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    • Several versions

    Reduced Set of Virulence Genes Allows High Accuracy Prediction of Bacterial Pathogenicity in Humans (Prediction of Bacterial Pathogenicity in Humans)

    Iraola, Gregorio, Vazquez, Gustavo, Spangenberg, Lucía, Naya, Hugo
    2012, Vol.7(8), p.e42144 [Peer Reviewed Journal]

    • Several versions

    MLSTar: automatic multilocus sequence typing of bacterial genomes in R

    Ferrés, Ignacio, Iraola, Gregorio
    PeerJ, 2018, Vol.6 [Peer Reviewed Journal]

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    Wedding higher taxonomic ranks with metabolic signatures coded in prokaryotic genomes

    Iraola, Gregorio, Naya, Hugo
    BioRxiv, Apr 22, 2016
    © ProQuest LLC All rights reserved, Biological Science Database, Publicly Available Content Database, ProQuest Biological Science Collection, ProQuest Natural Science Collection, ProQuest SciTech Collection, Natural Science Collection, ProQuest Central (new), ProQuest Central K-12, ProQuest Central Korea, SciTech Premium Collection, ProQuest Central Essentials, ProQuest One Academic
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    Title: Wedding higher taxonomic ranks with metabolic signatures coded in prokaryotic genomes
    Author: Iraola, Gregorio; Naya, Hugo
    Contributor: Naya, Hugo (pacrepositoryorg)
    Subject: Taxonomy ; Genomes ; Metabolism ; Phenotypic Plasticity ; Taxonomy ; Prokaryotes ; Genomics
    Description: Taxonomy of prokaryotes has remained a controversial discipline due to the extreme plasticity of microorganisms, causing inconsistencies between phenotypic and genotypic classifications. The genomics era has enhanced taxonomy but also opened new debates about the best practices for incorporating genomic data into polyphasic taxonomy protocols, which are fairly biased towards the identification of bacterial species. Here we use an extensive dataset of Archaea and Bacteria to prove that metabolic signatures coded in their genomes are informative traits that allow to accurately classify organisms coherently to higher taxonomic ranks, and to associate functional features with the definition of taxa. Our results support the ecological coherence of higher taxonomic ranks and reconciles taxonomy with traditional chemotaxonomic traits inferred from genomes. KARL, a simple and free tool useful for assisting polyphasic taxonomy or to perform functional prospections is also pre- sented (https://github.com/giraola/KARL).
    Is part of: BioRxiv, Apr 22, 2016
    Identifier: 10.1101/044115 (DOI)

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    MLSTar: automatic multilocus and core genome sequence typing in R

    Ferrés, Ignacio, Iraola, Gregorio
    PeerJ PrePrints, Mar 7, 2018
    © ProQuest LLC All rights reserved, ProQuest Science Journals, Science Database (Alumni edition), Biological Science Database, Publicly Available Content Database, ProQuest Biological Science Collection, ProQuest Central, ProQuest Natural Science Collection, ProQuest SciTech Collection, Natural Science Collection, ProQuest Central (new), ProQuest Central K-12, ProQuest Central Korea, SciTech Premium Collection, ProQuest Central Essentials, ProQuest Central China, ProQuest One Academic
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    Title: MLSTar: automatic multilocus and core genome sequence typing in R
    Author: Ferrés, Ignacio; Iraola, Gregorio
    Subject: Databases ; Genomes ; Multilocus Sequence Typing ; Bacteria ; Nucleotide Sequence ; Population Genetics ; Genomes ; Genetic Diversity ; Alleles ; Mlst ; Cgmlst ; Bacterial Genomics ; R Package ; Population Genomics
    Description: Multilocus sequence typing (MLST) is a standard tool in population genetics and bacterial epidemiology that assesses the genetic variation present in a reduced number of housekeeping genes (typically seven) along the genome. This methodology assigns arbitrary integer identifiers to genetic variations at these loci allowing to efficiently compare bacterial isolates using allele-based methods. Now, the increasing availability of whole-genome sequences for hundreds to thousands of strains from the same bacterial species has motivated to upgrade the resolution of traditional MLST schemes using larger gene sets or even the core genome (cgMLST). The PubMLST database is the most comprehensive resource of described MLST and cgMLST schemes available for a wide variety of species. Here we present MLSTar as the first R package that allows to i) connect with the PubMLST database to select a target scheme, ii) screen a desired set of genomes to assign alleles and sequence types and iii) interact with...
    Is part of: PeerJ PrePrints, Mar 7, 2018
    Identifier: 21679843 (E-ISSN); 10.7287/peerj.preprints.26630v2 (DOI)

