Results 41 to 50 of about 129,780 (292)

metagenome-atlas/atlas: Use python 3.8, ruamel.yaml>17 and panday 1.2

, 2021
ATLAS - Three commands to start analyzing your metagenome ...
Silas Kieser, Jackson M. Tsuji, Richard Allen White III, Christopher Bottoms, Joe Brown, Sean M. Colby, Vladimir Mikryukov, wangzc, Chris Overall, Mattias de Hollander, C. Titus Brown, Colin Brislawn   +11 more
core   +1 more source

High throughput whole rumen metagenome profiling using untargeted massively parallel sequencing

BMC Genetics, 2012
Background Variation of microorganism communities in the rumen of cattle (Bos taurus) is of great interest because of possible links to economically or environmentally important traits, such as feed conversion efficiency or methane emission levels.
Ross Elizabeth M, Moate Peter J, Bath Carolyn R, Davidson Sophie E, Sawbridge Tim I, Guthridge Kathryn M, Cocks Ben G, Hayes Ben J   +7 more
doaj   +1 more source

Enterobacteriaceae and Bacteroidaceae provide resistance to travel-associated intestinal colonization by multi-drug resistant Escherichia coli

Gut Microbes, 2022
Previous studies have shown high acquisition risks of extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E) among international travelers visiting antimicrobial resistance (AMR) hotspots.
Matthew Davies, Gianluca Galazzo, Jarne M. van Hattem, Maris S. Arcilla, Damian C. Melles, Menno D. de Jong, Constance Schultsz, Petra Wolffs, Alan McNally, Willem van Schaik, John Penders   +10 more
doaj   +1 more source

A Bioinformatician's Guide to Metagenomics [PDF]

Microbiology and Molecular Biology Reviews, 2008
SUMMARYAs random shotgun metagenomic projects proliferate and become the dominant source of publicly available sequence data, procedures for the best practices in their execution and analysis become increasingly important. Based on our experience at the Joint Genome Institute, we describe the chain of decisions accompanying a metagenomic project from ...
Kunin, V., Copeland, A., Lapidus, A., Mavromatis, K., Hugenholtz, P.   +4 more
openaire   +5 more sources

Presence of neutrophil extracellular traps (NETs) in different types of human urinary tract infections (UTI). A pilot study

Frontiers in Immunology
IntroductionActivated polymorphonuclear neutrophils (PMN) release neutrophil extracellular traps (NETs) composed of a web-like DNA core, concomitant with nuclear histones, granular peptides and enzymes.
Lena Schröder Alvarez, Lena Schröder Alvarez, Iván Conejeros, Gabriel Espinosa, Constanza Salinas-Varas, Benjamin Ott, Markus Weigel, Markus Weigel, Can Imirzalioglu, Can Imirzalioglu, Moritz Fritzenwanker, Moritz Fritzenwanker, Anita C. Windhorst, Torsten Hain, Torsten Hain, Anja Taubert, Carlos Hermosilla, Florian Wagenlehner, Florian Wagenlehner   +18 more
doaj   +1 more source

metagenome-atlas/atlas: With new GTDB v05

, 2020
ATLAS - Three commands to start analysing your metagenome ...
Silas Kieser, Jackson M. Tsuji, Richard Allen White III, Christopher Bottoms, Joe Brown, Sean M. Colby, Chris Overall, Mattias de Hollander, C. Titus Brown, Colin Brislawn   +9 more
core   +1 more source

metagenome-atlas/atlas: V2.0.0

, 2019
<p>ATLAS - Three commands to start analysing your metagenome data</p ...
Silas Kieser, Joe Brown
core   +1 more source

metagenome-atlas/atlas: Toiminnot

, 2021
This is a major update of metagenome-atlas. It was developed for the 3-day course in Finnland, that's also why it has a finish release name. What is new?
Silas Kieser, Richard Allen White III, Joe Brown, Vladimir Mikryukov, Yan Hui, Jackson M. Tsuji, Christopher Bottoms, Sean M. Colby, wangzc, Chris Overall, Mattias de Hollander, C. Titus Brown, Colin Brislawn   +12 more
core   +1 more source

Mining virulence genes using metagenomics.

PLoS ONE, 2011
When a bacterial genome is compared to the metagenome of an environment it inhabits, most genes recruit at high sequence identity. In free-living bacteria (for instance marine bacteria compared against the ocean metagenome) certain genomic regions are ...
Pedro Belda-Ferre, Raúl Cabrera-Rubio, Andrés Moya, Alex Mira   +3 more
doaj   +1 more source

metagenome-atlas/atlas: Use parquet and pyfastx to handle large gene catalogs

, 2022
What's Changed Make atlas handle large gene catalogs using parquet and pyfastx (Fix #515) parquet files can be opened in python with import pandas as pd coverage = pd.read_parquet("working_dir/Genecatalog/counts/median_coverage.parquet") coverage ...
Silas Kieser, Richard Allen White III, Joe Brown, Vladimir Mikryukov, Roshni Biswas, Yan Hui, Jackson M. Tsuji, Christopher Bottoms, Cedric Midoux, Jie Zhu, Sean M. Colby, wangzc, Chris Overall, Mattias de Hollander, C. Titus Brown, Colin Brislawn   +15 more
core   +1 more source