Results 41 to 50 of about 140,801 (215)

Metagenome-assembled genomes of Cyanobacteria in cryoconite

, 2022
These data are associated with the manuscript "Metagenomics reveals global-scale contrasts in nitrogen cycling and cyanobacterial light harvesting mechanisms in glacier cryoconite".
Takumi Murakami (10828728)
core   +1 more source

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

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

Multilocus sequence typing breathes life into a microbial metagenome [PDF]

, 2006
Shot-gun sequencing of DNA isolated from the environment and the assembly of metagenomes from the resulting data has considerably advanced the study of microbial diversity.
Vandamme Peter, Dowson, Chris G., Mahenthiralingam Eshwar, Dowson Chris G., Adam Baldwin, Pavel Drevinek, Vandamme, Peter, Elke Vanlaere, John J LiPuma, Vanlaere, Elke, Dowson, Christopher G., LiPuma, John J., Drevinek, Pavel, LiPuma John J., Baldwin Adam, Peter Vandamme, Baldwin, Adam, Chris G Dowson, Eshwar Mahenthiralingam, Drevinek Pavel, Vanlaere Elke, Dowson, Chris G, Mahenthiralingam, Eshwar, LiPuma, John J   +23 more
core   +2 more sources

metagenome-atlas/atlas: Large gene catalogs

, 2022
What's Changed Make atlas handle large gene catalogs using parquet and pyfastx parquet files can be opened in python with import pandas as pd coverage = pd.read_parquet("working_dir/Genecatalog/counts/median_coverage.parquet") coverage.set_index ...
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

Dissecting the role of the human microbiome in COVID-19 via metagenome-assembled genomes

Nature Communications, 2022
Here, using whole-metagenome shotgun sequencing data from patients with COVID-19 and controls, the authors reconstruct 11,584 microbial metagenome-assembled genomes (MAGs) including 5,403 non-redundant MAGs, revealing microbiota and metabolic pathways ...
Shanlin Ke, Scott T. Weiss, Yang-Yu Liu
doaj   +1 more source

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

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

MMINP: A computational framework of microbe-metabolite interactions-based metabolic profiles predictor based on the O2-PLS algorithm

Gut Microbes, 2023
The gut metabolome acts as an intermediary between the gut microbiota and host, and has tremendous diagnostic and therapeutic potential. Several studies have utilized bioinformatic tools to predict metabolites based on the different aspects of the gut ...
Wenli Tang, Huimin Zheng, Shuangbin Xu, Pan Li, Li Zhan, Xiao Luo, Zehan Dai, Qianwen Wang, Guangchuang Yu   +8 more
doaj   +1 more source

metagenome-atlas/atlas: Allow parameters in init qc

, 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, wangzc, Chris Overall, Mattias de Hollander, C. Titus Brown, Colin Brislawn   +10 more
core   +1 more source