Josh Earl Email and Phone Number

Guiding bioinformaticians in current generation DNA sequencing, genomics, microbiomics, administering databases and high performance compute clusters, writing SOPs for our CAP and CLIA certified diagnostics lab, programming, writing papers, reading papers, the works.

Primarily the same responsibilities of the previous Research Instructor position, however new added responsibilities include overseeing the technical computer hardware/software development of a new COVID-19 testing lab. This included creating software to automatically interpret output of high throughput PCR Quantstudio machine tests, and workflow to integrate data into multiple health system and laboratory information systems. I also wrote and implemented standard operating procedure (SOP) creation and validation for laboratory information management systems (LIMS) for CLIA certification. Workflow development for all sequencers to final datasets and reports, which includes whole genome (bacterial) sequencing on Pacific Biosciences Sequel and Illumina Miseq/Nextseq assembly pipelines, a novel highly accurate microbiome sequencing to organism identification using Pacbio Sequel, pipeline implementation of COVID-19 strain identification using Pacbio Sequel, and currently developing a new novel fungal microbiome identification pipeline to match the same degree of granularity as our bacterial microbiome identification pipeline. In addition to doing lectures for multiple graduate level courses (phylogenetics, database information mining), I also run two weekly education clubs teaching statistical analysis in the R framework and using the Linux operating system for scientific research.

Responsible for bioinformatics software and hardware development to support new Genomic Sequencing Center. Oversee bioinformatics programming group (2 bioinformatics programmers), graduate student mentorship in bioinformatics and assist teaching bioinformatics graduate classes. Continuing management, support and independent development of all bioinformatics research and analysis in prokaryote and eukaryote sequencing efforts. DNA sequencing technologies overseen include Pacific Biosciences RSII, Pacific Biosciences Sequel, Illumina Nextseq, and Roche Life Sciences 454. Management and system administration of Centos 6 Linux cluster computing system for DNA sequencing analysis and support for department. Development of multiple analysis pipelines for NGS (next generation sequencing) data analysis, including a novel 16S whole gene sequencing and clustering analysis pipeline in Ruby and R, whole genome assembly and annotation, and comparative genomic analysis pipelines for bacterial genomes using statistical techniques, transcriptome analysis with RNAseq.

Responsible for the setup and continued maintenance of over 10 Windows/Linux servers for genomic analysis/data storage (including virtualized environments for specific analyses using both Hyper-V and VirtualBox). Oversaw installation and implementation of current generation sequencing technology of the Pacific Biosciences RS sequencer, both software and hardware. Developed pipelines for whole genome assembly and comparative genome analysis using current computational algorithms tailored for two sequencing methodologies (Roche 454 and Pacific Biosciences RSII). Developed programs to automate and facilitate genomic/genetic analysis for various data types. Implemented user friendly SQL database backed online tools with Ruby on Rails web application design, and database management protocol. Oversee the acquisition and configuration of computer systems for genetic research projects running mainly Centos/Fedora linux or Windows Server 2008.

Part of a quality control team that verified and implemented routines to asses quality goals being reached in a pharmaceutical laboratory environment.Troubleshot equipment, including both computer systems as well as various laboratory equipment.Maintained and monitored mission critical hardware

Part of a quality control department which tested pharmaceutical products via SOP FDA microbiology testing. Including all selective and differential microbiological testing for microbial organisms monitored by the FDA. Monitored total organism counts for manufacturing plants, including water for injection, and basic biosafety lvl 2 environmental testing.Well versed in a broad spectrum of microbial tests, including plating to selective/differential agars/strips for both aerobic and anaerobic conditions.