Genomics fellowship with CDPH

Genomics fellowship with CDPH

2-year bioinformatics fellowship with the Connecticut Department of Public Health (CDPH)

CDPH Qualifications

  • Advanced degree in Biology, Computational Biology, Bioinformatics or related field is preferred
  • Experience developing custom scripts using standard bioinformatics tools for pathogen genomics and implementing metagenomics computational tools
  • Experience working with high throughput sequencing datasets (e.g. whole exome sequencing, whole genome sequencing, RNA-seq, ChIP-seq, ATAC-seq, etc.) in a Linux and/or cloud environment
  • Experience/or Knowledge with genomics laboratory techniques
  • Proficiency in one or more programming languages (e.g. C++, Python, R, Java, Perl, Unix, SQL) and Knowledge and experience with Jupyter notebooks and/or knitr to generate and share reports preferred.
  • Experience working with common bioinformatic tools (e.g. BWA, GATK) and file formats (e.g. BAM, VCF).
  • Experience with collaborative development environments, including management of shared repositories (github), and other data management systems (Excel, Access, Tableau)
  • Experience in developing analytical pipelines (e.g. using snakemake)
  • Experience working with High Performance Computing clusters (e.g. SLURM) and workflow manager (e.g. CWL, WDL, Snakemake).
  • Experience working with data quality assessment to evaluate overall quality score of the sequencing reads, presence of adaptors, carry-over and contamination
  • Experience with pathogen genomics, especially SARS-CoV-2, Mycobacterium tuberculosis, antimicrobial resistance, and enteric pathogens

The candidate would be officially employed at Yale as a research scientist and be contracted to work with the CDPH. The CDPH would prefer for the candidate to work at their lab in Rocky Hill, CT, though remote options are available. The work would be 75% leading pathogen genomics programs for the CDPH, and the rest of the time working on collaborative projects with my lab. This is a fantastic opportunity to gain real experience in public health while also conducting genomic epidemiology research with our lab. The salary is VERY competitive. Start date is ASAP. Please send your CV and cover letter to Nathan Grubaugh at to apply.

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