Publications

Bacteria and mobile genetic elements have coevolved in a long arms race, generating diverse defense and counter-defense systems now better understood through modern genomic tools. These insights highlight conserved bacterial defense mechanisms as promising targets for developing broad, microbiome-focused antibacterial therapies.

We performed a large-scale in-depth analysis of the defensomes of 7,759 high-quality bacterial population genomes reconstructed from soil, marine, and human gut environments. Our results provide a detailed picture of the multiple immune barriers present in environmentally distinct bacterial communities.

In this book, the reader is introduced to state-of-the-art computational methods designed to manage, analyze, and generally leverage epigenomic and epitranscriptomic data.

I summarize lessons taken from high-dimensional methylome data analyses and recent efforts that we and others are developing to leverage such findings into meaningful biological insights.

In this opinion article, we propose that highly conserved DNA methyltransferases represent a unique opportunity for bacterial epigenomic studies.

We perform a comprehensive DNA methylome analysis of C. difficile using 36 human isolates and observe a high level of epigenomic diversity.

We propose a model where the different genetic plasticity and amplitude of host range between elements explain the co-occurrence of integrative and extrachromosomal elements in microbial populations.

We found that transferred genes are concentrated in only ~1% of the chromosomal regions (hotspots) in 80 bacterial species.

Our results reconcile previous studies by showing that R-M systems are more abundant in promiscuous species, wherein they establish preferential paths of genetic exchange.

We analyzed the distribution of R-M systems in 2,261 prokaryote genomes and found their frequency to be strongly dependent on the presence of MGEs.

This review addresses the current status and emerging trends of genome plasticity in human stem cells, underscoring the need for new regulatory standards.

We find that newly acquired IS2 elements are consistently inserted around abrupt DNA compositional shifts, particularly in the form of switch sites of GC skew.

Herein we review our current knowledge on bacterial genome instability, with particular emphasis on findings gained from E. coli.

We provide an overview on the potential implications of marker-free plasmids and perspectives for their successful biotechnological use.

In this work we performed an extensive screening of human mtDNA deletions and evaluated the association between breakpoint density and sequence motifs.

We investigated the influence of hypoxia and prolonged passaging on the expression of genes involved in DNA repair and cell-cycle regulation.

We evaluated the potential of boronic acid functionalized magnetic particles for the one-step capture of a human monoclonal antibody.

Different transpososomes are assembled in each step of the IS2 transposition pathway.

This review highlights several bioinformatic tools for detection of potentially unstable DNA regions.

We evaluated the abundance and distribution of direct, inverted, and tandem repeats in 36 natural plasmids.

This review focuses on major instability determinants in pDNA, an important step towards designing safer molecules.

A simple non-linear mathematical function is proposed to predict recombination frequencies in bacterial plasmid DNA.

This work highlights the impact of mutational hot spots on expression and cloning plasmid vectors.

This is the first evidence for siderophore synthesis in S. erythraea and one of the first examples of non-polyketide secondary metabolite production by this organism.