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(2026). The endomicrobiome and weed invasiveness in Mediterranean ecosystems worldwide. In: Nature Communications, 2026.

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(2026). Gypsum as a repository of extinct and extant biosignatures at Salar de Pajonales, northern Chile. In: Frontiers in Astronomy and Space Sciences, p. 1693302, 2026.

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(2026). Functional Shifts in the Gut DNA Virome in a Long-Distance Migratory Shorebird During the Pre-Migratory Fattening. In: Molecular Ecology, (35), 6, pp. e70315.

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(2026). Distinct taxonomic signatures in the rhizobiome of two native plants from the polyextreme Salar de Huasco ecosystem. In: Environmental Microbiome, (21), pp. 42.

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(2026). Complete Mitochondrial Genomes Recovered From Environmental Metagenomics Samples Can Facilitate Non-Intrusive Population Genetic/Genomics Studies in the South American Sea Lion. In: Environmental DNA, (8), 1, pp. e70213.

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(2025). Sustainable Open Production of Short-Medium-Chain Length Polyhydroxyalkanoates from Crude Glycerol in Batch and Fed-Batch Bioreactors by Pseudomonas frigusceleri MPC6. In: ACS Sustainable Chemistry & Engineering, (13), 43, pp. 18448-18461.

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(2025). Rhizosphere and soil metagenomes and metagenome-assembled genomes from the Byers Peninsula, Livingston Island (62° S), Antarctica. In: Microbiology Resource Announcements, (14), 7, pp. e00171-25.

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(2025). Occurrence and flux of polycyclic aromatic hydrocarbons in settling particulate matter from the water column in Fildes Bay, Antarctica. In: Czech Polar Reports, (15), 1, pp. 97-109.

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(2025). Life on the edge: Microbial diversity, resistome, and virulome in soils from the union glacier cold desert. In: Science of the Total Environment, (957), pp. 177594.

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(2025). Habitat Anthropization Shapes the Skin Bacteriome of Dolphins: A Red Flag About Health. In: Aquatic Conservation: Marine and Freshwater Ecosystems, (35), 6, pp. e70166.

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(2025). Fungal endophytes modulate the negative effects induced by Persistent Organic Pollutants in the antarctic plant Colobanthus quitensis. In: Physiologia Plantarum, (177), 1, pp. e70079.

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(2025). From sewage to genomes: Expanding our understanding of the urban and semi-urban wastewater RNA virome. In: Environmental Research, (276), pp. 121509.

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(2025). Distribution and bioconcentration of semivolatile organic compounds (SVOCs) in soils and vascular plant Colobanthus quitensis from Sub-Antarctic and Antarctic regions. In: Science of the Total Environment, (963), pp. 178494.

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(2024). The nasal mycobiome of individuals with allergic rhinitis and asthma differs from that of healthy controls in composition, structure and function. In: Frontiers in Microbiology, (15), pp. 1464257.

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(2024). Pediatric urinary tract infections caused by poultry-associated Escherichia coli. In: Microbiology Spectrum, (12), 7, pp. e03415-23.

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(2024). Occurrence and diffusive air-seawater exchanges of organochlorine pesticides (OCPs) and polychlorinated biphenyls (PCBs) in Fildes Bay, King George Island, Antarctica. In: Science of The Total Environment, (908), pp. 168323.

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(2024). Microbiome alterations are associated with apolipoprotein E mutation in Octodon degus and humans with Alzheimer's disease. In: iScience, (27), 8, 2024.

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(2024). Microbial Sequence Typing Strategies for Genetic and Genomic Data. In: Genetics and Evolution of Infectious Diseases, pp. 427-463.

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(2024). Fungal endophyte symbionts enhance plant adaptation in Antarctic habitats. In: Physiologia Plantarum, (176), 6, pp. e14589.

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(2024). Detection of SARS-CoV-2 in Wastewater Associated with Scientific Stations in Antarctica and Possible Risk for Wildlife. In: Microorganisms, (12), 4, pp. 743.

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(2024). Characterization of the oral mycobiome of Portuguese with allergic rhinitis and asthma. In: Current Research in Microbial Sciences, (7), pp. 100300.

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(2023). The oral bacteriomes of patients with allergic rhinitis and asthma differ from that of healthy controls. In: Frontiers in Microbiology, (14), pp. 1197135.

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(2023). Spatially and temporally explicit metagenomes and metagenome-assembled genomes from the Comau Fjord (42° S), Patagonia. In: Microbiology Resource Announcements, (12), 6, pp. e00059-23.

