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 …
[HTML][HTML] Deciphering the multi-scale, quantitative cis-regulatory code
S Kim, J Wysocka - Molecular cell, 2023 - cell.com
Uncovering the cis-regulatory code that governs when and how much each gene is
transcribed in a given genome and cellular state remains a central goal of biology. Here, we …
transcribed in a given genome and cellular state remains a central goal of biology. Here, we …
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 …
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 …
[HTML][HTML] Smart breeding driven by big data, artificial intelligence, and integrated genomic-enviromic prediction
The first paradigm of plant breeding involves direct selection-based phenotypic observation,
followed by predictive breeding using statistical models for quantitative traits constructed …
followed by predictive breeding using statistical models for quantitative traits constructed …
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 …
[HTML][HTML] 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 …
[HTML][HTML] Comprehensive analysis of single cell ATAC-seq data with SnapATAC
Identification of the cis-regulatory elements controlling cell-type specific gene expression
patterns is essential for understanding the origin of cellular diversity. Conventional assays to …
patterns is essential for understanding the origin of cellular diversity. Conventional assays to …