Job Description:
The Bioinformatician will provide bioinformatics expertise and support for metagenomic sequence analysis, including benchmarking and evaluation of different free and open source (F/OSS) and Commercial off the Shelf (CotS) software products for pathogen genomics, metagenomics and metatranscriptomics. MAJOR DUTIES AND RESPONSIBILITIES: -Design and manage large-scale sequence databases to enable the rapid integration, querying, and selective enrichment or depletion of large metagenomic shotgun sequence datasets. The Bioinformatician is expected to draw on the following disciplines and skills: 1) database design, management and tuning; 2) scripting and programming; 3) statistical analysis; 4) algorithmic selection and optimization; 5) visualization of complex datasets. These efforts include design and customization of small-scale, local applications for data access, analysis and visualization; the development and administration of database systems; and the identification and implementation of new techniques and technologies for advanced analysis of complex biological data. -Design, program, test, modify, enhance, maintain, and support novel and existing bioinformatics applications and pipelines for metagenomic analysis, pathogen identification and characterization, using both open source (ex: MEGAN, MetaGeneMark, kraken, CLARK, etc.) and commercial off-the shelf software applications as appropriate. -Develop, in consultation with CDC project team representatives, standardized pipelines or toolchains for metagenomic analysis of different sample types, configure and deploy them into the CDC Bioinformatics computing environment, and use these for standardized benchmarking of laboratory extraction and sample preparation methods. -Assist with the development and maintenance of comprehensive and highly-curated genomic sequence databases, including: microbial and pathogen-specific genomic sequences for inclusion or exclusion of known pathogens; plant and animal genomic sequences for exclusion of host DNA; signature databases for known virulence and antimicrobial resistance markers; and databases of known straintype or pathotype-specific markers. This requirement requires the design, implementation of gigabase-scale, high-performance databases of genomic and/or signature sequences drawn from public and limited-access sequencing activities. -Develop scripts and software to automate scientific data analysis using Python, Perl/BioPerl, Ruby and Java. Documented, authoritative source code to all software and scripts developed during the period of performance for this contract will be maintained in a managed GitLab source code repository in CDC’s bioinformatics computing environment. It is also expected that any useful software tools developed during the course of this work will be published as open source software on approved public source code repositories (eg: http://www.github.com/CDCgov). -Receive next generation metagenomic shotgun sequencing data from both internal and external collaborators, perform standardized quality assurance and control procedures on the raw sequence reads, and analyze them using established metagenomic pipelines and methods. Metagenomic sequence data shall be derived from both spiked blood, sputum, and stool samples, with multiple replicates, representing different specimen processing and extraction techniques, and different platforms. -Develop and refine quantitative methods to compare multiple metagenomic datasets in order to advise the project team on optimal parameters for sample processing, extraction and sequencing. -Consult with internal and external partners on strategies and solutions for data retention, storage and management. MINIMUM QUALIFICATIONS: Education and Experience: Advanced degree, from an accredited academic institution, in scientific or technical discipline, including bioinformatics, computational biology or field related to the responsibilities of the position. At least 4 years of experience in the development and optimization of bioinformatics workflows and genomic/metagenomics analysis methods and applications. 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 publicly available data repositories (i.e. NCBI, EMBL, and DDBJ). -Experience using molecular, immunological, and cell biology techniques. 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 Python, Perl/BioPerl. Ruby and/or Java. -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. -Experience with Access, BioNumerics and statistical software. -Ability to work independently and yet maintain the flexibility to respond to requests for support of ongoing projects. 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 To apply for this position: visit our Career Center, which can also be reached by visiting www.ihrc.com/Careers and clicking on the “View Opportunities” link.
