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 …
Chromatin accessibility profiling by ATAC-seq
The assay for transposase-accessible chromatin using sequencing (ATAC-seq) provides a
simple and scalable way to detect the unique chromatin landscape associated with a cell …
simple and scalable way to detect the unique chromatin landscape associated with a cell …
JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles
JA Castro-Mondragon, R Riudavets-Puig… - Nucleic acids …, 2022 - academic.oup.com
Abstract JASPAR (http://jaspar. genereg. net/) is an open-access database containing
manually curated, non-redundant transcription factor (TF) binding profiles for TFs across six …
manually curated, non-redundant transcription factor (TF) binding profiles for TFs across six …
JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles
I Rauluseviciute, R Riudavets-Puig… - Nucleic Acids …, 2024 - academic.oup.com
Abstract JASPAR (https://jaspar. elixir. no/) is a widely-used open-access database
presenting manually curated high-quality and non-redundant DNA-binding profiles for …
presenting manually curated high-quality and non-redundant DNA-binding profiles for …
ChIP-Atlas 2021 update: a data-mining suite for exploring epigenomic landscapes by fully integrating ChIP-seq, ATAC-seq and Bisulfite-seq data
Abstract ChIP-Atlas (https://chip-atlas. org) is a web service providing both GUI-and API-
based data-mining tools to reveal the architecture of the transcription regulatory landscape …
based data-mining tools to reveal the architecture of the transcription regulatory landscape …
Epigenetic regulation of T cell exhaustion
Chronic antigen stimulation during viral infections and cancer can lead to T cell exhaustion,
which is characterized by reduced effector function and proliferation, and the expression of …
which is characterized by reduced effector function and proliferation, and the expression of …
Characterizing cis-regulatory elements using single-cell epigenomics
Cell type-specific gene expression patterns and dynamics during development or in disease
are controlled by cis-regulatory elements (CREs), such as promoters and enhancers …
are controlled by cis-regulatory elements (CREs), such as promoters and enhancers …
ReMap 2022: a database of Human, Mouse, Drosophila and Arabidopsis regulatory regions from an integrative analysis of DNA-binding sequencing experiments
F Hammal, P De Langen, A Bergon… - Nucleic acids …, 2022 - academic.oup.com
Abstract ReMap (https://remap. univ-amu. fr) aims to provide manually curated, high-quality
catalogs of regulatory regions resulting from a large-scale integrative analysis of DNA …
catalogs of regulatory regions resulting from a large-scale integrative analysis of DNA …
Cis-regulatory sequences in plants: their importance, discovery, and future challenges
The identification and characterization of cis-regulatory DNA sequences and how they
function to coordinate responses to developmental and environmental cues is of paramount …
function to coordinate responses to developmental and environmental cues is of paramount …
cis-Regulatory Elements in Plant Development, Adaptation, and Evolution
cis-Regulatory elements encode the genomic blueprints that ensure the proper
spatiotemporal patterning of gene expression necessary for appropriate development and …
spatiotemporal patterning of gene expression necessary for appropriate development and …