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    Phylogenetic and Genome-Wide Deep-Sequencing Analyses of Canine Parvovirus Reveal Co-Infection with Field Variants and Emergence of a Recent Recombinant Strain

    Pérez, Ruben, Calleros, Lucía, Marandino, Ana, Sarute, Nicolás, Iraola, Gregorio, Grecco, Sofia, Blanc, Hervé, Vignuzzi, Marco, Isakov, Ofer, Shomron, Noam, Carrau, Lucía, Hernández, Martín, Francia
    PLoS ONE, 2014, Vol.9(11) [Peer Reviewed Journal]

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    Campylobacter geochelonis sp. nov. isolated from the western Hermann's tortoise (Testudo hermanni hermanni)

    Piccirillo, Alessandra, Niero, Giulia, Calleros, Lucía, Pérez, Ruben, Naya, Hugo, Iraola, Gregorio
    International journal of systematic and evolutionary microbiology, September 2016, Vol.66(9), pp.3468-3476 [Peer Reviewed Journal]
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    Title: Campylobacter geochelonis sp. nov. isolated from the western Hermann's tortoise (Testudo hermanni hermanni)
    Author: Piccirillo, Alessandra; Niero, Giulia; Calleros, Lucía; Pérez, Ruben; Naya, Hugo; Iraola, Gregorio
    Subject: Phylogeny ; Campylobacter -- Classification ; Turtles -- Microbiology
    Description: During a screening study to determine the presence of species of the genus Campylobacter in reptiles, three putative strains (RC7, RC11 and RC20T) were isolated from different individuals of the western Hermann's tortoise (Testudo hermanni hermanni). Initially, these isolates were characterized as representing Campylobacterfetus subsp. fetus by multiplex PCR and partial 16S rRNA gene sequence analysis. Further whole- genome characterization revealed considerable differences compared to other Campylobacter species. A polyphasic study was then undertaken to determine the exact taxonomic position of the isolates. The three strains were characterized by conventional phenotypic tests and whole genome sequencing. We generated robust phylogenies that showed a distinct clade containing only these strains using the 16S rRNA and atpA genes and a set of 40 universal proteins. Our phylogenetic analysis demonstrates their designation as representing a novel species and this was further confirmed using...
    Is part of: International journal of systematic and evolutionary microbiology, September 2016, Vol.66(9), pp.3468-3476
    Identifier: 1466-5034 (E-ISSN); 27266587 Version (PMID); 10.1099/ijsem.0.001219 (DOI)

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    Campylobacter ornithocola sp. nov., a new member of the Campylobacter lari group isolated from wild bird faecal samples

    Caceres, Alberto, Muñoz, Ivo, Iraola, Gregorio, Díaz-Viraqué, Florencia, Collado, Luis
    International journal of systematic and evolutionary microbiology, 23 January 2017, Vol.67(6), pp.1643-1649 [Peer Reviewed Journal]

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    The Tritryps comparative repeatome: insights on repetitive element evolution in Trypanosomatid pathogens

    Pita, Sebastian, Diaz-Viraque, Florencia, Iraola, Gregorio, Robello, Carlos
    BioRxiv, Aug 8, 2018
    © ProQuest LLC All rights reserved, Biological Science Database, Publicly Available Content Database, ProQuest Biological Science Collection, ProQuest Natural Science Collection, ProQuest SciTech Collection, Natural Science Collection, ProQuest Central (new), ProQuest Central K-12, ProQuest Central Korea, SciTech Premium Collection, ProQuest Central Essentials, ProQuest One Academic
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    Title: The Tritryps comparative repeatome: insights on repetitive element evolution in Trypanosomatid pathogens
    Author: Pita, Sebastian; Diaz-Viraque, Florencia; Iraola, Gregorio; Robello, Carlos
    Contributor: Robello, Carlos (pacrepositoryorg)
    Subject: Deoxyribonucleic Acid–DNA ; Genomes ; Protozoa ; Eukaryotes ; DNA Sequencing ; Transposons ; Parasites ; Genomes ; Deoxyribonucleic Acid–DNA ; Pathogens
    Description: The major human pathogens Trypanosoma cruzi, Trypanosoma brucei and Leishmania major are collectively known as the Tritryps. The initial comparative analysis of their genomes has uncovered that Tritryps share a great number of genes, but repetitive DNA seems to be extremely variable between them. However, the in-depth characterization of repetitive DNA in these pathogens has been in part neglected, mainly due to the well-known technical challenges of studying repetitive sequences from de novo assemblies using short reads. Here, we compared the repetitive DNA repertories between the Tritryps genomes using genome-wide, low-coverage Illumina sequencing coupled to RepeatExplorer analysis. Our work demonstrates that this extensively implemented approach for studying higher eukaryote repeatomes is also useful for protozoan parasites like trypanosomatids, as we recovered previously observed differences in the presence and amount of repetitive DNA families. Additionally, our estimations of repetitive...
    Is part of: BioRxiv, Aug 8, 2018
    Identifier: 10.1101/387217 (DOI)

