Single-cell omics: experimental workflow, data analyses and applications

F Sun, H Li, D Sun, S Fu, L Gu, X Shao, Q Wang… - Science China Life …, 2025 - Springer
Cells are the fundamental units of biological systems and exhibit unique development
trajectories and molecular features. Our exploration of how the genomes orchestrate the …

Diverse clonal fates emerge upon drug treatment of homogeneous cancer cells

Y Goyal, GT Busch, M Pillai, J Li, RH Boe, EI Grody… - Nature, 2023 - nature.com
Even among genetically identical cancer cells, resistance to therapy frequently emerges
from a small subset of those cells,,,,,–. Molecular differences in rare individual cells in the …

Unraveling non-genetic heterogeneity in cancer with dynamical models and computational tools

M Pillai, E Hojel, MK Jolly, Y Goyal - Nature Computational Science, 2023 - nature.com
Individual cells within an otherwise genetically homogenous population constantly undergo
fluctuations in their molecular state, giving rise to non-genetic heterogeneity. Such diversity …

Gene-expression memory-based prediction of cell lineages from scRNA-seq datasets

AS Eisele, M Tarbier, AA Dormann, V Pelechano… - nature …, 2024 - nature.com
Assigning single cell transcriptomes to cellular lineage trees by lineage tracing has
transformed our understanding of differentiation during development, regeneration, and …

Retrospective identification of cell-intrinsic factors that mark pluripotency potential in rare somatic cells

N Jain, Y Goyal, MC Dunagin, CJ Cote, IA Mellis… - Cell Systems, 2024 - cell.com
Pluripotency can be induced in somatic cells by the expression of OCT4, KLF4, SOX2, and
MYC. Usually only a rare subset of cells reprogram, and the molecular characteristics of this …

Integration of quantitative methods and mathematical approaches for the modeling of cancer cell proliferation dynamics

M Cotner, S Meng, T Jost, A Gardner… - … of Physiology-Cell …, 2023 - journals.physiology.org
Physiological processes rely on the control of cell proliferation, and the dysregulation of
these processes underlies various pathological conditions, including cancer. Mathematical …

Craniofacial developmental biology in the single-cell era

KC Tseng, JG Crump - Development, 2023 - journals.biologists.com
The evolution of a unique craniofacial complex in vertebrates made possible new ways of
breathing, eating, communicating and sensing the environment. The head and face develop …

Retrospective identification of intrinsic factors that mark pluripotency potential in rare somatic cells

N Jain, Y Goyal, MC Dunagin, CJ Cote, IA Mellis… - …, 2023 - pmc.ncbi.nlm.nih.gov
Pluripotency can be induced in somatic cells by the expression of the four “Yamanaka”
factors OCT4, KLF4, SOX2, and MYC. However, even in homogeneous conditions, usually …

Transformer-based modeling of Clonal Selection and Expression Dynamics reveals resistance mechanisms in breast cancer

ND Maulding, J Zou, W Zhou, C Metcalfe… - npj Systems Biology …, 2025 - nature.com
Understanding transcriptional heterogeneity in cancer cells and its implication for treatment
response is critical to identify how resistance occurs and may be targeted. Such …

Toward a systems-level probing of tumor clonality

EI Grody, A Abraham, V Shukla, Y Goyal - Iscience, 2023 - cell.com
Cancer has been described as a genetic disease that clonally evolves in the face of
selective pressures imposed by cell-intrinsic and extrinsic factors. Although classical models …