List of works - Ruy Jauregui

A metaproteomics approach to elucidate host and pathogen protein expression during catheter-associated urinary tract infections (CAUTIs).

scientific article

A robust nitrifying community in a bioreactor at 50 °C opens up the path for thermophilic nitrogen removal

scientific article

An entropy-reducing data representation approach for bioinformatic data.

scientific article published in January 2018

Application of a Novel "Pan-Genome"-Based Strategy for Assigning RNAseq Transcript Reads to Staphylococcus aureus Strains

scientific article (publication date: 2015)

AromaDeg, a novel database for phylogenomics of aerobic bacterial degradation of aromatics

scientific article published on December 2014

Bacterial Diversity in Bentonites, Engineered Barrier for Deep Geological Disposal of Radioactive Wastes.

scientific article published on 30 May 2015

Beyond microarrays: find key transcription factors controlling signal transduction pathways

scientific article

Characterisation of the human uterine microbiome in non-pregnant women through deep sequencing of the V1-2 region of the 16S rRNA gene

scientific article

Comparing the anterior nare bacterial community of two discrete human populations using Illumina amplicon sequencing

scientific article published on 16 January 2014

Degradation of Benzene by Pseudomonas veronii 1YdBTEX2 and 1YB2 Is Catalyzed by Enzymes Encoded in Distinct Catabolism Gene Clusters

scientific article

Draft Genome Sequence of Pseudomonas veronii Strain 1YdBTEX2.

scientific article

Draft Genome Sequence of Rhodococcus sp. Strain 311R.

scientific article published on 21 May 2015

Draft Genome Sequence of the Naphthalene Degrader Herbaspirillum sp. Strain RV1423.

scientific article published on 20 March 2014

EGENES: transcriptome-based plant database of genes with metabolic pathway information and expressed sequence tag indices in KEGG.

scientific article published on 27 April 2007

Effect of dental cements on peri-implant microbial community: comparison of the microbial communities inhabiting the peri-implant tissue when using different luting cements.

scientific article published on 21 March 2015

Exploring the bacterial assemblages along the human nasal passage

scientific article published on 21 May 2016

Exploring the transcriptome of Staphylococcus aureus in its natural niche

scientific article

First Draft Genome Sequence of the Acidovorax caeni sp. nov. Type Strain R-24608 (DSM 19327).

scientific article

Functional soil metagenomics: elucidation of polycyclic aromatic hydrocarbon degradation potential following 12 years of in situ bioremediation.

scientific article published on 12 April 2017

Genetic Diversity in Invasive Populations of Argentine Stem Weevil Associated with Adaptation to Biocontrol ⬇️

scientific article published on 14 July 2020

Genome analysis of Escherichia coli promoter sequences evidences that DNA static curvature plays a more important role in gene transcription than has previously been anticipated

scientific article published on 18 January 2006

Genome sequence of Pseudopithomyces chartarum, causal agent of facial eczema (pithomycotoxicosis) in ruminants, and identification of the putative sporidesmin toxin gene cluster ⬇️

Genome-scale computational analysis of DNA curvature and repeats in Arabidopsis and rice uncovers plant-specific genomic properties. ⬇️

scientific article

Gut microbial functional maturation and succession during human early life.

scientific article published on 24 April 2018

High individuality of respiratory bacterial communities in a large cohort of adult cystic fibrosis patients under continuous antibiotic treatment

scientific article

High-fiber and high-protein diets shape different gut microbial communities, which ecologically behave similarly under stress conditions, as shown in a gastrointestinal simulator

scientific article published on 4 July 2016

High-rate activated sludge communities have a distinctly different structure compared to low-rate sludge communities, and are less sensitive towards environmental and operational variables

scientific article published on 7 May 2016

High-resolution transcriptomic analysis of the adaptive response of Staphylococcus aureus during acute and chronic phases of osteomyelitis.

scientific article

Identification of composite promoter modules in inflammation-regulated genes.

scientific article published on 26 February 2009

In vitro colonisation of the distal colon by Akkermansia muciniphila is largely mucin and pH dependent.

scientific article published on 8 November 2016

Linking Microbial Community and Catabolic Gene Structures during the Adaptation of Three Contaminated Soils under Continuous Long-Term Pollutant Stress

scientific article published on 5 February 2016

Maternal obesity is associated with gut microbial metabolic potential in offspring during infancy.

scientific article

Methylobacterium, a major component of the culturable bacterial endophyte community of wild Brassica seed

scientific article published on 10 July 2020

Mineral and organic growing media have distinct community structure, stability and functionality in soilless culture systems

scientific article

Modelling the Molecular Interactions in the Flower Developmental Network of Arabidopsis thaliana.

scientific article published in January 2011

Modelling the molecular interactions in the flower developmental network of Arabidopsis thaliana.

scientific article published in January 2010

One-year calorie restriction impacts gut microbial composition but not its metabolic performance in obese adolescents.

scientific article published on 2 March 2017

Optimized cryopreservation of mixed microbial communities for conserved functionality and diversity

scientific article

Presence does not imply activity: DNA and RNA patterns differ in response to salt perturbation in anaerobic digestion.

scientific article published on 9 November 2016

Product Diversity Linked to Substrate Usage in Chain Elongation by Mixed-Culture Fermentation

scientific article published on 10 May 2016

Reinforcement of intestinal epithelial barrier by arabinoxylans in overweight and obese subjects: A randomized controlled trial: Arabinoxylans in gut barrier

scientific article published on 3 February 2017

Relationship between codon usage and sequence-dependent curvature of genomes

scientific article published on 01 January 1998

Relationship between whole proteome aminoacid composition and static DNA curvature.

scientific article published in January 2000

Target genes of the MADS transcription factor SEPALLATA3: integration of developmental and hormonal pathways in the Arabidopsis flower

scientific article

The full-scale anaerobic digestion microbiome is represented by specific marker populations.

scientific article

The microbial community structure of the cotton rat nose.

scientific article published on 26 August 2015

The temporal dynamics of bacterial communities across human anterior nares.

scientific article

Trade-off between mesophilic and thermophilic denitrification: rates vs. sludge production, settleability and stability

scientific article

Validating T-RFLP as a sensitive and high-throughput approach to assess bacterial diversity patterns in human anterior nares

scientific article

List of works by Ruy Jauregui

A metaproteomics approach to elucidate host and pathogen protein expression during catheter-associated urinary tract infections (CAUTIs).

