Computational principles and challenges in single-cell data integration

R Argelaguet, ASE Cuomo, O Stegle… - Nature biotechnology, 2021 - nature.com
The development of single-cell multimodal assays provides a powerful tool for investigating
multiple dimensions of cellular heterogeneity, enabling new insights into development …

Single-cell RNA sequencing analysis: a step-by-step overview

S Slovin, A Carissimo, F Panariello, A Grimaldi… - RNA bioinformatics, 2021 - Springer
Thanks to innovative sample-preparation and sequencing technologies, gene expression in
individual cells can now be measured for thousands of cells in a single experiment. Since its …

Active eosinophils regulate host defence and immune responses in colitis

A Gurtner, C Borrelli, I Gonzalez-Perez, K Bach, IE Acar… - Nature, 2023 - nature.com
In the past decade, single-cell transcriptomics has helped to uncover new cell types and
states and led to the construction of a cellular compendium of health and disease. Despite …

Expanding the boundaries of RNA sequencing as a diagnostic tool for rare Mendelian disease

HD Gonorazky, S Naumenko, AK Ramani… - The American Journal of …, 2019 - cell.com
Gene-panel and whole-exome analyses are now standard methodologies for mutation
detection in Mendelian disease. However, the diagnostic yield achieved is at best 50 …

Spearheading future omics analyses using dyngen, a multi-modal simulator of single cells

R Cannoodt, W Saelens, L Deconinck… - Nature …, 2021 - nature.com
We present dyngen, a multi-modal simulation engine for studying dynamic cellular
processes at single-cell resolution. dyngen is more flexible than current single-cell …

Concepts and limitations for learning developmental trajectories from single cell genomics

S Tritschler, M Büttner, DS Fischer, M Lange… - …, 2019 - journals.biologists.com
Single cell genomics has become a popular approach to uncover the cellular heterogeneity
of progenitor and terminally differentiated cell types with great precision. This approach can …

A pooled single-cell genetic screen identifies regulatory checkpoints in the continuum of the epithelial-to-mesenchymal transition

JL McFaline-Figueroa, AJ Hill, X Qiu, D Jackson… - Nature …, 2019 - nature.com
Integrating single-cell trajectory analysis with pooled genetic screening could reveal the
genetic architecture that guides cellular decisions in development and disease. We applied …

Single cell analysis of adult mouse skeletal muscle stem cells in homeostatic and regenerative conditions

S Dell'Orso, AH Juan, KD Ko, F Naz… - …, 2019 - journals.biologists.com
Dedicated stem cells ensure postnatal growth, repair and homeostasis of skeletal muscle.
Following injury, muscle stem cells (MuSCs) exit from quiescence and divide to reconstitute …

Context-specific transcription factor functions regulate epigenomic and transcriptional dynamics during cardiac reprogramming

NR Stone, CA Gifford, R Thomas, KJB Pratt… - Cell stem cell, 2019 - cell.com
Ectopic expression of combinations of transcription factors (TFs) can drive direct lineage
conversion, thereby reprogramming a somatic cell's identity. To determine the molecular …

Emergent dynamics of adult stem cell lineages from single nucleus and single cell RNA-Seq of Drosophila testes

AA Raz, GS Vida, SR Stern, S Mahadevaraju… - Elife, 2023 - elifesciences.org
Proper differentiation of sperm from germline stem cells, essential for production of the next
generation, requires dramatic changes in gene expression that drive remodeling of almost …