Results 11 to 20 of about 7,727 (208)

SAMSA: a comprehensive metatranscriptome analysis pipeline [PDF]

BMC Bioinformatics, 2016
BackgroundAlthough 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.
Danielle G. Lemay, David A. Mills, Ian Korf, Samuel T. Westreich   +3 more
core   +6 more sources

Incorporating Scale Uncertainty into Differential Expression Analyses Using ALDEx2. [PDF]

Curr Protoc
Abstract Differential abundance or expression analyses are routinely performed on metagenomic, metatranscriptomic, and amplicon sequencing data. In such datasets, analysts usually have no information regarding the true scale (i.e., size) of the microbial community or sample under study, with inter‐sample differences in sequencing depth instead being ...
Dos Santos SJ, Gloor GB.
europepmc   +2 more sources

Insights Into Sequences of Viral and Bacterial Origin in the Metatranscriptome of Centaurea cyanus L. Susceptible and Resistant to Acetolactate Synthase (ALS)-Inhibiting Herbicides. [PDF]

Environ Microbiol Rep
Metatranscriptomic analysis of Centaurea cyanus revealed diverse plant‐associated viral and bacterial sequences in herbicide‐susceptible and ‐resistant biotypes. While novel partitiviruses occurred independently of resistance status, differences in bacterial community composition may suggest a potential role of the plant microbiome in responses to ...
Marcinkowska K, Wrzesińska-Krupa B, Obrępalska-Stęplowska A.   +2 more
europepmc   +2 more sources

MetaGT: A pipeline for de novo assembly of metatranscriptomes with the aid of metagenomic data

Frontiers in Microbiology, 2022
While metagenome sequencing may provide insights on the genome sequences and composition of microbial communities, metatranscriptome analysis can be useful for studying the functional activity of a microbiome.
Daria Shafranskaya, Varsha Kale, Rob Finn, Alla L. Lapidus, Anton Korobeynikov, Andrey D. Prjibelski, Andrey D. Prjibelski   +6 more
doaj   +1 more source

Understanding human health through metatranscriptomics

Trends in Molecular Medicine, 2023
Metatranscriptomics has revolutionized our ability to explore and understand transcriptional programs in microbial communities. Moreover, it has enabled us to gain deeper and more specific insight into the microbial activities in human gut, respiratory, oral, and vaginal communities. Perhaps the most important contribution of metatranscriptomics arises,
Teija Ojala, Esko Kankuri, Matti Kankainen   +2 more
openaire   +4 more sources

Reverse engineering environmental metatranscriptomes clarifies best practices for eukaryotic assembly

BMC Bioinformatics, 2023
Background Diverse communities of microbial eukaryotes in the global ocean provide a variety of essential ecosystem services, from primary production and carbon flow through trophic transfer to cooperation via symbioses.
Arianna I. Krinos, Natalie R. Cohen, Michael J. Follows, Harriet Alexander   +3 more
doaj   +1 more source

Functional Profiling of Unfamiliar Microbial Communities Using a Validated De Novo Assembly Metatranscriptome Pipeline. [PDF]

PLoS ONE, 2016
BACKGROUND:Metatranscriptomic landscapes can provide insights in functional relationships within natural microbial communities. Analysis of complex metatranscriptome datasets of these communities poses a considerable bioinformatic challenge since they ...
Mark Davids, Floor Hugenholtz, Vitor Martins dos Santos, Hauke Smidt, Michiel Kleerebezem, Peter J Schaap   +5 more
doaj   +1 more source

Sizing up metatranscriptomics [PDF]

The ISME Journal, 2012
Abstract A typical marine bacterial cell in coastal seawater contains only ∼200 molecules of mRNA, each of which lasts only a few minutes before being degraded. Such a surprisingly small and dynamic cellular mRNA reservoir has important implications for understanding the bacterium’s responses to environmental signals, as well as for our ...
Mary Ann, Moran, Brandon, Satinsky, Scott M, Gifford, Haiwei, Luo, Adam, Rivers, Leong-Keat, Chan, Jun, Meng, Bryndan P, Durham, Chen, Shen, Vanessa A, Varaljay, Christa B, Smith, Patricia L, Yager, Brian M, Hopkinson   +12 more
openaire   +2 more sources

Current trends in RNA virus detection through metatranscriptome sequencing data

FEBS Open Bio, 2023
With advances in sequencing technology, metatranscriptome sequencing from a variety of environmental and biological sources has revealed the existence of various previously unknown RNA viruses. This review presents recent major RNA virome studies sampled
So Nakagawa, Shoichi Sakaguchi, Atsushi Ogura, Katsuhiko Mineta, Toshinori Endo, Yoshiyuki Suzuki, Takashi Gojobori   +6 more
doaj   +1 more source

Exploring the Change of Host and Microorganism in Chronic Obstructive Pulmonary Disease Patients Based on Metagenomic and Metatranscriptomic Sequencing

Frontiers in Microbiology, 2022
BackgroundChronic obstructive pulmonary disease (COPD) is a universal respiratory disease resulting from the complex interactions between genes and environmental conditions. The process of COPD is deteriorated by repeated episodes of exacerbations, which
Jing Yang, Qiang Zhang, Jun Zhang, Yan Ouyang, Zepeng Sun, Xinlong Liu, Feng Qaio, Li-Qun Xu, Yunfei Niu, Jian Li   +9 more
doaj   +1 more source