Bioinformatics Coordinator, Breeding Insight Program
The Breeding Insight Program seeks a Bioinformatics Coordinator to lead the integration of genotypic and phenotypic data, statistical analyses, and breeding decision support efforts for USDA-ARS specialty plant and animal breeders.
With the support of the USDA-ARS, Breeding Insight at Cornell University is the first large-scale public-sector effort to systematically apply genomic information to the breeding of specialty crops and animals. The project will implement and use breeding and genomic data management systems to enhance the capacity of public-sector breeding programs to deliver increased rates of genetic gain. The breeding, genomic, and phenotypic data management systems will include databases, analytics, and decision support tools for breeders. A wide range of open source tools and platforms have already been built for breeding efforts in major crops and animals. This project will leverage these software development efforts, and focus on integration, cloud deployment, and ease of use for small breeding programs.
The Bioinformatics Coordinator, in concert with the software engineering team, will work as part of a national initiative to extend the application of genotypic information to routine development of specialty crops and animals. Breeding of specialty crops and animals has lagged behind major crops and livestock, though these specialty species together have equal economic value to the major crops and provide valuable nutrition and flavor to diets. One of Breeding Insight's aims is to accelerate breeding efforts by integrating the use of phenomics (trait analysis) with genomics and natural variation to increase the rate of genetic gain to create healthy, nutritious, and sustainable specialty crops and animals.
The Bioinformatics Coordinator will have expertise in genomic and statistical analyses, and will be responsible for working directly with the breeders to run and analyze GWAS, GS, and QTL studies to make selection decisions. The Bioinformatics Coordinator will also participate in weekly meetings, annual visits, and provide breeder support. Through the process of supporting these programs, the Bioinformatics Coordinator will gain the experience necessary to set use-case and development priorities.
The Ithaca-based Bioinformatics Coordinator will be a highly visible person central to the success of Breeding Insight and will report to the Sr. Program Manager. The Breeding Insight project integrates a team of USDA-ARS breeders (based at research locations across the US), with a software development team and a scientific team (based in Ithaca).
The Coordinator performs the following critical responsibilities:
Coordinates with breeders at 5 breeding locations across the US to understand their breeding objectives, data analytic needs, and to manage project deliverables.
Works with PIs and breeders at USDA centers and universities to develop workflows for genomic-phenomic data analyses, specify use-cases that clearly spell out the computational and interface requirements of the breeders, and form project plans to develop key capabilities and integrate Breeding Insight into each breeding program.
Overall, combines these communications into a regular process in conjunction with the development cycle implemented by the software team to ensure a well-defined roadmap of new methods and features.
In communication with breeders, designs and helps execute evaluation experiments and analyses of features introduced by Breeding Insight on which follow-up requirement documents are based.
This position is an initial two-year term appointment with the possibility of extension contingent upon continued funding.
The coordinator will be recruited based on core competency in several different areas, including GWAS, linkage mapping, QTL studies, genomic selection, bioinformatics, and project management.
A PhD in the field of quantitative genetics, molecular breeding, plant or animal genetics, biological informatics, molecular biology, or related field, plus at least three years' postdoctoral or equivalent post PhD experience is required.
Above all, the coordinator must have demonstrated exceptional verbal and written communication skills.
The ability to conduct statistical analyses on large data sets and interpret results for decision making is required.
Must be proficient with Linux/Unix systems, Python/perl, and shell scripting.
Experience with multiple animals or crops, and experience working with diverse teams are preferred.
Knowledge of information technologies, analytics, and methods appropriate for polyploid genomic data and/or image analysis are beneficial.
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