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 …

[HTML][HTML] Statistics or biology: the zero-inflation controversy about scRNA-seq data

R Jiang, T Sun, D Song, JJ Li - Genome biology, 2022 - Springer
Researchers view vast zeros in single-cell RNA-seq data differently: some regard zeros as
biological signals representing no or low gene expression, while others regard zeros as …

Transcription factors interact with RNA to regulate genes

O Oksuz, JE Henninger, R Warneford-Thomson… - Molecular cell, 2023 - cell.com
Transcription factors (TFs) orchestrate the gene expression programs that define each cell's
identity. The canonical TF accomplishes this with two domains, one that binds specific DNA …

[HTML][HTML] Transcription factors associated with abiotic and biotic stress tolerance and their potential for crops improvement

EH Baillo, RN Kimotho, Z Zhang, P Xu - Genes, 2019 - mdpi.com
In field conditions, crops are adversely affected by a wide range of abiotic stresses including
drought, cold, salt, and heat, as well as biotic stresses including pests and pathogens. These …

EnhancerAtlas 2.0: an updated resource with enhancer annotation in 586 tissue/cell types across nine species

T Gao, J Qian - Nucleic acids research, 2020 - academic.oup.com
Enhancers are distal cis-regulatory elements that activate the transcription of their target
genes. They regulate a wide range of important biological functions and processes …

[HTML][HTML] Controlling gene expression with deep generative design of regulatory DNA

J Zrimec, X Fu, AS Muhammad, C Skrekas… - Nature …, 2022 - nature.com
Abstract Design of de novo synthetic regulatory DNA is a promising avenue to control gene
expression in biotechnology and medicine. Using mutagenesis typically requires screening …

[HTML][HTML] Intrinsically disordered regions direct transcription factor in vivo binding specificity

S Brodsky, T Jana, K Mittelman, M Chapal, DK Kumar… - Molecular cell, 2020 - cell.com
Transcription factors (TFs) that bind common DNA motifs in vitro occupy distinct sets of
promoters in vivo, raising the question of how binding specificity is achieved. TFs are …

[HTML][HTML] Plant transcription factors involved in drought and associated stresses

M Hrmova, SS Hussain - International journal of molecular sciences, 2021 - mdpi.com
Transcription factors (TFs) play a significant role in signal transduction networks spanning
the perception of a stress signal and the expression of corresponding stress-responsive …

Deep conservation of the enhancer regulatory code in animals

ES Wong, D Zheng, SZ Tan, NI Bower, V Garside… - Science, 2020 - science.org
INTRODUCTION In animals, gene regulatory networks specify cell identity in space and
time. Transcription of genes in these networks is modulated by a class of cis-regulatory …

Genetic engineering of microalgae for enhanced lipid production

CF Muñoz, C Südfeld, MIS Naduthodi… - Biotechnology …, 2021 - Elsevier
Microalgae have the potential to become microbial cell factories for lipid production. Their
ability to convert sunlight and CO 2 into valuable lipid compounds has attracted interest from …