The Breeding Insight Biometrics Coordinator will lead the integration of statistical analyses from genotypic and phenotypic data to provide breeding-decision support efforts for USDA-ARS specialty plant and animal breeders. The Coordinator, in concert with the science and software engineering teams, 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.  Breeding Insight currently supports 18 ARS breeding programs.

The Biometrics Coordinator will have expertise on applying genetic principles to enable interpretation of biological phenomena and provide information that guide strategies and optimize resources in specialty breeding programs.

The Biometrics Coordinator is responsible for working directly with the breeders to assist them in implementing optimal experimental and trial design, data processing for statistical analyses, and contribute to breeding decisions support tool creation at BI. The Biometrics Coordinator will also participate in weekly meetings, annual site visits, and provide breeding decision support. Through the process of supporting these programs, the Biometrics Coordinator will gain the experience necessary to set use-case and development priorities.

The Biometrics Coordinator will be a highly visible person central to the success of Breeding Insight and will report to the Breeding Coordinator. The Breeding Insight project integrates a team of USDA-ARS breeders (based at research locations across the US), with a scientific team and a software development team.

The Research Software Engineer will lead the creation and development of biologically tailored software and applications for integration with Breeding Insight’s core software platform to enhance breeding decisions for USDA-ARS specialty plant and animal breeders. This position, in concert with the science and software engineering teams, will work as part of a national initiative within the USDA-ARS to extend the application and use of genotypic information to routine development of specialty crops and animals. Breeding of specialty crops and animals has lagged behind major crops and livestock in funding and technology advances, 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 integrated web-based software to increase the rate of genetic gain to create healthy, nutritious, and sustainable specialty crops and animals.  Breeding Insight currently supports 18 ARS breeding programs.

The Research Software Engineer will have expertise in creating biological software with easy-to-use user interfaces for isolated analyses and data visualization, such as, but not limited to, image analysis phenotypic data extraction, interpreting sensor and/or drone data as phenotypes, and data visualization in user-friendly interfaces.  The Research Software Engineer will also participate in weekly meetings, annual site visits, and provide breeder support. Through the process of supporting these programs, the Research Software Engineer will gain the experience necessary to set use-case and development priorities.

The Research Software Engineer will be a highly visible person central to the success of Breeding Insight and will report to the Breeding Coordinator. The Breeding Insight project integrates a team of USDA-ARS breeders (based at research locations across the US), with a scientific team and a software development team.

We are looking to hire one researcher with a background in bioinformatics of phenomic data. Strong skills in scripting and pipeline development are necessary, as are proven written and verbal communication skills. Researchers with experience in human, animal, and non-model organisms are especially encouraged to apply.

The successful researcher will work as part of the Breeding Insight program at Cornell University to collaborate with USDA-ARS breeders on a diversity of research projects across multiple breeding programs within USDA. Primary responsibilities for this position include:

• Developing customized image analysis pipelines to extract quantitative phenotyping data for key breeding targets
• Performing statistical analyses and extracting actionable interpretations from phenotyping data
• Preparing reports, manuscripts, and presentations of research results.

This position reports to the Executive Administrative Assistant and is tasked with providing various types of technical support to both Breeding Insight Coordinators and ARS specialty crop breeders. This position also works closely with the Communications and Training Lead, Data Curators, as well as interacting with the Biotechnology Resource Center core facilities at the Institute of Biotechnology and service providers. This is an in-person or hybrid position located in Ithaca, NY (cannot be fully remote).

Primary responsibilities include:

• Traveling to USDA-ARS locations within the US and assisting ARS breeders for short-term surge support including tissue sampling prep, tagging plants, digitizing records, phenotyping support (including set up of equipment), and providing additional support as needed.
• Assisting BI Coordinators to provide support where needed for a short duration either remote or on-site, prioritized by breeding cycle demands.
• Assisting in non-standard protocol development, recommendation of modifications for optimization, and deployment.
• Assisting BI Coordinators with scheduling, designing, and developing complex experiments for genomic and phenomic data collection.
• Collection of tissue samples for DNA, RNA, protein, and metabolite extractions with moderately complex record keeping.
• Managing the BI order tracking database and assisting breeders with sample submission to service providers and/or coordinating shipments from collaborators of large-scale, multi-collaborator projects.
• Procurement of laboratory supplies, maintenance of available inventory, and management of supplies disbursement to breeding groups.
• Assisting the Communications and Training Lead in BI-led training workshops (remote, virtual, or hybrid) and creating and maintaining SOPs for BI-deployed technologies and services.
• Occasionally assist the Data curation team in preparing data for loading into BreedBase and retrieval of stored data for downstream applications.