Results 51 to 60 of about 1,783 (178)

SAMSA: a comprehensive metatranscriptome analysis pipeline

BMC Bioinformatics, 2016
Abstract Background Although metatranscriptomics—the study of diverse microbial population activity based on RNA-seq data—is rapidly growing in popularity, there are limited options for biologists to analyze this type of data.
Samuel T. Westreich, Ian Korf, David A. Mills, Danielle G. Lemay   +3 more
openaire   +5 more sources

Relating the metatranscriptome and metagenome of the human gut [PDF]

Proceedings of the National Academy of Sciences, 2014
Significance Recent years have seen incredible growth in both the scale and specificity of projects analyzing the microbial organisms living in and on the human body (the human microbiome). Such studies typically require subjects to report to clinics for sample collection, a complicated practice that is impractical for large studies ...
E. A. Franzosa, X. C. Morgan, Segata, Nicola, L. Waldron, J. Reyes, AM Earl, G. Giannoukos, MR Boylan, D. Ciulla, D. Gevers, J. Izard, WS Garrett, AT Chan, C. Huttenhower   +13 more
openaire   +3 more sources

Advancing periodontitis microbiome research: integrating design, analysis, and technology

Frontiers in Cellular and Infection Microbiology
Periodontitis, a chronic inflammatory disease affecting 20%-50% of adults worldwide, is driven by polymicrobial synergy and dysbiosis. Despite numerous studies on the oral microbiota in periodontitis, significant heterogeneity exists between findings ...
Yibing Han, Pei-Hui Ding
doaj   +1 more source

Transcriptional activity of the giant barrel sponge, Xestospongia muta Holobiont: Molecular Evidence for Metabolic Interchange

Frontiers in Microbiology, 2015
Compared to our understanding of the taxonomic composition of the symbiotic microbes in marine sponges, the functional diversity of these symbionts is largely unknown.
Cara L Fiore, Micheline eLabrie, Jessica K Jarett, Michael P. Lesser   +3 more
doaj   +1 more source

Distribution of COG functional categories of the mouse cecal metatranscriptome.

, 2016
Distribution of COG functional categories of the mouse cecal metatranscriptome.
Vitor Martins dos Santos (526472), Mark Davids (426774), Floor Hugenholtz (164819), Hauke Smidt (228430), Peter J. Schaap (216954), Michiel Kleerebezem (16314)   +5 more
core   +1 more source

Molecular evidence of domoic acid production in the high Arctic Qikiqtaaluk Region of Inuit Nunangat

Limnology and Oceanography Letters, Volume 11, Issue 6, November 2026.
Abstract Domoic acid, a neurotoxin produced by the diatom Pseudo‐nitzschia, is an increasing concern in Arctic marine environments. Shellfish harvesting occurs in many Canadian Arctic waterways in Inuit Nunangat and is the main vector for human domoic acid exposure, but most toxin monitoring has occurred in the Pacific Arctic region.
Patrick L. White, Gordon Lax, Margaret Mars Brisbin, Arianna I. Krinos, Harriet Alexander, Jenifer S. Spence, Maria A. Cavaco, Terry Noah, Megan E. Roberts, Simon Shyka‐Brown, Marty Kuluguqtuq, Laisa Audlaluk‐Watsko, Meeka Kiguktak, Stephanie Waterman, Andrew K. Hamilton, David Didier, Maya P. Bhatia, Erin M. Bertrand   +17 more
wiley   +1 more source

SARS‐CoV‐2 triggered oxidative stress and abnormal energy metabolism in gut microbiota

MedComm, 2022
Specific roles of gut microbes in COVID‐19 progression are critical. However, the circumstantial mechanism remains elusive. In this study, shotgun metagenomic or metatranscriptomic sequencing was performed on fecal samples collected from 13 COVID‐19 ...
Tuoyu Zhou, Jingyuan Wu, Yufei Zeng, Junfeng Li, Jun Yan, Wenbo Meng, Huawen Han, Fengya Feng, Jufang He, Shuai Zhao, Ping Zhou, Ying Wu, Yanlin Yang, Rong Han, Weilin Jin, Xun Li, Yunfeng Yang, Xiangkai Li   +17 more
doaj   +1 more source

Supplementary table S2 - Annotation table - C. quitensis metatranscriptome

, 2018
Colobanthus quitensis, reference metatranscriptome annotation table, including phylum information and normalized expression (Trimmed means of M-values)
Gabriel Ballesteros (3904243)
core   +1 more source

Supplementary Table 4C: Statistics of reads retained through bioinformatic processing of iTAG data for the 11 samples and control samples and metatranscriptome data.

, 2020
Dataset: IODP360 - iTAG and metatranscriptome dataSupplementary Table 4C: Metatranscriptome data summary for cellular activities presented and statistics on sequencing and removal of potential contaminant sequences: Statistics of reads retained through ...
Edgcomb, Virginia P.
core   +1 more source

Automated reconstruction of reproducible protein databases with RepDBmaker

Protein Science, Volume 35, Issue 11, November 2026.
Abstract RepDBmaker is a reproducible Snakemake pipeline designed for the automated construction of large‐scale protein sequence databases. It enables the seamless downloading of sequences from different public databases and the integration of user‐specified proteomes.
Giacomo Mutti, Toni Gabaldón
wiley   +1 more source