Associate Scientist II

Job Description

Key Responsibilities

Engineer, maintain, & improve upon pipeline code base for bioinformatics processing & analysis of various genomics data types.

Enable code reuse across different Linux environments / computing architecture deployed across research sites.

Facilitate internal & external data availability to bioinformaticians.

Develop & maintain structured data repositories for semi-automated computational reassessment & record keeping.

Develop & support R Shiny applications to enable data query, visualization & custom web-interfaces of data analytics processes & pipelines.

Interface with research-serving IT specialists to assure availability of appropriate HPC resources (compute, storage, networking).

Leverage bioinformatics & genomics data knowledge to gather requirements from stakeholders & collect feedback for continued development & support.

Engage in effective communications with stakeholders & other team members via asynchronous collaboration tools (e.g. Microsoft Teams).

Utilize R & Python, including experience with web-app frameworks such as R Shiny & Flask.

Build workflows & pipelines to support Illumina NGS data generation, processing, & analysis (particularly Bulk RNAseq and scRNA-seq).

Structure data storage technologies including relational &/or NoSQL.

Generate ML models for data classification & analysis such as KNN, Random Forest, &/or SVN.

Use version control systems such as Git or GitHub, & software project management systems such as Jira.

Wrangle, manage, & leverage large datasets such as patient cohorts & public data repositories.

Utilize contemporary interactive data visualization methods such as R Shiny, D 3, or Spotfire.

Use pipeline building tools including CWL &/or Snakemake.

Utilize tools & data formats related to gene expression, enrichment analysis, genetic, genomic, or epigenetic data such as encountered when analyzing high-throughput transcriptomic, whole exome, whole genome, whole methylome, GWAS, or targeted resequencing data.