Bibliografías temáticas / Human metagenomic

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Literatura académica sobre el tema "Human metagenomic"

Autor: Grafiati
Publicado: 10 de marzo de 2023

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Artículos de revistas sobre el tema "Human metagenomic"

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Nalbantoglu, O. Ufuk. "Information Theoretic Metagenome Assembly Allows the Discovery of Disease Biomarkers in Human Microbiome." Entropy 23, no. 2 (2021): 187. http://dx.doi.org/10.3390/e23020187.

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Quantitative metagenomics is an important field that has delivered successful microbiome biomarkers associated with host phenotypes. The current convention mainly depends on unsupervised assembly of metagenomic contigs with a possibility of leaving interesting genetic material unassembled. Additionally, biomarkers are commonly defined on the differential relative abundance of compositional or functional units. Accumulating evidence supports that microbial genetic variations are as important as the differential abundance content, implying the need for novel methods accounting for the genetic va
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Filipic, Brankica, Katarina Novovic, David J. Studholme, et al. "Shotgun metagenomics reveals differences in antibiotic resistance genes among bacterial communities in Western Balkans glacial lakes sediments." Journal of Water and Health 18, no. 3 (2020): 383–97. http://dx.doi.org/10.2166/wh.2020.227.

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Abstract Long-term overuse of antibiotics has driven the propagation and spreading of antibiotic resistance genes (ARGs) such as efflux pumps in the environment, which can be transferred to clinically relevant pathogens. This study explored the abundance and diversity of ARGs and mobile genetic elements within bacterial communities from sediments of three Western Balkans glacial lakes: Plav Lake (high impact of human population), Black Lake (medium impact of human population) and Donje Bare Lake (remote lake, minimal impact of human population) via shotgun metagenomics. Assembled metagenomic s
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Bai, Geng-Hao, Sheng-Chieh Lin, Yi-Hsiang Hsu, and Shih-Yen Chen. "The Human Virome: Viral Metagenomics, Relations with Human Diseases, and Therapeutic Applications." Viruses 14, no. 2 (2022): 278. http://dx.doi.org/10.3390/v14020278.

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The human body is colonized by a wide range of microorganisms. The field of viromics has expanded since the first reports on the detection of viruses via metagenomic sequencing in 2002. With the continued development of reference materials and databases, viral metagenomic approaches have been used to explore known components of the virome and discover new viruses from various types of samples. The virome has attracted substantial interest since the outbreak of the coronavirus disease 2019 (COVID-19) pandemic. Increasing numbers of studies and review articles have documented the diverse virome
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Simon, Carola, and Rolf Daniel. "Metagenomic Analyses: Past and Future Trends." Applied and Environmental Microbiology 77, no. 4 (2010): 1153–61. http://dx.doi.org/10.1128/aem.02345-10.

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ABSTRACTMetagenomics has revolutionized microbiology by paving the way for a cultivation-independent assessment and exploitation of microbial communities present in complex ecosystems. Metagenomics comprising construction and screening of metagenomic DNA libraries has proven to be a powerful tool to isolate new enzymes and drugs of industrial importance. So far, the majority of the metagenomically exploited habitats comprised temperate environments, such as soil and marine environments. Recently, metagenomes of extreme environments have also been used as sources of novel biocatalysts. The empl
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Zorrilla, Francisco, Filip Buric, Kiran R. Patil, and Aleksej Zelezniak. "metaGEM: reconstruction of genome scale metabolic models directly from metagenomes." Nucleic Acids Research 49, no. 21 (2021): e126-e126. http://dx.doi.org/10.1093/nar/gkab815.

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Abstract Metagenomic analyses of microbial communities have revealed a large degree of interspecies and intraspecies genetic diversity through the reconstruction of metagenome assembled genomes (MAGs). Yet, metabolic modeling efforts mainly rely on reference genomes as the starting point for reconstruction and simulation of genome scale metabolic models (GEMs), neglecting the immense intra- and inter-species diversity present in microbial communities. Here, we present metaGEM (https://github.com/franciscozorrilla/metaGEM), an end-to-end pipeline enabling metabolic modeling of multi-species com
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Kasmanas, Jonas Coelho, Alexander Bartholomäus, Felipe Borim Corrêa, et al. "HumanMetagenomeDB: a public repository of curated and standardized metadata for human metagenomes." Nucleic Acids Research 49, no. D1 (2020): D743—D750. http://dx.doi.org/10.1093/nar/gkaa1031.

