Overlapping genes in natural and engineered genomes
BW Wright, MP Molloy, PR Jaschke - Nature Reviews Genetics, 2022 - nature.com
Modern genome-scale methods that identify new genes, such as proteogenomics and
ribosome profiling, have revealed, to the surprise of many, that overlap in genes, open …
ribosome profiling, have revealed, to the surprise of many, that overlap in genes, open …
What, where, and how: regulation of translation and the translational landscape in plants
Translation is a crucial step in gene expression and plays a vital role in regulating various
aspects of plant development and environmental responses. It is a dynamic and complex …
aspects of plant development and environmental responses. It is a dynamic and complex …
Damage on plants activates Ca2+-dependent metacaspases for release of immunomodulatory peptides
T Hander, ÁD Fernández-Fernández, RP Kumpf… - Science, 2019 - science.org
INTRODUCTION Cellular damage caused by wounding triggers signals to alert the
surrounding tissue. As a universal process in all multicellular organisms, these signals …
surrounding tissue. As a universal process in all multicellular organisms, these signals …
Beyond read-counts: Ribo-seq data analysis to understand the functions of the transcriptome
L Calviello, U Ohler - Trends in Genetics, 2017 - cell.com
By mapping the positions of millions of translating ribosomes in the cell, ribosome profiling
(Ribo-seq) has established its role as a powerful tool to study gene expression. Several …
(Ribo-seq) has established its role as a powerful tool to study gene expression. Several …
Updated MS²PIP web server delivers fast and accurate MS² peak intensity prediction for multiple fragmentation methods, instruments and labeling techniques
MS²PIP is a data-driven tool that accurately predicts peak intensities for a given peptide's
fragmentation mass spectrum. Since the release of the MS²PIP web server in 2015, we have …
fragmentation mass spectrum. Since the release of the MS²PIP web server in 2015, we have …
The Arabidopsis PeptideAtlas: harnessing worldwide proteomics data to create a comprehensive community proteomics resource
KJ Van Wijk, T Leppert, Q Sun, SS Boguraev… - The Plant …, 2021 - academic.oup.com
We developed a resource, the Arabidopsis PeptideAtlas (www. peptideatlas.
org/builds/arabidopsis/), to solve central questions about the Arabidopsis thaliana proteome …
org/builds/arabidopsis/), to solve central questions about the Arabidopsis thaliana proteome …
Sensitive determination of proteolytic proteoforms in limited microscale proteome samples
Protein N termini unambiguously identify truncated, alternatively translated or modified
proteoforms with distinct functions and reveal perturbations in disease. Selective enrichment …
proteoforms with distinct functions and reveal perturbations in disease. Selective enrichment …
Discovery of noncanonical translation initiation sites through mass spectrometric analysis of protein N termini
Translation initiation generally occurs at AUG codons in eukaryotes, although it has been
shown that non-AUG or noncanonical translation initiation can also occur. However, the …
shown that non-AUG or noncanonical translation initiation can also occur. However, the …
CircCode: a powerful tool for identifying circRNA coding ability
P Sun, G Li - Frontiers in genetics, 2019 - frontiersin.org
Circular RNAs (circRNAs), which play vital roles in many regulatory pathways, are
widespread in many species. Although many circRNAs have been discovered in plants and …
widespread in many species. Although many circRNAs have been discovered in plants and …
Translation initiation landscape profiling reveals hidden open-reading frames required for the pathogenesis of tomato yellow leaf curl Thailand virus
Plant viruses with densely packed genomes employ noncanonical translational strategies to
increase the coding capacity for viral function. However, the diverse translational strategies …
increase the coding capacity for viral function. However, the diverse translational strategies …