Research Scientist, Bioinformatics & Computational Genomics

Key Responsibilities

• Develop and support computational pipelines for genomic data processing and analysis.
• Perform sequence analysis, read processing, and variant discovery from next-generation sequencing datasets.
• Generate high-quality variant datasets, including VCF files, for downstream research and breeding applications.
• Perform genome assembly analyses (including scaffold-level assembly where applicable) and compare assemblies and genomic regions across multiple reference genomes.
• Identify SNPs and other sequence variants relevant to research and breeding objectives.
• Able to design primers informed by comparative genomic analysis across multiple reference genomes.
• Support difficult marker-related problems by providing sequence-based analysis and computational interpretation.
• Retrieve, organize, and analyze genomic and associated metadata from relational databases, including SQL-based systems.
• Write scripts and automated workflows in Python, R, bash, or similar languages to streamline analysis and reporting.
• Document methods, results, and workflows clearly and reproducibly, and present findings to internal teams.
• Work independently on assigned analyses while coordinating with the manager and relevant collaborators as needed.
• Support projects across multiple crops, with the ability to perform analysis across species.

Required Qualifications

• PhD in Bioinformatics, Computational Biology, Genomics, Genetics, Plant Biology, or a closely related field.
• Strong computational genomics background with hands-on experience in several of the following areas: variant calling, genome assembly pipeline development, primer design.
• Strong programming skills, with the ability to independently develop and troubleshoot scripts and workflows in a Linux environment. Proficiency in Python and at least one additional analysis language or environment such as R or bash.
• Experience working in Linux-based computational environments.
• Experience handling large-scale genomics datasets.
• Experience generating, processing, and interpreting sequence-based outputs such as assemblies, alignments, and VCF files.
• Experience comparing genomic data across multiple references, assemblies, or sequence datasets.
• Working knowledge of molecular biology sufficient to support marker and primer design decisions, even if the role is not bench-based.
• Experience with relational databases and the ability to retrieve and manipulate data using SQL.
• Strong organizational skills, scientific judgment, and the ability to manage multiple tasks with limited supervision.
• Strong written and verbal communication skills and the ability to document analyses clearly.
• Cultural sensitivity and ability to work effectively in a diverse team environment.
• Must be legally authorized to work in the United States.

Preferred Qualifications

• Experience in plant genomics, crop genetics, or computational support of breeding programs.
• Experience analyzing data from multiple crop species or transferring analysis strategies across species.
• Experience with comparative genomics across diverse germplasm or multiple reference genomes.
• Experience building reproducible workflows for routine genomic analysis.
• Experience supporting molecular marker development through computational sequence analysis.
• Ability to grow into an increasingly independent role and take ownership of technically demanding analyses.