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Abstract Metagenomics became a standard strategy to comprehend the functional potential of microbial communities, including the human microbiome. Currently, the number of metagenomes in public repositories is increasing exponentially. The Sequence Read Archive (SRA) and the MG-RAST are the two main repositories for metagenomic data. These databases allow scientists to reanalyze samples and explore new hypotheses. However, mining samples from them can be a limiting factor, since the metadata available in these repositories is often misannotated, misleading, and decentralized, creating an overly
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Nayfach, Stephen, David Páez-Espino, Lee Call, et al. "Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome." Nature Microbiology 6, no. 7 (2021): 960–70. http://dx.doi.org/10.1038/s41564-021-00928-6.

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AbstractBacteriophages have important roles in the ecology of the human gut microbiome but are under-represented in reference databases. To address this problem, we assembled the Metagenomic Gut Virus catalogue that comprises 189,680 viral genomes from 11,810 publicly available human stool metagenomes. Over 75% of genomes represent double-stranded DNA phages that infect members of the Bacteroidia and Clostridia classes. Based on sequence clustering we identified 54,118 candidate viral species, 92% of which were not found in existing databases. The Metagenomic Gut Virus catalogue improves detec
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Rahman, Mohammad Arifur, and Huzefa Rangwala. "IDMIL: an alignment-free Interpretable Deep Multiple Instance Learning (MIL) for predicting disease from whole-metagenomic data." Bioinformatics 36, Supplement_1 (2020): i39—i47. http://dx.doi.org/10.1093/bioinformatics/btaa477.

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Abstract Motivation The human body hosts more microbial organisms than human cells. Analysis of this microbial diversity provides key insight into the role played by these microorganisms on human health. Metagenomics is the collective DNA sequencing of coexisting microbial organisms in an environmental sample or a host. This has several applications in precision medicine, agriculture, environmental science and forensics. State-of-the-art predictive models for phenotype predictions from metagenomic data rely on alignments, assembly, extensive pruning, taxonomic profiling and reference sequence
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Jaiani, Ekaterine, Ia Kusradze, Tamar Kokashvili, et al. "Microbial Diversity and Phage–Host Interactions in the Georgian Coastal Area of the Black Sea Revealed by Whole Genome Metagenomic Sequencing." Marine Drugs 18, no. 11 (2020): 558. http://dx.doi.org/10.3390/md18110558.

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Viruses have the greatest abundance and highest genetic diversity in marine ecosystems. The interactions between viruses and their hosts is one of the hot spots of marine ecology. Besides their important role in various ecosystems, viruses, especially bacteriophages and their gene pool, are of enormous interest for the development of new gene products with high innovation value. Various studies have been conducted in diverse ecosystems to understand microbial diversity and phage–host interactions; however, the Black Sea, especially the Eastern coastal area, remains among the least studied ecos
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Liu, Michael Y., Paul Worden, Leigh G. Monahan, et al. "Evaluation of ddRADseq for reduced representation metagenome sequencing." PeerJ 5 (September 19, 2017): e3837. http://dx.doi.org/10.7717/peerj.3837.

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BackgroundProfiling of microbial communities via metagenomic shotgun sequencing has enabled researches to gain unprecedented insight into microbial community structure and the functional roles of community members. This study describes a method and basic analysis for a metagenomic adaptation of the double digest restriction site associated DNA sequencing (ddRADseq) protocol for reduced representation metagenome profiling.MethodsThis technique takes advantage of the sequence specificity of restriction endonucleases to construct an Illumina-compatible sequencing library containing DNA fragments
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Tesis sobre el tema "Human metagenomic"

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Rampelli, Simone <1985&gt. "Metagenomic trajectory of gut microbiome in the human lifespan." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2014. http://amsdottorato.unibo.it/6333/1/Rampelli_thesis_2014.pdf.

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Co-evolving with the human host, gut microbiota establishes configurations, which vary under the pressure of inflammation, disease, ageing, diet and lifestyle. In order to describe the multi-stability of the microbiome-host relationship, we studied specific tracts of the bacterial trajectory during the human lifespan and we characterized peculiar deviations from the hypothetical development, caused by disease, using molecular techniques, such as phylogenetic microarray and next-generation sequencing. Firstly, we characterized the enterocyte-associated microbiota in breast-fed infants and ad
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Rampelli, Simone <1985&gt. "Metagenomic trajectory of gut microbiome in the human lifespan." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2014. http://amsdottorato.unibo.it/6333/.

