Results 91 to 100 of about 1,840,918 (247)

Semi-automatic in silico gap closure enabled de novo assembly of two Dehalobacter genomes from metagenomic data. [PDF]

PLoS ONE, 2012
Typically, the assembly and closure of a complete bacterial genome requires substantial additional effort spent in a wet lab for gap resolution and genome polishing.
Shuiquan Tang, Yunchen Gong, Elizabeth A Edwards   +2 more
doaj   +1 more source

A Metagenome‐Assembled Genome Catalog From the Global Ruminant Microbiomes

Animal Research and One Health, EarlyView.
The Ruminant Gastrointestinal MAG Catalog (RGMC) is a comprehensive global resource offering 40,812 strain‐level genomes across 53 bacterial and 4 archaeal classes. It greatly surpasses prior efforts in scale and diversity, serving as an essential foundation for research in ruminant nutrition, microbial function, and methane mitigation.
Shizhe Zhang, Qiushuang Li, Bingzi Ouyang, Wenxing Wang, Xiang Zhou, Xiumin Zhang, Rong Wang, Zhiliang Tan, Min Wang   +8 more
wiley   +1 more source

Machine learning based prediction of functional capabilities in metagenomically assembled microbial genomes [PDF]

, 2018
Abstract The increasing popularity of genome resolved meta genomics - the binning of genomes of potentially uncultured organisms direct from the environmental DNA - has resulted in a deluge of draft genomes. There is a pressing need to develop methods to interpret this data.
Farrell, Fred, Soyer, Orkun S., Quince, Christopher   +2 more
openaire   +1 more source

ExMODE: A comprehensive resource for extremophile genomic and functional exploration

iMetaOmics, EarlyView.
ExMODE (https://db.genomics.cn/exmode/) integrates 3518 samples to build a unified extremophile resource, which hosts 1.35 billion habitat‐specific non‐redundant genes, 5.25 million representative protein structures, 67,026 metagenome‐assembled genomes (MAGs), and 164,132 biosynthetic gene clusters (BGCs). By combining sequence‐, structure‐, and genome‐
Denghui Li, Kailong Ma, Xiaoqiang Li, Jieni Wang, Zhen Cui, Yulu Zhang, Weiwen Wang, Jiawei Tong, Yang Guo, Zongan Wang, Peiyun Zeng, Jieyu Wang, Xiaokai Xu, Nannan Zhang, Yingying Zhang, Jing Chen, Qingjiang Hu, Wenzhen Yang, Zhiyong Li, Tao Yang, Wensi Du, Zhicheng Xu, Zhen Yue, Jian Wang, Guangyi Fan, Weijia Zhang, Xun Xu, Liujie Huo, Xiaofeng Wei, Liang Meng, Shanshan Liu   +30 more
wiley   +1 more source

Benchmarking short-, long- and hybrid-read assemblers for metagenome sequencing of complex microbial communities

Microbiology
Metagenome community analyses, driven by the continued development in sequencing technology, is rapidly providing insights in many aspects of microbiology and becoming a cornerstone tool. Illumina, Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio) are the leading technologies, each with their own advantages and drawbacks.
Gleb Goussarov, Mohamed Mysara, Ilse Cleenwerck, Jürgen Claesen, Natalie Leys, Peter Vandamme, Rob Van Houdt   +6 more
openaire   +2 more sources

Multi‐omics reveals gastrointestinal metabolic disorder‐induced diarrhea in postpartum dairy cows

iMetaOmics, EarlyView.
Nutritional diarrhea is a pervasive, costly challenge in dairy production. Using integrated metagenomic and metabolomic profiling, we identified coordinated microbial and metabolic alterations across the rumen, hindgut, and serum. In the rumen, enrichment of Prevotella sp.
Weixuan Tang, Yangyi Hao, Jiawei Zhang, Yajing Wang, Zhijun Cao, Hongjian Yang, Wei Wang, Shengli Li   +7 more
wiley   +1 more source

Metagenome-assembled microbial genomes (n = 3,448) of the oral microbiomes of Tibetan and Duroc pigs

Scientific Data
Compared with leaner breeds, local Chinese pig breeds have distinct intestinal microbial, as determined by metagenomic techniques, and the interactions between oral microorganisms and their hosts are also gradually being clarified. However, the high host genome content means that few metagenome-based oral microbiomes have been reported.
Hong Hu, Ying Huang, Fuyan Yang, Liangru Ma, Junjie Zhang, Xu Deng, Nan Ma, Kunping Wang, Ye Tao, Qin Lin, Yanfei Li, Xi Bai, Hongbin Pan   +12 more
openaire   +3 more sources

Metagenomic and culture‐based insights into host and plasmid contexts of high‐risk ARGs in poultry farm environments

iMetaOmics, EarlyView.
Shotgun metagenomics and culture‐based isolate genomics revealed position‐associated high‐risk antibiotic resistance genes (ARGs) signals across poultry manure piles and surrounding soils. Culture‐confirmed Enterobacteriaceae and IncHI2A‐related blaNDM‐5 plasmid backgrounds further highlight priority host‐ARG‐plasmid contexts for farm antimicrobial ...
Yaling Wang, Lianwei Ye, Linan He, Zhenlong Wu, Yiwen Yang, Sheng Chen   +5 more
wiley   +1 more source

Metagenome-assembled-genomes (MAGs)

, 2022
MAGs were constructed using snakemake metagenome workflow in anvi'o (Eren et al., 2015).  A detailed explanation on the workflow (such as the softwares used in anvi'o) can be found in the supplementary material of the paper.
Ömer Coskun (9725927)
core   +1 more source

Multi‐omics–driven precision medicine

iMeta, EarlyView.
Multi‐omics‐driven precision medicine (MODPM) provides a multiscale, continuously learnable framework that integrates genomics, epigenomics, transcriptomics, proteomics, metabolomics, microbiome profiles, and clinical data. Powered by artificial intelligence and foundation models, MODPM enables cross‐modal representation learning, contextual modeling ...
Huibo Li, Zhe Zhao, Yifan Zhang, Yao Ma, Gaofei Hu, Min Zeng, Zhanqun Yang, Zixuan Zhao, Xin Zhou, Wei Hu, Yuxuan Sun, Meng Su, Jun Li, Matthew Whiteman, Wei Fu, Chao Zhong, Lemin Zheng, Long Chen, Hairong Lv, Rongsheng Zhao, Yi Zhun Zhu   +20 more
wiley   +1 more source