Gene regulatory network inference in the era of single-cell multi-omics
P Badia-i-Mompel, L Wessels, S Müller-Dott… - Nature Reviews …, 2023 - nature.com
The interplay between chromatin, transcription factors and genes generates complex
regulatory circuits that can be represented as gene regulatory networks (GRNs). The study …
regulatory circuits that can be represented as gene regulatory networks (GRNs). The study …
Charting plant gene functions in the multi-omics and single-cell era
T Depuydt, B De Rybel, K Vandepoele - Trends in Plant Science, 2023 - cell.com
Despite the increased access to high-quality plant genome sequences, the set of genes with
a known function remains far from complete. With the advent of novel bulk and single-cell …
a known function remains far from complete. With the advent of novel bulk and single-cell …
Coordinated control of neuronal differentiation and wiring by sustained transcription factors
The large diversity of cell types in nervous systems presents a challenge in identifying the
genetic mechanisms that encode it. Here, we report that nearly 200 distinct neurons in the …
genetic mechanisms that encode it. Here, we report that nearly 200 distinct neurons in the …
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 …
Robust discovery of gene regulatory networks from single-cell gene expression data by Causal Inference Using Composition of Transactions
A Shojaee, SC Huang - Briefings in Bioinformatics, 2023 - academic.oup.com
Gene regulatory networks (GRNs) drive organism structure and functions, so the discovery
and characterization of GRNs is a major goal in biological research. However, accurate …
and characterization of GRNs is a major goal in biological research. However, accurate …
Structure-primed embedding on the transcription factor manifold enables transparent model architectures for gene regulatory network and latent activity inference
Background Modeling of gene regulatory networks (GRNs) is limited due to a lack of direct
measurements of genome-wide transcription factor activity (TFA) making it difficult to …
measurements of genome-wide transcription factor activity (TFA) making it difficult to …
Neural cell diversity in the light of single-cell transcriptomics
SM Fernández-Moya, AJ Ganesh, M Plass - Transcription, 2023 - Taylor & Francis
The development of highly parallel and affordable high-throughput single-cell
transcriptomics technologies has revolutionized our understanding of brain complexity …
transcriptomics technologies has revolutionized our understanding of brain complexity …
PMF-GRN: a variational inference approach to single-cell gene regulatory network inference using probabilistic matrix factorization
Inferring gene regulatory networks (GRNs) from single-cell data is challenging due to
heuristic limitations. Existing methods also lack estimates of uncertainty. Here we present …
heuristic limitations. Existing methods also lack estimates of uncertainty. Here we present …
[HTML][HTML] Stem cells tightly regulate dead cell clearance to maintain tissue fitness
Billions of cells are eliminated daily from our bodies,,–. Although macrophages and dendritic
cells are dedicated to migrating and engulfing dying cells and debris, many epithelial and …
cells are dedicated to migrating and engulfing dying cells and debris, many epithelial and …
Discogen: Learning to discover gene regulatory networks
Accurately inferring Gene Regulatory Networks (GRNs) is a critical and challenging task in
biology. GRNs model the activatory and inhibitory interactions between genes and are …
biology. GRNs model the activatory and inhibitory interactions between genes and are …