Biology subjects

Wolfgruber, T.

Publications and source records attributed to Wolfgruber, T..

3 recordsLinked to original sources

bioRxiv2019

Placenta microbiome diversity is associated with maternal pre-pregnancy obesity and placenta biogeography

Recently there has been considerable debate in the scientific community regarding the placenta as the host of a unique microbiome. No studies have addressed the associations of clinical conditions such as maternal obesity, or localizations on the placental microbiome. We examined the placental microbiome in a multi-ethnic maternal pre-pregnant obesity cohort using controls for environmental contaminants and an optimized microbiome protocol to enrich low bacterial biomass samples. We confirmed that a distinct placenta microbiome does exist, as compared to the environmental background. The placenta microbiome consists predominantly of Lactobacillus, Enterococcus and Chryseobacterium. Moreover, the microbiome in the placentas of obese pre-pregnant mothers are less diverse when compared to those of mothers of normal pre-pregnancy weight. Lastly, microbiome richness also decreases from the maternal side to fetal side. In summary, our study reveals associations of placental microbiome with placenta biogeography and with maternal pre-pregnant obesity.

microbiology↗

bioRxiv2018

GranatumX: A community engaging and flexible software environment for single-cell analysis

We present GranatumX, a next-generation software environment for single-cell data analysis. GranatumX is inspired by the interactive web tool Granatum. It enables biologists to access the latest single-cell bioinformatics methods in a web-based graphical environment. It also offers software developers the opportunity to rapidly promote their own tools with others in customizable pipelines. The architecture of GranatumX allows for easy inclusion of plugin modules, named Gboxes, that wrap around bioinformatics tools written in various programming languages and on various platforms. GranatumX can be run on the cloud or private servers and generate reproducible results. It is a community-engaging, flexible, and evolving software ecosystem for scRNA-Seq analysis, connecting developers with bench scientists. GranatumX is freely accessible at http://garmiregroup.org/granatumx/app.

bioinformatics↗

bioRxiv2017

Granatum: a graphical single-cell RNA-seq analysis pipeline for genomics scientists

BackgroundSingle-cell RNA sequencing (scRNA-Seq) is an increasingly popular platform to study heterogeneity at the single-cell level.\n\nComputational methods to process scRNA-Seq have limited accessibility to bench scientists as they require significant amounts of bioinformatics skills.\n\nResultsWe have developed Granatum, a web-based scRNA-Seq analysis pipeline to make analysis more broadly accessible to researchers. Without a single line of programming code, users can click through the pipeline, setting parameters and visualizing results via the interactive graphical interface Granatum conveniently walks users through various steps of scRNA-Seq analysis. It has a comprehensive list of modules, including plate merging and batch-effect removal, outlier-sample removal, gene filtering, geneexpression normalization, cell clustering, differential gene expression analysis, pathway/ontology enrichment analysis, protein-networ interaction visualization, and pseudo-time cell series construction.\n\nConclusionsGranatum enables broad adoption of scRNA-Seq technology by empowering the bench scientists with an easy-to-use graphical interface for scRNA-Seq data analysis. The package is freely available for research use at http://garmiregroup.org/granatum/app

bioinformatics↗