Results 81 to 90 of about 95,247 (306)

Challenges in benchmarking metagenomic profilers [PDF]

, 2021
Accurate microbial identification and abundance estimation are crucial for metagenomics analysis. Various methods for classification of metagenomic data and estimation of taxonomic profiles, broadly referred to as metagenomic profilers, have been ...
Shi Huang, Laxmi Parida, Zhu, Qiyun, Yoshiki Vázquez-Baeza, Haiminen, Niina, Meng Zhang, Niina Haiminen, Ho-Cheol Kim, Knight, Rob, Yang-Yu Liu, Liu, Yang-Yu, Rob Knight, Zheng Sun, Vázquez-Baeza, Yoshiki, Parida, Laxmi, Kim, Ho Cheol, Qiyun Zhu, Sun, Zheng, Kim, Ho-Cheol, Anna Paola Carrieri, Zhang, Meng, Huang, Shi, Carrieri, Anna Paola, Liu, Yang Yu   +23 more
core   +1 more source

A Microbial Lipid‐ATP Synthase Axis Fuels NK Cell Antitumor Activity

Advanced Science, EarlyView.
This study focuses on the mechanism by which gut microbiota‐derived outer membrane vesicles (OMVs) regulate NK cell antitumor activity. B. intestinalis is identified to decrease extra‐intestinal tumor growth via its OMVs enriched in sphingosine (SP).
Kaiyuan Yu, Xinyu Sun, Wanxia Ma, Jianming Yang, Xuan Sun, Lisong Zhang, Yumeng Liu, Tianshu Ren, Qi Wang, Jingyu Wang, Xiao Li, Xianping Peng, Liu Yang, Junqiang Lv, Zhi Yao, Zhi‐Song Zhang, Quan Wang   +16 more
wiley   +1 more source

Metagenomic analysis: the challenge of the data bonanza [PDF]

Briefings in Bioinformatics, 2012
Several thousand metagenomes have already been sequenced, and this number is set to grow rapidly in the forthcoming years as the uptake of high-throughput sequencing technologies continues. Hand-in-hand with this data bonanza comes the computationally overwhelming task of analysis. Herein, we describe some of the bioinformatic approaches currently used
Chris I. Hunter, Alex L. Mitchell, Philip Jones, Craig McAnulla, Sebastien Pesseat, Maxim Scheremetjew, Sarah Hunter   +6 more
openaire   +2 more sources

Phylogenetic classification of short environmental DNA fragments

, 2008
Krause L, Diaz NN, Goesmann A, et al. Phylogenetic classification of short environmental DNA fragments. Nucleic Acids Research. 2008;36(7):2230-2239.Metagenomics is providing striking insights into the ecology of microbial communities.
Nattkemper, Tim Wilhelm ; https://orcid.org/, Krause, Lutz, Kelley, Scott, Stoye, Jens, Stoye, Jens ; https://orcid.org/, Diaz, Naryttza N., Goesmann, Alexander ; https://orcid.org/, Nattkemper, Tim W., Rohwer, Forest, Goesmann, Alexander, Edwards, Robert A.   +10 more
core   +1 more source

Metadata of metagenomic analysis of nasopharyngeal Covid-infected people

, 2023
Metadata of metagenomic analysis of nasopharyngeal Covid-infected ...
Fernando Perez (6409748)
core   +1 more source

MFPD: A Multiple Fungal Pathogen Detection Pipeline Across Diverse Habitats

Advanced Science, EarlyView.
The MFPD pipeline integrates a comprehensive ITS reference database of fungal pathogens, optimized parameters, and algorithms tailored for both full‐length and subregion sequences that balance accuracy and computational efficiency; it enables high‐throughput, species‐level identification from amplicon sequencing data, supporting large‐scale ...
Yi Shen, Xinrun Yang, Jiabao Yu, Yaozhong Zhang, Tianjie Yang, Yang Gao, Xiaofang Wang, Alexandre Jousset, Waseem Raza, Fang‐Jie Zhao, Qirong Shen, Gaofei Jiang, Zhong Wei, Yangchun Xu   +13 more
wiley   +1 more source

Analysis of composition-based metagenomic classification [PDF]

BMC Genomics, 2012
An essential step of a metagenomic study is the taxonomic classification, that is, the identification of the taxonomic lineage of the organisms in a given sample. The taxonomic classification process involves a series of decisions. Currently, in the context of metagenomics, such decisions are usually based on empirical studies that consider one ...
Higashi, Susan, Barreto, André, Cantão, Maurício, de Vasconcelos, Ana   +3 more
openaire   +3 more sources

Tales from the crypt and coral reef: the successes and challenges of identifying new herpesviruses using metagenomics.

, 2015
Herpesviruses are ubiquitous double-stranded DNA viruses infecting many animals, with the capacity to cause disease in both immunocompetent and immunocompromised hosts.
Charlotte J. Houldcroft, Houldcroft, CJ, Breuer, J, Judith Breuer   +3 more
core   +1 more source

Engineering Microbial Particles for Next‐Generation Biomedical Platforms

Advanced Science, EarlyView.
Microbe‐derived particles (MDPs), which include extracellular vesicles, outer membrane vesicles, inclusion bodies, polysaccharide particles, and virus‐like particles, represent a rapidly expanding category of bioinspired nanomaterials. With their natural origin, intrinsic biocompatibility, and highly programmable functionality, MDPs serve as a ...
Yuting Li, Yunjie Lu, Ziyan Huang, Jianjiang Chen, Yanbin Liu, Lei Qin, Chao Wang, Yumin Wu   +7 more
wiley   +1 more source

FANTOM: Functional and taxonomic analysis of metagenomes [PDF]

BMC Bioinformatics, 2013
Abstract Background Interpretation of quantitative metagenomics data is important for our understanding of ecosystem functioning and assessing differences between various environmental samples. There is a need for an easy to use tool to explore the often complex metagenomics data in taxonomic and functional context.
Kemal Sanli, Fredrik H. Karlsson, Intawat Nookaew, Jens Nielsen   +3 more
openaire   +4 more sources