Recent publications

Bacteria in metastatic sites: Unveiling hidden players in cancer progression
Bacteria exhibit key features of cancer metastasis, such as motility, invasion, and modulation of the tumor microenvironment. They …
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Bacteria in metastatic sites: Unveiling hidden players in cancer progression
Women in STEM becoming independent: The journey to independence is an immensely gratifying odyssey
This year at JEM, we are highlighting women in science by sharing their stories and amplifying their voices. In this Viewpoint, we hear …
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Estudiando las funciones de la microbiota intestinal: presente y futuro de la metatranscriptómica
La microbiota intestinal es el conjunto de microorganismos (bacterias, virus y hongos, entre otros) que residen en el delicado …
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Estudiando las funciones de la microbiota intestinal: presente y futuro de la metatranscriptómica
Microbiome confounders and quantitative profiling challenge predicted microbial targets in colorectal cancer development
Despite substantial progress in cancer microbiome research, recognized confounders and advances in absolute microbiome quantification …
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Microbiome confounders and quantitative profiling challenge predicted microbial targets in colorectal cancer development
Single-cell approaches in human microbiome research
Microbial culturing and meta-omic profiling technologies have significantly advanced our understanding of the taxonomic and functional …
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Single-cell approaches in human microbiome research
Clinical practices underlie COVID-19 patient respiratory microbiome composition and its interactions with the host
Understanding the pathology of COVID-19 is a global research priority. Early evidence suggests that the respiratory microbiome may be …
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Benchmarking microbiome transformations favors experimental quantitative approaches to address compositionality and sampling depth biases
While metagenomic sequencing has become the tool of preference to study host-associated microbial communities, downstream analyses and …
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Endogenous IFNB expression predicts outcome in critical patients with COVID-19
Although the subject of intensive preclinical and clinical research, controversy on the protective versus deleterious effects of …
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Determination of the gene regulatory network of a genome-reduced bacterium highlights alternative regulation independent of transcription factors
Here, we determined the relative importance of different transcriptional mechanisms in the genome-reduced bacterium Mycoplasma …
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Determination of the gene regulatory network of a genome-reduced bacterium highlights alternative regulation independent of transcription factors
Tracking humans and microbes
The Human Microbiome Project put the health-associated microbes found in humans on centre stage. The project’s second phase shows how …
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Integrated culturing, modeling and transcriptomics uncovers complex interactions and emergent behavior in a three-species synthetic gut community
The composition of the human gut microbiome is well resolved, but predictive understanding of its dynamics is still lacking. Here, we …
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Alternative transcriptional regulation in genome-reduced bacteria
Transcription is a core process of bacterial physiology, and as such it must be tightly controlled, so that bacterial cells maintain …
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Insights into the mechanisms of basal coordination of transcription using a genome-reduced bacterium
Coordination of transcription in bacteria occurs at supra-operonic scales, but the extent, specificity, and mechanisms of such …
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Bacterial antisense RNAs are mainly the product of transcriptional noise
cis-Encoded antisense RNAs (asRNAs) are widespread along bacterial transcriptomes. However, the role of most of these RNAs remains …
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The yin–yang of kinase activation and unfolding explains the peculiarity of Val600 in the activation segment of BRAF
Many driver mutations in cancer are specific in that they occur at significantly higher rates than – presumably – functionally …
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Comparative “-omics” in Mycoplasma pneumoniae clinical isolates reveals key virulence factors
The human respiratory tract pathogen M. pneumoniae is one of the best characterized minimal bacterium. Until now, two main groups of …
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Distinguishing between productive and abortive promoters using a random forest classifier in Mycoplasma pneumoniae
Distinguishing between promoter-like sequences in bacteria that belong to true or abortive promoters, or to those that do not initiate …
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Defining a minimal cell: essentiality of small ORF s and nc RNA s in a genome‐reduced bacterium
Identifying all essential genomic components is critical for the assembly of minimal artificial life. In the genome-reduced bacterium …
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Assessing the hodgepodge of non-mapped reads in bacterial transcriptomes: real or artifactual RNA chimeras?
Background - RNA sequencing methods have already altered our view of the extent and complexity of bacterial and eukaryotic …
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Comprehensive Methylome Characterization of Mycoplasma genitalium and Mycoplasma pneumoniae at Single-Base Resolution
In the bacterial world, methylation is most commonly associated with restriction-modification systems that provide a defense mechanism …
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