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 …
Redefining fundamental concepts of transcription initiation in bacteria
Despite enormous progress in understanding the fundamentals of bacterial gene regulation,
our knowledge remains limited when compared with the number of bacterial genomes and …
our knowledge remains limited when compared with the number of bacterial genomes and …
Disentangling direct from indirect relationships in association networks
Networks are vital tools for understanding and modeling interactions in complex systems in
science and engineering, and direct and indirect interactions are pervasive in all types of …
science and engineering, and direct and indirect interactions are pervasive in all types of …
[HTML][HTML] Genomic and functional analyses of fungal and bacterial consortia that enable lignocellulose breakdown in goat gut microbiomes
The herbivore digestive tract is home to a complex community of anaerobic microbes that
work together to break down lignocellulose. These microbiota are an untapped resource of …
work together to break down lignocellulose. These microbiota are an untapped resource of …
[HTML][HTML] Systematic exploration of Escherichia coli phage–host interactions with the BASEL phage collection
Bacteriophages, the viruses infecting bacteria, hold great potential for the treatment of
multidrug-resistant bacterial infections and other applications due to their unparalleled …
multidrug-resistant bacterial infections and other applications due to their unparalleled …
RegulonDB 11.0: Comprehensive high-throughput datasets on transcriptional regulation in Escherichia coli K-12
Genomics has set the basis for a variety of methodologies that produce high-throughput
datasets identifying the different players that define gene regulation, particularly regulation …
datasets identifying the different players that define gene regulation, particularly regulation …
[HTML][HTML] Deep learning suggests that gene expression is encoded in all parts of a co-evolving interacting gene regulatory structure
Understanding the genetic regulatory code governing gene expression is an important
challenge in molecular biology. However, how individual coding and non-coding regions of …
challenge in molecular biology. However, how individual coding and non-coding regions of …
RSAT 2022: regulatory sequence analysis tools
W Santana-Garcia, JA Castro-Mondragon… - Nucleic Acids …, 2022 - academic.oup.com
Abstract RSAT (Regulatory Sequence Analysis Tools) enables the detection and the
analysis of cis-regulatory elements in genomic sequences. This software suite performs (i) …
analysis of cis-regulatory elements in genomic sequences. This software suite performs (i) …
Prokaryotic single-cell RNA sequencing by in situ combinatorial indexing
Despite longstanding appreciation of gene expression heterogeneity in isogenic bacterial
populations, affordable and scalable technologies for studying single bacterial cells have …
populations, affordable and scalable technologies for studying single bacterial cells have …
PRODORIC: state-of-the-art database of prokaryotic gene regulation
PRODORIC is worldwide one of the largest collections of prokaryotic transcription factor
binding sites from multiple bacterial sources with corresponding interpretation and …
binding sites from multiple bacterial sources with corresponding interpretation and …