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Regulatory architecture of cell identity genes and housekeeping genes
Trends in Cell Biology, 2023Gene regulation and chromosome architecture are intimately linked. Genes with prominent roles in cell identity are often regulated by clusters of enhancer elements. By contrast, a recent study shows housekeeping genes are often regulated through clustering of promoters. We discuss here new regulatory insights for these two types of genes.
Alessandra, Dall'Agnese, Richard, Young
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Genes controlling plant architecture
Current Opinion in Biotechnology, 2006Plant architecture, referring here to the aerial part of a higher plant, is mainly determined by factors affecting shoot branching, plant height and inflorescence morphology. Significant progress has been made in isolating and characterizing genes that are directly involved in the formation of plant architecture, especially those controlling the ...
Yonghong, Wang, Jiayang, Li
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Modeling gene regulatory networks using neural network architectures
Nature Computational Science, 2021Gene regulatory networks (GRNs) encode the complex molecular interactions that govern cell identity. Here we propose DeepSEM, a deep generative model that can jointly infer GRNs and biologically meaningful representation of single-cell RNA sequencing (scRNA-seq) data. In particular, we developed a neural network version of the structural equation model
Hantao Shu +6 more
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Gene dynamics and nuclear architecture during differentiation
Differentiation, 2008Recent advances have demonstrated that placing genes in a specific nuclear context plays an important role in the regulation of coordinated gene expression, thus adding an additional level of complexity to the mechanisms of gene regulation. Differentiation processes are characterized by dynamic changes in gene activation and silencing.
Christian, Schöfer +1 more
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Chromatin Architectures and Hox Gene Collinearity
2013Ever since the observation that collinearity, that is, the sequential activity of Hox genes based on their relative positions within their gene clusters, is conserved throughout most of the animal kingdom, the question has been raised as to what are the underlying molecular mechanisms.
Noordermeer, D. and Duboule, D.
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Riboswitch-Mediated Gene Regulation: Novel RNA Architectures Dictate Gene Expression Responses
Annual Review of Microbiology, 2016Riboswitches are RNA elements that act on the mRNA with which they are cotranscribed to modulate expression of that mRNA. These elements are widely found in bacteria, where they have a broad impact on gene expression. The defining feature of riboswitches is that they directly recognize a physiological signal, and the resulting shift in RNA structure ...
Anna V, Sherwood, Tina M, Henkin
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Blue Gene/Q resource management architecture
2010 3rd Workshop on Many-Task Computing on Grids and Supercomputers, 2010As supercomputers scale to a million processor cores and beyond, the underlying resource management architecture needs to provide a flexible mechanism to manage the wide variety of workloads executing on the machine. In this paper we describe the novel approach of the Blue Gene/Q (BG/Q) supercomputer in addressing these workload requirements by ...
Tom Budnik +5 more
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