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(2023). Seasonal and Spatially Distributed Viral Metagenomes from Comau Fjord (42° S), Patagonia. In: Microbiology Resource Announcements, pp. e00082–23.

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(2023). Role of Microbes in the degradation of organic semivolatile compounds in polar ecosystems: A review. In: Science of The Total Environment, pp. 163046.

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(2023). Nasal Bacteriomes of Patients with Asthma and Allergic Rhinitis Show Unique Composition, Structure, Function and Interactions. In: Microorganisms, (11), 3, pp. 683.

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(2023). Metagenomic profiling pipelines improve taxonomic classification for 16S amplicon sequencing data. In: Scientific Reports, (13), 1, pp. 13957.

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(2023). Levels of persistent organic pollutants (POPs) in the Antarctic atmosphere over time (1980 to 2021) and estimation of their atmospheric half-lives.. In: Atmospheric Chemistry and Physics Discussions, pp. 1–28.

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(2023). Fecal Metagenomes and Metagenome-Assembled Genomes from the South American Sea Lion (Otaria flavescens) from the Comau Fjord (42° S), Patagonia. In: Microbiology Resource Announcements, (12), 5, pp. e00183-23.

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(2023). Exploring the Influence of Small-Scale Geographical and Seasonal Variations Over the Microbial Diversity in a Poly-extreme Athalosaline Wetland. In: Current Microbiology, (80), 9, pp. 297.

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(2023). Continuous bioreactors enable high-level bioremediation of diesel-contaminated seawater at low and mesophilic temperatures using Antarctic bacterial consortia: Pollutant analysis and microbial community composition. In: Environmental Pollution, (321), pp. 121139.

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(2023). Characterization of the upper respiratory tract microbiota in Chilean asthmatic children reveals compositional, functional, and structural differences. In: Frontiers in Allergy, (4), pp. 1223306.

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(2023). A First Insight into the Microbial and Viral Communities of Comau Fjord—A Unique Human-Impacted Ecosystem in Patagonia (42° S). In: Microorganisms, (11), 4, pp. 904.

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(2022). Transcriptomic analyses reveal increased expression of dioxygenases, monooxygenases, and other metabolizing enzymes involved in anthracene degradation in the marine alga Ulva lactuca. In: Frontiers in Plant Science, (13).

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(2022). The Genome of the Marine Alga Ulva compressa (Chlorophyta) Reveals Protein-Coding Genes with Similarity to Plants and Green Microalgae, but Also to Animal, Bacterial, and Fungal Genes. In: International Journal of Molecular Sciences, (23), 13, pp. 7279.

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(2022). Source and acquisition of rhizosphere microbes in Antarctic vascular plants. In: Frontiers in microbiology, pp. 3376.

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(2022). Predicting climate change-related genetic offset for the endangered southern South American conifer Araucaria araucana. In: Forest Ecology and Management, (504), pp. 119856.

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(2022). Nasopharyngeal metatranscriptome profiles of infants with bronchiolitis and risk of childhood asthma: a multicentre prospective study. In: European Respiratory Journal, (60), 1.

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(2022). Long-term interactions of salmonella enteritidis with a lytic phage for 21 days in high nutrients media. In: Frontiers in cellular and infection microbiology, pp. 596.

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(2022). Influence of Physical-Chemical Soil Parameters on Microbiota Composition and Diversity in a Deep Hyperarid Core of the Atacama Desert. In: Frontiers in Microbiology, (12).

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(2022). Comparative Analysis of Metagenomics and Metataxonomics for the Characterization of Vermicompost Microbiomes. In: Frontiers in microbiology.

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(2022). Annotating unknown species of urban microorganisms on a global scale unveils novel functional diversity and local environment association. In: Environmental Research, (207), pp. 112183.

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(2021). Rhodococcus comparative genomics reveals a phylogenomic-dependent non-ribosomal peptide synthetase distribution: insights into biosynthetic gene cluster connection to an orphan metabolite. In: Microbial genomics, (7), 7.

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(2021). Radiation-induced toxicity in rectal epithelial stem cell contributes to acute radiation injury in rectum. In: Stem Cell Research & Therapy, (12), 1, pp. 1–14.

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(2021). Phosphate-Arsenic Interactions in Halophilic Microorganisms of the Microbial Mat from Laguna Tebenquiche: from the Microenvironment to the Genomes. In: Microbial Ecology, 81(4):, pp. 941-953.

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(2021). Patterns of the fecal microbiota in the Juan Fernández fur seal (Arctocephalus philippii). In: MicrobiologyOpen, (10), 4, pp. e1215.

