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Design and manage the Agile group responsible for creating analytics for data stored on the NIH consortiums GUDMAP and RBK. This analytics are not only best-practices pipelines written in Nextflow, but also integrates seamlessly with the consortiums' data-hub, in terms of initiation, and data ingress/egress. It is built with the flexibility to utilize on premises HPC, or a custom built AWS architecture (including many serverless resources) for low-cost, highly-available queueing, compute, and reporting. It can also be easily adapted to almost any running environment using custom configs. The entire pipeline utilizes dockerized micro-services which is orchestrated by Nextflow.
Manage a small agile team to create a proof of concept AWS architecture to run Nextflow pipelines in the cloud. It utilizes low-cost, highly-availability queueing, compute, and storage resources.
Creating a pipeline run tracking tool for the Bioinformatics Core Facility at UT Southwestern Medical Center. This tool utilizes AWS serverless offerings, including REST-API and a website for run tracking.
The Strand Lab website was designed to not only provide a location to share information about the lab, but also provide a means to showcase the lab's data and biorepository. The single-cell data is displayed using CZI's cellxgene visualization tool as well as pre-generated genome-wide visualization of the expression data. The lab has an extensive biorepository of human lower urinary tract biosamples and de-identified clinical data as well as H&E images are available for viewing and filtering on the website. The site is hosted serverlessly on AWS.
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Single-cell RNA-sequencing of adult human prostates and urethras from organ donors, and BPH (glandular and stromal) patients as well as adult mouse lower urinary tracts.
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This pipeline conducts end-to-end RNA-seq analysis on replicates stored in the GenitoUrinary Development Molecular Anatomy Project and ReBuilding the Kidney consortium. This pipeline was created in a collaboration between the Strand Lab and Bioinformatics Core Facility (BICF) at UT Southwestern Medical Center.This pipeline conducts end-to-end RNA-seq analysis on replicates stored in the GenitoUrinary Development Molecular Anatomy Project and ReBuilding the Kidney consortium. This pipeline was created in a collaboration between the Strand Lab and Bioinformatics Core Facility (BICF) at UT Southwestern Medical Center.
This code was used for the single-cell RNA-sequencing analysis in the Strand Lab at UT Southwestern Medical Center
BICF Cellranger count Analysis Workflow is a wrapper for the cellranger count tool from 10x Genomics. This pipeline, used by the Bioinformatics Core Facility at UT Southwestern, takes fastq files from 10x Genomics single-cell gene expression libraries and passes them to cellranger count, managing parallelization of multiple runs, as well as, aggregation as appropriate. This pipeline is primarily used with a SLURM cluster on BioHPC, but it should be able to run on any system that Nextflow supports. Additionally, this pipeline is designed to work using a simple web interface.
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Spatial transcriptomics of treatment naive and 5-alpha reductase inhibitior treated human BPH tissue
Dissected verumontanum region and peripheral zone region from a normal human prostate sample were digested into single-cell suspensions, cells were subject to single-cell RNA-sequencing using the 10x Genomics platform
Single-cell RNA-sequencing of adult human prostates and urethras from organ donors, and BPH (glandular and stromal) patients.
Single-cell RNA-sequencing of adult mouse prostates and urethras.
Sequencing data relating to the in preparation publication: 'Single cell analysis of mouse and human prostate reveals novel fibroblasts with specialized distribution and microenvironment interactions'
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