Results 71 to 80 of about 30,341 (174)

SIMPER analysis of genera accounting for >75% of dissimilarity between thermophilic and mesophilic microbial communities based on metagenome binning.

, 2013
SIMPER analysis of genera accounting for >75% of dissimilarity between thermophilic and mesophilic microbial communities based on metagenome binning.
Jane Khudyakov (476902), Amitha P. Reddy (476899), Christopher W. Simmons (476900), Michael P. Thelen (200081), Steven W. Singer (162486), Patrik D’haeseleer (476901), Masood Hadi (331952), Helcio Burd (162438), Blake A. Simmons (108789), Jean S. VanderGheynst (254496)   +9 more
core   +1 more source

The Oral Microbiome of King Richard III of England

American Journal of Biological Anthropology, Volume 191, Issue 1, September 2026.
ABSTRACT Objectives Metagenomic investigations of ancient dental calculus provide insights into oral health, disease, and diet. Here, we analyze the dental calculus metagenome of King Richard III of England (1452–1485). Materials and Methods Dental calculus DNA was extracted from three teeth of King Richard III and shotgun sequenced to a depth of ...
Irina M. Velsko, Alexander Hübner, Zandra Fagernäs, James A. Fellows Yates, Allison E. Mann, Courtney A. Hofman, Andrew T. Ozga, Cecil M. Lewis Jr., Camilla Speller, Sarah Fiddyment, Michael Francken, Joachim Wahl, Johannes Krause, Anita Radini, Turi King, Christina Warinner   +15 more
wiley   +1 more source

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

From short to long: The impact of read length on metagenome assembly and binning

Methods in Ecology and Evolution
Metagenome sequencing not only plays a pivotal role in unravelling the genetic diversity and functional potential of microbial communities but also facilitates the discovery of genome context for microbial dark matter.
Xi Peng, Xingsheng Yang, Danrui Wang, Bo Zhao, Kai Feng, Qing He, Shang Wang, Ye Deng   +7 more
doaj   +1 more source

Evaluating the potential of assembler-binner combinations in recovering low-abundance and strain-resolved genomes from human metagenomes

Heliyon
Human-associated microbial communities are a complex mixture of bacterial species and diverse strains prevalent at varying abundances. Due to the inherent limitations of metagenomic assemblers and genome binning tools in recovering low-abundance species (
Hajra Qayyum, Muhammad Sarfraz Talib, Amjad Ali, Masood Ur Rehman Kayani   +3 more
doaj   +1 more source

Foundation Models for Microbiome Research: From Sequence Semantics to Community Dynamics and Multimodal World Models

Advanced Genetics, Volume 7, Issue 3, September 2026.
Microbiome foundation models are framed as a multiscale route from sequence semantics to community ecology, multimodal alignment and future world models. By learning transferable representations across cohorts, habitats and perturbations, this roadmap highlights how microbiome AI can move beyond association‐driven analysis toward interpretable ...
Haohong Zhang, Zixin Kang, Kang Ning
wiley   +1 more source

Binning meets taxonomy:TaxVAMB improves metagenome binning using bi-modal variational autoencoder

A common procedure for studying the microbiome is binning the sequenced contigs into metagenome-assembled genomes. Currently, unsupervised and self-supervised deep learning based methods using co-abundance and sequence based motifs such as ...
Gobbi, Alex, Nielsen, Mads, Rasmussen, Simon, Dougherty, Peter Erdmann, Kutuzova, Svetlana, Olsen, Nikoline S., Riber, Leise, Piera, Pau, Nissen, Jakob Nybo, Forero-Junco, Laura Milena, Christensen, Svend, Hansen, Lars Hestbjerg, Westergaard, Jesper Cairo, Nor Nielsen, Knud   +13 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

Antarctic soil microbiomes encode structurally conserved and phylogenetically diverse beta‐lactamases

iMetaOmics, Volume 3, Issue 3, September 2026.
An integrative metagenomic framework combining sequence, structural, and functional inference reveals a phylogenetically diverse and structurally conserved repertoire of putative beta‐lactamases across Antarctic soil microbiomes, with predominance of class A and subclass B3 enzymes and limited but detectable associations with mobile genetic elements ...
José Coche‐Miranda, Patricio Arros, Nicolás Canales, Camilo Berríos‐Pastén, Gastón Azziz, Rosalba Lagos, Julieta Orlando, Francisco P. Chávez, Andrés E. Marcoleta   +8 more
wiley   +1 more source

Evidence tiers for strain‐resolved long‐read metagenomics

iMetaOmics, Volume 3, Issue 3, September 2026.
Long‐read metagenomics links variants, repeats, and mobile elements across individual molecules and can reveal lineage turnover that is obscured at the species level. The strength of the resulting inference, however, depends on the type and genomic span of the recovered linkage. We distinguish four evidence units—strain profiles, local haplotype blocks,
Yanhua Han, Yunjuan Peng, Minghui Li, Xiaoyuan Wei, Jianmin Chai, Jiangchao Zhao, Ying Li, Feilong Deng   +7 more
wiley   +1 more source