MedlineRanker: flexible ranking of biomedical literature

Fontaine, Jean-Fred; Barbosa-Silva, Adriano; Schaefer, Martin H.; Huska, Matthew R.; Muro, Enrique M.; Andrade‐Navarro, Miguel A.

doi:10.1093/nar/gkp353

Cited by 117 publications

(96 citation statements)

References 15 publications

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“…Reads with the 16S rDNA forward oligonucleotide sequence CCGCGRCTGCTGGCGC, containing G instead of A at the penultimate position of the 3′ end, were likely due to a primer synthesis or sequencing artifact (Lazarevic et al, 2010) and were not removed from the dataset provided other quality criteria were met. After trimming primer sequences, reads <200 or >290 nt and those that incompletely covered the E. coli 16S rRNA gene positions 288–514, determined using the RDP pyrosequencing tool Aligner (Cole et al, 2009), were discarded, leaving 31,577 sequences. Sequences were examined for potential chimeras using the MG-RAST server (Meyer et al, 2008).…”

Section: Methodsmentioning

confidence: 99%

Altered Gut Microbiota and Endocannabinoid System Tone in Obese and Diabetic Leptin-Resistant Mice: Impact on Apelin Regulation in Adipose Tissue

Geurts¹,

Lazarević²,

Derrien³

et al. 2011

Front. Microbio.

285

254

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Growing evidence supports the role of gut microbiota in the development of obesity, type 2 diabetes, and low-grade inflammation. The endocrine activity of adipose tissue has been found to contribute to the regulation of glucose homeostasis and low-grade inflammation. Among the key hormones produced by this tissue, apelin has been shown to regulate glucose homeostasis. Recently, it has been proposed that gut microbiota participate in adipose tissue metabolism via the endocannabinoid system (eCB) and gut microbiota-derived compounds, namely lipopolysaccharide (LPS). We have investigated gut microbiota composition in obese and diabetic leptin-resistant mice (db/db) by combining pyrosequencing and phylogenetic microarray analysis of 16S ribosomal RNA gene sequences. We observed a significant higher abundance of Firmicutes, Proteobacteria, and Fibrobacteres phyla in db/db mice compared to lean mice. The abundance of 10 genera was significantly affected by the genotype. We identified the roles of the eCB and LPS in the regulation of apelinergic system tone (apelin and APJ mRNA expression) in genetic obese and diabetic mice. By using in vivo and in vitro models, we have demonstrated that both the eCB and low-grade inflammation differentially regulate apelin and APJ mRNA expression in adipose tissue. Finally, deep-gut microbiota profiling revealed that the gut microbial community of type 2 diabetic mice is significantly different from that of their lean counterparts. This indicates specific relationships between the gut microbiota and the regulation of the apelinergic system. However, the exact roles of specific bacteria in shaping the phenotype of db/db mice remain to be determined.

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Section: Methodsmentioning

confidence: 99%

Altered Gut Microbiota and Endocannabinoid System Tone in Obese and Diabetic Leptin-Resistant Mice: Impact on Apelin Regulation in Adipose Tissue

Geurts¹,

Lazarević²,

Derrien³

et al. 2011

Front. Microbio.

285

254

View full text Add to dashboard Cite

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“…Shortly, raw sequencing reads were quality and length filtered (≥150 bp). Rarefaction analysis was performed for phylotype clusters of 97, 95, and 90% similarity by using the tools of the RDP’s Pyrosequencing Pipeline (Cole et al, 2009). Datasets were normalized to the same number of sequences.…”

Section: Methodsmentioning

confidence: 99%

Similar Diversity of Alphaproteobacteria and Nitrogenase Gene Amplicons on Two Related Sphagnum Mosses

Bragina¹,

Maier²,

Berg³

et al. 2012

Front. Microbio.

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Sphagnum mosses represent a main vegetation component in ombrotrophic wetlands. They harbor a specific and diverse microbial community with essential functions for the host. To understand the extend of host specificity and impact of environment, Sphagnum fallax and Sphagnum angustifolium, two phylogenetically closely related species, which show distinct habitat preference with respect to the nutrient level, were analyzed by a multifaceted approach. Microbial fingerprints obtained by PCR-single-strand conformation polymorphism of 16S rRNA and nitrogenase-encoding (nifH) genes were highly similar for both Sphagnum species. Similarity was confirmed for colonization patterns obtained by fluorescence in situ hybridization (FISH) coupled with confocal laser scanning microscopy (CLSM): Alphaproteobacteria were the main colonizers inside the hyaline cells of Sphagnum leaves. A deeper survey of Alphaproteobacteria by 16S rRNA gene amplicon sequencing reveals a high diversity with Acidocella, Acidisphaera, Rhodopila, and Phenylobacterium as major genera for both mosses. Nitrogen fixation is an important function of Sphagnum-associated bacteria, which is fulfilled by microbial communities of Sphagna in a similar way. NifH libraries of Sphagnum-associated microbial communities were characterized by high diversity and abundance of Alphaproteobacteria but contained also diverse amplicons of other taxa, e.g., Cyanobacteria and Deltaproteobacteria. Statistically significant differences between the microbial communities of both Sphagnum species could not be discovered in any of the experimental approach. Our results show that the same close relationship, which exists between the physical, morphological, and chemical characteristics of Sphagnum mosses and the ecology and function of bog ecosystems, also connects moss plantlets with their associated bacterial communities.

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“…It can thus be applied to prepare training data for document categorization and ranking applications such as MedlineRanker (Fontaine et al, 2009) (Supplementary Fig. S15).…”

Section: User Cases/usefulnessmentioning

confidence: 99%

MyMiner: a web application for computer-assisted biocuration and text annotation

et al. 2012

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Motivation: The exponential growth of scientific literature has resulted in a massive amount of unstructured natural language data that cannot be directly handled by means of bioinformatics tools. Such tools generally require structured data, often generated through a cumbersome process of manual literature curation. Herein, we present MyMiner, a free and user-friendly text annotation tool aimed to assist in carrying out the main biocuration tasks and to provide labelled data for the development of text mining systems. MyMiner allows easy classification and labelling of textual data according to user-specified classes as well as predefined biological entities. The usefulness and efficiency of this application have been tested for a range of real-life annotation scenarios of various research topics.

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MedlineRanker: flexible ranking of biomedical literature

Cited by 117 publications

References 15 publications

Altered Gut Microbiota and Endocannabinoid System Tone in Obese and Diabetic Leptin-Resistant Mice: Impact on Apelin Regulation in Adipose Tissue

Altered Gut Microbiota and Endocannabinoid System Tone in Obese and Diabetic Leptin-Resistant Mice: Impact on Apelin Regulation in Adipose Tissue

Similar Diversity of Alphaproteobacteria and Nitrogenase Gene Amplicons on Two Related Sphagnum Mosses

MyMiner: a web application for computer-assisted biocuration and text annotation

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