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Co-evolving with the human host, gut microbiota establishes configurations, which vary under the pressure of inflammation, disease, ageing, diet and lifestyle. In order to describe the multi-stability of the microbiome-host relationship, we studied specific tracts of the bacterial trajectory during the human lifespan and we characterized peculiar deviations from the hypothetical development, caused by disease, using molecular techniques, such as phylogenetic microarray and next-generation sequencing. Firstly, we characterized the enterocyte-associated microbiota in breast-fed infants and ad
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Huang, Kun. "Evolutionary analysis of the human microbiome using ancient metagenomic samples." Doctoral thesis, Università degli studi di Trento, 2021. http://hdl.handle.net/11572/318833.

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Studying the evolutionary history of human microbiome members is indispensable to understanding how our microbiota complexity has been shaped over time. While recent decades have witnessed remarkable progress in investigation of the human microbiome within different evolutionary contexts, reconstructing a time-resolved divergence history for human microbiome members is still extremely challenging. Longitudinal metagenomics studies have shown the potential of addressing such challenges, but it is limited in tracking the evolutionary change in a short term. By contrast, leveraging the microbial
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Gaudin, Maxime. "Human RNA bait library depletion for human (viral) pathogen discovery using shotgun metagenomic sequencing." Thesis, Aix-Marseille, 2018. http://www.theses.fr/2018AIXM0697/document.

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La métagénomique virale est une approche prometteuse pour la détection et l’identification sans a priori de potentiels nouveaux pathogènes.Cependant, son utilisation reste encore marginale en raison de l’importante contamination des viromes par les séquences nucléiques de l’hôte.L'objectif de cette thèse était d’améliorer l’approche de métagénomique pour le diagnostic clinique de maladies infectieuses virales en augmentant le ratio de séquences pathogène/hôte par déplétion des acides nucléiques humains.Le premier chapitre consiste en une synthèse bibliographique des approches de métagénomique
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Easton, S. "Functional and metagenomic analysis of the human tongue dorsum using phage display." Thesis, University College London (University of London), 2009. http://discovery.ucl.ac.uk/18512/.

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It is well established that mixed microbial communities contain organisms which have not been studied by conventional culture-based methods. In the human oral cavity this number is estimated at around 50%. Commensal bacteria develop and maintain an intimate relationship with human cells without triggering proinflammatory mechanisms and this study aims to explore this by searching for bacterial proteins which facilitate binding to the human tongue dorsum and wider oral cavity. Metagenomic DNA from the human tongue dorsum of 9 volunteers was extracted and a phage display library created, to our
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Szczepanska, Anna. "Functional metagenomic analysis of carbohydrate degrading enzymes from the human gut microbiota." Thesis, University of East Anglia, 2011. https://ueaeprints.uea.ac.uk/47983/.

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The gut microbiota is a complex and diverse microbial community that is adapted to a carbohydrate-rich ecosystem. Plant cell wall components (cellulose, hemicelluloses and pectins), resistant starch and various oligosaccharides reach the colon by escaping digestion in the upper gastrointestinal tract. Fermentation of these dietary carbohydrates by the gut microbiota has well-recognised beneficial effects on host health. The microbial community in the human gut requires specific enzymes to efficiently degrade these carbohydrates. In this project, a culture-independent approach based on function
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Al-Jarbou, Ahmed. "Metagenomic analysis of the human mouth virus population and characterisation of two lytic viruses." Thesis, University of Leicester, 2009. http://hdl.handle.net/2381/8221.

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Viruses are biological agents that infect cellular organisms. Most viruses are bacteriophages, these are the most abundant biological entities on earth. Not much is known about virus diversity in the human mouth, including dental plaque, compared to other environments. A culture-independent based approach was tried using metagenomic analysis to characterize uncultured virus gene fragments in human dental plaque. The isolated viral genomes were amplified using a multiple displacement amplification method. Eighty, eleven and ten clones were sequenced from three volunteers, respectively. TBLASTX
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Tansirichaiya, Supathep. "Investigation of mobile genetic elements and antimicrobial resistance genes in human oral metagenomic DNA." Thesis, University College London (University of London), 2017. http://discovery.ucl.ac.uk/10041034/.

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Antibiotic resistance is currently one of the major global healthcare problems. Bacteria can become resistant by acquiring resistance genes from other bacteria. This process is usually facilitated by mobile genetic elements (MGEs), a type of DNA that can move from one site to another site within bacterial genome, and often between bacterial cells. The human oral cavity has been shown to harbour various antimicrobial resistance genes (ARGs). The aim of this research is to study the fundamental biology and the association between MGEs and ARGs present in human oral bacteria by both sequence and
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Temisak, Sasithon. "Assessing the accuracy of metagenomic analysis of microorganisms involved in human diseases using control materials." Thesis, St George's, University of London, 2015. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.703283.

