Challenges and best practices in omics benchmarking
TG Brooks, NF Lahens, A Mrčela, GR Grant - Nature Reviews Genetics, 2024 - nature.com
Technological advances enabling massively parallel measurement of biological features—
such as microarrays, high-throughput sequencing and mass spectrometry—have ushered in …
such as microarrays, high-throughput sequencing and mass spectrometry—have ushered in …
Best practices on the differential expression analysis of multi-species RNA-seq
Advances in transcriptome sequencing allow for simultaneous interrogation of differentially
expressed genes from multiple species originating from a single RNA sample, termed dual …
expressed genes from multiple species originating from a single RNA sample, termed dual …
Systematic comparison and assessment of RNA-seq procedures for gene expression quantitative analysis
LA Corchete, EA Rojas, D Alonso-López… - Scientific reports, 2020 - nature.com
RNA-seq is currently considered the most powerful, robust and adaptable technique for
measuring gene expression and transcription activation at genome-wide level. As the …
measuring gene expression and transcription activation at genome-wide level. As the …
Polyploidy, the nucleotype, and novelty: the impact of genome doubling on the biology of the cell
Polyploidy is a key mechanism of genome evolution and speciation, particularly in plants.
Many aspects of polyploidy have been elucidated with the tools that have become available …
Many aspects of polyploidy have been elucidated with the tools that have become available …
Selecting between-sample RNA-Seq normalization methods from the perspective of their assumptions
C Evans, J Hardin, DM Stoebel - Briefings in bioinformatics, 2018 - academic.oup.com
RNA-Seq is a widely used method for studying the behavior of genes under different
biological conditions. An essential step in an RNA-Seq study is normalization, in which raw …
biological conditions. An essential step in an RNA-Seq study is normalization, in which raw …
DEBrowser: interactive differential expression analysis and visualization tool for count data
Background Sequencing data has become a standard measure of diverse cellular activities.
For example, gene expression is accurately measured by RNA sequencing (RNA-Seq) …
For example, gene expression is accurately measured by RNA sequencing (RNA-Seq) …
Genome editing as a tool to achieve the crop ideotype and de novo domestication of wild relatives: case study in tomato
The ideotype is a theoretical model of an archetypal cultivated plant. Recent progress in
genome editing is aiding the pursuit of this ideal in crop breeding. Breeding is relatively …
genome editing is aiding the pursuit of this ideal in crop breeding. Breeding is relatively …
Characterization of the Tomato ARF Gene Family Uncovers a Multi-Levels Post-Transcriptional Regulation Including Alternative Splicing
Background The phytohormone auxin is involved in a wide range of developmental
processes and auxin signaling is known to modulate the expression of target genes via two …
processes and auxin signaling is known to modulate the expression of target genes via two …
TomExpress, a unified tomato RNA‐Seq platform for visualization of expression data, clustering and correlation networks
The TomExpress platform was developed to provide the tomato research community with a
browser and integrated web tools for public RNA‐Seq data visualization and data mining. To …
browser and integrated web tools for public RNA‐Seq data visualization and data mining. To …
Several geranylgeranyl diphosphate synthase isoforms supply metabolic substrates for carotenoid biosynthesis in tomato
Geranylgeranyl diphosphate (GGPP) produced by GGPP synthase (GGPPS) serves as a
precursor for many plastidial isoprenoids, including carotenoids. Phytoene synthase (PSY) …
precursor for many plastidial isoprenoids, including carotenoids. Phytoene synthase (PSY) …