Temporal modelling using single-cell transcriptomics

J Ding, N Sharon, Z Bar-Joseph - Nature Reviews Genetics, 2022 - nature.com
Methods for profiling genes at the single-cell level have revolutionized our ability to study
several biological processes and systems including development, differentiation, response …

Tempora: cell trajectory inference using time-series single-cell RNA sequencing data

TN Tran, GD Bader - PLoS computational biology, 2020 - journals.plos.org
Single-cell RNA sequencing (scRNA-seq) can map cell types, states and transitions during
dynamic biological processes such as tissue development and regeneration. Many …

[HTML][HTML] A hitchhiker's guide to single-cell transcriptomics and data analysis pipelines

R Nayak, Y Hasija - Genomics, 2021 - Elsevier
Single-cell transcriptomics (SCT) is a tour de force in the era of big omics data that has led to
the accumulation of massive cellular transcription data at an astounding resolution of single …

The triumphs and limitations of computational methods for scRNA-seq

PV Kharchenko - Nature methods, 2021 - nature.com
The rapid progress of protocols for sequencing single-cell transcriptomes over the past
decade has been accompanied by equally impressive advances in the computational …

scEpath: energy landscape-based inference of transition probabilities and cellular trajectories from single-cell transcriptomic data

S Jin, AL MacLean, T Peng, Q Nie - Bioinformatics, 2018 - academic.oup.com
Motivation Single-cell RNA-sequencing (scRNA-seq) offers unprecedented resolution for
studying cellular decision-making processes. Robust inference of cell state transition paths …

Critical downstream analysis steps for single-cell RNA sequencing data

Z Zhang, F Cui, C Lin, L Zhao, C Wang… - Briefings in …, 2021 - academic.oup.com
Single-cell RNA sequencing (scRNA-seq) has enabled us to study biological questions at
the single-cell level. Currently, many analysis tools are available to better utilize these …

[HTML][HTML] Identifying cell populations with scRNASeq

TS Andrews, M Hemberg - Molecular aspects of medicine, 2018 - Elsevier
Single-cell RNASeq (scRNASeq) has emerged as a powerful method for quantifying the
transcriptome of individual cells. However, the data from scRNASeq experiments is often …

Single‐cell sequencing methodologies: from transcriptome to multi‐dimensional measurement

Y Chen, J Song, Q Ruan, X Zeng, L Wu, L Cai… - Small …, 2021 - Wiley Online Library
Cells are the basic building blocks of biological systems, with inherent unique molecular
features and development trajectories. The study of single cells facilitates in‐depth …

Time-resolved single-cell RNA-seq using metabolic RNA labelling

F Erhard, AE Saliba, A Lusser, C Toussaint… - Nature Reviews …, 2022 - nature.com
Single-cell RNA genomics technologies are revolutionizing biomedical science by profiling
single cells with unprecedented resolution, providing fundamental insights into the role of …

Simulating multiple faceted variability in single cell RNA sequencing

X Zhang, C Xu, N Yosef - Nature communications, 2019 - nature.com
The abundance of new computational methods for processing and interpreting
transcriptomes at a single cell level raises the need for in silico platforms for evaluation and …