Eleven grand challenges in single-cell data science

D Lähnemann, J Köster, E Szczurek, DJ McCarthy… - Genome biology, 2020 - Springer
The recent boom in microfluidics and combinatorial indexing strategies, combined with low
sequencing costs, has empowered single-cell sequencing technology. Thousands—or even …

Principles and challenges of modeling temporal and spatial omics data

B Velten, O Stegle - Nature Methods, 2023 - nature.com
Studies with temporal or spatial resolution are crucial to understand the molecular dynamics
and spatial dependencies underlying a biological process or system. With advances in high …

Single-nucleus profiling of human dilated and hypertrophic cardiomyopathy

M Chaffin, I Papangeli, B Simonson, AD Akkad, MC Hill… - Nature, 2022 - nature.com
Heart failure encompasses a heterogeneous set of clinical features that converge on
impaired cardiac contractile function, and presents a growing public health concern …

Screening cell–cell communication in spatial transcriptomics via collective optimal transport

Z Cang, Y Zhao, AA Almet, A Stabell, R Ramos… - Nature …, 2023 - nature.com
Spatial transcriptomic technologies and spatially annotated single-cell RNA sequencing
datasets provide unprecedented opportunities to dissect cell–cell communication (CCC) …

Human distal airways contain a multipotent secretory cell that can regenerate alveoli

MC Basil, FL Cardenas-Diaz, JJ Kathiriya, MP Morley… - Nature, 2022 - nature.com
The human lung differs substantially from its mouse counterpart, resulting in a distinct distal
airway architecture affected by disease pathology in chronic obstructive pulmonary disease …

[HTML][HTML] Lineage tracing reveals the phylodynamics, plasticity, and paths of tumor evolution

D Yang, MG Jones, S Naranjo, WM Rideout, KHJ Min… - Cell, 2022 - cell.com
Tumor evolution is driven by the progressive acquisition of genetic and epigenetic
alterations that enable uncontrolled growth and expansion to neighboring and distal tissues …

Tissue-resident memory and circulating T cells are early responders to pre-surgical cancer immunotherapy

AM Luoma, S Suo, Y Wang, L Gunasti, CBM Porter… - Cell, 2022 - cell.com
Neoadjuvant immune checkpoint blockade has shown promising clinical activity. Here, we
characterized early kinetics in tumor-infiltrating and circulating immune cells in oral cancer …

CellRank for directed single-cell fate mapping

M Lange, V Bergen, M Klein, M Setty, B Reuter… - Nature …, 2022 - nature.com
Computational trajectory inference enables the reconstruction of cell state dynamics from
single-cell RNA sequencing experiments. However, trajectory inference requires that the …

Alveolar regeneration through a Krt8+ transitional stem cell state that persists in human lung fibrosis

M Strunz, LM Simon, M Ansari, JJ Kathiriya… - Nature …, 2020 - nature.com
The cell type specific sequences of transcriptional programs during lung regeneration have
remained elusive. Using time-series single cell RNA-seq of the bleomycin lung injury model …

Sublethal cytochrome c release generates drug-tolerant persister cells

H Kalkavan, MJ Chen, JC Crawford, G Quarato… - Cell, 2022 - cell.com
Drug-tolerant persister cells (persisters) evade apoptosis upon targeted and conventional
cancer therapies and represent a major non-genetic barrier to effective cancer treatment …