Cell lineage and communication network inference via optimization for single-cell transcriptomics
Nucleic Acids Research, 2019 The use of single-cell transcriptomics has become a major approach to delineate cell subpopulations and the transitions between them. While various computational tools using different mathematical methods have been developed to infer clusters, marker ...
Shuxiong Wang +3 more
semanticscholar +1 more source
STOCHASTIC DYNAMICS OF CELL LINEAGE IN TISSUE HOMEOSTASIS. [PDF]
, 2019 During epithelium tissue maintenance, lineages of cells differentiate and proliferate in a coordinated way to provide the desirable size and spatial organization of different types of cells.
Chen, Weitao, Nie, Qing, Qiu, Yuchi
core +2 more sources
Human haematopoietic stem cell lineage commitment is a continuous process
Nature Cell Biology, 2017 Blood formation is believed to occur through stepwise progression of haematopoietic stem cells (HSCs) following a tree-like hierarchy of oligo-, bi- and unipotent progenitors.
Lars Velten +16 more
semanticscholar +1 more source
Notch/Delta signaling constrains reengineering of pro-T cells by PU.1 [PDF]
, 2006 PU.1 is essential for early stages of mouse T cell development but antagonizes it if expressed constitutively. Two separable mechanisms are involved: attenuation and diversion. Dysregulated PU.1 expression inhibits pro-T cell survival, proliferation, and
Adams, Stephanie L. +8 more
core +3 more sources
A Computational Model for Understanding Stem Cell, Trophectoderm and Endoderm Lineage Determination [PDF]
, 2008 Background: Recent studies have associated the transcription factors, Oct4, Sox2 and Nanog as parts of a self-regulating network which is responsible for maintaining embryonic stem cell properties: self renewal and pluripotency.
Chickarmane, Vijay, Peterson, Carsten
core +3 more sources
bioRxiv, 2018 Simultaneous measurement of cell lineage and cell fates is a longstanding goal in biomedicine. Here we describe EMBLEM, a strategy to track cell lineage using endogenous mitochondrial DNA variants in ATAC-seq data.
Jin Xu +6 more
semanticscholar +1 more source
The transcription factor TCF-1 enforces commitment to the innate lymphoid cell lineage
Nature Immunology, 2019 Innate lymphoid cells (ILCs) play important functions in immunity and tissue homeostasis, but their development is poorly understood. Through the use of single-cell approaches, we examined the transcriptional and functional heterogeneity of ILC ...
C. Harly +9 more
semanticscholar +1 more source
Unraveling Heterogeneity in Epithelial Cell Fates of the Mammary Gland and Breast Cancer. [PDF]
, 2019 Fluidity in cell fate or heterogeneity in cell identity is an interesting cell biological phenomenon, which at the same time poses a significant obstacle for cancer therapy.
Doh, Hanna +3 more
core +1 more source
The differential response to Fgf signalling in cells internalized at different times influences lineage segregation in preimplantation mouse embryos [PDF]
Open Biology, 2013 Lineage specification in the preimplantation mouse embryo is a regulative process. Thus, it has been difficult to ascertain whether segregation of the inner-cell-mass (ICM) into precursors of the pluripotent epiblast (EPI) and the differentiating ...
Samantha A. Morris +3 more
doaj +1 more source
Tracking cell lineages in 3D by incremental deep learning
eLife, 2022 Deep learning is emerging as a powerful approach for bioimage analysis. Its use in cell tracking is limited by the scarcity of annotated data for the training of deep-learning models. Moreover, annotation, training, prediction, and proofreading currently
Ko Sugawara +2 more
doaj +1 more source