Integrating phylogenies into single-cell RNA sequencing analysis allows comparisons across species, genes, and cells

SH Church, JL Mah, CW Dunn - Plos Biology, 2024 - journals.plos.org
Comparisons of single-cell RNA sequencing (scRNA-seq) data across species can reveal
links between cellular gene expression and the evolution of cell functions, features, and …

The making of a proprioceptor: a tale of two identities

JC de Nooij, N Zampieri - Trends in Neurosciences, 2023 - cell.com
Proprioception, the sense of body position in space, has a critical role in the control of
posture and movement. Aside from skin and joint receptors, the main sources of …

Multicellular factor analysis of single-cell data for a tissue-centric understanding of disease

ROR Flores, JD Lanzer, D Dimitrov, B Velten… - Elife, 2023 - elifesciences.org
Biomedical single-cell atlases describe disease at the cellular level. However, analysis of
this data commonly focuses on cell-type-centric pairwise cross-condition comparisons …

[HTML][HTML] A single-cell transcriptional timelapse of mouse embryonic development, from gastrula to pup

C Qiu, BK Martin, IC Welsh, RM Daza, TM Le, X Huang… - bioRxiv, 2023 - ncbi.nlm.nih.gov
The house mouse, Mus musculus, is an exceptional model system, combining genetic
tractability with close homology to human biology. Gestation in mouse development lasts …

[PDF][PDF] Lineage motifs as developmental modules for control of cell type proportions

M Tran, A Askary, MB Elowitz - Developmental Cell, 2024 - cell.com
In multicellular organisms, cell types must be produced and maintained in appropriate
proportions. One way this is achieved is through committed progenitor cells or extrinsic …

A logic-incorporated gene regulatory network deciphers principles in cell fate decisions

G Xue, X Zhang, W Li, L Zhang, Z Zhang, X Zhou… - Elife, 2024 - elifesciences.org
Organisms utilize gene regulatory networks (GRN) to make fate decisions, but the regulatory
mechanisms of transcription factors (TF) in GRNs are exceedingly intricate. A longstanding …

A single-nucleus atlas of seed-to-seed development in Arabidopsis

TA Lee, T Nobori, N Illouz-Eliaz, J Xu, B Jow, JR Nery… - bioRxiv, 2023 - biorxiv.org
Extensive studies of the reference plant Arabidopsis have enabled deep understandings of
tissues throughout development, yet a census of cell types and states throughout …

CADD v1. 7: using protein language models, regulatory CNNs and other nucleotide-level scores to improve genome-wide variant predictions

M Schubach, T Maass, L Nazaretyan… - Nucleic Acids …, 2024 - academic.oup.com
Abstract Machine Learning-based scoring and classification of genetic variants aids the
assessment of clinical findings and is employed to prioritize variants in diverse genetic …

[HTML][HTML] RDA coupled with deep sequencing detects somatic SVA-retrotranspositions and mosaicism in the human brain

J Möhner, M Scheuren, V Woronzow… - Frontiers in Cell and …, 2023 - frontiersin.org
Cells of the developing human brain are affected by the progressive acquisition of genetic
and epigenetic alterations that have been reported to contribute to somatic mosaicism in the …

[HTML][HTML] A single-cell time-lapse of mouse prenatal development from gastrula to birth

C Qiu, BK Martin, IC Welsh, RM Daza, TM Le, X Huang… - Nature, 2024 - nature.com
The house mouse (Mus musculus) is an exceptional model system, combining genetic
tractability with close evolutionary affinity to humans,. Mouse gestation lasts only 3 weeks …