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. The successful candidate will be a full-time employee of IHRC, Inc. and will be assigned to the Office of Advanced Molecular Detection (AMD) at the CDC, 1600 Clifton Road, Atlanta, GA, to provide scientific and technical support for the AMD initiative. 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.[Click Here to Access the Original Job Post]
The Bioinformatician will provide bioinformatics expertise and support for metagenomic sequence analysis, including benchmarking and evaluation of different free and open source (F/OSS) and Commercial off the Shelf (CotS) software products for pathogen genomics, metagenomics and metatranscriptomics. MAJOR DUTIES AND RESPONSIBILITIES: -Design and manage large-scale sequence databases to enable the rapid integration, querying, and selective enrichment or depletion of large metagenomic shotgun sequence datasets. The Bioinformatician is expected to draw on the following disciplines and skills: 1) database design, management and tuning; 2) scripting and programming; 3) statistical analysis; 4) algorithmic selection and optimization; 5) visualization of complex datasets. These efforts include design and customization of small-scale, local applications for data access, analysis and visualization; the development and administration of database systems; and the identification and implementation of new techniques and technologies for advanced analysis of complex biological data. -Design, program, test, modify, enhance, maintain, and support novel and existing bioinformatics applications and pipelines for metagenomic analysis, pathogen identification and characterization, using both open source (ex: MEGAN, MetaGeneMark, kraken, CLARK, etc.) and commercial off-the shelf software applications as appropriate. -Develop, in consultation with CDC project team representatives, standardized pipelines or toolchains for metagenomic analysis of different sample types, configure and deploy them into the CDC Bioinformatics computing environment, and use these for standardized benchmarking of laboratory extraction and sample preparation methods. -Assist with the development and maintenance of comprehensive and highly-curated genomic sequence databases, including: microbial and pathogen-specific genomic sequences for inclusion or exclusion of known pathogens; plant and animal genomic sequences for exclusion of host DNA; signature databases for known virulence and antimicrobial resistance markers; and databases of known straintype or pathotype-specific markers. This requirement requires the design, implementation of gigabase-scale, high-performance databases of genomic and/or signature sequences drawn from public and limited-access sequencing activities. -Develop scripts and software to automate scientific data analysis using Python, Perl/BioPerl, Ruby and Java. Documented, authoritative source code to all software and scripts developed during the period of performance for this contract will be maintained in a managed GitLab source code repository in CDC’s bioinformatics computing environment. It is also expected that any useful software tools developed during the course of this work will be published as open source software on approved public source code repositories (eg: http://www.github.com/CDCgov). -Receive next generation metagenomic shotgun sequencing data from both internal and external collaborators, perform standardized quality assurance and control procedures on the raw sequence reads, and analyze them using established metagenomic pipelines and methods. Metagenomic sequence data shall be derived from both spiked blood, sputum, and stool samples, with multiple replicates, representing different specimen processing and extraction techniques, and different platforms. -Develop and refine quantitative methods to compare multiple metagenomic datasets in order to advise the project team on optimal parameters for sample processing, extraction and sequencing. -Consult with internal and external partners on strategies and solutions for data retention, storage and management. MINIMUM QUALIFICATIONS: Education and Experience: Advanced degree, from an accredited academic institution, in scientific or technical discipline, including bioinformatics, computational biology or field related to the responsibilities of the position. At least 4 years of experience in the development and optimization of bioinformatics workflows and genomic/metagenomics analysis methods and applications. 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 publicly available data repositories (i.e. NCBI, EMBL, and DDBJ). -Experience using molecular, immunological, and cell biology techniques. 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 Python, Perl/BioPerl. Ruby and/or Java. -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. -Experience with Access, BioNumerics and statistical software. -Ability to work independently and yet maintain the flexibility to respond to requests for support of ongoing projects. 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 To apply for this position: visit our Career Center, which can also be reached by visiting www.ihrc.com/Careers and clicking on the “View Opportunities” link.
Requeriments :
Skills :
- Bioinformatics
- Biology
- Cell Biology
- Database design
- genomic
- JavaScript
- Machine Learning
- Next Generation Sequencing
- Pathology
- Programing in Python
- Programing Skills
- Programming in Java
- Programming in PERL
- Programming in R
- Software Design
- Statistics
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. The successful candidate will be a full-time employee of IHRC, Inc. and will be assigned to the Office of Advanced Molecular Detection (AMD) at the CDC, 1600 Clifton Road, Atlanta, GA, to provide scientific and technical support for the AMD initiative. 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.[Click Here to Access the Original Job Post]