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"Visualizing the Hidden Half: Plant-Microbe Interactions in the Rhizosphere" Plant roots and the associated rhizosphere constitute a dynamic environment that fosters numerous intra- and interkingdom interactions, including metabolite exchange between plants and soil mediated by root exudates and the...
Elmore JR, Dexter GN, Baldino H, Huenemann JD, Francis R, Peabody GL 5th, Martinez-Baird J, Riley LA, Simmons T, Coleman-Derr D, Guss AM, Egbert RG. High-throughput genetic engineering of nonmodel and undomesticated bacteria via iterative site-specific genome integration. Sci Adv. 2023 Mar 10;9(10)...
Metabolite exchange between plant roots and their associated rhizosphere microbiomes underpins plant growth promotion by microbes. Sorghum bicolor is a cereal crop that feeds animals and humans and is used for bioethanol production. Its root tips exude large amounts of a lipophilic benzoquinone...
A major challenge in biotechnology and biomanufacturing is the identification of a set of biomarkers for perturbations and metabolites of interest. Here, we develop a data-driven, transcriptome-wide approach to rank perturbation-inducible genes from time-series RNA sequencing data for the discovery...
HDF5 file containing 10,000 hydraulic transmissivity inputs and the corresponding hydraulic pressure field outputs for a two-dimensional saturated flow model of the Hanford Site. The inputs are generated by sampling a 1,000-dimensional Kosambi-Karhunen-Loève (KKL) model of the transmissivity field...
The Sequel II System Sequencer is a high-throughput DNA sequencer machine developed and manufactured by PacBio , and is designed for high throughput, production-scale sequencing laboratories. Originally released in 2015, the Sequel system provides Single Molecule, Real-Time (SMRT) sequencing core...
Human infections caused by viral pathogens trigger a complex gamut of host responses that limit disease, resolve infection, generate immunity, and contribute to severe disease or death. Here, we present experimental methods and multi-omics data capture approaches representing the global host...
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LIQUID Software Overview LIQUID provides users with the capability to process high throughput data and contains a customizable target library and scoring model per project needs. The graphical user interface provides visualization of multiple lines of spectral evidence for each lipid identification...
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pmartR Software Overview The pmartR package provides a single software tool for QC (filtering and normalization), exploratory data analysis (EDA), and statistical analysis (robust to missing data) and includes numerous visualization capabilities of mass spectrometry (MS) omics data (proteomic...
The Phenotypic Response of the Soil Microbiome to Environmental Perturbations Project (Soil Microbiome SFA) at Pacific Northwest National Laboratory is a Genomic Sciences Program Science Focus Area (SFA) Project operating under the Environmental Microbiome Science Research Area. The Soil Microbiome...
Datasets
23
Fusarium sp. DS682 Proteogenomics Statistical Data Analysis of SFA dataset download: 10.25584/KSOmicsFspDS682/1766303 . GitHub Repository Source: https://github.com/lmbramer/Fusarium-sp.-DS-682-Proteogenomics MaxQuant Export Files (txt) Trelliscope Boxplots (jsonp) Fusarium Report (.Rmd, html)...