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(2021). Living to the High Extreme: Unraveling the Composition, Structure, and Functional Insights of Bacterial Communities Thriving in the Arsenic-Rich Salar de Huasco Altiplanic Ecosystem. In: Microbiology Spectrum, (9) 1, pp. e00444-21.

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(2021). Genetic characterization of salmonella infantis with multiple drug resistance profiles isolated from a poultry-farm in Chile. In: Microorganisms, (9), 11, pp. 2370.

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(2021). COVID-19 drug practices risk antimicrobial resistance evolution. In: The Lancet Microbe, (2), 4, pp. e135–e136.

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(2021). Composition and structure of the skin microbiota of rorquals off the Eastern South Pacific. In: FEMS Microbiology Ecology, (97), 5, pp. fiab050.

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(2021). A global metagenomic map of urban microbiomes and antimicrobial resistance. In: Cell, (184), 13, pp. 3376–3393.

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(2020). Origin, genomic diversity and microevolution of the Clostridium difficile B1/NAP1/RT027/ST01 strain in Costa Rica, Chile, Honduras and Mexico. Microbial Genomics, https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000355.

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(2020). Monitoring the occurrence of microplastic ingestion in Otariids along the Peruvian and Chilean coasts. Marine Pollution Bulletin, https://www.sciencedirect.com/science/article/abs/pii/S0025326X20300849.

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(2020). In infants with severe bronchiolitis: dual-transcriptomic profiling of nasopharyngeal microbiome and host response. Pediatric Research, https://www.nature.com/articles/s41390-019-0742-8.

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(2020). Copper-induced concomitant increases in photosynthesis, respiration, and C, N and S assimilation revealed by transcriptomic analyses in Ulva compressa (Chlorophyta). BMC plant biology, https://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-019-2229-5.

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(2020). Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment. Nature Medicine, https://www.nature.com/articles/s41591-020-0894-4.

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(2020). Biotransformation of 2, 4, 6-Trinitrotoluene by Pseudomonas sp. TNT3 isolated from Deception Island, Antarctica. Environmental Pollution, https://www.sciencedirect.com/science/article/pii/S0269749119320378.

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(2020). Sequences of Endophytic Fungal and Bacterial Communities from Araucaria araucana [(Molina) K. Koch, 1869] in the Coastal and Andes Mountain Ranges, Chile. In: Microbiology Resource Announcements, (9), 27, pp. e00544–20.

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(2020). Rapid sequence modification in the highly polymorphic region (HPR) of the hemagglutinin gene of the infectious salmon anaemia virus (ISAV) suggests intra-segmental template switching recombination. In: Journal of Fish Diseases, 00, pp. 1–14.

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(2020). Genomic variation and arsenic tolerance emerged as niche specific adaptations by different Exiguobacterium strains isolated from the extreme Salar de Huasco environment in Chilean--Altiplano. In: Frontiers in Microbiology, (11), pp. 1632.

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(2020). Evaluation of computational methods for human microbiome analysis using simulated data. In: PeerJ, (8), pp. e9688.

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(2019). Variability in Genomic and Virulent Properties of Porphyromonas gingivalis Strains Isolated From Healthy and Severe Chronic Periodontitis Individuals. Frontiers in Cellular and Infection Microbiology, https://www.frontiersin.org/articles/10.3389/fcimb.2019.00246/full.

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(2019). The Transcription Factor ArcA Modulates Salmonella’s Metabolism in Response to Neutrophil Hypochlorous Acid-Mediated Stress. Frontiers in Microbiology, https://www.frontiersin.org/articles/10.3389/fmicb.2019.02754/full.

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(2019). Global genetic cartography of urban metagenomes and anti-microbial resistance. BioRxiv, https://www.biorxiv.org/content/10.1101/724526v4.

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(2019). Arsenic response of three altiplanic Exiguobacterium strains with different tolerance levels against the metalloid species: a proteomics study. Frontiers in Microbiology, https://www.frontiersin.org/articles/10.3389/fmicb.2019.02161/full.

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(2019). Analysis of co-regulated abundance of genes associated with arsenic and phosphate metabolism in Andean Microbial Ecosystems. BioRxiv, https://www.biorxiv.org/content/10.1101/870428v1.abstract.

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(2019). Altered middle ear microbiome in children with chronic otitis media with effusion and respiratory illnesses. Frontiers in Cellular and Infection Microbiology, https://www.frontiersin.org/articles/10.3389/fcimb.2019.00339/full.

