Results 51 to 60 of about 162,178 (247)

Pavian: interactive analysis of metagenomics data for microbiome studies and pathogen identification

Bioinform., 2019
SUMMARY Pavian is a web application for exploring classification results from metagenomics experiments. With Pavian, researchers can analyze, visualize, and transform results from various classifiers - such as Kraken, Centrifuge, and MethaPhlAn - using ...
F. Breitwieser, S. Salzberg
semanticscholar   +1 more source

Biotechnological applications of functional metagenomics in the food and pharmaceutical industries [PDF]

, 2015
peer-reviewedMicroorganisms are found throughout nature, thriving in a vast range of environmental conditions. The majority of them are unculturable or difficult to culture by traditional methods.
Alvarez-Ordonez, Avelino, Cotter, Paul D., Coughlan, Laura M., Hill, Colin   +3 more
core   +1 more source

Hydrogen cyanide in the rhizosphere: not suppressing plant pathogens, but rather regulating availability of phosphate

Frontiers in Microbiology, 2016
Plant growth promoting rhizobacteria produce chemical compounds with different benefits for the plant. Among them, HCN is recognized as a biocontrol agent, based on its ascribed toxicity against plant pathogens.
Tomaž Rijavec, Tomaž Rijavec, Aleš Lapanje, Aleš Lapanje, Aleš Lapanje   +4 more
doaj   +1 more source

A Vavilovian approach to discovering crop-associated microbes with potential to enhance plant immunity [PDF]

, 2014
Through active associations with a diverse community of largely non-pathogenic microbes, a plant may be thought of as possessing an “extended genotype,” an interactive cross-organismal genome with potential, exploitable implications for plant immunity ...
Broders, Kirk, Hale, Iago L., Iriarte, Gloria   +2 more
core   +3 more sources

Pattern-Recognition Receptors and Cervical Microbiome in Patients with Early Miscarriages

International Journal of Inflammation
Early miscarriages are one of the main causes of reproductive losses. The objective of this study was to estimate Toll- and NOD-like receptors mRNA expression levels and their correlation with microbiome composition in the endocervix of patients with 1st
Mariya V. Gryaznova, Olesya N. Kozarenko, Victoria M. Ivannikova, Yuliya D. Smirnova, Inna Y. Burakova, Oxana B. Altukhova, Natalia I. Samborskaya, Mikhail Y. Syromyatnikov, Alexander Y. Maslov, Olga P. Lebedeva   +9 more
doaj   +1 more source

Maximal viral information recovery from sequence data using VirMAP

Nature Communications, 2018
Viral taxonomic characterization from metagenomic data suffers from high background noise and signal crosstalk. Here, the authors develop VirMAP, a novel pipeline for analyses of metagenomic data that classifies viral reconstructions independent of ...
Nadim J Ajami, Matthew C. Wong, Matthew C. Ross, Richard E. Lloyd, Joseph F. Petrosino   +4 more
doaj   +1 more source

Metagenome of a polluted river reveals a reservoir of metabolic and antibiotic resistance genes

Environmental Microbiome, 2019
Background Yamuna, a major tributary of Ganga, which flows through the national capital region of Delhi, is among the major polluted rivers in India. The accumulation of various effluents, toxic chemicals, heavy metals, and increased organic load in the ...
Parul Mittal, Vishnu Prasoodanan PK, Darshan B. Dhakan, Sanjiv Kumar, Vineet K. Sharma   +4 more
doaj   +1 more source

New techniques to characterise the vaginal microbiome in pregnancy [PDF]

, 2016
Understanding of the vaginal microbiome in health and disease is essential to screen, detect and manage complications in pregnancy. One of the major complications of pregnancy is preterm birth, which is the leading world-wide cause of death and ...
Kaakoush, N, Mendz, G, Quinlivan, J
core   +3 more sources

An overlooked phenomenon: complex interactions of potential error sources on the quality of bacterial de novo genome assemblies

BMC Genomics
Background Parameters adversely affecting the contiguity and accuracy of the assemblies from Illumina next-generation sequencing (NGS) are well described.
Zoltán Rádai, Alex Váradi, Péter Takács, Nikoletta Andrea Nagy, Nicholas Schmitt, Eszter Prépost, Gábor Kardos, Levente Laczkó   +7 more
doaj   +1 more source

The gut mycobiome of the Human Microbiome Project healthy cohort

Microbiome, 2017
Background Most studies describing the human gut microbiome in healthy and diseased states have emphasized the bacterial component, but the fungal microbiome (i.e., the mycobiome) is beginning to gain recognition as a fundamental part of our microbiome ...
Andrea K. Nash, Thomas A. Auchtung, Matthew C. Wong, Daniel P. Smith, Jonathan R. Gesell, Matthew C. Ross, Christopher J. Stewart, Ginger A. Metcalf, Donna M. Muzny, Richard A. Gibbs, Nadim J. Ajami, Joseph F. Petrosino   +11 more
doaj   +1 more source