SEQanswers

Go Back   SEQanswers > Jobs Forums > Academic/Non-Profit Jobs



Similar Threads
Thread Thread Starter Forum Replies Last Post
NGS Metagenomics Bacterial Enteric Pathogens Sub-typing Wet Lab Fellowship at CDC Mercaptan Academic/Non-Profit Jobs 0 09-28-2016 08:57 AM
antimicrobial resistance frequencies database sphil Bioinformatics 0 03-23-2015 06:36 AM

Reply
 
Thread Tools
Old 07-17-2017, 11:22 AM   #1
Mercaptan
Junior Member
 
Location: Atlanta

Join Date: Aug 2012
Posts: 4
Default Antimicrobial resistance Bioinformatics Fellowship - CDC - Atlanta, Georgia

BIOINFORMATICS FELLOW
Population antimicrobial resistance discovery in stools associated with foodborne illness using NGS

Centers for Disease Control and Prevention, Atlanta, GA

A bioinformatics fellowship is available in the Culture Independent and Metagenomic Subtyping group (CIMS) in the Enteric Diseases Laboratory Branch (EDLB) in the Division of Foodborne, Waterborne, and Environmental Diseases in the National Center for Emerging and Zoonotic Infectious Diseases at the Centers for Disease Control and Prevention (CDC).

Antimicrobial resistance (AMR) determinant detection and quantification directly from healthy and disease state stool samples is of strong public health interest. Current AMR assays are culture-based, which has limitations that we are interested in overcoming using shotgun sequencing and AMR-targeted amplicon sequencing in a metagenomic context. The fellow will work with a group of bioinformatics and laboratory scientists in CIMS to develop bioinformatics approaches for the analysis of shotgun sequencing and amplicon sequencing data for AMR content.

In conjunction with the National Antimicrobial Resistance Surveillance Team in EDLB and other partners, CIMS will be generating AMR profiles of stools from healthy individuals as well as individuals who are suffering from cases of bacterial foodborne illness. These AMR profiles will be generated through shotgun metagenomics sequencing of stool DNA using the Illumina HiSeq platform, as well as short (~200 bp) amplicon sequencing of known AMR gene targets amplified from stool DNA.

Questions include:
  • How can AMRs be accurately quantified and linked to antimicrobial activity of health consequence from metagenomic shotgun sequencing and AMR amplicon sequencing?
  • How much AMR content is found in the stools of Americans without foodborne illness?
  • Can AMRs be linked back to their host bacterium using different sequencing strategies?

Activities include:
  • Development of pipelines for extraction and quantification of AMR content from metagenomic shotgun sequencing and targeted AMR amplicon NGS data
  • Curation of AMR determinant databases both in house and with external collaborators
  • Analysis of metagenomic shotgun and amplicon AMR data from hundreds of healthy stool samples to improve understanding of background AMR content
  • Analysis of AMR data from outbreak associated stool samples for AMR content associated with foodborne pathogens and commensal organisms

Qualifications:
  • Master’s degree in biological sciences, microbiology, bioinformatics, or related field (graduation within last three years)
  • Strong UNIX command line bioinformatics tool experience required
  • Proven experience with command line NGS data QC, alignment, quantification, and phylogeny tools required
  • Experience with Python, Perl, and/or R is desirable
  • Experience with metagenomics, comparative genomics, amplicon, and AMR-related research and bioinformatics tools and databases a plus

Stipend is based on degree attained and other experience. This is a one year fellowship appointment through the Oak Ridge Institute for Science and Education program administered through the Department of Energy. For more information, please contact Andrew Huang care of [email protected].
Mercaptan is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 03:27 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO