SCNS: a graphical tool for reconstructing executable regulatory networks from single-cell genomic data
Background Reconstruction of executable mechanistic models from single-cell gene
expression data represents a powerful approach to understanding developmental and …
expression data represents a powerful approach to understanding developmental and …
Computational tools for stem cell biology
For over half a century, the field of developmental biology has leveraged computation to
explore mechanisms of developmental processes. More recently, computational approaches …
explore mechanisms of developmental processes. More recently, computational approaches …
One model fits all: combining inference and simulation of gene regulatory networks
The rise of single-cell data highlights the need for a nondeterministic view of gene
expression, while offering new opportunities regarding gene regulatory network inference …
expression, while offering new opportunities regarding gene regulatory network inference …
IQCELL: A platform for predicting the effect of gene perturbations on developmental trajectories using single-cell RNA-seq data
T Heydari, M A. Langley, CL Fisher… - PLoS Computational …, 2022 - journals.plos.org
The increasing availability of single-cell RNA-sequencing (scRNA-seq) data from various
developmental systems provides the opportunity to infer gene regulatory networks (GRNs) …
developmental systems provides the opportunity to infer gene regulatory networks (GRNs) …
[HTML][HTML] Integration of single-cell multi-omics for gene regulatory network inference
The advancement of single-cell sequencing technology in recent years has provided an
opportunity to reconstruct gene regulatory networks (GRNs) with the data from thousands of …
opportunity to reconstruct gene regulatory networks (GRNs) with the data from thousands of …
Concepts and limitations for learning developmental trajectories from single cell genomics
Single cell genomics has become a popular approach to uncover the cellular heterogeneity
of progenitor and terminally differentiated cell types with great precision. This approach can …
of progenitor and terminally differentiated cell types with great precision. This approach can …
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 …
Inferring better gene regulation networks from single-cell data
MPH Stumpf - Current Opinion in Systems Biology, 2021 - Elsevier
Networks can provide a graphical representation of complex systems, including gene
regulation processes. They can also provide a basis for further quantitative and …
regulation processes. They can also provide a basis for further quantitative and …
Building with a scaffold: emerging strategies for high-to low-level cellular modeling
T Ideker, D Lauffenburger - TRENDS in Biotechnology, 2003 - cell.com
Computational cellular models are becoming crucial for the analysis of complex biological
systems. An important new paradigm for cellular modeling involves building a …
systems. An important new paradigm for cellular modeling involves building a …
Single-cell transcriptional analysis to uncover regulatory circuits driving cell fate decisions in early mouse development
Motivation: Transcriptional regulatory networks controlling cell fate decisions in mammalian
embryonic development remain elusive despite a long time of research. The recent …
embryonic development remain elusive despite a long time of research. The recent …