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 …
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins
AD Rouillard, GW Gundersen, NF Fernandez… - Database, 2016 - academic.oup.com
Genomics, epigenomics, transcriptomics, proteomics and metabolomics efforts rapidly
generate a plethora of data on the activity and levels of biomolecules within mammalian …
generate a plethora of data on the activity and levels of biomolecules within mammalian …
Single cell RNA-sequencing of pluripotent states unlocks modular transcriptional variation
AA Kolodziejczyk, JK Kim, JCH Tsang, T Ilicic… - Cell stem cell, 2015 - cell.com
Embryonic stem cell (ESC) culture conditions are important for maintaining long-term self-
renewal, and they influence cellular pluripotency state. Here, we report single cell RNA …
renewal, and they influence cellular pluripotency state. Here, we report single cell RNA …
Modeling gene regulatory networks using neural network architectures
Gene regulatory networks (GRNs) encode the complex molecular interactions that govern
cell identity. Here we propose DeepSEM, a deep generative model that can jointly infer …
cell identity. Here we propose DeepSEM, a deep generative model that can jointly infer …
CellNet: network biology applied to stem cell engineering
Somatic cell reprogramming, directed differentiation of pluripotent stem cells, and direct
conversions between differentiated cell lineages represent powerful approaches to engineer …
conversions between differentiated cell lineages represent powerful approaches to engineer …
Common genetic variation drives molecular heterogeneity in human iPSCs
Technology utilizing human induced pluripotent stem cells (iPS cells) has enormous
potential to provide improved cellular models of human disease. However, variable genetic …
potential to provide improved cellular models of human disease. However, variable genetic …
From time-series transcriptomics to gene regulatory networks: A review on inference methods
M Marku, V Pancaldi - PLOS Computational Biology, 2023 - journals.plos.org
Inference of gene regulatory networks has been an active area of research for around 20
years, leading to the development of sophisticated inference algorithms based on a variety …
years, leading to the development of sophisticated inference algorithms based on a variety …
Inference of cell type-specific gene regulatory networks on cell lineages from single cell omic datasets
Cell type-specific gene expression patterns are outputs of transcriptional gene regulatory
networks (GRNs) that connect transcription factors and signaling proteins to target genes …
networks (GRNs) that connect transcription factors and signaling proteins to target genes …
STGRNS: an interpretable transformer-based method for inferring gene regulatory networks from single-cell transcriptomic data
J Xu, A Zhang, F Liu, X Zhang - Bioinformatics, 2023 - academic.oup.com
Motivation Single-cell RNA-sequencing (scRNA-seq) technologies provide an opportunity to
infer cell-specific gene regulatory networks (GRNs), which is an important challenge in …
infer cell-specific gene regulatory networks (GRNs), which is an important challenge in …
Good cell culture practice for stem cells and stem-cell-derived models
The first guidance on Good Cell Culture Practice dates back to 2005. This document
expands this to aspects of quality assurance for in vitro cell culture focusing on the …
expands this to aspects of quality assurance for in vitro cell culture focusing on the …