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 …
Hold out the genome: a roadmap to solving the cis-regulatory code
CG de Boer, J Taipale - Nature, 2024 - nature.com
Gene expression is regulated by transcription factors that work together to read cis-
regulatory DNA sequences. The 'cis-regulatory code'—how cells interpret DNA sequences …
regulatory DNA sequences. The 'cis-regulatory code'—how cells interpret DNA sequences …
Expanding the coverage of regulons from high-confidence prior knowledge for accurate estimation of transcription factor activities
Gene regulation plays a critical role in the cellular processes that underlie human health and
disease. The regulatory relationship between transcription factors (TFs), key regulators of …
disease. The regulatory relationship between transcription factors (TFs), key regulators of …
Single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain
Cytosine DNA methylation is essential in brain development and is implicated in various
neurological disorders. Understanding DNA methylation diversity across the entire brain in a …
neurological disorders. Understanding DNA methylation diversity across the entire brain in a …
Dynamic 3D genome reorganization during senescence: defining cell states through chromatin
Cellular senescence, a cell state characterized by growth arrest and insensitivity to growth
stimulatory hormones, is accompanied by a massive change in chromatin organization …
stimulatory hormones, is accompanied by a massive change in chromatin organization …
Idiosyncratic and dose-dependent epistasis drives variation in tomato fruit size
Epistasis between genes is traditionally studied with mutations that eliminate protein activity,
but most natural genetic variation is in cis-regulatory DNA and influences gene expression …
but most natural genetic variation is in cis-regulatory DNA and influences gene expression …
Frontiers and techniques in plant gene regulation
Understanding plant gene regulation has been a priority for generations of plant scientists.
However, due to its complex nature, the regulatory code governing plant gene expression …
However, due to its complex nature, the regulatory code governing plant gene expression …
[PDF][PDF] DNA-guided transcription factor cooperativity shapes face and limb mesenchyme
Transcription factors (TFs) can define distinct cellular identities despite nearly identical DNA-
binding specificities. One mechanism for achieving regulatory specificity is DNA-guided TF …
binding specificities. One mechanism for achieving regulatory specificity is DNA-guided TF …
Physical interaction between MSL2 and CLAMP assures direct cooperativity and prevents competition at composite binding sites
N Eggers, F Gkountromichos, S Krause… - Nucleic Acids …, 2023 - academic.oup.com
MSL2, the DNA-binding subunit of the Drosophila dosage compensation complex,
cooperates with the ubiquitous protein CLAMP to bind MSL recognition elements (MREs) on …
cooperates with the ubiquitous protein CLAMP to bind MSL recognition elements (MREs) on …
GENA-LM: A Family of Open-Source Foundational DNA Language Models for Long Sequences
The field of genomics has seen substantial advancements through the application of artificial
intelligence (AI), with machine learning revealing the potential to interpret genomic …
intelligence (AI), with machine learning revealing the potential to interpret genomic …