Charting plant gene functions in the multi-omics and single-cell era
T Depuydt, B De Rybel, K Vandepoele - Trends in Plant Science, 2023 - cell.com
Despite the increased access to high-quality plant genome sequences, the set of genes with
a known function remains far from complete. With the advent of novel bulk and single-cell …
a known function remains far from complete. With the advent of novel bulk and single-cell …
Multi‐omics network‐based functional annotation of unknown Arabidopsis genes
T Depuydt, K Vandepoele - The Plant Journal, 2021 - Wiley Online Library
Unraveling gene function is pivotal to understanding the signaling cascades that control
plant development and stress responses. As experimental profiling is costly and labor …
plant development and stress responses. As experimental profiling is costly and labor …
Plant Regulomics: a data‐driven interface for retrieving upstream regulators from plant multi‐omics data
High‐throughput technology has become a powerful approach for routine plant research.
Interpreting the biological significance of high‐throughput data has largely focused on the …
Interpreting the biological significance of high‐throughput data has largely focused on the …
Advances in omics and bioinformatics tools for systems analyses of plant functions
K Mochida, K Shinozaki - Plant and Cell Physiology, 2011 - academic.oup.com
Omics and bioinformatics are essential to understanding the molecular systems that underlie
various plant functions. Recent game-changing sequencing technologies have revitalized …
various plant functions. Recent game-changing sequencing technologies have revitalized …
Machine learning: its challenges and opportunities in plant system biology
Sequencing technologies are evolving at a rapid pace, enabling the generation of massive
amounts of data in multiple dimensions (eg, genomics, epigenomics, transcriptomic …
amounts of data in multiple dimensions (eg, genomics, epigenomics, transcriptomic …
Towards revealing the functions of all genes in plants
The great recent progress made in identifying the molecular parts lists of organisms
revealed the paucity of our understanding of what most of the parts do. In this review, we …
revealed the paucity of our understanding of what most of the parts do. In this review, we …
Omics-guided metabolic pathway discovery in plants: Resources, approaches, and opportunities
Plants produce a vast array of metabolites, the biosynthetic routes of which remain largely
undetermined. Genome-scale enzyme and pathway annotations and omics technologies …
undetermined. Genome-scale enzyme and pathway annotations and omics technologies …
Decoding genes with coexpression networks and metabolomics–'majority report by precogs'
K Saito, MY Hirai, K Yonekura-Sakakibara - Trends in plant science, 2008 - cell.com
Following the sequencing of whole genomes of model plants, high-throughput decoding of
gene function is a major challenge in modern plant biology. In view of remarkable technical …
gene function is a major challenge in modern plant biology. In view of remarkable technical …
Integrated omics approaches in plant systems biology
Understanding cellular metabolic systems is vital not only for determining the function of
enzymatic genes, but also for elucidating the coordination among various metabolic …
enzymatic genes, but also for elucidating the coordination among various metabolic …
Omics meet networks—using systems approaches to infer regulatory networks in plants
MA Moreno-Risueno, W Busch, PN Benfey - Current Opinion in Plant …, 2010 - Elsevier
Many genomic-scale datasets in plants have been generated over the last few years. This
substantial achievement has led to impressive progress, including some of the most detailed …
substantial achievement has led to impressive progress, including some of the most detailed …