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 …

Genome annotation is a tedious task that is mostly done by automated methods; however,
the accuracy of these approaches has been questioned since the beginning of the …

Many steps in the evolution of cellular life are still mysterious. We suggest that the ribosome
may represent one important missing link between compositional (or metabolism-first), RNA …

Annotation of gene expression in prokaryotes often finds itself corrected due to small
variations of the annotated gene regions observed between different (sub)-species. It has …

For more than 30 years, we have understood that genes may be organized within genomic
DNA in complex spatial arrangements. In particular, gene-coding sequences can overlap: a …

Experimental evidence is increasingly being used to reassess the quality and accuracy of
genome annotation. Proteomics data used for this purpose, called proteogenomics, can …

As sequence data continues to be generated at a logarithmic rate our dependence on
effective in silico gene prediction methods is also increasing. Herein, I review the current …

The pathogenic Legionella bacteria are notorious for delivering numerous effector proteins
into the host cell with the aim of disturbing and hijacking cellular processes for their benefit …

The present study describes the behavior of a natural phenanthrene-degrading consortium
(CON), a synthetic consortium (constructed with isolated strains from CON) and an isolated …

Assembly of genes into operons is generally viewed as an important process during the
continual adaptation of microbes to changing environmental challenges. However, the …