Eduardo Rocha

The SPARK (Spread of Population-wide Antibiotic Resistance in Klebsiella) project, funded by the JPIAMR instrument of the European Union H2020 programme, seeks to address the complex issue of transmission of antimicrobial resistance genes and […]

Towards the design of new nitrogen fixing symbionts Elucidate how the capacity to establish a nitrogen fixing symbiosis with legumes has been acquired by new bacterial taxons via a lab-evolution experiment should allow developping […]

Bacterial genomes are mainly composed of two types of replicons: chromosomes and plasmids. Plasmids are accessory mobile genetic elements acquired by horizontal transfer between strains or species. Their domestication by new hosts is of […]

Prokaryotes evolve rapidly new functionalities by horizontal gene transfer delivered by mobile genetic elements (MGE). MGE increase relatedness between individuals and thereby might also promote the establishment of microbial social networks. Many studies have […]

Klebsiella pneumoniae is one of the most urgent threats to public health given its increasing resistance to antimicrobial agents including carbapenems, considered as last-resort antibiotics.  In this project we aim to understand the ecological, epidemiological and […]

Selection and mutation in bacteria Evolution is an intrinsically stochastic process that involves a time lag between the generation of the polymorphisms and their moderation by selection. During the very initial stages of sequence […]

Replication-associated gene dosage effects Maximal growth rates are central to microbial life-history strategies because there is a trade-off between fast growth in copiotrophs and scavenging potential in slow-growing oligotrophs. When E. coli’s generation time […]

The evolutionary roles of repeats Stress is often faced in nature, whether from lack of nutrients, arrival of competitors or predators, or the presence of toxic substances. The survival of stressed organisms can be […]

Inter-species horizontal transfer Tuberculosis was initially considered as a clonal population with no known acquisition of genetic material by horizontal genetic transfer, although it carries IS elements with similarity to IS elements from other […]

IntegronFinder is a program that detects integrons in DNA sequences. The program is available on a webserver (Galaxy), or by command line (IntegronFinder on github). Integrons are major genetic element, notorious for their major […]

Scans a set of protein sequences for type IV secretion systems and relaxases using HMM profiles. See Guglielmini et al. (2011) for our criteria to class loci on the basis of this output. Except […]

T3SSscan and FLAGscan use hmm profiles to scan a set of bacterial protein sequences for the presence of key components of: non-flagellar type III secretion systems (“NF-T3SS” database), flagella (“Flagellum”) or both (“NF-T3SS+Flagellum”).Eight proteins […]

While there were efficient methods for detecting strict repeats or detecting already characterised repeats, there was no software available for detecting approximate repeats in large DNA sequences allowing for weighted substitutions and indels in […]

Intragenic duplications of genetic material have important biological roles because of their consequences in terms of protein sequence and structure. We developed Swelfe to find internal repeats at three levels. Swelfe quickly identifies statistically […]

Growthpred predicts bacterial minimal doubling times by analysing codon usage bias in genomes and metagenomes. The program takes a set of DNA protein coding sequences, searches for ribosomal protein coding genes and translates all […]

Macromolecular System Finder (MacSyFinder) provides a flexible framework to model the properties of molecular systems (cellular machinery or pathway) including their components, evolutionary associations with other systems and genetic architecture. Modelled features also include […]

Repeatoire is a bioinformatics tool for locating DNA repeats inside of sequenced (but not necessarily assembled) genomes. Specifically, our focus is on repeat families, i.e. related sets of repeats that share a similar role […]

CapsuleFinder is a program that detects capsule systems with high accuracy in proteic sequences.  It is based on the use of HMM profiles for the detection of the essential proteins of capsule biogenesis and  requires computational models describing […]

The database TXSSdb includes all results from our works on the detection of protein secretion systems in 1,528 complete genomes of bacteria with diderm-LPS cellular enveloppes. It is by far the most complete database […]

Protein secretion systems are key virulence factors of all major bacterial pathogens with an LPS-containing outer membrane: Shigella, Escherichia coli, Yersinia pestis, Salmonella, Pseudomonas aeruginosa, Helicobacter pylori, Vibrio cholerae, etc. Protein secretion systems are […]

Non-Flagellar Type III Secretion Systems (NF-T3SS, or injectisomes) are bacterial machineries partially homologous to the bacterial flagellum, which allow direct injection of bacterial effectors from bacterial cytoplasm to eukaryotic cells via a molecular needle […]

This website allows to query a dataset of 947 conjugative systems, 646 non-conjugative T4SS and 1,180 mobilization systems retrieved from 2,269 complete genome sequences. These systems were detected with protein profiles of T4SS components, […]