Transposable Element Mediated Innovation in Gene Regulatory Landscapes of Cells: Re‐Visiting the “Gene‐Battery” Model
Sign Up to like & getrecommendations! Published in 2018 at "BioEssays"
DOI: 10.1002/bies.201700155
Abstract: Transposable elements (TEs) are no longer considered to be “junk” DNA. Here, we review how TEs can impact gene regulation systematically. TEs encode various regulatory elements that enables them to regulate gene expression. RJ Britten… read more here.
Keywords: gene battery; gene; gene regulatory; battery model ... See more keywords
Initiated by CREB: Resolving Gene Regulatory Programs in Learning and Memory
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DOI: 10.1002/bies.201900045
Abstract: Consolidation of long‐term memory is a highly and precisely regulated multistep process. The transcription regulator cAMP response element‐binding protein (CREB) plays a key role in initiating memory consolidation. With time processing, first the cofactors are… read more here.
Keywords: creb resolving; initiated creb; gene regulatory; resolving gene ... See more keywords
Appendages and gene regulatory networks: Lessons from the limbless
Sign Up to like & getrecommendations! Published in 2018 at "genesis"
DOI: 10.1002/dvg.23078
Abstract: Among squamate reptiles, dozens of lineages have independently evolved complete or partial limb reduction. This remarkable convergence of limbless and limb‐reduced phenotypes provides multiple natural replicates of different ages to explore the evolution and development… read more here.
Keywords: limb; limb reduced; gene regulatory; appendages gene ... See more keywords
A gene regulatory architecture that controls region‐independent dynamics of oligodendrocyte differentiation
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DOI: 10.1002/glia.23569
Abstract: Oligodendrocytes (OLs) facilitate information processing in the vertebrate central nervous system via axonal ensheathment. The structure and dynamics of the regulatory network that mediates oligodendrogenesis are poorly understood. We employed bioinformatics and meta‐analysis of high‐throughput… read more here.
Keywords: gene regulatory; regulatory architecture; model; differentiation ... See more keywords
Gene Regulatory Networks from Single Cell Data for Exploring Cell Fate Decisions.
Sign Up to like & getrecommendations! Published in 2019 at "Methods in molecular biology"
DOI: 10.1007/978-1-4939-9224-9_10
Abstract: Single cell experimental techniques now allow us to quantify gene expression in up to thousands of individual cells. These data reveal the changes in transcriptional state that occur as cells progress through development and adopt… read more here.
Keywords: single cell; gene regulatory; cell data; regulatory networks ... See more keywords
A gene regulatory network for root hair development
Sign Up to like & getrecommendations! Published in 2019 at "Journal of Plant Research"
DOI: 10.1007/s10265-019-01100-2
Abstract: Root hairs play important roles for the acquisition of nutrients, microbe interaction and plant anchorage. In addition, root hairs provide an excellent model system to study cell patterning, differentiation and growth. Arabidopsis root hairs have… read more here.
Keywords: regulatory network; root hairs; gene regulatory; root ... See more keywords
Fitting structure to function in gene regulatory networks
Sign Up to like & getrecommendations! Published in 2017 at "History and Philosophy of the Life Sciences"
DOI: 10.1007/s40656-017-0164-z
Abstract: Cascades of transcriptional regulation are the common source of the forward drive in all developmental systems. Increases in complexity and specificity of gene expression at successive stages are based on the collaboration of varied combinations… read more here.
Keywords: transcription; gene regulatory; fitting structure; regulatory networks ... See more keywords
Computational methods for Gene Regulatory Networks reconstruction and analysis: A review
Sign Up to like & getrecommendations! Published in 2019 at "Artificial intelligence in medicine"
DOI: 10.1016/j.artmed.2018.10.006
Abstract: In the recent years, the vast amount of genetic information generated by new-generation approaches, have led to the need of new data handling methods. The integrative analysis of diverse-nature gene information could provide a much-sought… read more here.
Keywords: analysis; gene regulatory; used network; computational methods ... See more keywords
A framework to shift basins of attraction of gene regulatory networks through batch reinforcement learning.
Sign Up to like & getrecommendations! Published in 2020 at "Artificial intelligence in medicine"
DOI: 10.1016/j.artmed.2020.101853
Abstract: A major challenge in gene regulatory networks (GRN) of biological systems is to discover when and what interventions should be applied to shift them to healthy phenotypes. A set of gene activity profiles, called basin… read more here.
Keywords: shift; gene regulatory; batch reinforcement; reinforcement learning ... See more keywords
The Gene-Regulatory Footprint of Aging Highlights Conserved Central Regulators
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DOI: 10.1016/j.celrep.2020.108203
Abstract: Summary Many genes and pathways have been linked to aging, yet our understanding of underlying molecular mechanisms is still lacking. Here, we measure changes in the transcriptome, histone modifications, and DNA methylome in three metabolic… read more here.
Keywords: regulatory footprint; aging highlights; gene regulatory; highlights conserved ... See more keywords
Transitions in lineage specification and gene regulatory networks in hematopoietic stem/progenitor cells over human development
Sign Up to like & getrecommendations! Published in 2021 at "Cell Reports"
DOI: 10.1016/j.celrep.2021.109698
Abstract: Summary Human hematopoiesis is a dynamic process that starts in utero 18–21 days post-conception. Understanding the site- and stage-specific variation in hematopoiesis is important if we are to understand the origin of hematological disorders, many… read more here.
Keywords: regulatory networks; gene regulatory; hematopoietic stem; stem progenitor ... See more keywords