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Metagenomics is the study of the collective genomes of the members of a microbial community. In contrast to conventional culture methods, sequence-based metagenomics exclusively relies on sequence analysis without culturing microorganisms. This approach has revolutionised our understanding of the complexity of microbiomes. As such, microbial profiling, particularly of microbiomes in humans that appear to play key roles in numerous disease phenotype, may provide information to help define associated underlying aetiological mechanisms. However, a number of available metagenomic approaches have d
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Ahiska, Bartu. "Reference-free identification of genetic variation in metagenomic sequence data using a probabilistic model." Thesis, University of Oxford, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.561121.

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Microorganisms are an indispensable part of our ecosystem, yet the natural metabolic and ecological diversity of these organisms is poorly understood due to a historical reliance of microbiology on laboratory grown cultures. The awareness that this diversity cannot be studied by laboratory isolation, together with recent advances in low cost scalable sequencing technology, have enabled the foundation of culture-independent microbiology, or metagenomics. The study of environmental microbial samples with metagenomics has led to many advances, but a number of technological and methodological chal
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Libros sobre el tema "Human metagenomic"

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Nelson, Karen E. Metagenomics of the human body. Springer, 2011.

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Nelson, Karen E., ed. Metagenomics of the Human Body. Springer New York, 2011. http://dx.doi.org/10.1007/978-1-4419-7089-3.

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Nelson, Karen E. Metagenomics of the human body. Springer, 2011.

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Epigenetics and human health: Linking hereditary, environmental, and nutritional aspects. Wiley-VCH, 2010.

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Probiotic bacteria and their effect on human health and well-being. Karger, 2013.

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Raffaetà, Roberta. Metagenomic Futures: How Microbiome Research Is Reconfiguring Health and What It Means to Be Human. Taylor & Francis Group, 2022.

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Raffaetà, Roberta. Metagenomic Futures: How Microbiome Research Is Reconfiguring Health and What It Means to Be Human. Taylor & Francis Group, 2022.

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Raffaetà, Roberta. Metagenomic Futures: How Microbiome Research Is Reconfiguring Health and What It Means to Be Human. Routledge, 2022.

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Raffaetà, Roberta. Metagenomic Futures: How Microbiome Research Is Reconfiguring Health and What It Means to Be Human. Routledge, Chapman & Hall, Incorporated, 2022.

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Raffaetà, Roberta. Metagenomic Futures: How Microbiome Research Is Reconfiguring Health and What It Means to Be Human. Taylor & Francis Group, 2022.

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Capítulos de libros sobre el tema "Human metagenomic"

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Bermúdez-Humarán, Luis G. "Metagenomic analysis of the human microbiome." In The Human Microbiota and Chronic Disease. John Wiley & Sons, Inc., 2016. http://dx.doi.org/10.1002/9781118982907.ch6.

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Bhatia, Sonu, Vivek Tiwari, Neetu Sharma, Abhinashi Singh Sodhi, and Navneet Batra. "Metagenomic Insights of Human Oral Microbiome." In Genomic, Proteomics, and Biotechnology. CRC Press, 2022. http://dx.doi.org/10.1201/9781003220831-10.

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Wang, Jun. "Human Gut Microbial Gene by Metagenomic Sequencing." In Encyclopedia of Metagenomics. Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4614-6418-1_752-1.

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Wang, Jun. "Human Gut Microbial Genes by Metagenomic Sequencing." In Encyclopedia of Metagenomics. Springer US, 2015. http://dx.doi.org/10.1007/978-1-4899-7478-5_752.

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Li, Huiying. "Metagenomic Study, Human Skin Microbiome Associated with Acne, Project." In Encyclopedia of Metagenomics. Springer US, 2015. http://dx.doi.org/10.1007/978-1-4899-7475-4_532.

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Li, Huiying. "Metagenomic Study, Human Skin Microbiome Associated with Acne, Project." In Encyclopedia of Metagenomics. Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4614-6418-1_532-4.

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Singh, Hemender, Indu Sharma, and Varun Sharma. "Epidemiological Perspectives of Human Health Through Metagenomic Research." In Metagenomics: Techniques, Applications, Challenges and Opportunities. Springer Singapore, 2020. http://dx.doi.org/10.1007/978-981-15-6529-8_9.

