Bioinformatician

Posted on by Micaela Brun
Job ID:
Job date: 2017-06-30
End Date:

Company : IHRC 

Country :

Role : Other 


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Job Description:
The successful candidate will be a full-time employee of IHRC, Inc. and will be assigned to the Respiratory Diseases Branch (RDB) within the Division of Bacterial Diseases (DBD), at the CDC, 1600 Clifton Road, Atlanta, GA to provide bioinformatics support services for the Pneumonia Response and Surveillance Laboratory.

SCOPE OF WORK

The Bioinformatician will support the development and implementation of bioinformatics data analysis pipelines to analyze data generated by next generation sequencing platforms for the detection of respiratory pathogens. The Bioinformatician will design and implement a bioinformatics infrastructure to support whole genome and metagenomics data analysis for the identification of respiratory pathogens including the optimization of comparative genomics analysis techniques and other high performance computing-required analyses. Additionally, the Bioinformatician will be involved in the testing and validation of in-house bioinformatics workflows in order to allow their dissemination to international partner laboratories.

MAJOR DUTIES AND RESPONSIBILITIES

  • Design and implement microbial comparative genomic analysis pipelines.
  • Optimize bioinformatics workflows to assist in the decision making processes for the selection of an optimal sequence assembly and gene finder predictions.
  • Process and analyze next generation sequencing data from the Illumina and PacBio sequencing platforms.
  • Perform post-processing of raw sequencing reads using multiple bioinformatics tools such as FastQC, or PRINSEQ for quality assurance, adapter removal and trimming.
  • Perform assembly and mapping to reference genomes to call variants (SNPs, INDELS)
  • Create shell scripts and Python scripts to generate an automated pipeline that takes in raw reads and performs each step automatically on CDC’s bioinformatics scientific cluster.
  • Work with MySQL and JavaScript libraries to develop a visualization program to analyze meta-data from a bacterial species.
  • Provide in-depth analysis of data and interpret trends, critical components, and identify any potential problems associated with design or execution of next generation sequencing projects.
  • Analyze and troubleshoot any and all problems associated with the Research and Development (R&D) of bioinformatics analyses on high-performance computing environments.
  • Provide documentation on all aspects of performance of bioinformatics workflows.
  • Prepare Standard Operating Procedures (SOPs) as instructed for all platforms.
  • Attend staff meetings when requested.
  • Present data orally when requested and assist in providing hands-on training for next generation sequencing data analysis procedures.
MINIMUM QUALIFICATIONS

Education and Experience: MS degree in bioinformatics, computational biology or related field

Required:

  • Experience performing quality control, assembly, annotation, and analysis of data generated by next generation sequencing platforms
  • Proficiency with open source and commercially available software for bioinformatics analysis of next generation sequencing data
  • Proficiency with computer programming languages (JavaScript, Python, R, and/or Perl) and the use of publicaly available data repositories (i.e. NCBI, EMBL, and DDBJ)
  • Experience using molecular, immunological, and cell biology techniques
  • Proficiency with Microsoft Word, Excel, and PowerPoint
  • Excellent attention to detail and the ability to efficiently organize multiple priorities
  • Experience writing project, reports, research protocols and manuscripts
  • Documentation of daily work with good laboratory practice compliance
Desirable:
  • Proficiency with different technologies for the generation of bacterial genomic libraries for next generation sequencing
  • Experience with metagenomics data analysis, comparative genomics and genome-based typing systems
  • Experience with SQL
  • Experience with machine learning
  • Experience performing bioinformatics analysis in a cluster computing environment
  • Ability to work and build coalitions with partners involved, and develop strategies to effectively convey information to partners
  • Ability to work independently and yet maintain the flexibility to respond to the needs of the RDB
  • Experience with Access, BioNumerics and statistical software
Language Skills:

The candidate must possess excellent oral and written communication skills in English

REQUIREMENT:

Must be United States citizen or permanent resident or have authorization for employment in the United States

SALARY: Commensurate with qualifications and experience

Requeriments :

Skills :

Areas :

Additional Info:
IHRC, Inc. provides scientific, information management and administrative program support to various Centers, Institutes and Offices of the Centers for Disease Control and Prevention (CDC) under several contracts.

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IHRC, INC. IS AN EQUAL OPPORTUNITY AND AFFIRMATIVE ACTION EMPLOYER. It is the policy of IHRC, Inc. to provide equal employment opportunities without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, age, and veteran or disability status and to take affirmative action in accordance with applicable laws and Executive Orders.

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