[HTML][HTML] Best practices for single-cell analysis across modalities

L Heumos, AC Schaar, C Lance, A Litinetskaya… - Nature Reviews …, 2023 - nature.com
Recent advances in single-cell technologies have enabled high-throughput molecular
profiling of cells across modalities and locations. Single-cell transcriptomics data can now …

[PDF][PDF] Wound healing, fibroblast heterogeneity, and fibrosis

HE Talbott, S Mascharak, M Griffin, DC Wan… - Cell stem cell, 2022 - cell.com
Fibroblasts are highly dynamic cells that play a central role in tissue repair and fibrosis.
However, the mechanisms by which they contribute to both physiologic and pathologic …

Single-cell profiling to explore pancreatic cancer heterogeneity, plasticity and response to therapy

S Bärthel, C Falcomatà, R Rad, FJ Theis, D Saur - Nature cancer, 2023 - nature.com
Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal cancer entity characterized by a
heterogeneous genetic landscape and an immunosuppressive tumor microenvironment …

[HTML][HTML] Statistical and machine learning methods for spatially resolved transcriptomics data analysis

Z Zeng, Y Li, Y Li, Y Luo - Genome biology, 2022 - Springer
The recent advancement in spatial transcriptomics technology has enabled multiplexed
profiling of cellular transcriptomes and spatial locations. As the capacity and efficiency of the …

[HTML][HTML] Single-cell and spatial transcriptomics: deciphering brain complexity in health and disease

M Piwecka, N Rajewsky, A Rybak-Wolf - Nature Reviews Neurology, 2023 - nature.com
In the past decade, single-cell technologies have proliferated and improved from their
technically challenging beginnings to become common laboratory methods capable of …

[HTML][HTML] A relay velocity model infers cell-dependent RNA velocity

S Li, P Zhang, W Chen, L Ye, KW Brannan, NT Le… - Nature …, 2024 - nature.com
RNA velocity provides an approach for inferring cellular state transitions from single-cell
RNA sequencing (scRNA-seq) data. Conventional RNA velocity models infer universal …

[HTML][HTML] The specious art of single-cell genomics

T Chari, L Pachter - PLOS Computational Biology, 2023 - journals.plos.org
Dimensionality reduction is standard practice for filtering noise and identifying relevant
features in large-scale data analyses. In biology, single-cell genomics studies typically begin …

[HTML][HTML] UniTVelo: temporally unified RNA velocity reinforces single-cell trajectory inference

M Gao, C Qiao, Y Huang - Nature Communications, 2022 - nature.com
The recent breakthrough of single-cell RNA velocity methods brings attractive promises to
reveal directed trajectory on cell differentiation, states transition and response to …

[HTML][HTML] Recent advances in the field of single-cell proteomics

V Petrosius, EM Schoof - Translational Oncology, 2023 - Elsevier
The field of single-cell omics is rapidly progressing. Although DNA and RNA sequencing-
based methods have dominated the field to date, global proteome profiling has also entered …

DeepVelo: Single-cell transcriptomic deep velocity field learning with neural ordinary differential equations

Z Chen, WC King, A Hwang, M Gerstein, J Zhang - Science advances, 2022 - science.org
Recent advances in single-cell sequencing technologies have provided unprecedented
opportunities to measure the gene expression profile and RNA velocity of individual cells …