A robust nitrifying community in a bioreactor at 50 °C opens up the path for thermophilic nitrogen removal

An entropy-reducing data representation approach for bioinformatic data.

Application of a Novel "Pan-Genome"-Based Strategy for Assigning RNAseq Transcript Reads to Staphylococcus aureus Strains

AromaDeg, a novel database for phylogenomics of aerobic bacterial degradation of aromatics

Bacterial Diversity in Bentonites, Engineered Barrier for Deep Geological Disposal of Radioactive Wastes.

Beyond microarrays: find key transcription factors controlling signal transduction pathways

Characterisation of the human uterine microbiome in non-pregnant women through deep sequencing of the V1-2 region of the 16S rRNA gene

Comparing the anterior nare bacterial community of two discrete human populations using Illumina amplicon sequencing

Degradation of Benzene by Pseudomonas veronii 1YdBTEX2 and 1YB2 Is Catalyzed by Enzymes Encoded in Distinct Catabolism Gene Clusters

Draft Genome Sequence of Pseudomonas veronii Strain 1YdBTEX2.

Draft Genome Sequence of Rhodococcus sp. Strain 311R.

Draft Genome Sequence of the Naphthalene Degrader Herbaspirillum sp. Strain RV1423.

EGENES: transcriptome-based plant database of genes with metabolic pathway information and expressed sequence tag indices in KEGG.

Effect of dental cements on peri-implant microbial community: comparison of the microbial communities inhabiting the peri-implant tissue when using different luting cements.

Exploring the bacterial assemblages along the human nasal passage

Exploring the transcriptome of Staphylococcus aureus in its natural niche

First Draft Genome Sequence of the Acidovorax caeni sp. nov. Type Strain R-24608 (DSM 19327).

Functional soil metagenomics: elucidation of polycyclic aromatic hydrocarbon degradation potential following 12 years of in situ bioremediation.

Genetic Diversity in Invasive Populations of Argentine Stem Weevil Associated with Adaptation to Biocontrol ⬇️

Genome analysis of Escherichia coli promoter sequences evidences that DNA static curvature plays a more important role in gene transcription than has previously been anticipated

Genome sequence of Pseudopithomyces chartarum, causal agent of facial eczema (pithomycotoxicosis) in ruminants, and identification of the putative sporidesmin toxin gene cluster ⬇️

Genome-scale computational analysis of DNA curvature and repeats in Arabidopsis and rice uncovers plant-specific genomic properties. ⬇️

Gut microbial functional maturation and succession during human early life.

High individuality of respiratory bacterial communities in a large cohort of adult cystic fibrosis patients under continuous antibiotic treatment

High-fiber and high-protein diets shape different gut microbial communities, which ecologically behave similarly under stress conditions, as shown in a gastrointestinal simulator

High-rate activated sludge communities have a distinctly different structure compared to low-rate sludge communities, and are less sensitive towards environmental and operational variables

High-resolution transcriptomic analysis of the adaptive response of Staphylococcus aureus during acute and chronic phases of osteomyelitis.

Identification of composite promoter modules in inflammation-regulated genes.

In vitro colonisation of the distal colon by Akkermansia muciniphila is largely mucin and pH dependent.

Linking Microbial Community and Catabolic Gene Structures during the Adaptation of Three Contaminated Soils under Continuous Long-Term Pollutant Stress

Maternal obesity is associated with gut microbial metabolic potential in offspring during infancy.

Methylobacterium, a major component of the culturable bacterial endophyte community of wild Brassica seed

Mineral and organic growing media have distinct community structure, stability and functionality in soilless culture systems

Modelling the Molecular Interactions in the Flower Developmental Network of Arabidopsis thaliana.

Modelling the molecular interactions in the flower developmental network of Arabidopsis thaliana.

One-year calorie restriction impacts gut microbial composition but not its metabolic performance in obese adolescents.

Optimized cryopreservation of mixed microbial communities for conserved functionality and diversity

Presence does not imply activity: DNA and RNA patterns differ in response to salt perturbation in anaerobic digestion.

Product Diversity Linked to Substrate Usage in Chain Elongation by Mixed-Culture Fermentation

Reinforcement of intestinal epithelial barrier by arabinoxylans in overweight and obese subjects: A randomized controlled trial: Arabinoxylans in gut barrier

Relationship between codon usage and sequence-dependent curvature of genomes

Relationship between whole proteome aminoacid composition and static DNA curvature.

Target genes of the MADS transcription factor SEPALLATA3: integration of developmental and hormonal pathways in the Arabidopsis flower

The full-scale anaerobic digestion microbiome is represented by specific marker populations.

The microbial community structure of the cotton rat nose.

The temporal dynamics of bacterial communities across human anterior nares.

Trade-off between mesophilic and thermophilic denitrification: rates vs. sludge production, settleability and stability

Validating T-RFLP as a sensitive and high-throughput approach to assess bacterial diversity patterns in human anterior nares