Single-cell genomics in plants: current state, future directions, and hurdles to overcome

JT Cuperus - Plant Physiology, 2022 - academic.oup.com
Single-cell genomics has the potential to revolutionize the study of plant development and
tissue-specific responses to environmental stimuli by revealing heretofore unknown players …

A systematic evaluation of single-cell RNA-sequencing imputation methods

W Hou, Z Ji, H Ji, SC Hicks - Genome biology, 2020 - Springer
Background The rapid development of single-cell RNA-sequencing (scRNA-seq)
technologies has led to the emergence of many methods for removing systematic technical …

Targeted Perturb-seq enables genome-scale genetic screens in single cells

D Schraivogel, AR Gschwind, JH Milbank, DR Leonce… - Nature …, 2020 - nature.com
The transcriptome contains rich information on molecular, cellular and organismal
phenotypes. However, experimental and statistical limitations constrain sensitivity and …

The application of single‐cell RNA sequencing in vaccinology

A Noé, TN Cargill, CM Nielsen… - Journal of …, 2020 - Wiley Online Library
Single‐cell RNA sequencing allows highly detailed profiling of cellular immune responses
from limited‐volume samples, advancing prospects of a new era of systems immunology …

Antigen identification and high-throughput interaction map** by reprogramming viral entry

CS Dobson, AN Reich, S Gaglione, BE Smith, EJ Kim… - Nature …, 2022 - nature.com
Deciphering immune recognition is critical for understanding a broad range of diseases and
for the development of effective vaccines and immunotherapies. Efforts to do so are limited …

[HTML][HTML] Inflation-collapse dynamics drive patterning and morphogenesis in intestinal organoids

NP Tallapragada, HM Cambra, T Wald, SK Jalbert… - Cell stem cell, 2021 - cell.com
How stem cells self-organize to form structured tissues is an unsolved problem. Intestinal
organoids offer a model of self-organization as they generate stem cell zones (SCZs) of …

Method of moments framework for differential expression analysis of single-cell RNA sequencing data

MC Kim, R Gate, DS Lee, A Tolopko, A Lu, E Gordon… - Cell, 2024 - cell.com
Differential expression analysis of single-cell RNA sequencing (scRNA-seq) data is central
for characterizing how experimental factors affect the distribution of gene expression …

SCITO-seq: single-cell combinatorial indexed cytometry sequencing

B Hwang, DS Lee, W Tamaki, Y Sun, A Ogorodnikov… - Nature …, 2021 - nature.com
The development of DNA-barcoded antibodies to tag cell surface molecules has enabled
the use of droplet-based single-cell sequencing (dsc-seq) to profile protein abundances …

A robust and scalable graph neural network for accurate single-cell classification

Y Zeng, Z Wei, Z Pan, Y Lu, Y Yang - Briefings in Bioinformatics, 2022 - academic.oup.com
Single-cell RNA sequencing (scRNA-seq) techniques provide high-resolution data on
cellular heterogeneity in diverse tissues, and a critical step for the data analysis is cell type …

Tools and concepts for interrogating and defining cellular identity

KL McKinley, D Castillo-Azofeifa, OD Klein - Cell Stem Cell, 2020 - cell.com
Defining the mechanisms that generate specialized cell types and coordinate their functions
is critical for understanding organ development and renewal. New tools and discoveries are …