Computational approaches and challenges in spatial transcriptomics

S Fang, B Chen, Y Zhang, H Sun, L Liu… - Genomics …, 2023 - academic.oup.com
The development of spatial transcriptomics (ST) technologies has transformed genetic
research from a single-cell data level to a two-dimensional spatial coordinate system and …

Studying stochastic systems biology of the cell with single-cell genomics data

G Gorin, JJ Vastola, L Pachter - Cell Systems, 2023 - cell.com
Recent experimental developments in genome-wide RNA quantification hold considerable
promise for systems biology. However, rigorously probing the biology of living cells requires …

Advancing root developmental research through single-cell technologies

M Minne, Y Ke, M Saura-Sanchez… - Current opinion in plant …, 2022 - Elsevier
Single-cell RNA-sequencing has greatly increased the spatiotemporal resolution of root
transcriptomics data, but we are still only scratching the surface of its full potential. Despite …

Quantifying cancer cell plasticity with gene regulatory networks and single-cell dynamics

SM Groves, V Quaranta - Frontiers in Network Physiology, 2023 - frontiersin.org
Phenotypic plasticity of cancer cells can lead to complex cell state dynamics during tumor
progression and acquired resistance. Highly plastic stem-like states may be inherently drug …

scGIR: deciphering cellular heterogeneity via gene ranking in single-cell weighted gene correlation networks

F Xu, H Hu, H Lin, J Lu, F Cheng, J Zhang… - Briefings in …, 2024 - academic.oup.com
Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool for investigating
cellular heterogeneity through high-throughput analysis of individual cells. Nevertheless …

A review of single-cell transcriptomics and epigenomics studies in maternal and child health

C Shu, K Street, CV Breton, TM Bastain, ML Wilson - Epigenomics, 2024 - Taylor & Francis
Single-cell sequencing technologies enhance our understanding of cellular dynamics
throughout pregnancy. We outlined the workflow of single-cell sequencing techniques and …

DNA Barcoding Technology for Lineage Recording and Tracing to Resolve Cell Fate Determination

IS Kim - Cells, 2023 - mdpi.com
In various biological contexts, cells receive signals and stimuli that prompt them to change
their current state, leading to transitions into a future state. This change underlies the …

TIPD: A Probability Distribution-Based Method for Trajectory Inference from Single-Cell RNA-Seq Data

J Xie, Y Yin, J Wang - Interdisciplinary Sciences: Computational Life …, 2021 - Springer
Single-cell RNA-seq technology provides an unprecedented opportunity to allow
researchers to study the biological heterogeneity during cell differentiation and development …

Inferring cell differentiation maps from lineage tracing data

P Sashittal, R Zhang, B Law, A Strzalkowski, H Schmidt… - bioRxiv, 2024 - biorxiv.org
During development, mulitpotent cells differentiate through a hierarchy of increasingly
restricted progenitor cell types until they realize specialized cell types. A cell differentiation …

Network Control of Cell Identity and Plasticity in Small Cell Lung Cancer

SM Groves - 2022 - search.proquest.com
Epigenetic heterogeneity underlies acquired resistance to therapy in several cancer types.
Small cell lung cancer (SCLC) is a particularly recalcitrant form of lung cancer that …