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Models trained to predict differential expression across plant organs identify distal and proximal regulatory regions

https://doi.org/10.1101/2024.06.04.597477

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Lessons from Domestication: Targeting Cis-Regulatory Elements for Crop Improvement

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Accessible chromatin regions and their functional interrelations with gene transcription and epigenetic modifications in sorghum genome

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The Sorghum bicolor genome and the diversification of grasses

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Improved maize reference genome with single-molecule technologies

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Identification of a functional transposon insertion in the maize domestication gene tb1

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The prevalence, evolution and chromatin signatures of plant regulatory elements

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A foundational large language model for edible plant genomes

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Conserved noncoding genomic sequences associated with a flowering-time quantitative trait locus in maize

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Open chromatin reveals the functional maize genome

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Evolutionarily informed deep learning methods for predicting relative transcript abundance from DNA sequence

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Attaining the promise of plant gene editing at scale

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Enhancing genetic gain in the era of molecular breeding

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Independent and Parallel Evolution of New Genes by Gene Duplication in Two Origins of C4 Photosynthesis Provides New Insight into the Mechanism of Phloem Loading in C4 Species

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PLAZA 5.0: extending the scope and power of comparative and functional genomics in plants

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Expression Atlas update: gene and protein expression in multiple species

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Phytozome: a comparative platform for green plant genomics

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MaizeGDB 2018: the maize multi-genome genetics and genomics database

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MOROKOSHI: Transcriptome Database in Sorghum bicolor

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Cis-regulatory sequences in plants: Their importance, discovery, and future challenges

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A comparative transcriptional landscape of maize and sorghum obtained by single-molecule sequencing

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G-Boxes, Bigfoot Genes, and Environmental Response: Characterization of Intragenomic Conserved Noncoding Sequences inArabidopsis

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Differentially Regulated Orthologs in Sorghum and the Subgenomes of Maize

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DNA methylation and gene expression regulation associated with vascularization in Sorghum bicolor

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The Sorghum bicolor reference genome: improved assembly, gene annotations, a transcriptome atlas, and signatures of genome organization

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The B73 Maize Genome: Complexity, Diversity, and Dynamics

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De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes

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Dynamics of gene expression during development and expansion of vegetative stem internodes of bioenergy sorghum

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FloraBERT: cross-species transfer learning withattention-based neural networks for geneexpression prediction

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Automated conserved non-coding sequence (CNS) discovery reveals differences in gene content and promoter evolution among grasses

inferredcites →https://doi.org/10.3835/plantgenome2015.04.0025openalex-snapshot

An Expanded Maize Gene Expression Atlas based on RNA Sequencing and its Use to Explore Root Development

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1079/9781836994572.0002openalex-snapshot

Spatial Omics in Plants: Current Achievements, Challenges, and Future Directions

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