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(2019). A first insight into the structure and function of rhizosphere microbiota in Antarctic plants using shotgun metagenomic. Polar Biology, https://link.springer.com/article/10.1007/s00300-019-02556-7.

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(2019). In-Depth Genomic and Phenotypic Characterization of the Antarctic Psychrotolerant Strain Pseudomonas sp. MPC6 Reveals Unique Metabolic Features, Plasticity, and Biotechnological Potential. Frontiers in Microbiology, https://www.frontiersin.org/articles/10.3389/fmicb.2019.01154/full.

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(2019). Genomic and Physiological Traits of the Marine Bacterium Alcaligenes aquatilis QD168 Isolated From Quintero Bay, Central Chile, Reveal a Robust Adaptive Response to Environmental Stressors. Frontiers in Microbiology, https://www.frontiersin.org/articles/10.3389/fmicb.2019.00528/full.

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(2018). The transcription factor SlyA from Salmonella Typhimurium regulates genes in response to hydrogen peroxide and sodium hypochlorite. Research in Microbiology, https://doi.org/10.1016/j.resmic.2018.04.003.

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(2018). The Tracheal Microbiota in Patients with a Tracheostomy Before, During, and After an Acute Respiratory Infection.. The Pediatric infectious disease journal, https://journals.lww.com/pidj/Abstract/publishahead/The_Tracheal_Microbiota_in_Patients_with_a.96738.aspx.

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(2018). Mutation and recombination in pathogen evolution: Relevance, methods and controversies. Infection, Genetics and Evolution, https://doi.org/10.1016/j.meegid.2017.09.029.

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(2018). Microbial sequence typing in the genomic era. Infection, Genetics and Evolution, https://doi.org/10.1016/j.meegid.2017.09.022.

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(2018). Metagenomic exploration of soils microbial communities associated to Antarctic vascular plants. PeerJ Preprints, https://10.7287/peerj.preprints.26508v1.

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(2018). Genomic Analysis of 48 Paenibacillus larvae Bacteriophages. Viruses, http://www.mdpi.com/1999-4915/10/7/377.

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(2018). Genome sequence of two members of the chloroaromatic-degrading MT community: Pseudomonas reinekei MT1 and Achromobacter xylosoxidans MT3. Journal of Biotechnology, (275), pp. 13-16, https://doi.org/10.1016/j.jbiotec.2018.03.019.

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(2018). Cyclic AMP regulates bacterial persistence through repression of the oxidative stress response and SOS-dependent DNA repair in uropathogenic Escherichia coli. mBio, (9), 1, https://doi.org/10.1128/mBio.02144-17.

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(2018). Copper-induced increased expression of genes involved in photosynthesis, carotenoid synthesis and C assimilation in the marine alga Ulva compressa. BMC Genomics, https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-5226-4.

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(2018). Complete genome sequence of the marine Rhodococcus sp. H-CA8f isolated from Comau fjord in Northern Patagonia, Chile. Marine Genomics, https://doi.org/10.1016/j.margen.2018.01.004.

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(2018). Comparative genomic analysis of a new tellurite-resistant Psychrobacter strain isolated from the Antarctic Peninsula. PeerJ, (2018), 2, https://doi.org/10.7717/peerj.4402.

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(2017). The temporal dynamics of the tracheal microbiome in tracheostomised patients with and without lower respiratory infections. PLoS ONE, (12), 8, https://doi.org/10.1371/journal.pone.0182520.

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(2017). Multilocus Sequence Typing of Pathogens: Methods, Analyses, and Applications. Methods, Analyses, and Applications.. Genetics and Evolution of Infectious Diseases: Second Edition, pp. 383-404, https://doi.org/10.1016/B978-0-12-799942-5.00016-0.

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(2017). Genome sequence of streptomyces sp. H-KF8, a marine actinobacterium isolated from a northern chilean patagonian fjord. Genome Announcements, (5), 6, https://doi.org/10.1128/genomeA.01645-16.

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(2017). Draft genome sequences of five Enterococcus species isolated from the gut of patients with suspected Clostridium difficile infection. Genome Announcements, (5), 20, https://doi.org/10.1128/genomeA.00379-17.

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(2017). DNA Barcoding analysis of seafood accuracy in Washington, D.C. restaurants. PeerJ, https://peerj.com/articles/3234/.

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(2017). Computational Methods for Human Microbiome Analysis. Current protocols in microbiology, (47), pp. 1E.14.1-1E.14.17, https://doi.org/10.1002/cpmc.41.

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(2017). Comparative genomics analysis of a new Exiguobacterium strain from salar de huasco reveals a repertoire of stress-related genes and arsenic resistance. Frontiers in Microbiology, (8), MAR, https://doi.org/10.3389/fmicb.2017.00456.

