Quantitative Genetics Intern

Summary

Alta Genetics is a livestock genetics company associated with URUS. The Quantitative Genetics Intern will develop, validate, document, and apply genetic evaluations for economically and biologically relevant traits in internal beef and dairy breeding programs using phenotypic, pedigree, and genomic data. The role also involves reproducible analytical workflow development, quality assurance, technical communication, and project collaboration.

Responsibilities

• Contribute to the development of one or more genetic evaluations for traits relevant to internal beef and dairy breeding programs
• Define analysis populations, contemporary groups, fixed and random effects, and other model specifications in collaboration with team geneticists
• Estimate or evaluate genetic parameters and implement single-step genomic evaluations using appropriate programs within the BLUPF90 family
• Compare alternative data edits, model specifications, or evaluation scenarios and summarize implications for prediction quality and operational use
• Prepare, integrate, and quality-control phenotypic, pedigree, and genomic datasets used in assigned evaluations
• Assess evaluation outputs for convergence, data integrity, predictive performance, bias, stability, biological plausibility, and suitability for use in breeding decisions
• Develop reproducible scripts and workflows for data preparation, program execution, results processing, validation, and reporting
• Document datasets, code, parameter files, methods, assumptions, quality-control rules, analytical decisions, limitations, and results to support reproducibility and future implementation
• Participate in regular project meetings, communicate progress and technical risks, and incorporate feedback from quantitative genetics and business stakeholders
• Prepare and deliver a final technical report and presentation summarizing methods, results, limitations, and recommended next steps
• A documented, reproducible genetic-evaluation workflow for the assigned trait or traits
• Analysis-ready datasets and quality-control summaries, subject to applicable data-governance requirements
• Validated evaluation outputs with a concise assessment of model performance, limitations, and implementation readiness
• A final technical report, presentation, and organized handoff of code, parameter files, and supporting documentation

Skills

• Currently enrolled in a PhD program in quantitative genetics, animal breeding, animal science, genetics, genomics, or a closely related discipline
• Practical experience conducting genetic evaluations in livestock, preferably cattle
• Hands-on experience implementing single-step BLUP or single-step genomic BLUP evaluations using the BLUPF90 family of programs
• Sound understanding of mixed models, breeding value estimation, genomic relationship matrices, genetic parameter estimation, prediction accuracy, and evaluation validation
• Experience working with phenotypic, pedigree, and genomic data, including data editing, quality control, and construction of analysis-ready files
• Proficiency in Python for data manipulation, workflow development, quality control, or result processing
• Ability to write clear, well-documented, reproducible code and maintain organized analytical records
• Strong analytical judgment, attention to detail, problem-solving skills, and ability to work independently while seeking input when needed
• Effective written and verbal communication skills, including the ability to explain technical methods and findings to scientific and cross-functional audiences
• Experience with Fortran is strongly preferred
• Experience working in Linux or Unix environments and using shell scripting, job scheduling, or high-performance computing resources is preferred

Qualifications

Must Haves

• Currently enrolled in a PhD program in quantitative genetics, animal breeding, animal science, genetics, genomics, or a closely related discipline
• Practical experience conducting genetic evaluations in livestock, preferably cattle
• Hands-on experience implementing single-step BLUP or single-step genomic BLUP evaluations using the BLUPF90 family of programs
• Sound understanding of mixed models, breeding value estimation, genomic relationship matrices, genetic parameter estimation, prediction accuracy, and evaluation validation
• Experience working with phenotypic, pedigree, and genomic data, including data editing, quality control, and construction of analysis-ready files
• Proficiency in Python for data manipulation, workflow development, quality control, or result processing
• Ability to write clear, well-documented, reproducible code and maintain organized analytical records
• Strong analytical judgment, attention to detail, problem-solving skills, and ability to work independently while seeking input when needed
• Effective written and verbal communication skills, including the ability to explain technical methods and findings to scientific and cross-functional audiences

Nice to Haves

• experience with Fortran is strongly preferred
• Experience working in Linux or Unix environments and using shell scripting, job scheduling, or high-performance computing resources is preferred

Benefits

• Remote internship with regular collaboration across the Product Development and Innovation team.
• Day-to-day supervision and technical coaching will be provided by a senior quantitative geneticist.