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Computational Biologist - Microbial Genomics

Employer
CosmosID
Location
Germantown, Maryland, US
Salary
Competitive
Closing date
May 30, 2022

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Sector
Academic / Research
Field
Informatics / GIS
Discipline
Ecology
Salary Type
Salary
Employment Type
Full time
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Job Description
POSITION SUMMARY

This role will be responsible for developing and maintaining critical database infrastructure for metagenomic assays. Important note: this job description is in regard to genomic reference databases, not database administrator work for database systems.

The focus of the position will be updating and maintaining reference databases utilizing accumulated public and proprietary data in both standard and proprietary technologies. Critical to this activity will be version control, documentation, and validation of metagenomic databases.

The candidate will work well with a multidisciplinary team. This exciting opportunity will involve preparation of peer-reviewed as well as white paper publications on methods, theory, and validation of complex metagenomic database structures with the support of a diverse team of bioinformaticists, software developers, clinical specialists, sales, and microbiologists.

Responsibilities:

Generating, validating, and updating genomic databases, including:
  • Develop SOPs for database updates to confirm that they work, including validation and quality control tests
  • Run validation of databases with bioinformatics team
  • Work with custom client databases (where client proprietary genomes are added) to work within the same validation tests as standard genomic databases
  • If there's a database issue, determine what happened
  • Document standard and custom databases and updates
  • Keep track of any new update requests
  • Keep track of taxonomic name changes
  • Sign off on validation of databases
  • Project manage database updates

Documentation
  • Critical to this role is a rigorous attention to detail in documentation. Some of this documentation will be required by clinical regulatory authorities.

Multi-Team Collaboration (Product, Engineering, Support)
  • Working closely with the Chief Algorithms Officer and VP of Engineering in order to gather performance metrics for various databases
  • Ability to research new publications on microbiome, reproduce the publication results and suggest what would be valuable for future addition to products in terms of technical methods or tools
  • The position will mainly support internal microbiome and clinical metagenomic database curation needs, however some custom database development will also be required for customers in the microbiome, pharmaceutical, epidemiological, and basic science fields

The right candidate will possess the following:
  • Bachelor's degree in bioinformatics, computational biology, computer science, molecular biology, genomics, biochemistry, microbial ecology or a related field with 5 years of experience or master's degree in related field with 2 years of experience or PhD; or an equivalent combination of education and or experience in a related field
  • Strong Computational Skills
    • Strong working knowledge of Python and or R scripting, Bash programming, as well as proficiency with command line tools in Unix/Linux
    • Experience with relational (or similar) databases
  • Microbial Knowledge
    • Experience in microbial phylogenomics
    • Isolate characterization knowledge (for example, clinically relevant species or strains, MLST, genome information, important genes)
    • Experience working with microbial databases like GTDB and Refseq
  • Bioinformatics Knowledge (need to understand and clearly describe):
    • Broad knowledge of NGS applications such as whole genome sequencing, 16S and other amplicons, RNA-seq, microbiome analysis, and functional analysis
    • Understanding of and experience working with large DNA/RNA sequence datasets and common bioinformatics software tools, algorithms, and workflows. Applications include ontologies, pathways, networks, and/or phylogenetics at both the individual gene and genomic scales
    • Phylogenetic Analysis (multiple sequence alignment, tree building)
    • Statistical methods for microbiome science
  • Excellent oral and written communication skills and fluency in English
  • Excellent task management and self-organizational skills
Company DescriptionCosmosID is a Next-Generation bioinformatics and sequencing provider focused on microbial genomics.
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