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Schnabl, Bernd. "Metagenomic Applications and the Potential for Understanding Chronic Liver Disease." In Metagenomics of the Human Body. Springer New York, 2011. http://dx.doi.org/10.1007/978-1-4419-7089-3_13.

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Jones, B. V., and C. G. M. Gahan. "Metagenomic Analysis of Bile Salt Hydrolases in the Human Gut Microbiome." In Encyclopedia of Metagenomics. Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4614-6418-1_777-1.

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Jones, Brian V., and C. G. M. Gahan. "Metagenomic Analysis of Bile Salt Hydrolases in the Human Gut Microbiome." In Encyclopedia of Metagenomics. Springer US, 2015. http://dx.doi.org/10.1007/978-1-4899-7478-5_777.

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Actas de conferencias sobre el tema "Human metagenomic"

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Zhang, J., Q. Chen, Y. Qiu, W. Zeng, and X. Wei. "5 Cases of Talaromycosis in Human Immunodeficiency Virus-Uninfected Patients Early Diagnosed by Metagenomic Next-Generation Sequencing." In American Thoracic Society 2020 International Conference, May 15-20, 2020 - Philadelphia, PA. American Thoracic Society, 2020. http://dx.doi.org/10.1164/ajrccm-conference.2020.201.1_meetingabstracts.a5485.

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Qi, Xianghui, Lang Xu, Zexi Yang, et al. "Cloning and analysis of xylose isomerase from metagenome." In International conference on Human Health and Medical Engineering. WIT Press, 2014. http://dx.doi.org/10.2495/hhme130211.

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Nuhamunada, Matin, Gregorius Altius Pratama, Setianing Wikanthi, Mohamad Khoirul Anam, R. Ludhang Pradhipta Rizki, and Nastiti Wijayanti. "Data Mining and Comparative Analysis of Human Skin Microbiome from EBI Metagenomics Database." In 2018 1st International Conference on Bioinformatics, Biotechnology, and Biomedical Engineering (BioMIC). IEEE, 2018. http://dx.doi.org/10.1109/biomic.2018.8610588.

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Informes sobre el tema "Human metagenomic"

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Beckstrom-Sternberg, Stephen. Bioinformatic Tools for Metagenomic Analysis of Pathogen Backgrounds and Human Microbial Communities. Defense Technical Information Center, 2010. http://dx.doi.org/10.21236/ada581677.

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Mizrahi, Itzhak, and Bryan A. White. Exploring the role of the rumen microbiota in determining the feed efficiency of dairy cows. United States Department of Agriculture, 2011. http://dx.doi.org/10.32747/2011.7594403.bard.

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Expanding world hunger calls for increasing available food resources. Ruminants have the remarkable ability to convert human-indigestible plant biomass into human-digestible food products, due to a complex microbiome residing in the rumen compartment of their upper digestive tract. One way to tackle the problem of diminishing food resources is to increase the animals' energetic efficiency, i.e., the efficiency with which they convert energy from feed, thereby increasing food availability while lowering the environmental burden, as these animals would produce more and eat less. We hypothesize t
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Mizrahi, Itzhak, and Bryan A. White. Uncovering rumen microbiome components shaping feed efficiency in dairy cows. United States Department of Agriculture, 2015. http://dx.doi.org/10.32747/2015.7600020.bard.

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Ruminants provide human society with high quality food from non-human-edible resources, but their emissions negatively impact the environment via greenhouse gas production. The rumen and its resident microorganisms dictate both processes. The overall goal of this project was to determine whether a causal relationship exists between the rumen microbiome and the host animal's physiology, and if so, to isolate and examine the specific determinants that enable this causality. To this end, we divided the project into three specific parts: (1) determining the feed efficiency of 200 milking cows, (2)
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Haynes, Dr Edward, Chris Conyers, Dr Marc Kennedy, Roy Macarthur, Sam McGreig, and Dr John Walshaw. What is the Burden of Antimicrobial Resistance Genes in Selected Ready-to-Eat Foods? Food Standards Agency, 2021. http://dx.doi.org/10.46756/sci.fsa.bsv485.

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This study was designed to get a broad estimate of the presence and the types of antimicrobial resistance genes across 52 simple ready-to-eat foods. It was also carried out to understand the benefits and drawbacks of using metagenomic sequencing, a fairly new technology, to study AMR genes. An antimicrobial is any substance that kills or inhibits the growth of microorganisms. It includes antibiotics which are used to treat bacterial infections in both humans and animals. Given the relevant selective pressures, the bacteria itself can change and find ways to survive the effects of an antimicrobi
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