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(2016). Redefining Healthy Urine: A Cross-Sectional Exploratory Metagenomic Study of People With and Without Bladder Dysfunction. Journal of Urology, (196), 2, pp. 579-587, https://doi.org/10.1016/j.juro.2016.01.088.

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(2016). Metataxonomic and metagenomic approaches vs. culture-based techniques for clinical pathology. Frontiers in Microbiology, (7), APR, https://doi.org/10.3389/fmicb.2016.00484.

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(2016). Genome sequence of Clostridium paraputrificum 373-A1 isolated in Chile from a patient infected with Clostridium difficile. Genome Announcements, (4), 6, https://doi.org/10.1128/genomeA.01178-16.

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(2016). Draft genome sequence of a multi-metal resistant bacterium Pseudomonas putida ATH-43 isolated from Greenwich Island, Antarctica. Frontiers in Microbiology, (7), NOV, https://doi.org/10.3389/fmicb.2016.01777.

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(2015). Integrating microbial and host transcriptomics to characterize asthma-associated microbial communities. BMC Medical Genomics, (8), 1, https://doi.org/10.1186/s12920-015-0121-1.

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(2015). Dual transcriptomic profiling of host and microbiota during health and disease in pediatric asthma. PLoS ONE, (10), 6, https://doi.org/10.1371/journal.pone.0131819.

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(2015). Concordance and discordance of sequence survey methods for molecular epidemiology. PeerJ, (2015), 2, https://doi.org/10.7717/peerj.761.

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(2015). Composition, taxonomy and functional diversity of the oropharynx microbiome in individuals with schizophrenia and controls. PeerJ, (2015), 8, https://doi.org/10.7717/peerj.1140.

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(2014). Whole genome single-nucleotide variation profile-based phylogenetic tree building methods for analysis of viral, bacterial and human genomes. Genomics, (104), 1, pp. 1-7, https://doi.org/10.1016/j.ygeno.2014.06.001.

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(2014). Single-molecule long-read 16S sequencing to characterize the lung microbiome from mechanically ventilated patients with suspected pneumonia. Journal of Clinical Microbiology, (52), 11, pp. 3913-3921, https://doi.org/10.1128/JCM.01678-14.

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(2014). PathoScope 2.0: A complete computational framework for strain identification in environmental or clinical sequencing samples. Microbiome, (2), 1, https://doi.org/10.1186/2049-2618-2-33.

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(2014). Clinical PathoScope: Rapid alignment and filtration for accurate pathogen identification in clinical samples using unassembled sequencing data. BMC Bioinformatics, (15), 1, https://doi.org/10.1186/1471-2105-15-262.

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(2013). Tat exon 1 exhibits functional diversity during HIV-1 subtype C primary infection. Journal of Virology, (87), 10, pp. 5732-5745, https://doi.org/10.1128/JVI.03297-12.

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(2013). Phage cluster relationships identified through single gene analysis. BMC Genomics, (14), 1, https://doi.org/10.1186/1471-2164-14-410.

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(2013). Pathoscope: Species identification and strain attribution with unassembled sequencing data. Genome Research, (23), 10, pp. 1721-1729, https://doi.org/10.1101/gr.150151.112.

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(2013). Pathogen typing in the genomics era: MLST and the future of molecular epidemiology. Infection, Genetics and Evolution, (16), pp. 38-53, https://doi.org/10.1016/j.meegid.2013.01.009.

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(2012). The evolution of HIV: Inferences using phylogenetics. Molecular Phylogenetics and Evolution, (62), 2, pp. 777-792, https://doi.org/10.1016/j.ympev.2011.11.019.

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(2012). Population genomics and phylogeography of an Australian dairy factory derived lytic bacteriophage. Genome Biology and Evolution, (4), 3, pp. 382-393, https://doi.org/10.1093/gbe/evs017.

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(2012). Genetic diversity and molecular epidemiology of HIV transmission. Future Virology, (7), 3, pp. 239-252, https://doi.org/10.2217/fvl.12.4.

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(2011). Molecular phylodynamics and protein modeling of infectious salmon anemia virus (ISAV). BMC Evolutionary Biology, (11), 1, https://doi.org/10.1186/1471-2148-11-349.

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(2010). Androgen receptor gene CAG and GGN repeat polymorphisms in Chilean men with primary severe spermatogenic failure. Journal of Andrology, (31), 6, pp. 552-559, https://doi.org/10.2164/jandrol.109.008821.

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