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    Leptospira venezuelensis sp. nov., a new member of the intermediate group isolated from rodents, cattle and humans

    Puche, Rafael, Ferrés, Ignacio, Caraballo, Lizeth, Rangel, Yaritza, Picardeau, Mathieu, Takiff, Howard, Iraola, Gregorio
    International journal of systematic and evolutionary microbiology, February 2018, Vol.68(2), pp.513-517 [Peer Reviewed Journal]
    MEDLINE/PubMed (U.S. National Library of Medicine)
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    Title: Leptospira venezuelensis sp. nov., a new member of the intermediate group isolated from rodents, cattle and humans
    Author: Puche, Rafael; Ferrés, Ignacio; Caraballo, Lizeth; Rangel, Yaritza; Picardeau, Mathieu; Takiff, Howard; Iraola, Gregorio
    Subject: Leptospirosis ; Venezuela ; Intermediates ; Whole-Genome Sequencing ; Phylogeny ; Leptospira -- Classification
    Description: Three strains, CLM-U50, CLM-R50 and IVIC-Bov1, belonging to the genus Leptospira, were isolated in Venezuela from a patient with leptospirosis, a domestic rat (Rattus norvegicus) and a cow (Bos taurus), respectively. The initial characterisation of these strains based on the rrs gene (16S rRNA) suggested their designation as a novel species within the 'intermediates' group of the genus Leptospira. Further phylogenomic characterisation based on single copy core genes was consistent with their separation into a novel species. The average nucleotide identity between these three strains was >99 %, but below 89 % with respect to any previously described leptospiral species, also supporting their designation as a novel species. Given this evidence, these three isolates were considered to represent a novel species, for which the name Leptospiravenezuelensis sp. nov. is proposed, with CLM-U50 (=CIP 111407=DSM 105752) as the type strain.
    Is part of: International journal of systematic and evolutionary microbiology, February 2018, Vol.68(2), pp.513-517
    Identifier: 1466-5034 (E-ISSN); 29239713 Version (PMID); 10.1099/ijsem.0.002528 (DOI)

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    Complete Genome Sequence of Mycobacterium tuberculosis Strain MtURU-001, Isolated from a Rapidly Progressing Outbreak in Uruguay

    Greif, Gonzalo, Iraola, Gregorio, Berná, Luisa, Coitinho, Cecilia, Rivas, Carlos M, Naya, Hugo, Robello, Carlos
    Genome announcements, 23 January 2014, Vol.2(1) [Peer Reviewed Journal]
    MEDLINE/PubMed (U.S. National Library of Medicine)
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    Title: Complete Genome Sequence of Mycobacterium tuberculosis Strain MtURU-001, Isolated from a Rapidly Progressing Outbreak in Uruguay
    Author: Greif, Gonzalo; Iraola, Gregorio; Berná, Luisa; Coitinho, Cecilia; Rivas, Carlos M; Naya, Hugo; Robello, Carlos
    Subject: Biology;
    Description: Despite efficient control programs, large clonal outbreaks of tuberculosis (TB) may arise in low-risk populations. Recently, an unusual TB outbreak was reported in Uruguay, reaching an elevated disease attack rate (53 to 69%). Here, we report the genome sequence of the Mycobacterium tuberculosis strain associated with this rapidly progressing outbreak, named MtURU-001.
    Is part of: Genome announcements, 23 January 2014, Vol.2(1)
    Identifier: 2169-8287 (ISSN); 24459279 Version (PMID); 10.1128/genomeA.01220-13 (DOI)