states during
organogenesis. To interrogate this diversity during human development, we generate a …

Bioprinted 3D outer retina barrier uncovers RPE-dependent choroidal phenotype in advanced macular degeneration

MJ Song, R Quinn, E Nguyen, C Hampton, R Sharma… - Nature …, 2023 - nature.com
Age-related macular degeneration (AMD), a leading cause of blindness, initiates in the outer-
blood-retina-barrier (oBRB) formed by the retinal pigment epithelium (RPE), Bruch's …