A comprehensive survey of regulatory network inference methods using single cell RNA sequencing data
Gene regulatory network is a complicated set of interactions between genetic materials,
which dictates how cells develop in living organisms and react to their surrounding …
which dictates how cells develop in living organisms and react to their surrounding …
Computational methods for trajectory inference from single‐cell transcriptomics
Recent developments in single‐cell transcriptomics have opened new opportunities for
studying dynamic processes in immunology in a high throughput and unbiased manner …
studying dynamic processes in immunology in a high throughput and unbiased manner …
A comparison of single-cell trajectory inference methods
Trajectory inference approaches analyze genome-wide omics data from thousands of single
cells and computationally infer the order of these cells along developmental trajectories …
cells and computationally infer the order of these cells along developmental trajectories …
Static and dynamic DNA loops form AP-1-bound activation hubs during macrophage development
The three-dimensional arrangement of the human genome comprises a complex network of
structural and regulatory chromatin loops important for coordinating changes in transcription …
structural and regulatory chromatin loops important for coordinating changes in transcription …
SINCERITIES: inferring gene regulatory networks from time-stamped single cell transcriptional expression profiles
N Papili Gao, SMM Ud-Dean, O Gandrillon… - …, 2018 - academic.oup.com
Motivation Single cell transcriptional profiling opens up a new avenue in studying the
functional role of cell-to-cell variability in physiological processes. The analysis of single cell …
functional role of cell-to-cell variability in physiological processes. The analysis of single cell …
Single-cell-based analysis highlights a surge in cell-to-cell molecular variability preceding irreversible commitment in a differentiation process
A Richard, L Boullu, U Herbach, A Bonnafoux… - PLoS …, 2016 - journals.plos.org
In some recent studies, a view emerged that stochastic dynamics governing the switching of
cells from one differentiation state to another could be characterized by a peak in gene …
cells from one differentiation state to another could be characterized by a peak in gene …
Single-cell analysis in cancer genomics
Genetic changes and environmental differences result in cellular heterogeneity among
cancer cells within the same tumor, thereby complicating treatment outcomes. Recent …
cancer cells within the same tumor, thereby complicating treatment outcomes. Recent …
Pseudotime estimation: deconfounding single cell time series
JE Reid, L Wernisch - Bioinformatics, 2016 - academic.oup.com
Motivation: Repeated cross-sectional time series single cell data confound several sources
of variation, with contributions from measurement noise, stochastic cell-to-cell variation and …
of variation, with contributions from measurement noise, stochastic cell-to-cell variation and …
CellTree: an R/bioconductor package to infer the hierarchical structure of cell populations from single-cell RNA-seq data
Background Single-cell RNA sequencing is fast becoming one the standard method for
gene expression measurement, providing unique insights into cellular processes. A number …
gene expression measurement, providing unique insights into cellular processes. A number …
Inferring single-cell gene regulatory network by non-redundant mutual information
Gene regulatory network plays a crucial role in controlling the biological processes of living
creatures. Deciphering the complex gene regulatory networks from experimental data …
creatures. Deciphering the complex gene regulatory networks from experimental data …