Abstract RNA-sequencing (RNA-seq) has a wide variety of applications, but no single
analysis pipeline can be used in all cases. We review all of the major steps in RNA-seq data …

Previously, large-scale proteomics was possible only for organisms whose genomes were
sequenced, meaning the most common model organisms. The use of next-generation …

With combined technological advancements in high-throughput next-generation sequencing
and deep mass spectrometry-based proteomics, proteogenomics, ie the integrative analysis …

If validated, diet‐derived foreign microRNA absorption and function in consuming
vertebrates would drastically alter our understanding of nutrition and ecology. RNA …

Mass spectrometry–based proteomics has emerged as the leading method for detection,
quantification, and characterization of proteins. Nearly all proteomic workflows rely on …

Accurate annotation of all protein-coding sequences (CDSs) is an essential prerequisite to
fully exploit the rapidly growing repertoire of completely sequenced prokaryotic genomes …

Proteogenomics is an emerging approach to improve gene annotation and interpretation of
proteomics data. Here we present JUMPg, an integrative proteogenomics pipeline including …

Proteogenomics combines large-scale genomic and transcriptomic data with mass-
spectrometry-based proteomic data to discover novel protein sequence variants and …

The continuous development of analytical and experimental technologies as well as
instruments resulted in the development of very specialized experimental approaches that …

In shotgun proteomics, peptide and protein identification is most commonly conducted using
database search engines, the method of choice when reference protein sequences are …